DOI: 10.5061/dryad.bk3j9kdnc
title: Habitat association predicts population connectivity and persistence in flightless beetles: a population genomics approach within a dynamic archipelago

description: Habitat association has been proposed to affect evolutionary dynamics
 through its control on dispersal propensity, which is considered a key
 trait for lineage survival in habitats of low durational stability. The
 Habitat Constraint hypothesis predicts different micro- and
 macroevolutionary patterns for stable vs. dynamic habitat specialists, but
 the empirical evidence remains controversial and in insects mostly derives
 from winged lineages. We here use genome-wide SNP data to assess the
 effect of habitat association on the population dynamics of two closely
 related flightless lineages of the genus Eutagenia (Coleoptera:
 Tenebrionidae), which are co-distributed across the Cyclades islands in
 the Eastern Mediterranean but are associated with habitat types of
 different presumed stability: the psammophilous lineage is associated with
 dynamic sandy coastal habitats, while the geophilous lineage is associated
 with comparatively stable compact-soil habitats. Our comparative
 population genomic and demographic analyses support higher inter-island
 gene flow in the psammophilous lineage, presumably due to the physical
 properties of dynamic sand-dune habitats that promote passive dispersal.
 We also find consistent bottlenecks in the psammophilous demes, suggesting
 that lineage evolution in the dynamic habitat is punctuated by local
 extinction and recolonisation events. The inferred demographic processes
 are surprisingly uniform among psammophilous demes, but vary considerably
 among geophilous demes depending on historical island connectivity,
 indicating more stringent constraints on the dynamic-habitat lineage. This
 study extends the Habitat Constraint hypothesis by demonstrating that
 selection on dispersal traits is not the only mechanism that can drive
 consistent differences in evolutionary dynamics between stable vs. dynamic
 habitat specialists.
description: For a detailed description of data collection and processing,
 please refer to the relevant manuscript: Meramveliotakis, E., Ortego, J.,
 Anastasiou, I., Vogler, A. P., Papadopoulou, A. (ACCEPTED;
 Sep-2024)<em> </em>Habitat association predicts population
 connectivity and persistence in flightless beetles: a population genomics
 approach within a dynamic archipelago. <em>Molecular
 Ecology</em> Briefly, 318 samples were collected
 from 47 sampling sites (24 demes of the compact-soil
 "geophilous" <em>Eutagenia</em> clade and 23 demes
 of the sand-obligate "psammophilous"
 <em>Eutagenia</em> clade) across 14 Cyclades islands (Aegean,
 Greece). Each specimen was individually preserved in 100% ethanol and
 stored at -20°C. DNA extraction was performed following a commercial
 bead-based protocol (Biosprint® 96 DNA Blood kit, Qiagen®) as implemented
 in the automated KingFisher Flex system (Thermo Fisher scientific).
 Library preparation followed the double-digest Restriction site Associated
 DNA sequencing (ddRADseq) protocol of Peterson et al. (2012) (PLOS One, 7:
 e37135) with small modifications (Papadopoulou and Knowles, 2017;
 Evolution, 71: 2901-2917). DNA was double-digested with restriction
 enzymes EcoRI and Msel, unique barcodes (10bp) and adaptors were ligated
 to the digested fragments and individually barcoded products were pooled
 into libraries of 72-80 samples each. Each library was size-selected
 between 350 to 450 bp using a Pippin Prep™ instrument (Sage Science Inc.).
 Following size-selection, the fragments were PCR-amplified (8-10
 amplification cycles) using high-fidelity DNA polymerase (iProof™ ,
 Bio-Rad) and they were sequenced on the Illumina HiSeq2500 platform
 (single-end, 150bp reads) at the Centre for Applied Genomics (SickKids,
 Toronto, Ontario, Canada). Demultiplexing of the raw Illumina reads,
 <em>de novo</em> assembly to putative loci and genotype
 calling, was performed using the STACKS2 v2.64 pipeline (Rochette et al.,
 2019; Molecular Ecology, 28: 4737-4754).
description: # DATA FOR: Habitat association predicts population connectivity and
 persistence in flightless beetles: a population genomics approach within a
 dynamic archipelago ## GENERAL INFORMATION **Dataset overview** A detailed
 description of the general framework and specific methodology that were
 followed in order to generate and process all included files, can be found
 in the relevant publication (see bellow). This dataset has been generated
 following the double-digest Restriction site Associated DNA sequencing
 (ddRADseq) protocol of Peterson et al. (2012; PLoS ONE, 7: e37135) with
 small modifications (Papadopoulou and Knowles, 2017; Evolution, 71:
 2901-2917). The constructed libraries of 72-80 individuals each were
 size-selected (350-450 bp), PCR-amplified (8-10 cycles) and sequenced on
 the Illumina HiSeq2500 platform (single-end, 150 bp reads). Raw Illumina
 reads (demultiplexed) and relevant metadata have been deposited in the
 NCBI Sequence Read Archive (SRA), under BioProject PRJNA951918
 ([https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA951918](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA951918)). Demultiplexing of the raw Illumina reads, *de novo* assembly to putative loci and genotype calling, was performed using the STACKS2 v2.64 pipeline (Rochette et al., 2019; Molecular Ecology, 28: 4737-4754). **Corresponding author information** ``` Name: Emmanouil Meramveliotakis ORCID: https://orcid.org/0000-0002-6399-575X Affiliation: Department of Biological Sciences, Faculty of Pure and Applied Sciences, University of Cyprus, Nicosia, Cyprus email: emeram01@ucy.ac.cy ``` **Alternative contact information** ``` Name: Anna Papadopoulou ORCID: https://orcid.org/0000-0002-4656-4894 Affiliation: Department of Biological Sciences, Faculty of Pure and Applied Sciences, University of Cyprus, Nicosia, Cyprus email: papadopoulou.g.anna@ucy.ac.cy ``` **Related publication** ``` Meramveliotakis, E., Ortego, J., Anastasiou, I., Vogler, A. P., Papadopoulou, A. (ACCEPTED; Sep-2024) Habitat association predicts population connectivity and persistence in flightless beetles: a population genomics approach within a dynamic archipelago. Molecular Ecology ``` **Funding information** ``` This work is a product of the project EVOLHAB (EXCELLENCE/0421/0419), which was co-financed by the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation (RIF). During the course of this work EM was supported by the A. G. Leventis Foundation Educational Grants Scheme for doctoral students. This research was also partly supported by the Spanish Ministry of Economy and Competitiveness through the Severo Ochoa Program for Centres of Excellence in R + D + I (SEV-2012-0262). ``` ## NOTES FOR FILES #### File names When applicable, file names follow the pattern `eut.(01).R(02).(03).(04).(05).(06).(07).c(08).(09).(10).(file_extension)`, where: * `(01)` denotes the dataset type and can be defined as: * `eph` for the psammophilous lineage * `per` for all demes of the geophilous lineage * `per.nc` for the eastern (northern and southern sectors, and Donoussa) demes of the geophilous lineage * `per.w` for the western demes of the geophilous lineage * `(02)` denotes the missing data filtering percent threshold across all individuals in order to keep a RAD locus, as implemented in the `populations` program of the `STACKS2 v2.64` pipeline * `(03)` denotes the included sites after the `STACKS2` assembly and can be defined as: * `all` for including all variant sites per RAD locus * `wss` for including only the first SNP per RAD locus * `tot` for including both variant and invariant sites for each RAD locus * `(04)` denotes if loci that are potentially under selection (as identified using the `BAYESCAN` software) have been removed from the dataset and can be defined as: * `fSEL` to state that potential loci under selection have been removed * *blank* : to state that the filter has not been applied on the dataset * `(05)` denotes if highly variable loci have been removed from the dataset and can be defined as: * `fTH` to state that the highly variable loci have been removed * *blank* : to state that the filter has not been applied on the dataset * `(06)` denotes if the included variant sites have been filtered based on their sequencing depth and can be defined as: * `fDP` to state that a filter has been applied to remove low and artificially high depth variants * *blank* : to state that the filter has not been applied on the dataset * `(07)` denotes if the file includes only individuals of a specific deme (or deme pair) and can be defined as: * *two-letter and one-number pattern* : denotes that the file only includes data from the specific deme (e.g., "AD1") * \_two consecutive *two-letter and one-number patterns* : denotes that the file only includes data from the specific deme pair (e.g., "AD1AD2") * *blank* : to state that the file includes all relevant individuals (e.g., individuals from all psammophilous demes) * `(08)` denotes if an extra filter on variant missingness percentage has been applied (e.g., "c80" for 80% presence across all included individuals to retain a site) * `(09)` denotes if a minor allele count (mac) threshold has been applied and can be defined as: * `mac3` to state that all variants with a mac &lt; 3 have been excluded * *blank* : to state that the filter has not been applied on the dataset * `(10)` denotes if the dataset has been thinned to one variant per RAD locus after the application of the aforementioned filters and can be defined as: * `onesnp` to state that the dataset is thinned * *blank* : to state that the dataset has not been thinned * `(file_extension)` denotes the file type extension This naming pattern is mostly relevant to input files and especially to `vcf` files. #### VCF files `vcf` files may include either both variant and invariant sites for each RAD locus or only variant sites. The following columns are included: * `#CHROM`: RAD locus number/identifier * `POS`: Position of the SNP on the RAD locus * `ID`: Identifier of the SNP * `REF`: Reference base * `ALT`: Alternate base * `QUAL`: Quality score * `FILTER`: Filter status * `INFO`: Additional information * `NS`: Number of samples with data (only included for the variant sites) * `AF`: Allele frequency (only included for the variant sites) * `FORMAT`: Data format * `GT`: Genotype * `DP`: Read depth (only included for the variant sites) * `AD`: Allele depth (only included for the variant sites) * `GQ`: Genotype quality (only included for the variant sites) * `GL`: Genotype likelihood (only included for the variant sites) * **Sample columns:** One per individual, containing genotype information Note that missing data are coded as `./.` ## DESCRIPTION OF DIRECTORIES AND FILES ### *0\_data\_processing\_filters.zip* The compressed master directory **"0_data_processing_filters"**, contains a total of 16 directories and 60 files. The directory tree structure is visible bellow (files not shown): ``` 0_data_processing_filters ├── geophilous │   ├── 0_stacks2_output │   ├── 1_bayescan_outliers │   │   ├── 0_bayescan_input │   │   ├── 1_bayescan_output │   │   └── 2_bayescan_outliers_blacklist │   ├── 2_theta_outliers │   └── 3_filtered_datasets └── psammophilous ├── 0_stacks2_output ├── 1_bayescan_outliers │   ├── 0_bayescan_input │   ├── 1_bayescan_output │   └── 2_bayescan_outliers_blacklist ├── 2_theta_outliers └── 3_filtered_datasets ``` It is divided into two main directories (i.e., "geophilous" and "psammophilous"), corresponding to the two distinct datasets of *Eutagenia* lineages with distinct habitat association. Each of the two main directories is further divided into four sub-directories which correspond to different data generation and filtering steps. Specifically: ##### Sub-directories **0_stacks2_output** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 0_data_processing_filters/geophilous/0_stacks2_output/ ├── eut.per.nc.R30.all.vcf.gz ├── eut.per.nc.R30.wss.vcf.gz ├── eut.per.R30.all.vcf.gz ├── eut.per.R30.wss.vcf.gz ├── eut.per.w.R30.all.vcf.gz └── eut.per.w.R30.wss.vcf.gz ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 0_data_processing_filters/psammophilous/0_stacks2_output/ ├── eut.eph.R30.all.vcf.gz └── eut.eph.R30.wss.vcf.gz ``` It includes `*.vcf` files, as generated by the first run of the `populations` program in the `STACKS2 v2.64` pipeline. All files have been minimally filtered to include variants that are present in at least 30% of all individuals. **1_bayescan_outliers** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 0_data_processing_filters/geophilous/1_bayescan_outliers/ ├── 0_bayescan_input │   └── eut.per.R30.wss.txt ├── 1_bayescan_output │   ├── eut.per.R30.wss_n5Kth10nbp20p5Kb50Kpo1000_fst.txt │   └── eut.per.R30.wss_n5Kth10nbp20p5Kb50Kpo1000.sel └── 2_bayescan_outliers_blacklist ├── bayescan_eut.per.R30.wss_n5Kth10nbp20p5Kb50Kpo1000_outliers.tsv ├── bayescan_eut.per.R30.wss_n5Kth10nbp20p5Kb50Kpo1000.tsv ├── bayescan_outliers_fSEL.Rmd ├── blacklistBS.txt ├── convergence_plots.pdf └── plot_R.r ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 0_data_processing_filters/psammophilous/1_bayescan_outliers/ ├── 0_bayescan_input │   └── eut.eph.R30.wss.txt ├── 1_bayescan_output │   ├── eut.eph.R30.wss_n5Kth10nbp20p5Kb50Kpo1000_fst.txt │   └── eut.eph.R30.wss_n5Kth10nbp20p5Kb50Kpo1000.sel └── 2_bayescan_outliers_blacklist ├── bayescan_eut.eph.R30.wss_n5Kth10nbp20p5Kb50Kpo1000_outliers.tsv ├── bayescan_eut.eph.R30.wss_n5Kth10nbp20p5Kb50Kpo1000.tsv ├── bayescan_outliers_fSEL.Rmd ├── blacklistBS.txt ├── convergence_plots.pdf └── plot_R.r ``` Includes all relevant directories and files for the `BAYESCAN` analyses. Specifically: * The `0_bayescan_input` directories (one for each lineage specific dataset) include the input files. * The `1_bayescan_output` directories include the main output of the `BAYESCAN` analyses, which can be used as input to (a) identify outliers (`*_fst.txt` files), and (b) evaluate the convergence of the MCMC chain (`*.sel` files). * The `2_bayescan_outliers_blacklist` directories include the blacklisted RAD loci (`blacklistBS.txt`) that are potentially under selection and relevant files. Note that (a) the code to generate the files in this directory is included in the *R-markdown* file (`bayescan_outliers_fSEL.Rmd`), and (b) the included script `plot_R.r` is provided by the authors of `BAYESCAN` in the relevant repository ([https://github.com/mfoll/BayeScan](https://github.com/mfoll/BayeScan)). **2_theta_outliers** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 0_data_processing_filters/geophilous/2_theta_outliers/ ├── blacklist95.txt ├── blacklist975.txt ├── blacklist995.txt ├── blacklistIQRextreme.txt ├── blacklistIQRmild.txt ├── blacklistMC.txt └── theta_outliers_fTH.Rmd ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 0_data_processing_filters/psammophilous/2_theta_outliers/ ├── blacklist95.txt ├── blacklist975.txt ├── blacklist995.txt ├── blacklistIQRextreme.txt ├── blacklistIQRmild.txt ├── blacklistMC.txt └── theta_outliers_fTH.Rmd ``` Includes all relevant files (and code) to generate the blacklist of RAD loci with potentially inflated *theta* values (i.e., highly variable loci based on the number of segregating sites). The input files are located in the `0_stacks2_output` directories, while the different blacklist files are named based on the selected threshold (see `theta_outliers_fTH.Rmd`). **3_filtered_datasets** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 0_data_processing_filters/geophilous/3_filtered_datasets/ ├── blacklist.per.fSEL.fTH99.txt ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.vcf.gz ├── eut.per.nc.R30.tot.fSEL.fTH99.vcf.gz ├── eut.per.R30.all.fSEL.fTH99.fDP95.vcf.gz ├── eut.per.R30.tot.fSEL.fTH99.vcf.gz ├── eut.per.w.R30.all.fSEL.fTH99.fDP95.vcf.gz ├── eut.per.w.R30.tot.fSEL.fTH99.vcf.gz ├── per-depth-post-filt.pdf ├── per-depth-pre-filt.pdf ├── per.nc-depth-post-filt.pdf ├── per.nc-depth-pre-filt.pdf ├── per.w-depth-post-filt.pdf ├── per.w-depth-pre-filt.pdf └── variant_depth_filtering_fDP.Rmd ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 0_data_processing_filters/psammophilous/3_filtered_datasets/ ├── blacklist.eph.fSEL.fTH99.txt ├── eph-depth-post-filt.pdf ├── eph-depth-pre-filt.pdf ├── eut.eph.R30.all.fSEL.fTH99.fDP95.vcf.gz ├── eut.eph.R30.tot.fSEL.fTH99.vcf.gz └── variant_depth_filtering_fDP.Rmd ``` Includes the filtered `*.vcf` files. Any further filtering (i.e., extra filtering for missing data, minor allele frequency threshold and thinning to one variant per RAD locus) for downstream analyses is applied to these files, depending on the requirements of the relevant software. Additionally, the directory includes: * The `blacklist.*` text file, which is a combination of the two blacklists generated in the previous steps (i.e., the ones included in directories `1_bayescan_outliers` and `2_theta_outliers`) and it is used in the second run of the `populations` program as implemented in the `STACKS2` pipeline to remove the relevant outliers. * A set of `*.pdf` files which include box-plot graphs of the pre- and post-filtering variant depth distribution per specimen. * A `variant_depth_filtering_fDP.Rmd` *R-markdown* file with the code to apply sample-oriented filtering on variant depth. ### *1\_genetic\_variation\_statistics.zip* The compressed master directory `1_genetic_variation_statistics`, contains a total of 30 directories and 220 files. The directory tree structure is visible bellow (files not shown): ``` 1_genetic_variation_statistics/ ├── 0_genetic_diversity_pi_pixy │   ├── 0_vcf_files │   │   ├── geophilous │   │   └── psammophilous │   ├── 1_info │   │   ├── geophilous │   │   └── psammophilous │   └── 2_pixy_raw_output │   ├── geophilous │   └── psammophilous ├── 1_genetic_divergence_Dxy_pixy │   ├── 0_vcf_files │   │   ├── geophilous │   │   └── psammophilous │   ├── 1_info │   │   ├── geophilous │   │   └── psammophilous │   └── 2_pixy_raw_output │   ├── geophilous │   └── psammophilous └── 2_genetic_differentiation _Fst_pixy ├── 0_vcf_files │   ├── geophilous │   └── psammophilous ├── 1_info │   ├── geophilous │   └── psammophilous └── 2_pixy_raw_output ├── geophilous └── psammophilous ``` ##### Sub-directories **0_genetic_diversity_pi_pixy** ``` 1_genetic_variation_statistics/0_genetic_diversity_pi_pixy/ ├── 0_vcf_files │   ├── geophilous │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD1.c50.mod.vcf.gz │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD1.c50.mod.vcf.gz.tbi │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD2.c50.mod.vcf.gz │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD2.c50.mod.vcf.gz.tbi │   │   ├-- [...] │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI2.c50.mod.vcf.gz │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI2.c50.mod.vcf.gz.tbi │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI3.c50.mod.vcf.gz │   │   └── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI3.c50.mod.vcf.gz.tbi │   └── psammophilous │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD5.c50.mod.vcf.gz │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD5.c50.mod.vcf.gz.tbi │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD6.c50.mod.vcf.gz │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD6.c50.mod.vcf.gz.tbi │   ├-- [...] │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI5.c50.mod.vcf.gz │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI5.c50.mod.vcf.gz.tbi │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI6.c50.mod.vcf.gz │   └── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI6.c50.mod.vcf.gz.tbi ├── 1_info │   ├── geophilous │   │   ├── popmap.AD1.tsv │   │   ├── popmap.AD2.tsv │   │   ├-- [...] │   │   ├── popmap.TI2.tsv │   │   └── popmap.TI3.tsv │   └── psammophilous │   ├── popmap.AD5.tsv │   ├── popmap.AD6.tsv │   ├-- [...] │   ├── popmap.TI5.tsv │   └── popmap.TI6.tsv └── 2_pixy_raw_output ├── geophilous │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD1.c50.mod_pi.txt │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.AD2.c50.mod_pi.txt │   ├-- [...] │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI2.c50.mod_pi.txt │   └── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.TI3.c50.mod_pi.txt └── psammophilous ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD5.c50.mod_pi.txt ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.AD6.c50.mod_pi.txt ├-- [...] ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI5.c50.mod_pi.txt └── eut.eph.R30.tot.fSEL.fTH99.fDP95.TI6.c50.mod_pi.txt ``` It includes all input files to calculate genetic diversity (*π*) using the `PIXY v1.2.7` software. It is divided into: * The `0_vcf_files` directory, which includes the input `*.vcf` files (one per deme) and the corresponding `*.tbi` files (indexed `*.vcf` files using the `tabix` software). Both variant and invariant sites that are present in at least 50% of the individuals of each deme are included. The files have been generated following the guidelines of the `PIXY` documentation (see [https://pixy.readthedocs.io/en/latest/#](https://pixy.readthedocs.io/en/latest/#)) * The `1_info` directory, which includes population maps for each deme. * The `2_pixy_raw_output` directory, which includes the raw output files of `PIXY`. These files can be used to estimate average genetic diversity per deme. **1_genetic_divergence_Dxy_pixy** ``` 1_genetic_variation_statistics/1_genetic_divergence_Dxy_pixy/ ├── 0_vcf_files │   ├── geophilous │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   │   ├── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   └── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   └── psammophilous │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   └── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi ├── 1_info │   ├── geophilous │   │   ├── popmap.per.nc.pairs.tsv │   │   ├── popmap.per.pairs.tsv │   │   └── popmap.per.w.pairs.tsv │   └── psammophilous │   └── popmap.eph.pairs.tsv └── 2_pixy_raw_output ├── geophilous │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod_dxy.txt │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod_dxy.txt │   └── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod_dxy.txt └── psammophilous └── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod_dxy.txt ``` It includes all input files to calculate pairwise genetic divergence (*Dxy*) using the `PIXY` software. It is divided into: * The `0_vcf_files` directory, which includes the input `*.vcf` files and the corresponding `*.tbi` files. Both variant and invariant sites that are present in at least 70% of the individuals are included. The files have been generated following the guidelines of the `PIXY` documentation (see [https://pixy.readthedocs.io/en/latest/#](https://pixy.readthedocs.io/en/latest/#)) * The `1_info` directory, which includes population maps. * The `2_pixy_raw_output` directory, which includes the raw output files of `PIXY`. These files can be used to estimate average pairwise genetic divergence. **2_genetic_differentiation_Fst_pixy** ``` 1_genetic_variation_statistics/2_genetic_differentiation _Fst_pixy/ ├── 0_vcf_files │   ├── geophilous │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   │   ├── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   │   └── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi │   └── psammophilous │   ├── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz │   └── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod.vcf.gz.tbi ├── 1_info │   ├── geophilous │   │   ├── popmap.per.nc.pairs.tsv │   │   ├── popmap.per.pairs.tsv │   │   └── popmap.per.w.pairs.tsv │   └── psammophilous │   └── popmap.eph.pairs.tsv └── 2_pixy_raw_output ├── geophilous │   ├── eut.per.nc.R30.tot.fSEL.fTH99.fDP95.c70.mod_fstHUD.txt │   ├── eut.per.R30.tot.fSEL.fTH99.fDP95.c70.mod_fstHUD.txt │   └── eut.per.w.R30.tot.fSEL.fTH99.fDP95.c70.mod_fstHUD.txt └── psammophilous └── eut.eph.R30.tot.fSEL.fTH99.fDP95.c70.mod_fstHUD.txt ``` It includes all input files to calculate pairwise genetic differentiation (*Fst*) using the `PIXY` software. It is divided into: * The `0_vcf_files` directory, which includes the input `*.vcf` files and the corresponding `*.tbi` files. Both variant and invariant sites that are present in at least 70% of the individuals are included. The files have been generated following the guidelines of the `PIXY` documentation (see [https://pixy.readthedocs.io/en/latest/#](https://pixy.readthedocs.io/en/latest/#)) * The `1_info` directory, which includes population maps. * The `2_pixy_raw_output` directory, which includes the raw output files of `PIXY`. These files can be used to estimate average pairwise genetic differentiation. ### *2\_genetic\_structure.zip* The compressed master directory `2_genetic_structure`, contains a total of 18 directories and 615 files. It is divided into two main directories (one for each dataset/lineage) with essentially identical sub-directory structure. The directory tree structure is visible bellow (files not shown): ``` 2_genetic_structure/ ├── geophilous │   ├── 0_structure_analyses │   │   ├── all_islands │   │   │   ├── input │   │   │   └── k_runs │   │   └── eastern_islands │   │   ├── input │   │   └── k_runs │   └── 1_pca_analyses │   ├── all_islands │   │   └── input │   └── eastern_islands │   └── input └── psammophilous ├── 0_structure_analyses │   ├── input │   └── k_runs └── 1_pca_analyses ``` ##### Sub-directories **0_structure_analyses** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 2_genetic_structure/geophilous/0_structure_analyses/ ├── all_islands │   ├── input │   │   ├── eut.per.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.str │   │   ├── extraparams │   │   ├── mainparams │   │   └── popmap.per.pairs.tsv │   └── k_runs │   ├── eut_per_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.1_f │   ├── eut_per_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.2_f │   ├-- [...] │   ├── eut_per_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.19_f │   └── eut_per_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.20_f └── eastern_islands ├── input │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.str │   ├── extraparams │   ├── mainparams │   └── popmap.per.nc.pairs.tsv └── k_runs ├── eut_per.nc_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.1_f ├── eut_per.nc_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.2_f ├-- [...] ├── eut_per.nc_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.19_f └── eut_per.nc_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.20_f ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 2_genetic_structure/psammophilous/0_structure_analyses/ ├── input │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.str │   ├── extraparams │   ├── mainparams │   └── popmap.eph.pairs.tsv └── k_runs ├── eut_eph_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.1_f ├── eut_eph_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K1.2_f ├-- [...] ├── eut_eph_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.19_f └── eut_eph_R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp_K10.20_f ``` It includes all input files to infer population genetic structure using the `STRUCTURE v2.3.4` software. For each dataset/lineage, there are two sub-directories: * The `input` directory, which includes: 1. The input `*.str` file for the `STRUCTURE` analysis that includes one variant per RAD locus (present in at least 80% of all individuals). Each diploid individual is represented by two consecutive rows. The input file includes the following columns: * **1st column**: Name of individual * **2nd column**: Population information * **Loci columns:** Genotype data. The coding of information follows the pattern: * `-9` =missing data * `1` = A * `2` = T * `3` = G * `4` = C * The `k_runs` directory, which includes the output of 10 different `STRUCTURE` runs (K=1-10) with 20 replicates per run. Note, that for the geophilous lineage, there are two directories, the `all_islands` which includes the aforementioned files for the analysis including all geophilous demes, and the `eastern islands` which includes the same type of files after excluding individuals sampled from the western islands and repeating the analysis. **1_pca_analyses** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 2_genetic_structure/geophilous/1_pca_analyses/ ├── all_islands │   └── input │   └── eut.per.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.vcf.gz └── eastern_islands └── input └── eut.per.nc.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.vcf.gz ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 2_genetic_structure/psammophilous/1_pca_analyses/ └── eut.eph.R30.all.fSEL.fTH99.fDP95.c80.mac3.onesnp.vcf.gz ``` It includes the `*.vcf` input files to perform a complementary PCA analyses using the `adegenet` R package, in order to evaluate the results of the aforementioned `STRUCTURE` analyses. ### *3\_genealogical\_inference\_svdquartets.zip* The compressed master directory `3_genealogical_inference_svdquartets`, contains a total of 2 directories and 4 files. It is divided into two main directories (one for each dataset/lineage). The directory tree structure is visible bellow: ``` 3_genealogical_inference_svdquartets/ ├── geophilous │   ├── eut.per.R30.all.fSEL.fTH99.fDP95.c30.mac3.onesnp.taxpart.nexus │   └── eut.per.R30.all.fSEL.fTH99.fDP95.c30.mac3.onesnp.vcf.gz └── psammophilous ├── eut.eph.R30.all.fSEL.fTH99.fDP95.c30.mac3.onesnp.taxpart.nexus └── eut.eph.R30.all.fSEL.fTH99.fDP95.c30.mac3.onesnp.vcf.gz ``` It includes the `*.nexus` input files for the `SVDQuartets` analyses and the corresponding `*.vcf` files that were used to generate them. ### *4\_demographic\_modelling\_fastsimcoal2.zip* The compressed master directory `4_demographic_modelling_fastsimcoal2`, contains a total of 706 directories and 1,404 files. It is divided into two main directories (one for each dataset/lineage) with identical sub-directory structure. The directory tree structure is visible bellow (files not shown): ``` 4_demographic_modelling_fastsimcoal2/ ├── geophilous │   ├── single_deme_models │   │   ├── 0_vcf_files │   │   └── 1_fastsimcoal2 │   │   ├── 0_sfs_data │   │   ├── 1_info │   │   └── 2_models │   │   ├── AD1 │   │   │   ├── per1.constant │   │   │   ├── per2.expansion │   │   │   ├── per3.contraction │   │   │   └── per4.instbot │   │   ├── AD2 │   │   │   ├── per1.constant │   │   │   ├── per2.expansion │   │   │   ├── per3.contraction │   │   │   └── per4.instbot │   │   ├-- [...] │   │   ├── TI2 │   │   │   ├── per1.constant │   │   │   ├── per2.expansion │   │   │   ├── per3.contraction │   │   │   └── per4.instbot │   │   └── TI3 │   │   ├── per1.constant │   │   ├── per2.expansion │   │   ├── per3.contraction │   │   └── per4.instbot │   └── two_deme_models │   ├── 0_vcf_files │   └── 1_fastsimcoal2 │   ├── 0_sfs_data │   ├── 1_info │   └── 2_models │   ├── AD1AD2 │   │   ├── iso1.complete_iso │   │   ├── iso2.contemporary_iso │   │   ├── mig1.contemporary_mig │   │   └── mig2.continuous_mig │   ├── AD1AD3 │   │   ├── iso1.complete_iso │   │   ├── iso2.contemporary_iso │   │   ├── mig1.contemporary_mig │   │   └── mig2.continuous_mig │   ├-- [...] │   ├── TI2SY3 │   │   ├── iso1.complete_iso │   │   ├── iso2.contemporary_iso │   │   ├── mig1.contemporary_mig │   │   └── mig2.continuous_mig │   └── TI2TI3 │   ├── iso1.complete_iso │   ├── iso2.contemporary_iso │   ├── mig1.contemporary_mig │   └── mig2.continuous_mig └── psammophilous ├── single_deme_models │   ├── 0_vcf_files │   └── 1_fastsimcoal2 │   ├── 0_sfs_data │   ├── 1_info │   └── 2_models │   ├── AD5 │   │   ├── per1.constant │   │   ├── per2.expansion │   │   ├── per3.contraction │   │   └── per4.instbot │   ├── AD6 │   │   ├── per1.constant │   │   ├── per2.expansion │   │   ├── per3.contraction │   │   └── per4.instbot │   ├-- [...] │   ├── TI5 │   │   ├── per1.constant │   │   ├── per2.expansion │   │   ├── per3.contraction │   │   └── per4.instbot │   └── TI6 │   ├── per1.constant │   ├── per2.expansion │   ├── per3.contraction │   └── per4.instbot └── two_deme_models ├── 0_vcf_files └── 1_fastsimcoal2 ├── 0_sfs_data ├── 1_info └── 2_models ├── AD5AD6 │   ├── iso1.complete_iso │   ├── iso2.contemporary_iso │   ├── mig1.contemporary_mig │   └── mig2.continuous_mig ├── AD5AD8 │   ├── iso1.complete_iso │   ├── iso2.contemporary_iso │   ├── mig1.contemporary_mig │   └── mig2.continuous_mig ├-- [...] ├── TI6SY4 │   ├── iso1.complete_iso │   ├── iso2.contemporary_iso │   ├── mig1.contemporary_mig │   └── mig2.continuous_mig └── TI6SY5 ├── iso1.complete_iso ├── iso2.contemporary_iso ├── mig1.contemporary_mig └── mig2.continuous_mig ``` ##### Sub-directories **single_deme_models** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 4_demographic_modelling_fastsimcoal2/geophilous/single_deme_models/ ├── 0_vcf_files │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.AD1.c70.onesnp.vcf.gz │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.AD2.c70.onesnp.vcf.gz │   ├-- [...] │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.TI2.c70.onesnp.vcf.gz │   └── eut.per.nc.R30.all.fSEL.fTH99.fDP95.TI3.c70.onesnp.vcf.gz └── 1_fastsimcoal2 ├── 0_sfs_data │   ├── AD1_MAFpop0.obs │   ├── AD2_MAFpop0.obs │   ├-- [...] │   ├── TI2_MAFpop0.obs │   └── TI3_MAFpop0.obs ├── 1_info │   ├── list.models.txt │   ├── list.popfile.txt │   ├── template.per1.constant.est │   ├── template.per1.constant.tpl │   ├── template.per2.expansion.est │   ├── template.per2.expansion.tpl │   ├── template.per3.contraction.est │   ├── template.per3.contraction.tpl │   ├── template.per4.instbot.est │   └── template.per4.instbot.tpl ├── 2_models │   ├── AD1 │   │   ├── per1.constant │   │   │   ├── AD1.per1.constant.est │   │   │   └── AD1.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── AD1.per2.expansion.est │   │   │   └── AD1.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── AD1.per3.contraction.est │   │   │   └── AD1.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── AD1.per4.instbot.est │   │   └── AD1.per4.instbot.tpl │   ├── AD2 │   │   ├── per1.constant │   │   │   ├── AD2.per1.constant.est │   │   │   └── AD2.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── AD2.per2.expansion.est │   │   │   └── AD2.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── AD2.per3.contraction.est │   │   │   └── AD2.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── AD2.per4.instbot.est │   │   └── AD2.per4.instbot.tpl │   ├-- [...] │   ├── TI2 │   │   ├── per1.constant │   │   │   ├── TI2.per1.constant.est │   │   │   └── TI2.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── TI2.per2.expansion.est │   │   │   └── TI2.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── TI2.per3.contraction.est │   │   │   └── TI2.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── TI2.per4.instbot.est │   │   └── TI2.per4.instbot.tpl │   └── TI3 │   ├── per1.constant │   │   ├── TI3.per1.constant.est │   │   └── TI3.per1.constant.tpl │   ├── per2.expansion │   │   ├── TI3.per2.expansion.est │   │   └── TI3.per2.expansion.tpl │   ├── per3.contraction │   │   ├── TI3.per3.contraction.est │   │   └── TI3.per3.contraction.tpl │   └── per4.instbot │   ├── TI3.per4.instbot.est │   └── TI3.per4.instbot.tpl └── setup.models.sh ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 4_demographic_modelling_fastsimcoal2/psammophilous/single_deme_models/ ├── 0_vcf_files │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.AD5.c70.onesnp.vcf.gz │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.AD6.c70.onesnp.vcf.gz │   ├-- [...] │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.TI5.c70.onesnp.vcf.gz │   └── eut.eph.R30.all.fSEL.fTH99.fDP95.TI6.c70.onesnp.vcf.gz └── 1_fastsimcoal2 ├── 0_sfs_data │   ├── AD5_MAFpop0.obs │   ├── AD6_MAFpop0.obs │   ├-- [...] │   ├── TI5_MAFpop0.obs │   └── TI6_MAFpop0.obs ├── 1_info │   ├── list.models.txt │   ├── list.popfile.txt │   ├── template.per1.constant.est │   ├── template.per1.constant.tpl │   ├── template.per2.expansion.est │   ├── template.per2.expansion.tpl │   ├── template.per3.contraction.est │   ├── template.per3.contraction.tpl │   ├── template.per4.instbot.est │   └── template.per4.instbot.tpl ├── 2_models │   ├── AD5 │   │   ├── per1.constant │   │   │   ├── AD5.per1.constant.est │   │   │   └── AD5.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── AD5.per2.expansion.est │   │   │   └── AD5.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── AD5.per3.contraction.est │   │   │   └── AD5.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── AD5.per4.instbot.est │   │   └── AD5.per4.instbot.tpl │   ├── AD6 │   │   ├── per1.constant │   │   │   ├── AD6.per1.constant.est │   │   │   └── AD6.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── AD6.per2.expansion.est │   │   │   └── AD6.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── AD6.per3.contraction.est │   │   │   └── AD6.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── AD6.per4.instbot.est │   │   └── AD6.per4.instbot.tpl │   ├-- [...] │   ├── TI5 │   │   ├── per1.constant │   │   │   ├── TI5.per1.constant.est │   │   │   └── TI5.per1.constant.tpl │   │   ├── per2.expansion │   │   │   ├── TI5.per2.expansion.est │   │   │   └── TI5.per2.expansion.tpl │   │   ├── per3.contraction │   │   │   ├── TI5.per3.contraction.est │   │   │   └── TI5.per3.contraction.tpl │   │   └── per4.instbot │   │   ├── TI5.per4.instbot.est │   │   └── TI5.per4.instbot.tpl │   └── TI6 │   ├── per1.constant │   │   ├── TI6.per1.constant.est │   │   └── TI6.per1.constant.tpl │   ├── per2.expansion │   │   ├── TI6.per2.expansion.est │   │   └── TI6.per2.expansion.tpl │   ├── per3.contraction │   │   ├── TI6.per3.contraction.est │   │   └── TI6.per3.contraction.tpl │   └── per4.instbot │   ├── TI6.per4.instbot.est │   └── TI6.per4.instbot.tpl └── setup.models.sh ``` It includes all input files for single-deme demographic analyses as implemented in `FASTSIMCOAL2 v27093`. For each dataset/lineage, there are two sub-directories and a relevant script: * The `0_vcf_files` directory, which includes a single `*.vcf` file per deme. These are the input files for the `easySFS.py` script ([https://github.com/isaacovercast/easySFS](https://github.com/isaacovercast/easySFS)), which was used to generate the deme-specific site frequency spectra (SFS). * The `1_fastsimcoal2` directory, which is further divided into: * The `0_sfs_data` directory includes one SFS file in `fastsimcoal2` format per deme, as estimated by the `easySFS.py` script. * The `1_info` directory includes: 1. A `list.models.txt` file with all model names 2. A `list.popfile.txt` file with three columns, where: * **Column 1:** deme identifiers * **Column 2:** deme effective population size (*Ne*), as estimated based on the *Ne=(θ/4μ)* equation, approximating *θ* using the nucleotide diversity (*π*) values from the PIXY analyses and an assumed mutation rate (*μ*) of *2.8×10⁻⁹*. * **Column 3:** sample size after projecting down, as estimated by the `easySFS.py` script. 3. Template `*.tpl` and `*.est` files for `fastsimcoal2` that are used by the provided `setup.models.sh` bash script to automatically create the four demographic models per deme * The `2_models` directory, which includes one sub-directory per deme, with the needed `*.tpl` and `*.est` files to run `fastsimcoal2`. * The `setup.models.sh` bash script, which uses the files in `1_info` directory to automatically create the `2_models` directory and its contents. **two_deme_models** ``` ################################################## ### GEOPHILOUS lineage dataset ################################################## 4_demographic_modelling_fastsimcoal2/geophilous/two_deme_models/ ├── 0_vcf_files │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.AD1AD2.c70.onesnp.vcf.gz │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.AD1AD3.c70.onesnp.vcf.gz │   ├-- [...] │   ├── eut.per.nc.R30.all.fSEL.fTH99.fDP95.TI2SY3.c70.onesnp.vcf.gz │   └── eut.per.nc.R30.all.fSEL.fTH99.fDP95.TI2TI3.c70.onesnp.vcf.gz └── 1_fastsimcoal2 ├── 0_sfs_data │   ├── AD1AD2.c70.onesnp_jointMAFpop1_0.obs │   ├── AD1AD3.c70.onesnp_jointMAFpop1_0.obs │   ├-- [...] │   ├── TI2SY3.c70.onesnp_jointMAFpop1_0.obs │   └── TI2TI3.c70.onesnp_jointMAFpop1_0.obs ├── 1_info │   ├── list.models.txt │   ├── list.popfile.txt │   ├── template.iso1.complete_iso.est │   ├── template.iso1.complete_iso.tpl │   ├── template.iso2.contemporary_iso.est │   ├── template.iso2.contemporary_iso.tpl │   ├── template.mig1.contemporary_mig.est │   ├── template.mig1.contemporary_mig.tpl │   ├── template.mig2.continuous_mig.est │   └── template.mig2.continuous_mig.tpl ├── 2_models │   ├── AD1AD2 │   │   ├── iso1.complete_iso │   │   │   ├── AD1AD2.iso1.complete_iso.est │   │   │   └── AD1AD2.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── AD1AD2.iso2.contemporary_iso.est │   │   │   └── AD1AD2.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── AD1AD2.mig1.contemporary_mig.est │   │   │   └── AD1AD2.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── AD1AD2.mig2.continuous_mig.est │   │   └── AD1AD2.mig2.continuous_mig.tpl │   ├── AD1AD3 │   │   ├── iso1.complete_iso │   │   │   ├── AD1AD3.iso1.complete_iso.est │   │   │   └── AD1AD3.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── AD1AD3.iso2.contemporary_iso.est │   │   │   └── AD1AD3.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── AD1AD3.mig1.contemporary_mig.est │   │   │   └── AD1AD3.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── AD1AD3.mig2.continuous_mig.est │   │   └── AD1AD3.mig2.continuous_mig.tpl │   ├-- [...] │   ├── TI2SY3 │   │   ├── iso1.complete_iso │   │   │   ├── TI2SY3.iso1.complete_iso.est │   │   │   └── TI2SY3.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── TI2SY3.iso2.contemporary_iso.est │   │   │   └── TI2SY3.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── TI2SY3.mig1.contemporary_mig.est │   │   │   └── TI2SY3.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── TI2SY3.mig2.continuous_mig.est │   │   └── TI2SY3.mig2.continuous_mig.tpl │   └── TI2TI3 │   ├── iso1.complete_iso │   │   ├── TI2TI3.iso1.complete_iso.est │   │   └── TI2TI3.iso1.complete_iso.tpl │   ├── iso2.contemporary_iso │   │   ├── TI2TI3.iso2.contemporary_iso.est │   │   └── TI2TI3.iso2.contemporary_iso.tpl │   ├── mig1.contemporary_mig │   │   ├── TI2TI3.mig1.contemporary_mig.est │   │   └── TI2TI3.mig1.contemporary_mig.tpl │   └── mig2.continuous_mig │   ├── TI2TI3.mig2.continuous_mig.est │   └── TI2TI3.mig2.continuous_mig.tpl └── setup.models.sh ################################################## ### PSAMMOPHILOUS lineage dataset ################################################## 4_demographic_modelling_fastsimcoal2/psammophilous/two_deme_models/ ├── 0_vcf_files │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.AD5AD6.c70.onesnp.vcf.gz │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.AD5AD8.c70.onesnp.vcf.gz │   ├-- [...] │   ├── eut.eph.R30.all.fSEL.fTH99.fDP95.TI6SY4.c70.onesnp.vcf.gz │   └── eut.eph.R30.all.fSEL.fTH99.fDP95.TI6SY5.c70.onesnp.vcf.gz └── 1_fastsimcoal2 ├── 0_sfs_data │   ├── AD5AD6.c70.onesnp_jointMAFpop1_0.obs │   ├── AD5AD8.c70.onesnp_jointMAFpop1_0.obs │   ├-- [...] │   ├── TI6SY4.c70.onesnp_jointMAFpop1_0.obs │   └── TI6SY5.c70.onesnp_jointMAFpop1_0.obs ├── 1_info │   ├── list.models.txt │   ├── list.popfile.txt │   ├── template.iso1.complete_iso.est │   ├── template.iso1.complete_iso.tpl │   ├── template.iso2.contemporary_iso.est │   ├── template.iso2.contemporary_iso.tpl │   ├── template.mig1.contemporary_mig.est │   ├── template.mig1.contemporary_mig.tpl │   ├── template.mig2.continuous_mig.est │   └── template.mig2.continuous_mig.tpl ├── 2_models │   ├── AD5AD6 │   │   ├── iso1.complete_iso │   │   │   ├── AD5AD6.iso1.complete_iso.est │   │   │   └── AD5AD6.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── AD5AD6.iso2.contemporary_iso.est │   │   │   └── AD5AD6.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── AD5AD6.mig1.contemporary_mig.est │   │   │   └── AD5AD6.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── AD5AD6.mig2.continuous_mig.est │   │   └── AD5AD6.mig2.continuous_mig.tpl │   ├── AD5AD8 │   │   ├── iso1.complete_iso │   │   │   ├── AD5AD8.iso1.complete_iso.est │   │   │   └── AD5AD8.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── AD5AD8.iso2.contemporary_iso.est │   │   │   └── AD5AD8.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── AD5AD8.mig1.contemporary_mig.est │   │   │   └── AD5AD8.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── AD5AD8.mig2.continuous_mig.est │   │   └── AD5AD8.mig2.continuous_mig.tpl │   ├-- [...] │   ├── TI6SY4 │   │   ├── iso1.complete_iso │   │   │   ├── TI6SY4.iso1.complete_iso.est │   │   │   └── TI6SY4.iso1.complete_iso.tpl │   │   ├── iso2.contemporary_iso │   │   │   ├── TI6SY4.iso2.contemporary_iso.est │   │   │   └── TI6SY4.iso2.contemporary_iso.tpl │   │   ├── mig1.contemporary_mig │   │   │   ├── TI6SY4.mig1.contemporary_mig.est │   │   │   └── TI6SY4.mig1.contemporary_mig.tpl │   │   └── mig2.continuous_mig │   │   ├── TI6SY4.mig2.continuous_mig.est │   │   └── TI6SY4.mig2.continuous_mig.tpl │   └── TI6SY5 │   ├── iso1.complete_iso │   │   ├── TI6SY5.iso1.complete_iso.est │   │   └── TI6SY5.iso1.complete_iso.tpl │   ├── iso2.contemporary_iso │   │   ├── TI6SY5.iso2.contemporary_iso.est │   │   └── TI6SY5.iso2.contemporary_iso.tpl │   ├── mig1.contemporary_mig │   │   ├── TI6SY5.mig1.contemporary_mig.est │   │   └── TI6SY5.mig1.contemporary_mig.tpl │   └── mig2.continuous_mig │   ├── TI6SY5.mig2.continuous_mig.est │   └── TI6SY5.mig2.continuous_mig.tpl └── setup.models.sh ``` It includes all input files for two-deme demographic analyses as implemented in `FASTSIMCOAL2 v27093`. For each dataset/lineage, there are two sub-directories and a relevant script: * The `0_vcf_files` directory, which includes a single `*.vcf` file per deme pair. These are the input files for the `easySFS.py` script, which were used to generate the joint site frequency spectra (jSFS) of the analysed deme pairs. * The `1_fastsimcoal2` directory, which is further divided into: * The `0_sfs_data` directory includes one jSFS file in `fastsimcoal2` format per deme pair, as estimated by the `easySFS.py` script. * The `1_info` directory includes: 1. A `list.models.txt` file with all demographic model names 2. A `list.popfile.txt` file with two columns, where: * **Column 1:** deme pair identifiers * **Column 2:** effective population size (*Ne*), as estimated based on the *Ne=(θ/4μ)* equation, approximating *θ* using the nucleotide diversity (*π*) values from the PIXY analyses and an assumed mutation rate (*μ*) of *2.8×10⁻⁹*. This effective population size corresponds to one of the two demes in the pair and was used as a fixed value in the demographic analyses. 3. Template `*.tpl` and `*.est` files for `fastsimcoal2` that are used by the provided `setup.models.sh` bash script to automatically create the four demographic models per deme pair * The `2_models` directory, which includes one sub-directory per deme pair, with the needed `*.tpl` and `*.est` files to run `fastsimcoal2`. * The `setup.models.sh` bash script, which uses the files in `1_info` directory to automatically create the `2_models` directory and its contents.