26 research outputs found
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 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
RAxML GeneTree 1allele Alignments
RAxML 1-allele Alignments. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephal
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