DOI: 10.5061/dryad.05qfttf9k
title: Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)

description: Evolutionary processes behind lineage divergence often involve
 multidimensional differentiation. However, in the context of recent
 divergences, the signals exhibited by each dimension may not converge. In
 such scenarios, incomplete lineage sorting, gene flow, and scarce
 phenotypic differentiation are pervasive. Here, we integrated genomic (RAD
 loci of 90 individuals), phenotypic (linear and geometric traits of 823
 and 411 individuals, respectively), spatial, and climatic data to
 reconstruct the evolutionary history of a speciation continuum of
 liolaemid lizards (Liolaemus kingii group). Specifically, we (i) inferred
 the population structure of the group and contrasted it with the
 phenotypic variability; (ii) assessed the role of post-divergence gene
 flow in shaping phylogeographic and phenotypic patterns; and (iii)
 explored eco-geographic drivers of diversification across time and space.
 We inferred eight genomic clusters exhibiting leaky genetic borders
 coincident with geographic transitions. We also found evidence of
 post-divergence gene flow resulting in transgressive phenotypic evolution
 in one species. Predicted ancestral niches unveiled suitable areas in
 southern and eastern Patagonia during glacial and interglacial periods.
 Our study underscores integrating different data and model-based
 approaches to determine the underlying causes of diversification, a
 challenge faced in the study of recently diverged groups. We also
 highlight Liolaemus as a model system for phylogeographic and broader
 evolutionary studies.
description: # Tracing evolutionary trajectories in the presence of gene flow in South
 American temperate lizards (Squamata: *Liolaemus kingii* group)
 ## Notes Specimens and
 tissues are hosted in the herpetological collection LJAMM-CNP
 (IPEEC-CONICET, Puerto Madryn, Argentina). Field trips were conducted in
 the Patagonia Steppe during the years 2000-2022. ## Usage Uncompress the
 data and follow the steps provided in the scripts to replicate the results
 presented in the manuscript ## File structure * `bpp_A00_MSci.zip`: bpp
 estimates of Multispecies Coalescent + introgression parameters. The
 script `phylogeography.R` includes the code used to estimate the support
 for the different introgression models through the Savage-Dickey density
 ratio. The rationale behind the analysis is detailed in the Supplementary
 Material. * `step1/`: Step 1 of the protocol implemented to reconstruct
 introgression events. * `bid_bag-sou/`: parameters of the `baguali` ⇄
 `south` introgression model. * `bid_cha-wes/`: parameters of the
 `chacabucoense` ⇄ `west` introgression model. * `bid_kin-des/`: parameters
 of the `kingii` ⇄ `deseado` introgression model. * `introg1_CF-attA/`:
 parameters of the `C-F` branch → `attenboroughi` introgression model. *
 `introg1_attA-CF/`: parameters of the `attenboroughi` → `C-F` branch
 introgression model. * `introg2_chaC-attA/`: parameters of the
 `chacabucoense` → `attenboroughi` introgression model. *
 `introg2_attA-chaC/`: parameters of the `chacabucoense` → `attenboroughi`
 introgression model. * `introg3_attA-wesC/`: parameters of the
 `attenboroughi` → `west` introgression model. * `introg3_wesC-attA/`:
 parameters of the `west` → `attenboroughi` introgression model. *
 `step2/`: Step 2 of the protocol implemented to reconstruct introgression
 events. Supported events of the step 1, according to the Savage-Density
 dickey ratio, were added sequentially in this step. *
 `introg1_bid_desD-kinD/`: parameters of the `kingii` ⇄ `deseado`
 introgression model. * `introg2_wesC-chaC`: parameters of the `kingii` ⇄
 `deseado` and `west` → `chacabucoense` introgression model. *
 `introg3_souB-bagB/`: parameters of the `kingii` ⇄ `deseado`, `west` →
 `chacabucoense`, and `south` → `baguali` introgression model. *
 `introg4_CF-attA/`: parameters of the `kingii` ⇄ `deseado`, `west` →
 `chacabucoense`, `south` → `baguali`, and `C-F` branch → `attenboroughi`
 introgression model. * `introg5_chaC-attA/`: parameters of the `kingii` ⇄
 `deseado`, `west` → `chacabucoense`, `south` → `baguali`, `C-F` branch →
 `attenboroughi`, and `chacabucoense` → `attenboroughi` introgression
 model. * `step3/`: parameters of the full introgression model of the
 *kingii* group. * `genomics.zip`: Filtered RAD loci data.
 Genomic data was obtained using the ddRADseq approach. *
 `populations.snps.maf0.01.geno`: Unlinked SNPs in `geno` format. Input for
 LEA. * `populations.snps.maf0.01.vcf`: Unlinked SNPs in `vcf` format. *
 `populations.snps.maf0.01.kin_des.vcf`: Unlinked SNPs of *L. kingii* and
 the "Deseado" clade in `vcf` format. *
 `populations.snps.maf0.01.net.vcf`: Unlinked SNPs in `vcf` format.
 Required by the `SNPs2CF()` R function to calculate the table of
 concordance factors. * `maps.zip`: Distribution maps of the
 lineages included in the *kingii* group and raster data used to estimate
 the influence of spatial/environmental factors on the genetic structure.
 Occurrence data for the specimens were obtained using GPS, primary
 literature sources, and online databases VertNet and GBIF. The range of
 each lineage was generated with the function `rangemap_hull()` function of
 the R package `rangemap` and exported as shapefiles (archives `.dbf`,
 `.prj`, `.shp`, and `.shx`). Also is included the whole range of the study
 group (files `fullrange.*` and `fullrange_crop.*` *
 `phenotype.zip`: Phenotypic data. Linear variables include: snout-vent
 length (SVL), arm length (AL), tibia-fibula length (TFL), head height
 (HH), head width (HW), snout length (SL), rostral-nasal distance (RND),
 auditory opening height (AH), auditory opening width (AW), rostral height
 (RH), mental height (MH), rostral width (RW), mental width (MW), anterior
 distance between orbits (ADO), and posterior distance between orbits
 (PDO). All these variables are measured in millimeters. Meristic variables
 include: number of scales in contact with the interparietal scale (SCI),
 number of scales in contact with mental scale (SCM), number of lorilabial
 scales (LS), number of supralabial scales (SS), number of infralabial
 scales (IS), number of scales around midbody (SAM), number of infradigital
 lamellae on the third finger (IL3), and number of precloacal pores (PP).
 Geometric morphometric data variables are defined in the Supplementary
 Material. * `dorsal_head_males.zip`: Images of the dorsal head view of
 male specimens. * `lineal_meristic_all.csv`: Raw morphometric data,
 including linear measurements and scale counts. * `phenoevol_allom.csv`:
 Phenotypic data of males and females corrected for allometry. *
 `phenoevol_m_allom.csv`: Phenotypic data of males corrected for allometry.
 * `phenoevol_f_allom.csv`: Phenotypic data of females corrected for
 allometry. * `grupoKingii_males.tps`: Two-dimensional landmarks
 coordinates. * `gm_males_red_nooutliers.tps`: Two-dimensional landmarks
 coordinates with outlier specimens removed. * `phenoevol_gm_raw.csv`:
 Two-dimensional landmarks coordinates in `csv` format. *
 `phenoevol_gm_pcscores.csv`: Principal component loadings of
 two-dimensional landmarks coordinates. * `phylo.zip`: Phylogenetic data,
 including: * Maximum likelihood tree of concatenated RAD loci
 (`out_all.treefile`). * SplitsTree network (`NNet_uncorrP.nex`). *
 Time-calibrated Bayesian phylogeny of the group (`mcc_median.tre`). *
 `sheets.zip`: Dataframes required to replicate the analyzes * Occurrence
 data of each lineage (`full_records.csv`). * Mapping of specimens to
 lineages included in the assessment of the spatial drivers of genetic
 structure and niche reconstructions (`mapping_seqs.csv`). * Mapping of
 specimens to lineages included in the geometric morphometric analyzes
 (`classif_gm.csv`). * Mapping of specimens to lineages included in the
 network reconstructions: * `popmap.txt`: used to obtain the table of
 concordance factors. * `net_pops.tsv`: used as input in PhyloNetworks to
 estimate the phylogenetic network of the group. *
 `delimitR.zip`: Data used to estimate the support for migration events
 between sister taxa: (i) *attenboroughi *- *somuncurae* clade, (ii)
 *baguali* - South group, (iii) *chacabucoense* - West group, and (iv)
 *kingii* - Deseado clade). The file `prediction.csv` shows the models of
 divergence supported by delimitR. * Files `*_popmap_easySFS.txt`: Mapping
 of specimens to lineages to be used in easySFS. * Files
 `*_easySFS_preview.txt`: Population size projection for construction of
 the site frequency spectrum. * Files `*_popmap_delimitR.txt`: Mapping of
 specimens to lineages to be used in delimitR. * `samples.tsv`: Information
 about the samples included in the study. ## Code The scripts required to
 reproduce the analyses are hosted in Zenodo and GitHub
 ().