We used a large number of wild-derived female house mice in oestrus or proestrus as subjects throughout this study (bred in captivity to control experience).
Descriptive information on the sample of dogs in the study, breed groups (according to The Kennel Club Organisation [ 28]), age, sex, weight and diet, are provided in Table 2.
In this study, breed origins of SNP alleles were assumed to be known without error but this may not hold for real data, which would introduce errors to the estimation of breed-specific SNP effects in BSAM.
Furthermore, we extracted nsSNP sets that did not overlap among the breeds in this study (breed-specific nsSNP) and identified 126, 26, 11, 10, and 8 for KWB, KNP, DUR, LAN, and YOR, respectively (Supplementary Table S3).
All species selected in this study breed in North America, all species pairs have large overlapping geographic ranges, and museum tissue samples were chosen such that species pairs would have roughly matching geographic sampling (Additional file 1: Table S1).
The gene frequency analysis evidenced significant differences among the studied breeds (FST = 0.325, p = 0.000).
Four alleles (A, B, C and D) and six genotypes (AA, AB, BB, CC, DD and CD) were identified in all studied breeds upon exon 3 analysis.
The NR6A1 c. 748T allele, associated with higher number of vertebrae, appeared to be fixed in most studied breeds except in Iberians.
The VRTN insertion (Ins allele) shows ample variability in all studied breeds although the allelic frequency of Ins seems to be larger in breeds with a greater history of genetic selection.
