Blanding's turtle location and microsatellite data

This dataset includes location and genetic data for Blanding's turtles sampled in Wood County, WI. The first sheet ("NestingFemaleData") includes data for females captured during terrestrial nesting surveys. Nesting areas are as described in the publication; any turtle captured outside of the seven main nesting areas identified are listed as "other". The second sheet ("NonNestingData") includes all other turtles, including adult males, adult females captured in aquatic locations, and juveniles of unknown sex. For all location data, "X" and "Y" are UTM coordinates (UTM zone 15N, WGS84 datum). When individuals were captured more than once, coordinates represent the centroid of all capture points. Missing data for microsatellites are represented as "xxx"

SAS Source Code for estimating genotyping error rates

Contains SAS script for estimating genotyping error rates using Mendelian incompatibilities

SNP_datasets

Contains the SNP datasets used for analysis of genotyping error rates from reference alignment, reference alignment rxstacks, de novo assembly and de novo assembly rxstacks

nuclear_emydura_group_beast_input

Nuclear data in nexus format used as the input for the Beast analysis

emydura.group

XML file used in the BEAST molecular clock analysis using only the Redbank Plains fossil calibration

reduced_gene_set_CR_ND4_phylogeny

This nexus file contains the sequence data for the reduced gene set (ND4 and CR) used to recover the phylogeny for mitochondrial haplotypes of Elseya novaeguineae, with E. branderhorsti haplotypes as outgroup

full_gene_set_12S_16S_CO1_CytB_phylogeny

This nexus file contains the sequence data for the full gene set (ND4, CR, 12s, 16s,Cox1, Cytb) used to confirm major nodes and refine bootstrap support for Elseya novaeguineae, with E. branderhorsti as outgroup

mtdna_emydura_group_beast_input

Mitochondrial data in nexus format used as the input for the Beast analysis

emydura_group_beast_trees_comb_1-7-5_output

Maximum clade credibility tree saved from figtree from the combined output of our Beast runs

Arlequin microsatellite input file

Arlequin microsatellite input file from six Chelonia mydas rookeries in the Atlantic, for 15 loci