FinalNuclearLoci_ECM7278

FinalNuclearLoci_ECM727

Probes for Anchored Hybrid Enrichment

Alignments and probe sequences used for anchored hybrid enrichment of anurans. Alignments are labeled by locus number and include sequences for Xenopus tropicalis (ind 1), Pseudacris feriarum (ind 2), Pseudacris nigrita (ind 3), Rana sphenocephala (ind 4). The 120-bp probe sequences and associated names are provided in "Amp2_XenRanNigFer.txt" and the key file associates the probe name with the locus number, species (ind 1-4), and site within the alignment

Phylogeographic Concordance Factor analyses

Phylogeographic Concordance Factor analyses and results. Includes SNAPP results for nuclear datasets, *BEAST results for mitochondrial datasets, (4-region and 5-region models for each), and PCF results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala

SNP datasets

SNP datasets for each species and summary table of SNP information. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala

RAxML GeneTree 1allele Alignments

RAxML 1-allele Alignments. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephal

RAxML Concatenated Alignments and Results

RAxML Concatenated Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephal

Python scripts

Python scripts for extracting SNPs from 1-allele RAxML (phylip) files; and script for summarizing bootstrap values from RAxML 2-allele results. Additional details are commented in each script

Supporting Information

Supporting information including supplementary methods on probe design and supplementary tables and figures

RAxML GeneTree 2alleles Alignments and Results

RAxML GeneTree 2alleles Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephal

Mitochondrial Datasets and Results

Mitochondrial alignments and RAxML results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephal