DOI: 10.5061/dryad.g68k008
title: Data from: Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican wolf (Canis lupus baileyi)

description: The Mexican gray wolf (Canis lupus baileyi) was historically distributed
 throughout the southwestern United States and northern Mexico. Extensive
 predator removal campaigns during the early 20th century, however,
 resulted in its eventual extirpation by the mid 1980s. At this time, the
 Mexican wolf existed only in three separate captive lineages (McBride,
 Ghost Ranch, and Aragón) descended from three, two, and two founders,
 respectively. These lineages were merged in 1995 to increase the available
 genetic variation, and Mexican wolves were reintroduced into Arizona and
 New Mexico in 1998. Despite the ongoing management of the Mexican wolf
 population, it has been suggested that a proportion of the Mexican wolf
 ancestry may be recently derived from hybridization with domestic dogs. In
 this study, we genotyped 87 Mexican wolves, including individuals from all
 three captive lineages and cross-lineage wolves, for more than 172,000
 single nucleotide polymorphisms (SNPs). We identified levels of genetic
 variation consistent with the pedigree record and effects of genetic
 rescue. To identify the potential to detect hybridization with domestic
 dogs, we compared our Mexican wolf genotypes with those from studies of
 domestic dogs and other gray wolves. The proportion of Mexican wolf
 ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and
 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and
 was consistent with simulated levels of incomplete lineage sorting.
 Overall, our results suggested that Mexican wolves lack biologically
 significant ancestry with dogs and have useful implications for the
 conservation and management of this endangered wolf subspecies.
description: READMEPlease read for more
 information and md5 checksums for the contents of this data
 repository.MW raw
 dataRaw fluorescence data
 from the BeadChip analysis. This is RAW, UNPROCESSED
 data.MW_raw_data.tar.gzMexican Wolf unprocessed genotypesRaw, Mexican wolf genotypes prior to any filtering in the standard PLINK format.MW.pedMexican wolf raw SNP locationsRaw, Mexican wolf SNP locations prior to any filtering in the standard PLINK format.MW.mapMexican Wolf Sample SpreadsheetA simple excel spreadsheet to convert sample IDs between BeadChip IDs, studbook numbers, and museum numbersMW-Samples.xlsxMexican wolf cleaned genotypes PEDThis file contain the filtered set of genotypes and sample information for the 84 samples (83 Mex Wolves and 1 domestic dog). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MW.clean.pedMexican wolf cleaned genotypes MAPThis file contains the SNP position data in the Plink 'map' format for the 62219 SNPs after filtering. See Table 1 in the manuscriptMW.clean.mapMERGED set of genotypes PEDThis file contains the unfiltered set of genotypes and sample information for the 1094 samples (89 Mex Wolves + 371 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.pedMERGED set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 169066 SNPs before filtering. See Table 1 in the manuscriptMERGED.mapMERGED clean set of genotypes PEDThis file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.clean.pedMERGED clean set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 118287 SNPs after filtering. See Table 1 in the manuscriptMERGED.clean.mapMERGED clean pruned set of genotypes PEDThis file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.clean.pruned.pedMERGED clean pruned set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 74876 SNPs after filtering and LD pruning. See Table 1 in the manuscriptMERGED.clean.pruned.mapLampLD 3-way local admixture results and phased genotypesThis file, once unpacked, contains the results of the local ancestry analysis using LAMP-LD v1.3. In addition to the numerous output files, there is a folder for each of the 38 chromosomes. Each chromosome's folder contains the LAMP-LD results. Most importantly, for each chromosome the phased genotypes generated using Beagle are found in the files chr#_phased.txt. I recommend following the code described at the GitHub page https://github.com/rfitak/Mexican_Wolf_SNPs to know exactly what each of the files represents.LampLD-3way.tar.gz