Table 1.
Summary of the datasets used in this study
| Dataset | Mexican wolves | Gray wolves | Dogs | Total | Autosomal SNPs | XY SNPs | Total SNPs | Call rate | Citation |
|---|---|---|---|---|---|---|---|---|---|
| MW | 83 | 0 | 1 | 84a | 166582 | 5532 | 172114 | 0.989 | This study |
| MW-cleaned | 83 | 0 | 1 | 84 | 62219 | 0 | 62219 | 0.989 | This study |
| MW-cleaned-pruned | 83 | 0 | 1 | 84 | 7295 | 0 | 7268 | 0.989 | This study |
| LUPA | 0 | 15 | 532 | 547 | 169066 | 5744 | 174810 | 0.983 | Vaysse et al. (2011) |
| NAC | 8 | 297 | 91 | 396 | 120671 | 3130 | 123801 | 0.946 | Cronin et al. (2014) |
| EURO | 0 | 59 | 0 | 59 | 131118 | 3430 | 134548 | 0.982 | Stronen et al. (2013) |
| HUSK | 0 | 0 | 10 | 10 | 166583 | 5532 | 172115 | 0.987 | Vernau et al. (2013) |
| Merged | 89b | 371 | 634 | 1094 | 169066 | 0 | 169066 | 0.861 | This study |
| Merged-cleaned | 88 | 299 | 634 | 1021 | 118287 | 0 | 118287 | 0.991 | This study |
| Merged-cleaned- pruned | 88 | 299 | 634 | 1021 | 74876 | 0 | 74876 | 0.991 | This study |
The Mexican wolf (MW) and Merged datasets are shown before quality control, after removal of low quality loci and individuals (“Cleaned”), and again after removal of loci in high linkage disequilibrium (“Pruned”). “Merged” datasets include the combination of MW, LUPA, NAC, EURO, and HUSK samples.
aEighty-four individuals remained after initial removal of 8 replicates and 4 with low call rate.
bTwo Mexican wolves overlapped both the MW and NAC datasets.