Complex patterns of diversification in the gray zone of speciation: Model-based approaches applied to Patagonian liolaemid lizards (Squamata: Liolaemus kingii clade)
Data files
Mar 31, 2023 version files 42.40 MB
-
appendixS1.csv
-
clust90_min37_46_subset.loci
-
concat_RADloci_permissive.treefile
-
concat_RADloci_strict.treefile
-
cytb_aligned.fasta
-
cytb_partitionedML.treefile
-
RADloci_clust90min23_permissive.loci
-
RADloci_clust90min93_strict.loci
-
README.txt
Sep 19, 2023 version files 364.07 MB
-
appendixS1.csv
-
clust90_min37_46_subset.loci
-
concat_RADloci_permissive.treefile
-
concat_RADloci_strict.treefile
-
cytb_aligned.fasta
-
cytb_partitionedML.treefile
-
data.zip
-
RADloci_clust90min23_permissive.loci
-
RADloci_clust90min93_strict.loci
-
README.md
Abstract
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.
README: 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
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
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 treecytb_aligned.fasta
(895.42 kB): aligned cytb matrix, including outgroupsclust90_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 informationdata.zip
: matrices needed to replicate the analyses of the GitHub repository (https://github.com/k-sanchez/Liolaemus_kingii_clade_phylogeography)PipeMaster/
: data to conduct demographic model selectionwest/
: data of the Western populationsfastas/
: folder with fasta matricespopmap.txt
: populations assignments
south/
: data of the Southern populationsfastas
: folder with fasta matricespopmap.txt
: populations assignments
kingii_deseado
: data of L. kingii and the "Deseado" cladefastas
: folder with fasta matricespopmap.txt
: populations assignments
PhyloNetworks/
: data to conduct phylogenetic network estimationsSNPs2CF/
: tables of concordance factorsstarting_tree.tre
: MSC phylogeny estimated in SNAPPER to start the network searchclust90_min37_46_subset_unphased.usnps.phy
: matrix of SNPs in PHYLIP format (output of the functionvcf2phylip()
)clust90_min37_46_subset.usnps.vcf
: matrix of SNPs in VCF format
bpp/
: data to conduct parameter estimations and posterior predictive simulations using bpppostPredSim_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 modelA00_MSC_gdi/
: posterior distribution of parameters of the MSC model