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.
README
Please read for more information and md5 checksums for the contents of this data repository.
MW raw data
Raw fluorescence data from the BeadChip analysis. This is RAW, UNPROCESSED data.
MW_raw_data.tar.gz
Mexican Wolf unprocessed genotypes
Raw, Mexican wolf genotypes prior to any filtering in the standard PLINK format.
MW.ped
Mexican wolf raw SNP locations
Raw, Mexican wolf SNP locations prior to any filtering in the standard PLINK format.
MW.map
Mexican Wolf Sample Spreadsheet
A simple excel spreadsheet to convert sample IDs between BeadChip IDs, studbook numbers, and museum numbers
MW-Samples.xlsx
Mexican wolf cleaned genotypes PED
This 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.ped
Mexican wolf cleaned genotypes MAP
This file contains the SNP position data
in the Plink 'map' format for the 62219 SNPs after
filtering. See Table 1 in the manuscript
MW.clean.map
MERGED set of genotypes PED
This 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.ped
MERGED set of SNPs MAP
This file contains the SNP position data
in the Plink 'map' format for the 169066 SNPs before
filtering. See Table 1 in the manuscript
MERGED.map
MERGED clean set of genotypes PED
This 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.ped
MERGED clean set of SNPs MAP
This file contains the SNP position data
in the Plink 'map' format for the 118287 SNPs after
filtering. See Table 1 in the manuscript
MERGED.clean.map
MERGED clean pruned set of genotypes PED
This 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.ped
MERGED clean pruned set of SNPs MAP
This 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 manuscript
MERGED.clean.pruned.map
LampLD 3-way local admixture results and phased genotypes
This 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