DOI: 10.5061/dryad.cfxpnvxjw
title: Disentangling complex histories of hybridisation: The genomic consequences of ancient and recent introgression in Channel Island monkeyflowers

description: Hybridization is a common feature of evolutionary radiations, but its
 genomic consequences vary depending on when it occurs. Since reproductive
 isolation takes time to accumulate, hybridization can occur at multiple
 points during divergence. Previous studies suggested that the taxonomic
 diversity in evolutionary radiations can help infer the timing of past
 gene flow events. Here, we assess the power of these approaches for
 revealing when gene flow occurred between two monkeyflower taxa (Mimulus
 aurantiacus) endemic to the Channel Islands of California. Coalescent
 simulations reveal that conventional four-taxon tests may not be capable
 of fully distinguishing between recent and ancient introgression, but
 genome-wide patterns of phylogenetic discordance vary predictably with
 different histories of hybridization. Using whole-genome sequencing and
 phylogenetic tests for introgression across the M. aurantiacus radiation,
 we identify signals of both ancient and recent hybridization that occurred
 between the island taxa and their ancestors. In addition, we find
 widespread selection against introgressed ancestry, consistent with
 polygenic barriers to gene flow. However, we also identify localized
 signals across the genome that may indicate adaptive introgression. This
 study highlights the power and challenges of trying to disentangle complex
 histories of hybridization. More broadly, our results illustrate the
 multiple roles that gene flow can play in evolutionary radiations:
 hybridization can expose genetic incompatibilities that contribute to
 reproductive isolation while also facilitating adaptation by transferring
 beneficial alleles between taxa. These findings underscore the dynamic
 interplay between the timing of hybridization and natural selection in
 shaping evolutionary trajectories within radiations.
description: Genome sequencing and variant calling  Leaf
 tissue from 27 plants was collected across four locations on Santa Cruz
 Island, California, USA (Table S1), consisting of red-flowered
 <em>parviflorus</em>, yellow-flowered
 <em>longiflorus</em>, and their putative hybrids. Tissue was
 dried in silica in the field, and DNA was isolated using the Zymo Plant
 and Seed DNA kit following the manufacturer’s instructions. Sequencing
 libraries were prepared according to Gaio et al (2022), with slight
 modifications. Bead-linked transposase from the Illumina Nextera XT Kit
 was used for initial tagmentation, generating insert sizes in the range of
 400 – 1200 bp. Multiplexed libraries were sequenced on the Illumina
 Novaseq 6000 using paired-end 150 bp reads at the University of Oregon’s
 Genomics Core Facility. New sequences from Santa Cruz
 Island were combined with previously generated whole genome sequences from
 various <em>M. aurantiacus </em>subspecies from Stankowski et
 al. (2019) and Short & Streisfeld (2023), resulting in a final
 dataset containing 74 individuals. Raw reads were filtered using
 <em>fastp</em> to remove reads with uncalled bases or poor
 quality scores (Chen et al. 2018). The retained reads were then aligned to
 the <em>M. aurantiacus</em> reference assembly (Stankowski et
 al 2019) using <em>BWA </em>version 0.7.17 (Li &
 Durbin 2009). An average of 90.56% of reads aligned (range: 75.45% –
 95.33%), and the average sequencing depth was 10× per individual (range:
 6–18×). PCR duplicates were marked using <em>Picard
 </em>(https://broadinstitute.github.io/picard/). Variant calling was
 performed following Stankowski et al. (2019). We then phased the VCF using
 <em>BEAGLE</em> (Browning & Browning 2007), and
 further filtered the VCF file for biallelic SNPs using <em>vcftools
 </em>(Danecek et al. 2011). The final data set contained 12,749,566
 SNPs across all 74 samples. Finally, we ran
 <em>UnifiedGenotyper</em> with the EMIT_ALL_CONFIDENT_SITES
 option to output all variant and invariant genotyped sites.
 <br><br>Admixture, PCA, and phylogenetic
 analysis <br><br>Prior research has consistently revealed four
 monophyletic clades delineating the taxa in <em>M.
 aurantiacus</em> (Stankowski and Streisfeld 2015; Chase et al 2017;
 Stankowski et al 2019; Short and Streisfeld 2023). Clade A consists
 entirely of subspecies <em>grandiflorus</em>; clade B shows
 <em>parviflorus</em> and <em>aridus</em> as sister
 taxa; clade C consists entirely of<em> aurantiacus</em>; and
 the remaining taxa (<em>longiflorus</em>,
 <em>calcyinus</em>, and the three lineages of
 <em>puniceus</em>) from southern California comprised the
 diverse clade D. To determine how the newly sequenced island samples were
 related to the other taxa in the complex, we used
 <em>Admixture</em> (Alexander et al. 2009) to estimate
 ancestry proportions from all samples, with the number of clusters (K) set
 between 2 and 11. We ran the cross-validation error function in
 <em>Admixture</em> and report results based on the value of K
 with the lowest cross-validation error. Because of the potential for
 ongoing hybridization between <em>parviflorus</em> and
 <em>longiflorus </em>on Santa Cruz Island (Wells 1980) and the
 phenotypic similarity between <em>longiflorus</em> from the
 island and mainland (Tulig 2000), we ran <em>Admixture</em>
 again using only these samples to identify putatively unadmixed
 individuals. Plants from the island that showed no evidence of admixture
 at K = 2 were used to assign individuals to subspecies. To further assess
 clustering patterns among these samples, we also performed a principal
 components analysis (PCA) in <em>Plink</em> using the 31
 samples from the island and the 7 <em>longiflorus</em> from
 the mainland. Admixed individuals were removed from further analysis, as
 they likely represented contemporary hybrids, which were not appropriate
 to include in the phylogenetic tests we used to estimate
 introgression. To determine the phylogenetic
 relationships of samples from the island and mainland, we generated a
 maximum likelihood consensus tree using <em>IQ-TREE</em>
 v1.6.12 (Nguyen et al. 2015).  We used a concatenated dataset consisting
 of 12,749,566 biallelic SNPs that did not include island samples that
 showed evidence of admixture in the above analyses (resulting in 63
 individuals, see Results). We used 1000 bootstrap replicates to provide
 support values at each node. Tests for the timing of
 admixture <br><br>To test for genome wide evidence of
 introgression, we used <em>dsuite</em> (Malinsky et al. 2021)
 to calculate the <em>f4</em>-ratio (Reich et al. 2009) for all
 possible trios of ingroup taxa, using <em>M. clevelandii
 </em>as the outgroup. The <em>f4</em>-ratio is derived
 from the <em>D-</em>statistics and their relatives, which
 measure asymmetries in the numbers of sites with ABBA and BABA patterns
 (where A and B are ancestral and derived alleles, respectively) across a
 phylogeny with three ingroup taxa and an outgroup that have the
 relationship (((P1, P2), P3) O). A significant excess of either pattern
 gives a nonzero value of <em>D</em>, which is taken as
 evidence that gene flow has occurred between P3 and one of the sister
 taxa. The <em>f4</em>-ratio then measures the proportion of
 the P2 genome that is derived from P3 and thus provides an estimate of the
 admixture proportion (Reich et al 2009). To estimate how introgression
 varied across the genome, we calculated another version of the admixture
 proportion (known as <em>f<sub>d</sub></em>;
 Martin et al 2015) in 100 kb non-overlapping windows using the
 <em>ABBABABAwindows.py</em> Python script (https://github.
 com/simonhmartin/genomics_general). Similar to the
 <em>f4</em>-ratio,
 <em>f<sub>d</sub></em> searches for asymmetries in
 the number of ABBA and BABA sites across the genome, but it has been
 optimized specifically for use in genomic windows. For the
 <em>f<sub>d</sub></em> analysis, mainland
 <em>longiflorus</em> was set as P1, Island
 <em>longiflorus</em> was P2, <em>parviflorus</em>
 was P3, and <em>M. clevelandii</em> was the outgroup (also
 referred to as Test 1, below).
 The <em>fbranch</em> statistic was designed to
 evaluate which taxa in an evolutionary radiation showed evidence of
 introgression and to assess the relative timing of that gene flow
 (Malinsky et al 2018, 2021). Specifically, given
 the <em>f4</em>-ratios calculated for all possible trios among
 a set of related taxa, <em>fbranch</em> uses the inferred
 phylogenetic relationship among these taxa, as well as variation in the
 phylogenetic distance between the sister taxa used as P1 and P2, to assign
 introgression to specific branches on a phylogenetic tree. The idea behind
 this test is the assumption that alleles introgressed into the common
 ancestor of P1 and P2 should be present in roughly equal proportions in
 both descendent lineages, making it difficult for any phylogenetic test to
 distinguish shared ancestral variation from introgression (Martin et al
 2013; Short and Streisfeld 2023). However, by gradually increasing the
 phylogenetic distance between the two sister taxa used in these
 tests, <em>fbranch</em> should be able to detect introgression
 that occurred at various points farther back in time (Malinsky et al.
 2021). Indeed, Malinsky et al (2018) used <em>fbranch</em> to
 conclude that there was extensive ancient hybridization between the
 ancestors of modern cichlid lineages, as well as recent hybridization
 among closely related species found in similar ecological
 niches. Despite the availability of this test,
 <em>fbranch</em> (or any 4-taxon test of introgression) might
 present challenges for distinguishing recent from ancient introgression
 (Fig S1). Although <em>fbranch</em> tests all possible trios
 of ingroup taxa in a phylogeny, it does not account for shared genetic
 variation between the P3 taxon and its relatives. For example, if P1 and
 P2 are more diverged from each other than the P3 taxon is to its immediate
 relatives, then variation that arose in the ancestor of P3 and its sister
 taxa would be shared in all descendant taxa. Thus, even if gene flow
 occurred recently between P3 and P2, we would detect a shared signal of
 introgression between P2 and all the relatives of P3 (Fig S1).
 Alternatively, the same shared pattern of introgression could be caused by
 ancient gene flow that occurred prior to the divergence of these sister
 taxa. Consequently, the same signals of introgression obtained from
 4-taxon tests can arise from distinct evolutionary histories, making it
 potentially difficult to determine whether introgression was recent or
 ancient. To test the ability of
 <em>fbranch</em> to distinguish between recent and ancient
 introgression, we performed neutral, coalescent simulations in msprime v.
 1.2.0 (Baumdicker et al. 2022). Specific details of each simulation can be
 found in the supplemental methods, but we began by testing three
 divergence times and three migration rates across three different
 demographic scenarios (Fig S2). We evaluated these scenarios using a
 common phylogenetic history that matched the evolutionary relationships
 found in the <em>M. aurantiacus</em> species complex (see
 Results). The specific scenarios included: <em>i)</em> ‘recent
 introgression,’ where gene flow occurred between
 <em>parviflorus</em> and Island
 <em>longiflorus</em> after the split between mainland and
 Island <em>longiflorus</em>; <em>ii</em>) ‘ancient
 introgression,’ where gene flow occurred between the ancestor of
 <em>parviflorus</em> and the ancestor of clades C and D; and
 <em>iii</em>) ‘recent and ancient introgression,’ which
 combined scenarios <em>i</em> and <em>ii</em> (Fig
 S2). <em>fbranch</em> was run separately for all divergence
 time and simulation scenario combinations, and then the different
 migration rates were tested for each demographic model using a single
 divergence time (see supplemental methods). Simulated results were
 compared to results from <em>fbranch</em> calculated from the
 empirical sequence data. In addition, we ran a fourth demographic scenario
 where no introgression occurred (to account for the effects of incomplete
 lineage sorting), which was used in the following section.
 The relationship between genome wide phylogenetic discordance and
 introgression To further describe the history of
 introgression with <em>parviflorus</em>, we explored patterns
 of phylogenetic discordance across the genome using
 <em>TWISST</em> (Martin & Van Belleghem 2017). Given a
 set of samples from multiple ingroup taxa, <em>TWISST</em>
 builds trees in genomic windows and then calculates the support for that
 topology among all possible topologies, which is referred to as the
 topology weighting. If all samples from each taxon are reciprocally
 monophyletic, then that topology is given a weighting of 1.0 for that
 window. Topological discordance among samples within a taxon will result
 in lower topology weightings for that window. We used
 <em>TWISST</em> to identify variation in the relationships
 among <em>aridus</em>, <em>parviflorus</em>,
 Island <em>longiflorus</em>, and mainland
 <em>longiflorus</em> in 100 kb genomic windows, with
 <em>M.</em> <em>clevelandii</em> as the outgroup.
 With four ingroup taxa, this resulted in 15 possible topologies, which
 were then partitioned into those that supported: <em>a</em>)
 the species tree, where <em>aridus</em> and
 <em>parviflorus </em>were sister and reciprocally monophyletic
 relative to Island <em>longiflorus</em> and mainland
 <em>longiflorus</em>; <em>b</em>) a set of recent
 introgression trees, where <em>parviflorus</em> and Island
 <em>longiflorus</em> were sister to one another relative to
 <em>aridus</em> and mainland <em>longiflorus</em>;
 and <em>c</em>) an ancient introgression tree, where
 <em>parviflorus</em> was sister to mainland and Island
 <em>longiflorus</em> relative to <em>aridus</em>.
 By quantifying variation in the support for these topologies across the
 genome, we should be able to identify how often ancient and recent
 introgression contributed to phylogenetic discordance. This is because
 adding a fourth ingroup taxon that is sister to P3 should allow us to
 distinguish the sharing of ancestral variation from signals caused by the
 introgression of lineage-specific alleles. However,
 topological discordance can also be influenced by incomplete lineage
 sorting (ILS). To test if these discordant topologies could be caused by
 ILS, we performed ten iterations of each of the simulated demographic
 scenarios described above, including the scenario with no introgression.
 We ran TWISST on each simulated dataset to count the number of windows
 that showed complete support for the recent or ancient introgression
 topologies (i.e., a topology weighting of 1.0). Under incomplete lineage
 sorting alone, we would expect to find support for both the recent and
 ancient introgression topologies in the simulation where no gene flow was
 allowed. To further confirm that these topology weightings were impacted
 by introgression, we calculated
 <em>F<sub>ST</sub></em> between
 <em>parviflorus</em> and Island
 <em>longiflorus</em> in all 100 kb non-overlapping windows
 that showed complete support for the species tree, the recent
 introgression tree, or the ancient introgression tree. Windows that
 matched the species tree or the ancient introgression tree are expected to
 show greater divergence between <em>parviflorus</em> and
 Island <em>longiflorus</em> than genomic regions reflecting
 recent introgression. This is because genomic windows where there has been
 recent introgression should have more allele sharing (and thus lower
 <em>F<sub>ST</sub></em>) between the pair of
 hybridizing taxa than genomic windows supporting the species tree (where
 there is no history of gene flow) or ancient introgression (where the
 signal may have been lost over time due to either selection or drift).
 <em>F<sub>ST</sub></em> was calculated using the
 <em>popgenwindows.py</em> Python script (https://github.com/simonhmartin/genomics_general), with only variant sites included. Finally, to distinguish between recent and ancient introgression, we compared the empirical distribution of tree topologies to the four simulated scenarios to determine which demographic history most closely resembled our observed results. The genomic consequences of introgression Introgression can have multiple consequences on patterns of genetic variation across the genome. For example, under a model where selection against gene flow is polygenic, we expect a positive relationship between introgression and recombination rate and a negative relationship between introgression and genetic differentiation (Brandvain et al. 2014, Schumer et al. 2018, Liu et al. 2022). To estimate the relationship between introgression and recombination rate, we partitioned the <em>f<sub>d</sub> </em>values calculated in 100 kb windows into quantile bins of recombination rates that were calculated previously in 500 kb windows by Stankowski et al. (2019). We then calculated the mean and 95% confidence intervals for <em>f<sub>d</sub> </em>within each recombination rate quantile bin and fit a linear model, with <em>f<sub>d</sub> </em>as the dependent variable and the recombination rate quantile bins as the independent variable. We then used the <em>emmeans</em> package (Lenth, 2019) to perform pairwise comparisons of the estimated marginal mean <em>f<sub>d</sub></em> values for the different quantile bins from the linear model. We used Spearman’s correlation coefficient to assess the relationship between <em>f<sub>d</sub> </em>and <em>F<sub>ST</sub></em>, calculated in the same 100 kb windows. In addition, we determined whether genetic diversity among the hybridizing island taxa varied relative to the mainland taxa. Specifically, we asked whether the nucleotide diversity (π) and effective population size in both island subspecies was similar to the other taxa in the complex. We calculated p in 100 kb windows using <em>PIXY</em> version 1.2.5 (Korunes & Samuk, 2021), with both variant and invariant sites included. To identify differences in the effective population sizes of these taxa, we used PSMC (Li and Durbin 2011) to estimate the effective population size through time for all samples from the island taxa and their most closely related mainland relatives. In accordance with Stankowski et al. (2023), we assumed a generation time of 2 years and a mutation rate of 7x10<sup>-9</sup> for these calculations. Identifying signatures of adaptive introgression Extensive heterogeneity in admixture across the genome raises the possibility that adaptive introgression has maintained foreign ancestry in particular regions. To determine whether regions of elevated f<sub>d</sub> display signatures of adaptive introgression between parviflorus and Island longiflorus, we calculated the frequency of Q95 sites found in windows across the genome (Racimo et al. 2017, Feng et al. 2024). Q95 sites are defined as those that are fixed (at a frequency of 1.0) in the donor taxon, near fixation (at a frequency greater than the 95<sup>th</sup> percentile) in the recipient taxon, and absent in the taxon that is sister to the recipient. Thus, any derived alleles that are present at high frequency in a recipient taxon that are also absent in its sister taxon but are fixed in a more distantly related donor taxon are candidates for adaptive introgression. Although other possibilities might generate an increase in the frequency of these Q95 sites (i.e., drift and bottlenecks), the Q95 statistic has been shown to be a powerful and reliable approach for detecting adaptive introgression (Racimo et al 2017). Moreover, genomic regions that display an excess of Q95 sites are even more likely to have been targets of positive selection, because selection will have correlated effects on linked sites. By contrast, other tests that rely on polymorphism or linkage disequilibrium are often less effective at detecting positive selection in introgressed regions due to known modifications of the haplotype structure and patterns of genetic diversity (Suarez-Gonzalez et al 2018; Moest et al 2020; Setter et al. 2020; Feng et al 2024), Thus, by identifying an elevated frequency of Q95 sites in 100 kb windows across the genome, we can identify genomic regions that may have been adaptively introgressed. To identify Q95 sites, we first identified all derived SNPs that were polymorphic among samples. Derived SNPs were defined as those where one nucleotide was fixed in <em>M. clevelandii</em> but a different nucleotide was present in at least one chromosome from samples of mainland <em>longiflorus</em>, Island <em>longiflorus</em>, <em>parviflorus</em>, or <em>aridus</em>. We then determined the number of derived sites that were fixed in <em>parviflorus</em>, absent in mainland <em>longiflorus</em>, and present in at least one haplotype in Island <em>longiflorus</em>. These represented sites that were introgressed from <em>parviflorus</em> into Island <em>longiflorus</em>. The 95th percentile of the allele frequency distribution among introgressed sites in Island <em>longiflorus</em> (=0.875) was used as a cutoff to identify adaptively introgressed sites (i.e., Q95 sites) (Racimo et al. 2017, Feng et al. 2024). For each 100 kb window, we then divided the number of Q95 sites by the total number of derived SNPs that were found on at least one chromosome in Island<em> longiflorus</em> to estimate the frequency of Q95 sites in each window. To identify signatures of adaptive introgression that were transferred from Island <em>longiflorus</em> into <em>parviflorus</em>, we identified derived SNPs that were fixed in Island <em>longiflorus</em>, present on at least one haplotype in <em>parviflorus</em>, but were absent in <em>aridus</em>. In this case, the 95<sup>th</sup> percentile of the allele frequency distribution in <em>parviflorus</em> included only sites fixed in <em>parviflorus</em>. We then divided the number of Q95 sites by the total number of derived SNPs that were present on at least one chromosome in <em>parviflorus </em>in 100 kb windows. To further explore signatures of introgression for the region with the highest frequency of Q95 sites across the genome, we calculated <em>f<sub>d</sub></em>, <em>d<sub>xy</sub></em>, <em>F<sub>ST</sub></em>, π, and the frequency of Q95 sites in 10 kb windows with 1000 bp steps. We calculated p and <em>d<sub>xy</sub></em> using <em>PIXY</em> version 1.2.5 (Korunes & Samuk, 2021), with both variant and invariant sites included, and <em>F<sub>ST</sub></em> was calculated using the <em>popgenwindows.py</em> Python script described above. Introgression will result in reduced <em>d<sub>xy</sub></em> and <em>F<sub>ST</sub></em> between a pair of hybridizing taxa, because the taxa share alleles in this region. By contrast, there should be a corresponding increase in genetic divergence between the recipient and its sister taxa.
description: # Disentangling complex histories of hybridisation: The genomic
 consequences of ancient and recent introgression in Channel Island
 monkeyflowers Dataset DOI:
 [10.5061/dryad.cfxpnvxjw](10.5061/dryad.cfxpnvxjw) ## Description of the
 data and file structure In this study we set out to examine the history
 and outcomes of introgression between a pair of parapatric, monkeyflower
 subspecies that are endemic to the Channel Islands of California. To do
 this we generated sequence data from leaf tissue collected from 27 plants
 across four locations on Santa Cruz Island, California, USA. These
 sequenced plants included red-flowered *parviflorus*, yellow-flowered
 *longiflorus*, and their putative hybrids. DNA was extracted from these
 leaves and sequenced using an Illumina Novaseq 6000. These 27 whole genome
 sequences were then combined with previous whole genome sequences
 generated from various members of the *Mimulus aurantaicus* species
 complex (Stankowski et al. 2019). To identify hybrid individuals among
 these Channel Island sequences, we performed a run of admixture using the
 74 samples from in our VCF file, and also an additional run of admixture
 using just these Channel Islands samples and mainland sequences of
 *longiflorus*. These admixture runs allowed us to identify 11 recent
 hybrids among our Channel Islands samples. These recent hybrids were
 excluded from all later analyses. We used the remaining 63 individuals to
 construct a species tree using IQTREE, and then used this species tree to
 perform tests for admixture. Specifically, we used dsuite to calculate the
 fbranch statistic (Malinsky et al. 2021), which revealed evidence of what
 appeared to be both recent and ancient introgression between the ancestors
 of *parviflorus* and *longiflorus*. To determine whether this is the case
 we performed simulations with different histories of gene flow using
 msprime (Baumdicker et al. 2022). This revealed that both recent
 hybridization, and recent plus ancient hybridization can lead to similar
 genome wide signals of introgression. However, patterns of topological
 discordance will vary depending on when hybridization occurred. By
 identifying genome wide variation in topological discordance we revealed
 that the most likely history of gene flow is one of both recent and
 ancient hybridization between these island endemics. Furthermore, by
 calculating the admixture proportion (*fd*) (Martin et al. 2015) in
 windows across the genome and then examining the relationship between *fd*
 and recombination rate, we provide evidence of recent selection against
 introgression between these subspecies. However, we also identified the
 near fixation of introgressed alleles in some regions of the genome,
 suggesting that adaptive introgression may also be contributing to genome
 wide levels of introgression. By examining a region on chromosome 5 we
 identified evidence of adaptive introgression from Channel Island
 *longiflorus* into *parviflorus*. Together the results of this study
 suggest that beneficial alleles can be shared between species when
 reproductive isolation is incomplete. Furthermore, it highlights how
 periodic bouts of hybridization do not prevent the continuation of
 speciation, and may in fact contribute to the progression of speciation by
 revealing barriers. Note: Cells marked as 'NA' represent missing
 values due to insufficient data for the calculation of statistics or
 missing data ### Files and variables #### File:
 iqtree\_keep\_admixture\_scores\_greater\_than\_0.99.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.min4.phy **Description:** Phylip format file of the whole genome sequences from the 61 individuals used to generate the species tree from IQTREE (Nguyen et al. 2015) #### File: no\_missing.biallelic.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.recode.vcf **Description:** VCF file containing all 74 individuals with no missing sites allowed #### File: iqtree\_keep\_admixture\_scores\_greater\_than\_0.99.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.min4.phy.contree.figtree.2 **Description:** Consensus species tree generated by IQTREE (Nguyen et al. 2015) #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.6.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=6. #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.5.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=5 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.4.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=4 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.3.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=3 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.2.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=2 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.8.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=8 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.7.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=7 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.9.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=9 #### File: biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.recode.vcf **Description:** VCF file containing all 74 individuals with only biallelic sites and phased using Beagle (Browning & Browning 2007). #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.10.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=10 #### File: no\_chr.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.11.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=11 #### File: no\_chr.no\_missing.biallelic.parv\_lon.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.2.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=2 for the Channel Islands samples and mainland *longiflorus* #### File: no\_chr.no\_missing.biallelic.parv\_lon.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.3.Q **Description:** Q-scores from admixture (Alexander et al. 2009) run at K=3 for the Channel Islands samples and mainland *longiflorus* #### File: admixture\_parv\_lon\_labels.csv **Description:** List of the sample names and taxonomic assignments of the Channel Islands samples and mainland *longiflorus* #### File: no\_chr.no\_missing.biallelic.parv\_lon.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.eigenvec **Description:** eigen vectors from a PCA on the Channel Islands samples and mainland *longiflorus* #### File: no\_chr.no\_missing.biallelic.parv\_lon.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.eigenval **Description:** eigen values from a PCA on the Channel Islands samples and mainland *longiflorus* #### File: pca\_parv\_lon\_pop\_labels.csv **Description:** List of the sample names and taxonomic assignments of the Channel Islands samples and mainland *longiflorus* #### File: labels\_2.csv **Description:** List of the sample names and taxonomic assignments for all 74 samples from the VCF. In this list the 11 recent hybrids are assigned as admixed. The taxnomic assignments in this list were used for all tests of admixture (fbranch, fd, q95) and topological discordance (TWISST). #### File: w\_100000.m100.lon\_lon\_isl\_parv\_clev.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.geno.fd.csv **Description:** The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using mainland *longiflorus* as P1, Island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: w\_100000.m100.ari\_parv\_lon\_isl\_clev.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.geno.fd.csv **Description:** The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using aridus as P1, *parviflorus* as P2, Island *longiflorus* as P3, and *M. clevelandii* as the outgroup ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: 100kb\_win\_data\_nonoverlap\_plos\_bio\_coords.csv **Description:** Coordinates of the 100kb windows with recombination rate estimates from Stankowski et al. 2019 ##### Variables * scaffold: Chromosome * start: Beginning of the window * end: End of the window #### File: Fst.w\_100000.m100.ari\_lon\_lon\_isl\_parv.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.geno.csv **Description:** pi, Fst, and dxy calculated in 100kb windows between *aridus*, *parviflorus*, *calycinus*, Channel Island *longiflorus*, and mainland *longiflorus*. ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window - pi_aridus: genetic diversity in *aridus* - pi_longiflorus: genetic diversity in mainland *longiflorus* - pi_longiflorus_island: genetic diversity in Channel Island *longiflorus* - pi_parviflorus: genetic diversity in *parviflorus* - pi_calycinus: genetic diversity in *calycinus* - dxy_aridus_longiflorus: genetic divergence between *aridus* and *longiflorus* - dxy_aridus_longiflorus_island: genetic divergence between *aridus* and Channel Island *longiflorus* - dxy_aridus_parviflorus: genetic divergence between *aridus* and *parviflorus* - dxy_aridus_calycinus: genetic divergence between *aridus* and *calycinus* - dxy_longiflorus_longiflorus_island: genetic divergence between *longiflorus* and Channel Island *longiflorus* - dxy_longiflorus_parviflorus: genetic divergence between *longiflorus* and *parviflorus* - dxy_longiflorus_calycinus: genetic divergence between *longiflorus* and *calycinus* - dxy_longiflorus_island_parviflorus: genetic divergence between *parviflorus* and Channel Island *longiflorus* - dxy_longiflorus_island_calycinus: genetic divergence between *calycinus* and Channel Island *longiflorus* - dxy_parviflorus_calycinus: genetic divergence between *parviflorus* and *calycinus* - Fst_aridus_longiflorus: genetic differentiation between *aridus* and *longiflorus* - Fst_aridus_longiflorus_island: genetic differentiation between *aridus* and Channel Island *longiflorus* - Fst_aridus_parviflorus: genetic differentiation between *aridus* and *parviflorus* - Fst_aridus_calycinus: genetic differentiation between *aridus* and *calycinus* - Fst_longiflorus_longiflorus_island: genetic differentiation between *longiflorus* and Channel Island *longiflorus* - Fst_longiflorus_parviflorus: genetic differentiation between *longiflorus* and *parviflorus* - Fst_longiflorus_calycinus: genetic differentiation between *longiflorus* and *calycinus* - Fst_longiflorus_island_parviflorus: genetic differentiation between *longiflorus* and Channel Island *longiflorus* - Fst_longiflorus_island_calycinus: genetic differentiation between *calycinus* and Channel Island *longiflorus* - Fst_parviflorus_calycinus: genetic differentiation between *parviflorus* and *calycinus* #### File: biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.geno **Description:** genotype file used for the calculation of *fd* and fst. See: [https://github.com/simonhmartin/genomics_general](https://github.com/simonhmartin/genomics_general) for details #### File: 100kb\_win\_data\_nonoverlap\_plos\_bio\_coords.bed **Description:** bed file of the coordinates of the 100kb windows with recombination rate estimates from Stankowski et al. 2019 #### File: Fbranch.tree\_2.newick **Description:** Newick format tree used for calculation of fbranch values for the empirical data #### File: tree\_2.newick **Description:** Newick format tree used as input in dsuite (Malinsky et al. 2021) #### File: iqtree\_keep\_admixture\_scores\_greater\_than\_0.99\_labels.csv **Description:** List of 61 individuals used to construct the species tree in iqtree #### File: channel\_islands\_2\_BBAA.txt **Description:** Output of dsuite (Malinsky et al. 2021) with calculated f4-ratio and Patterson's D-statistic values. ##### Variables * P1: Taxa used as P1 for the calculation of ABBA-BABA statistics * P2: Taxa used as P2 for the calculation of ABBA-BABA statistics * P3: Taxa used as P3 for the calculation of ABBA-BABA statistics * Dstatistic: Calculated value of Patterson's D * Z-score: Z-score of the calculated Patterson's D value * p-value: p-value of the calculated Patterson's D value * f4-ratio: Calculated value of the f4-ratio test for admixture * BBAA: count of BBAA sites * ABBA: count of ABBA sites * BABA: count of BABA sites #### File: channel\_islands\_2\_combine.txt **Description:** Output of dsuite (Malinsky et al. 2021) used as input to DtriosCombine #### File: channel\_islands\_2\_combine\_stderr.txt **Description:** Output of dsuite (Malinsky et al. 2021) used as input to DtriosCombine #### File: channel\_islands\_2\_Dmin.txt **Description:** Output of dsuite (Malinsky et al. 2021) ##### Variables * P1: Taxa used as P1 for the calculation of ABBA-BABA statistics * P2: Taxa used as P2 for the calculation of ABBA-BABA statistics * P3: Taxa used as P3 for the calculation of ABBA-BABA statistics * Dstatistic: Calculated value of Patterson's D * Z-score: Z-score of the calculated Patterson's D value * p-value: p-value of the calculated Patterson's D value * f4-ratio: Calculated value of the f4-ratio test for admixture * BBAA: count of BBAA sites * ABBA: count of ABBA sites * BABA: count of BABA sites #### File: channel\_islands\_2\_tree.txt **Description:** Output of dsuite (Malinsky et al. 2021) with calculated f4-ratio and Patterson's D-statistic values. ##### Variables * P1: Taxa used as P1 for the calculation of ABBA-BABA statistics * P2: Taxa used as P2 for the calculation of ABBA-BABA statistics * P3: Taxa used as P3 for the calculation of ABBA-BABA statistics * Dstatistic: Calculated value of Patterson's D * Z-score: Z-score of the calculated Patterson's D value * p-value: p-value of the calculated Patterson's D value * f4-ratio: Calculated value of the f4-ratio test for admixture * BBAA: count of BBAA sites * ABBA: count of ABBA sites * BABA: count of BABA sites #### File: Fbranch.channel\_islands\_2.txt **Description:** Fbranch values from dsuite (Malinsky et al. 2021) ##### Variables * branch: Branch on the phylogenetic test for which the test is being performed * branch_descendants: Taxa present on the branch * Outgroup: Calculated value of fbranch for outgroup * gra: Calculated value of fbranch for Mimulus grandiflorus * ari: Calculated value of fbranch for Mimulus aridus * par: Calculated value of fbranch for Mimulus parviflorus * aur: Calculated value of fbranch for Mimulus aurantiacus * cal: Calculated value of fbranch for Mimulus calycinus * OC: Calculated value of fbranch for Mimulus puniceus from Orange County, California * lon: Calculated value of fbranch for Mimulus longiflorus * isl_lon: Calculated value of fbranch for Mimulus longiflorus from the Santa Cruz Island, California * red: Calculated value of fbranch for the red ecotype of Mimulus puniceus * yellow: Calculated value of fbranch for the yellow ecotype of Mimulus puniceus #### File: LG10.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 10. Introgression from Island *longiflorus* into *parviflorus*. #### File: iqtree\_keep\_admixture\_scores\_greater\_than\_0.99.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.recode.vcf **Description:** VCF file containing the 61 individuals used for species tree construction. #### File: LG9.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 9. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG8.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 8. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG7.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 7. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG6.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 6. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG4.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 4. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG5.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 5. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG3.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 3. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG1.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 1. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG2.w\_10kb.s\_1000.N\_q95\_sites\_parv\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 2. Introgression from Island *longiflorus* into *parviflorus*. #### File: LG8.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 8. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG10.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 10. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG9.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 9. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG6.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 6. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG7.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 7. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG5.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 5. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG1.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 1. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG3.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 3. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG4.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 4. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG2.w\_10kb.s\_1000.N\_q95\_sites\_island\_lon\_VAF.txt **Description:** Number of Q95 sites in 10kb windows from chromosome 2. Introgression from *parviflorus* into Island *longiflorus*. #### File: LG\_1\_10.all\_confident\_sites.postBQSR.v1.UnifiedGenotyper.channel\_islands.vcf.gz **Description:** All sites VCF file used for the calculation of dxy and pi using pixy (Korunes & Samuk, 2021) #### File: parv.frq **Description:** Allele frequencies of all biallelic SNPs among the *parviflorus* samples #### File: island\_lon.frq **Description:** Allele frequencies of all biallelic SNPs among the Island *longiflorus* samples #### File: lon.frq **Description:** Allele frequencies of all biallelic SNPs among the mainland *longiflorus* samples #### File: clev.frq **Description:** Allele frequencies of all biallelic SNPs among the *clevelandii* samples #### File: ari.frq **Description:** Allele frequencies of all biallelic SNPs among the *aridus* samples #### File: PSMC\_results.zip **Description:** Zip file containing the PSMC results for all individuals of *aridus*, *parviflorus*, Island *longiflorus*, and mainland *longiflorus*. These files were used to estimate the historical effective populaiton size of these taxa. **Files:** * PSMC result for Mimulus aridus sample ARI_159357_83_S15_L006: split.ARI_159357_83_S15_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus aridus sample ARI_159357_84_S3_L006: split.ARI_159357_84_S3_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus aridus sample ARI_195935_1_S8_L006: split.ARI_195935_1_S8_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus aridus sample ARI_T84_79_S1_L006: split.ARI_T84_79_S1_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus calycinus sample CAL_T144_3_S47_L003: split.CAL_T144_3_S47_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus calycinus sample CAL_T150_10_S38_L003: split.CAL_T150_10_S38_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus calycinus sample CAL_T90_2_S44_L003: split.CAL_T90_2_S44_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus calycinus sample CAL_T91_7_S35_L003: split.CAL_T91_7_S35_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample ECSC_par_157_S347: split.ECSC_par_157_S347.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample ECSC_par_179_S276: split.ECSC_par_179_S276.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample ECSC_par_183_S287: split.ECSC_par_183_S287.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longilflorus sample LON_DPR_Y3_S34_L003: split.LON_DPR_Y3_S34_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longilflorus sample LON_SS_Y16_S39_L003: split.LON_SS_Y16_S39_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longilflorus sample LON_T33_1_S41_L003: split.LON_T33_1_S41_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longilflorus sample LON_T8_8_S50_L003: split.LON_T8_8_S50_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample PAR_KK161_S6_L006: split.PAR_KK161_S6_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample PAR_KK168_S32_L003: split.PAR_KK168_S32_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample PAR_KK180_S22_L006: split.PAR_KK180_S22_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample PAR_KK182_S16_L006: split.PAR_KK182_S16_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus puniceus sample RPR16_S23_L006: split.RPR16_S23_L006.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample RUT_DPR_R12_S53_L003: split.RUT_DPR_R12_S53_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample RUT_MBR4_R3_S42_L003: split.RUT_MBR4_R3_S42_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample RUT_SS_R19_S45_L003: split.RUT_SS_R19_S45_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample RUT_WTF_S48_L003: split.RUT_WTF_S48_L003.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_hyb_203_S320: split.SC2_hyb_203_S320.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_hyb_203_S320: split.SC2_lon_163_S278.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_164_S289: split.SC2_lon_164_S289.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_197_S300: split.SC2_lon_197_S300.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_199_S311: split.SC2_lon_199_S311.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_200_S321: split.SC2_lon_200_S321.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_200_S321: split.SC2_lon_200_S321.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus longiflorus sample SC2_lon_204_S340: split.SC2_lon_204_S340.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SC3_hyb_105_S339: split.SC3_hyb_105_S339.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SC3_hyb_177_S277: split.SC3_hyb_177_S277.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SC3_hyb_178_S288: split.SC3_hyb_178_S288.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample SC3_par_100_S309.: split.SC3_par_100_S309.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample SC3_par_170_S319: split.SC3_par_170_S319.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample SC3_par_173_S329: split.SC3_par_173_S329.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus parviflorus sample SC3_par_97_S298: split.SC3_par_97_S298.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_hyb_208_S349: split.SCB_hyb_208_S349.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_hyb_211_S330: split.SCB_hyb_211_S330.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_hyb_216_S299 split.SCB_hyb_216_S299.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_hyb_226_S310: split.SCB_hyb_226_S310.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_lon_207_S350: split.SCB_lon_207_S350.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_lon_209_S279: split.SCB_lon_209_S279.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_lon_218_S290: split.SCB_lon_218_S290.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_lon_221_S301: split.SCB_lon_221_S301.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc * PSMC result for Mimulus sample SCB_par_219_S348: split.SCB_par_219_S348.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.psmc #### File: pixy\_pi.txt **Description:** genetic diversity (pi) values calculated for all taxa in 100kb windows using pixy (Korunes & Samuk, 2021) ##### Variables * pop: Taxa * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of Window * avg_pi: average pi in window * no_sites: number of sites * count_diffs: number of differences * count_comparisons: number of comparisons * count_missing: number of missing #### File: ari.par.isl\_lon.lon.cle.output.weights.w\_100000.csv **Description:** Twisst (Martin & Van Belleghem 2017) topology weightings in 100kb windows for samples of *aridus*, *parviflorus*, Island *longiflorus*, and mainland *longiflorus* with *clevelandii* as the outgroup. #### File: ari.par.isl\_lon.lon.cle.output.phyml\_w\_100000.data.tsv **Description:** Trees in 100kb windows for samples of *aridus*, *parviflorus*, Island *longiflorus*, and mainland *longiflorus* with *clevelandii* as the outgroup. Generated using Simon Martin's `phymlWindows.py` script. See [https://github.com/simonhmartin/genomics_general](https://github.com/simonhmartin/genomics_general) for details. #### File: ari.par.isl\_lon.lon.cle.output.weights.w\_100000.window\_data\_100kb\_weights.csv **Description:** Twisst (Martin & Van Belleghem 2017) topology weightings in 100kb windows for samples of *aridus*, *parviflorus*, Island *longiflorus*, and mainland *longiflorus* with *clevelandii* as the outgroup. This file has window coordinates and phyml likelihoods for each window. #### File: x10\_gens\_recent.zip **Description:** Results from simulations with only recent gene flow with medium divergence (time to the root = 500,000 generations) **Files:** * Coodrinates of 100kb windows used for analysis: 100kb_win_data_nonoverlap_plos_bio_coords.bed * Coordinates and support for genomic trees built in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Genomic trees built in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) topologies in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_recent.txt * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * Plot of fbranch values with a max value of 0.2: max_color_0.2.png * Plot of fbranch values with a max value of 0.2: recent.fbranch.max_color_0.2.svg * Plot of fbranch values: recent_fbranch.png * Plot of fbranch values in SVG format: recent_fbranch.svg * Directory containing the output of twisst runs from the replicated runs of the simulation: recent_twisst_reps * Directory containing output from replicate run of simulaiton: rep_1 * Directory containing output from replicate run of simulaiton: rep_2 * Directory containing output from replicate run of simulaiton: rep_3 * Directory containing output from replicate run of simulaiton: rep_4 * Directory containing output from replicate run of simulaiton: rep_5 * Directory containing output from replicate run of simulaiton: rep_6 * Directory containing output from replicate run of simulaiton: rep_7 * Directory containing output from replicate run of simulaiton: rep_8 * Directory containing output from replicate run of simulaiton: rep_9 * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf * Processed VCF of simulated data in Simon Martin's geno format: sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno * List of individual haplotypes used for twisst run: twisst_haplotype_list * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, aurantiacus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, calycinus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, mainland *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, orange county *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calcyinus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated orange county *puniceus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, *parvfilorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: x10\_gens\_ancient.zip **Description:** Results from simulations with only ancient gene flow with medium divergence (time to the root = 500,000 generations) * Coodrinates of 100kb windows used for analysis: 100kb_win_data_nonoverlap_plos_bio_coords.bed * Coordinates and support for genomic trees built in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Genomic trees built in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) topologies in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Plot of fbranch values with a max value of 0.2: ancient.fbranch.max_color_0.2.svg * Plot of fbranch values:fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_ancient.txt * Plot of fbranch values in SVG format: fbranch.svg * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * Plot of fbranch values with a max value of 0.2: max_color_0.2.png * Directory containing output from replicate run of simulaiton: rep_1 * Directory containing output from replicate run of simulaiton: rep_2 * Directory containing output from replicate run of simulaiton: rep_3 * Directory containing output from replicate run of simulaiton: rep_4 * Directory containing output from replicate run of simulaiton: rep_5 * Directory containing output from replicate run of simulaiton: rep_6 * Directory containing output from replicate run of simulaiton: rep_7 * Directory containing output from replicate run of simulaiton: rep_8 * Directory containing output from replicate run of simulaiton: rep_9 * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf * Processed VCF of simulated data in Simon Martin's geno format: sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longilforus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longilforus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, orange county *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated orange county *puniceus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient_x10_divergence_time.vcf.geno.csv #### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: x10\_gens\_recent\_and\_ancient.zip **Description:** Results from simulations with both recent and ancient gene flow with medium divergence (time to the root = 500,000 generations) * Bed file with coordinates of 100kb windows:100kb_win_data_nonoverlap_plos_bio_coords.bed * SVG of fbranch results with max value of 0.2: ancient_plus_recent.fbranch.max_color_0.2.svg * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) topologies in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Plot of fbranch values: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_x10_divergence_time.txt * Plot of fbranch values in SVG format: fbranch.svg * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * Plot of fbranch values with a max value of 0.2: max_color_0.2.png * Directory containing output from replicate run of simulaiton: reps * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x10_divergence_time_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_x10_divergence_time_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_x10_divergence_time_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x10_divergence_time_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x10_divergence_time_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf * Processed VCF of simulated data in Simon Martin’s geno format: sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno * Tree used for fbranch calculaiton: simulation.Fbranch.tree.newick * Sample list used for fbranch calculaiton: simulation_sample_list.txt * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longilforus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longilforus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, orange county *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated orange county *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype puniceus as P1, island longiflorus as P2, parviflorus as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: recent\_and\_ancient.zip **Description:** Results from simulations with both recent and ancient gene flow with short divergence (time to the root = 50,000 generations) * Plot of fbranch values: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1.txt * Plot of fbranch values in SVG format: fbranch.svg * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.recent_plus_ancient_fbranch_x0.1_divergence_time.fbranch.png * SVG of fbranch results with max value of 0.2: max_color_0.2.recent_plus_ancient_fbranch_x0.1_divergence_time.fbranch.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1.vcf * Processed VCF of simulated data in Simon Martin’s geno format: sim_1_gens_gene_flow_0.1.vcf.geno * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, mainland *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated mainland *longiflorus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated Orange County (OC) *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv\ \ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1.vcf.geno.csv Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: only\_recent.zip **Description:** Results from simulations with only recent gene flow with short divergence (time to the root = 50,000 generations) * Plot of fbranch values: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_recent.txt * Plot of fbranch values in SVG format: fbranch.svg * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.only_recent_fbranch_x0.1_divergence_time.fbranch.png * SVG of fbranch results with max value of 0.2: max_color_0.2.only_recent_fbranch_x0.1_divergence_time.fbranch.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_recent.vcf * Processed VCF of simulated data in Simon Martin’s geno format: sim_1_gens_gene_flow_0.1_only_recent.vcf.geno * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, mainland *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated mainland *longiflorus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated Orange County (OC) *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: only\_ancient.zip **Description:** Results from simulations with only ancient gene flow with short divergence (time to the root = 50,000 generations) * Plot of fbranch values: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_ancient.txt * Plot of fbranch values in SVG format: fbranch.svg * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.only_ancient_fbranch_x0.1_divergence_time.fbranch.png * SVG of fbranch results with max value of 0.2: max_color_0.2.only_ancient_fbranch_x0.1_divergence_time.fbranch.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_ancient.vcf * Processed VCF of simulated data in Simon Martin’s geno format: sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, mainland *longiflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated mainland *longiflorus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated Orange County (OC) *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus* as P3, and *M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_ancient.vcf.geno.csv\ Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: x10\_no\_gene\_flow\.zip **Description:** Results from simulations with no gene flow with medium divergence (time to the root = 500,000 generations) * Directory containing output from replicate run of simulaiton: rep_0 * Directory containing output from replicate run of simulaiton: rep_1 * Directory containing output from replicate run of simulaiton: rep_2 * Directory containing output from replicate run of simulaiton: rep_3 * Directory containing output from replicate run of simulaiton: rep_4 * Directory containing output from replicate run of simulaiton: rep_5 * Directory containing output from replicate run of simulaiton: rep_6 * Directory containing output from replicate run of simulaiton: rep_7 * Directory containing output from replicate run of simulaiton: rep_8 * Directory containing output from replicate run of simulaiton: rep_9 * File containing list of commands used for the analysis of simulated data: workflow #### File: x20\_no\_gene\_flow\.zip **Description:** Results from simulations with no gene flow with long divergence (time to the root = 1,000,000 generations) * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_no_gene_flow.txt * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_no_gene_flow_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_no_gene_flow_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_no_gene_flow_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_no_gene_flow_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_no_gene_flow_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_no_gene_flow_x20_divergence_time.vcf * File containing list of commands used for the analysis of simulated data: workflow #### File: x20\_ancient.zip **Description:** Results from simulations with only ancient gene flow with long divergence (time to the root = 1,000,000 generations) * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_ancient.txt * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.sim_1_gens_gene_flow_0.1_only_ancient_fbranch.png * SVG of fbranch results with max value of 0.2: max_color_0.2.sim_1_gens_gene_flow_0.1_only_ancient_fbranch.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_ancient_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_Dmin.txt * Plot of fbranch values: sim_1_gens_gene_flow_0.1_only_ancient_fbranch.png * Plot of fbranch values in SVG format: sim_1_gens_gene_flow_0.1_only_ancient_fbranch.svg * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_ancient_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_ancient_x20_divergence_time.vcf * File containing list of commands used for the analysis of simulated data: workflow #### File: x20\_recent.zip **Description:** Results from simulations with only recent gene flow with long divergence (time to the root = 1,000,000 generations) * PNG of fbranch results: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_only_recent.txt * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.png * SVG of fbranch results with max value of 0.2: max_color_0.2.recent_fbranch_x2_divergence_time.svg * SVG of fbranch results: recent_fbranch_x2_divergence_time.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_only_recent_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_only_recent_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_only_recent_x20_divergence_time.vcf #### File: x20\_recent\_and\_ancient.zip **Description:** Results from simulations with both recent and ancient gene flow with long divergence (time to the root = 1,000,000 generations) * PNG of fbranch results: fbranch.png * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_gene_flow_0.1_x20_divergence_time.txt * Newick format tree used for calculation of Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.tree_2.newick * PNG of fbranch results with max value of 0.2: max_color_0.2.png * PNG of fbranch results with max value of 0.2: max_color_0.2.recent_plus_ancient_fbranch_x2_divergence_time.fbranch.png * SVG of fbranch results with max value of 0.2: max_color_0.2.recent_plus_ancient_fbranch_x2_divergence_time.fbranch.svg * SVG of fbranch results with max value of 0.2: max_color_0.2.svg * SVG of fbranch results: recent_plus_ancient_fbranch_x2_divergence_time.svg * Text file containing taxonomic assignment of samples from simulaiton: sample_list_2.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x20_divergence_time_BBAA.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_x20_divergence_time_combine_stderr.txt * Output of Dsuite (Malinsky et al. 2021) used for dtrioscombine: sim_1_gens_gene_flow_0.1_x20_divergence_time_combine.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x20_divergence_time_Dmin.txt * Calculated admixture statistics from simulated data: sim_1_gens_gene_flow_0.1_x20_divergence_time_tree.txt * VCF file containing simulated data: sim_1_gens_gene_flow_0.1_x20_divergence_time.vcf * File containing list of commands used for the analysis of simulated data: workflow #### File: 10kb\_fd\_fd\_Fst\_q95.zip **Description:** Fd, Fst, pi, dxy, and Q95 in 10kb windows with 1000bp steps. * Text file of dxy between aridus and parviflorus in 10kb windows with 1000bp steps: ari_par.w_10kb.s_100_dxy.txt\ **Variables** * pop1: Population 1 * pop2: population 2 * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_dxy: Average dxy * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites * The admixture proportion (fd) calculated in 10kb windows with 1000bp steps: clipped.w_10kb.m100.s1kb.ari_par_longiflorus_island_cle.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.geno.fd.csv\ **Variables:** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (fd) calculated in 10kb windows with 1000bp steps: clipped.w_10kb.m100.s1kb.lon_lon_isl_par_cle.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.geno.fd.csv **Variables:** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Genetic differentiation (Fst) calculated in 10kb windows with 1000bp steps: Fst.w_10kb.m100.s1kb.ari_lon_lon_isl_parv.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel_islands.geno.csv ##### Variables * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window - pi_aridus: genetic diversity in *aridus* - pi_longiflorus: genetic diversity in mainland *longiflorus* - pi_longiflorus_island: genetic diversity in Channel Island *longiflorus* - pi_parviflorus: genetic diversity in *parviflorus* - pi_calycinus: genetic diversity in *calycinus* - dxy_aridus_longiflorus: genetic divergence between *aridus* and *longiflorus* - dxy_aridus_longiflorus_island: genetic divergence between *aridus* and Channel Island *longiflorus* - dxy_aridus_parviflorus: genetic divergence between *aridus* and *parviflorus* - dxy_aridus_calycinus: genetic divergence between *aridus* and *calycinus* - dxy_longiflorus_longiflorus_island: genetic divergence between *longiflorus* and Channel Island *longiflorus* - dxy_longiflorus_parviflorus: genetic divergence between *longiflorus* and *parviflorus* - dxy_longiflorus_calycinus: genetic divergence between *longiflorus* and *calycinus* - dxy_longiflorus_island_parviflorus: genetic divergence between *parviflorus* and Channel Island *longiflorus* - dxy_longiflorus_island_calycinus: genetic divergence between *calycinus* and Channel Island *longiflorus* - dxy_parviflorus_calycinus: genetic divergence between *parviflorus* and *calycinus* - Fst_aridus_longiflorus: genetic differentiation between *aridus* and *longiflorus* - Fst_aridus_longiflorus_island: genetic differentiation between *aridus* and Channel Island *longiflorus* - Fst_aridus_parviflorus: genetic differentiation between *aridus* and *parviflorus* - Fst_aridus_calycinus: genetic differentiation between *aridus* and *calycinus* - Fst_longiflorus_longiflorus_island: genetic differentiation between *longiflorus* and Channel Island *longiflorus* - Fst_longiflorus_parviflorus: genetic differentiation between *longiflorus* and *parviflorus* - Fst_longiflorus_calycinus: genetic differentiation between *longiflorus* and *calycinus* - Fst_longiflorus_island_parviflorus: genetic differentiation between *longiflorus* and Channel Island *longiflorus* - Fst_longiflorus_island_calycinus: genetic differentiation between *calycinus* and Channel Island *longiflorus* - Fst_parviflorus_calycinus: genetic differentiation between *parviflorus* and *calycinus* * Genetic diversity (pi) of island longiflorus in 10kb windows with 1000bp steps: island_lon.w_10kb.s_100_pi.txt\ **Variables** * pop: Population * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_pi: Average pi * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites * Number of Q95 sites in 10kb windows with 1000bp steps: LG1.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG1.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG10.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG10.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG2.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG2.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG3.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG3.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG4.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG4.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG5.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG5.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG6.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG6.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG7.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG7.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG8.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG8.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG9.w_10kb.s_1000.N_q95_sites_island_lon_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Number of Q95 sites in 10kb windows with 1000bp steps: LG9.w_10kb.s_1000.N_q95_sites_parv_VAF.txt **Variables** * Chr: Chromosome * Start: Start of window * End: End of window * N_Q95: Number of Q95 sites * N_test_sites: Number of sites used to test for the Q95 statistic * N_sites: Total number of SNPs in window * Text file of dxy between island longiflorus and longiflorus in 10kb windows with 1000bp steps: lon_island_lon.w_10kb.s_100_dxy.txt **Variables** * pop1: Population 1 * pop2: population 2 * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_dxy: Average dxy * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites * Genetic diversity (pi) of longiflorus in 10kb windows with 1000bp steps: lon.w_10kb.s_100_pi.txt **Variables** * pop: Population * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_pi: Average pi * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites * Genetic diversity (pi) of parviflorus in 10kb windows with 1000bp steps: par.w_10kb.s_100_pi.txt **Variables** * pop: Population * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_pi: Average pi * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites * Text file of dxy between parviflorus and island longiflorus in 10kb windows with 1000bp steps: parv_island_lon.w_10kb.s_100_dxy.txt **Variables** * pop1: Population 1 * pop2: population 2 * chromosome: Chromosome * window_pos_1: Start of window * window_pos_2: End of window * avg_dxy: Average dxy * no_sites: Number of sites * count_diffs: Number of differences * count_comparisons: Number of comparisons * count_missing: Number of missing sites #### File: da.clipped.w\_100000.m100.ari\_parv\_lon\_isl\_clev.biallelic.phased.selected.filtered.postBQSR.v1.UnifiedGenotyper.channel\_islands.geno.fd.csv **Description:** fd, Fst, pixy dxy, pixy pi, da, and topology weightings in 100kb windows. ##### Variables * row_number: row number * scaffold: Chromosome * start: Start of window * end: End of window * mid: Approximate middle site of window * sites: Number of SNPs * sitesUsed: Number of SNPs used for fd calculation with *aridus* as P1, *parviflorus* as P2, and Island *longiflorus* as P3 with *clevelandii* as the outgroup * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson's D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinsky et al. 2021) * gene_count_per_window: Number of genes per window * cM.Mb: Recombination rate * Fst_aridus_longiflorus: Fst between aridus and longiflorus * Fst_aridus_longiflorus_island: Fst between aridus and Island longiflorus * Fst_aridus_parviflorus: Fst between aridus and parviflorus * Fst_aridus_calycinus: Fst between aridus and calycinus * Fst_longiflorus_longiflorus_island: Fst between longiflorus and Island longiflorus * Fst_longiflorus_parviflorus: Fst between longiflorus and parviflorus * Fst_longiflorus_calycinus: Fst between longiflorus and calycinus * Fst_longiflorus_island_parviflorus: Fst between parviflorus and Island longiflorus * Fst_longiflorus_island_calycinus: Fst between calycinus and Island longiflorus * Fst_parviflorus_calycinus: Fst between parviflorus and calycinus * average_dxy_ari_par: dxy between parviflorus and aridus * average_dxy_lon_isl_lon: dxy between longiflorus and Island longiflorus * average_dxy_par_isl_lon: dxy between parviflorus and Island longiflorus * average_dxy_par_lon: dxy between parviflorus and longiflorus * average_dxy_ari_isl_lon: dxy between aridus and Island longiflorus * average_dxy_ari_lon: dxy between aridus and longiflorus * lnL: tree likelihood from phyml for samples of aridus, parviflorus, Island longiflorus, and mainland longiflorus with clevelandii as the outgroup * topo1: Topology weighting for tree 1 * topo2: Topology weighting for tree 2 * topo3: Topology weighting for tree 3 * topo4: Topology weighting for tree 4 * topo5: Topology weighting for tree 5 * topo6: Topology weighting for tree 6 * topo7: Topology weighting for tree 7 * topo8: Topology weighting for tree 8 * topo9: Topology weighting for tree 9 * topo10: Topology weighting for tree 10 * topo11: Topology weighting for tree 11 * topo12: Topology weighting for tree 12 * topo13: Topology weighting for tree 13 * topo14: Topology weighting for tree 14 * topo15: Topology weighting for tree 15 * fd_isl_lon_par_ari: fd with a broken species tree island longiflorus and parviflorus as sister * average_pi_par: average pi in parviflorus * average_pi_lon: average pi in mainland longiflorus * average_pi_isl_lon: average pi in Island longiflorus * average_pi_ari: average pi in aridus * average_da_lon_isl_lon: average da between longiflorus and island longiflorus * average_da_ari_par: average da between aridus and parviflorus * average_da_par_isl_lon: average da between parviflorus and island longiflorus * average_da_par_lon: average da between parviflorus and mainland longiflorus * average_da_ari_isl_lon: average da between aridus and island longiflorus * average_da_ari_lon: average da between aridus and mainland longiflorus * Fd_lon_isl_lon_par_cle: fd with mainland lon as P1, island lon as P2, parviflorus as P3, and clevelandii as the outgroup * fd_ari_par_aur: fd with aridus as P1, parviflorus as P2, aurantiacus as P3, and clevelandii as the outgroup * fd_ari_par_cal: fd with aridus as P1, parviflorus as P2, calycinus as P3, and clevelandii as the outgroup * fd_ari_par_lon: fd with aridus as P1, parviflorus as P2, mainland longiflorus as P3, and clevelandii as the outgroup * fd_ari_par_oc: fd with aridus as P1, parviflorus as P2, orange county puniceus as P3, and clevelandii as the outgroup * fd_ari_par_yel: fd with aridus as P1, parviflorus as P2, yellow ecotype of puniceus as P3, and clevelandii as the outgroup * fd_ari_par_red: fd with aridus as P1, parviflorus as P2, red ecotype of puniceus as P3, and clevelandii as the outgroup #### File: simulated\_twisst\_recent\_and\_ancient.zip **Description:** Twisst results for ten replicate simulations with both recent and ancient gene flow with medium divergence (time to the root = 500,000 generations) * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Gzipped trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Combined Coordinates and likelihoods from trees in 100kb windows and TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.window_data_100kb_weights.csv * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv * Gzipped output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * Trees in 100kb windows: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Plot of genomewide twisst weightings: clipped.ari.par.isl_lon.lon.cle.output.phyml_w_100000.pdf * Boxplots of genomewide twisst weightings: clipped.ari.par.isl_lon.lon.cle.output.phyml_w_100000.weights_mean.pdf * Scatterplot of test 1 fd and introgression topologies: correlation_plot_test_1_fd_introgression_topologies.pdf * Scatterplot of test 2 fd and introgression topologies: correlation_plot_test_2_fd_introgression_topologies.pdf * Boxplot of the distribution of sites with a topology weighting of 1.0 from the replicate simulations: recent_and_ancient_simulation.topo_weightings_1.0_2.pdf * Directory containing the output of the replicate simulaiton runs: reps * Scatterplot of test 1 fd and ancient introgression topology weighting: test_1_correlation_plot_fd_ancient_introgression_topologies.pdf * Plot of the distribution of test 1 fd values in windows with topology weightings of 1.0 for the three topologies: test_1_fd_regions_with_topo_weighting_of_1.0_lon_isl_lon_twisst.pdf * Barplot of topology weightings in top 5% of test 1 fd windows: test_1_intro.stacked_barplot_top_5_percent.pdf * Scatterplot of test 2 fd and ancient introgression topology weighting: test_2_correlation_plot_fd_ancient_introgression_topologies.pdf * Plot of the distribution of test 2 fd values in windows with topology weightings of 1.0 for the three topologies: test_2_fd_regions_with_topo_weighting_of_1.0_lon_isl_lon_twisst.pdf * Barplot of topology weightings in top 5% of test 2 fd windows: test_2_intro.stacked_barplot_top_5_percent.pdf * Boxplot of the distribution of sites with a topology weighting of 1.0 from the replicate simulations: topo_weightings_1.0_ancient_plus_recent.pdf * rmarkdown containing commands used to make plots for test 1 fd values: twisst_test_1_fd.Rmd * rmarkdown containing commands used to make plots for test 2 fd values: twisst_test_2_fd.Rmd * rmarkdown containing commands used to plot twisst results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island *longiflorus* as P2, *parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_x10_divergence_time.vcf.geno.csv #### File: simulated\_twisst\_recent.zip **Description:** Twisst results for ten replicate simulations with only recent gene flow with medium divergence (time to the root = 500,000 generations) * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Gzipped trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Combined Coordinates and likelihoods from trees in 100kb windows and TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.window_data_100kb_weights.csv * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv * Gzipped output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * Trees in 100kb windows: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Plot of genomewide twisst weightings: clipped.ari.par.isl_lon.lon.cle.output.phyml_w_100000.pdf * Boxplots of genomewide twisst weightings: clipped.ari.par.isl_lon.lon.cle.output.phyml_w_100000.weights_mean.pdf * Scatterplot of test 1 fd and introgression topologies: correlation_plot_test_1_fd_introgression_topologies.pdf * Scatterplot of test 2 fd and introgression topologies: correlation_plot_test_2_fd_introgression_topologies.pdf * Boxplot of the distribution of sites with a topology weighting of 1.0 from the replicate simulations: recent_simulation.topo_weightings_1.0_2.pdf * Directory containing the output of the replicate simulaiton runs: recent_twisst_reps * Scatterplot of test 1 fd and ancient introgression topology weighting: test_1_correlation_plot_fd_ancient_introgression_topologies.pdf * Plot of the distribution of test 1 fd values in windows with topology weightings of 1.0 for the three topologies: test_1_fd_regions_with_topo_weighting_of_1.0_lon_isl_lon_twisst.pdf * Barplot of topology weightings in top 5% of test 1 fd windows: test_1_intro.stacked_barplot_top_5_percent.pdf * Scatterplot of test 2 fd and ancient introgression topology weighting: test_2_correlation_plot_fd_ancient_introgression_topologies.pdf * Plot of the distribution of test 2 fd values in windows with topology weightings of 1.0 for the three topologies: test_2_fd_regions_with_topo_weighting_of_1.0_lon_isl_lon_twisst.pdf * Barplot of topology weightings in top 5% of test 2 fd windows: test_2_intro.stacked_barplot_top_5_percent.pdf * Boxplot of the distribution of sites with a topology weighting of 1.0 from the replicate simulations: topo_weightings_1.0_recent.pdf * rmarkdown containing commands used to make plots for test 1 fd values: twisst_test_1_fd.Rmd * rmarkdown containing commands used to make plots for test 2 fd values: twisst_test_2_fd.Rmd * rmarkdown containing commands used to plot twisst results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_1_gens_gene_flow_0.1_only_recent_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: simulated\_twisst\_no\_gene\_flow\.zip **Description:** Twisst results for ten replicate simulations with no gene flow with medium divergence (time to the root = 500,000 generations) * Dirtectory containg replciate run of simulation with no gene flow: rep_0 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_1 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_2 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_3 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_4 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_5 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_6 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_7 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_8 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * Dirtectory containg replciate run of simulation with no gene flow: rep_9 * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * Fbranch (Malinsky et al. 2021) values from simulated data: Fbranch.sim_1_gens_no_gene_flow_x10_divergence_time.txt * Plot of mean test 1 fd values from simulated data: mean_Fd_test_1_no_gene_flow.pdf * Plot of mean test 2 fd values from simulated data: mean_Fd_test_2_no_gene_flow.pdf * rmarkdown with commands used to make fd plots: mean_simulated_fd_no_gene_flow.Rmd * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_BBAA.txt * Calculated admixture statistics from simulated data: sim_1_gens_no_gene_flow_x10_divergence_time_tree.txt * rmarkdown with commands used to plot TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) results: twisst.Rmd * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *aurantiacus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.aur.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *calycinus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.cal.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, island *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.isl_lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, *longiflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.lon.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, OC *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.OC.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, red ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.red.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aridus* as P1, *parviflorus* as P2, yellow ecotype *puniceus as P3, and M. clevelandii* as the outgroup: w_100000.m100.ari.par.yellow.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *aurantiacus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.aur.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *calycinus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.cal.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated *longiflorus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.lon.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated OC *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.OC.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated red ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.red.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) * The admixture proportion (*fd*) (Martin et al. 2015) calculated in 100 kb windows using simulated yellow ecotype *puniceus* as P1, island longiflorus *as P2, parviflorus as P3, and M. clevelandii* as the outgroup: w_100000.m100.yellow.isl_lon.par.cle.sim_no_gene_flow_x10_divergence_time.vcf.geno.csv * **Variables** * scaffold: Chromosome number * start: Beginning of the window * end: End of the window * mid: Approximate mid point of the window * sites: Number of SNPs in the window * sitesUsed: Number of sites used for the calculation of fd * ABBA: Pseudo count of ABBA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 2) * BABA: Pseudo count of BABA sites (including polymorphic sites) (See [Martin et al. 2015](https://doi.org/10.1093/molbev/msu269) Equation 3) * D: Patterson’s D * fd: The admixture proportion (*fd*) (Martin et al. 2015) * fdM: *fdM* (Malinksy et al. 2021) #### File: simulated\_twisst\_ancient.zip **Description:** Twisst results for ten replicate simulations with only ancient gene flow with medium divergence (time to the root = 500,000 generations) * Boxplot of the distribution of sites with a topology weighting of 1.0 from the replicate simulations: ancient_simulation.topo_weightings_1.0_2.pdf * Coordinates and likelihoods from trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.data.tsv * Gzipped trees in 100kb windows: ari.par.isl_lon.lon.cle.output.phyml_w_100000.trees.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv * Gzipped TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.csv.gz * TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) Topology weightings in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.output.weights.w_100000.window_data_100kb_weights.csv * Output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv * Gzipped output of TWISST ([Martin and Van Belleghem 2017](http://doi.org/10.1534/genetics.116.194720)) in 100kb windows using simulated taxa: ari.par.isl_lon.lon.cle.twisst.distance.w_100000.csv.gz * Trees in 100kb windows: ari.par.isl_lon.lon.cle.twisst.topologies.w_100000.trees * Directory containing the output of the replicate simulaiton runs: reps * rmarkdown containing commands used to plot twisst results: twisst.Rmd ## Code/software Computer scripts used for population genomic analyses are available on Github at: [https://github.com/awshort/Channel_Islands_monkeyflower_hybridization](https://github.com/awshort/Channel_Islands_monkeyflower_hybridization)