DOI: 10.5061/dryad.rn8pk0pds
title: Complex patterns of diversification in the gray zone of speciation: Model-based approaches applied to Patagonian liolaemid lizards (Squamata: Liolaemus kingii clade)

description: In this study, we detangled the evolutionary history of the Patagonian
 lizard clade Liolaemus kingii, coupling dense geographic sampling and
 novel computational analytical approaches. We analyzed nuclear and
 mitochondrial data (restriction DNA sequencing and cytochrome b) to
 hypothesize and evaluate species limits, phylogenetic relationships, and
 demographic histories. We also conducted posterior predictive simulations
 to assess the fit of the genomic data to the multispecies coalescent
 model. Our results show several instances of mito-nuclear discordance and
 consistent support for a reticulated history, supporting the view that the
 complex evolutionary history of the kingii clade is characterized by
 extensive gene flow and rapid diversification events. We discuss our
 findings in the contexts of the “gray zone” of speciation, phylogeographic
 patterns in the Patagonian region, and taxonomic outcomes.
description: # Complex patterns of diversification in the gray zone of speciation:
 Model-based approaches applied to Patagonian liolaemid lizards (Squamata:
 Liolaemus kingii clade)
 [https://doi.org/10.5061/dryad.rn8pk0pds](https://doi.org/10.5061/dryad.rn8pk0pds) This readme file was generated on 2023-Sep-18 by Kevin Sánchez # GENERAL INFORMATION * **Title of Dataset:** Supplementary data for the article "Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: *Liolaemus kingii* clade)" ## Author/Principal Investigator Information * **Name:** Kevin Sánchez * **ORCID:** 0000-0002-2364-2327 * **Institution:** IPEEC-CONICET * **Address:** Bv. Almirante Brown 2915 * **Email:** [kevin.imanol.sanchez@gmail.com](kevin.imanol.sanchez@gmail.com) ## Data information * **Date of data collection:** from 2000 to 2018 * **Geographic location of data collection:** Southern Patagonia, Argentina and Chile * **Information about funding sources that supported the collection of the data:** NSF, CONICET, ANPCYT # SHARING/ACCESS INFORMATION * **Licenses/restrictions placed on the data:** * **Links to publications that cite or use the data:** * **Links to other publicly accessible locations of the data:** * **Links/relationships to ancillary data sets:** * **Was data derived from another source?** If yes, list source(s): * **Recommended citation for this dataset:** Sánchez, Kevin et al. (2023), Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: *Liolaemus kingii* clade), Dryad, Dataset, https://doi.org/10.5061/dryad.rn8pk0pds # DATA & FILE OVERVIEW * **File List:** * `cytb_partitionedML.treefile` (49.71 kB): Maximum Likelihood cytb tree * `cytb_aligned.fasta` (895.42 kB): aligned cytb matrix, including outgroups * `clust90_min37_46_subset.loci` (4.71 MB): RAD loci from subset of 38 individuals (output of ipyrad) * `concat_RADloci_permissive.treefile` (5.70 kB): Maximum Likelihood concatenated RAD loci tree (permissive dataset) * `concat_RADloci_strict.treefile` (5.65 kB): Maximum Likelihood concatenated RAD loci tree (strict dataset) * `RADloci_clust90min93_strict.loci` (8.97 MB): RAD loci, strict dataset (output of ipyrad) * `RADloci_clust90min23_permissive.loci` (27.56 MB): RAD loci, permissive dataset (output of ipyrad) * `appendixS1.csv` (207.5 kB): voucher information * `data.zip`: matrices needed to replicate the analyses of the GitHub repository ([https://github.com/k-sanchez/Liolaemus_kingii_clade_phylogeography](https://github.com/k-sanchez/Liolaemus_kingii_clade_phylogeography)) * `PipeMaster/`: data to conduct demographic model selection * `west/`: data of the Western populations * `fastas/`: folder with fasta matrices * `popmap.txt`: populations assignments * `south/`: data of the Southern populations * `fastas`: folder with fasta matrices * `popmap.txt`: populations assignments * `kingii_deseado`: data of _L. kingii_ and the "Deseado" clade * `fastas`: folder with fasta matrices * `popmap.txt`: populations assignments * `PhyloNetworks/`: data to conduct phylogenetic network estimations * `SNPs2CF/`: tables of concordance factors * `starting_tree.tre`: MSC phylogeny estimated in SNAPPER to start the network search * `clust90_min37_46_subset_unphased.usnps.phy`: matrix of SNPs in PHYLIP format (output of the function `vcf2phylip()`) * `clust90_min37_46_subset.usnps.vcf`: matrix of SNPs in VCF format * `bpp/`: data to conduct parameter estimations and posterior predictive simulations using bpp * `postPredSim_MSC/`: data to conduct posterior predictive simulations, which includes the empirical posterior distribution of parameters (`mcmc.txt`) and the posterior distributions of parameters estimated from simulated datasets (`simulated_datasets/dataset{1..100}`) * `A00_MSCi/`: posterior distribution of parameters of the MSCi model * `A00_MSC_gdi/`: posterior distribution of parameters of the MSC model