coverage of the dataset. In addition, the samples selected for analysis are representative of the larger geographic clustering pattern based analysis on genome-wide SNP data. Based on clustering analysis of 48K SNP data in the program STRUCTURE conducted in [33], coyotes from southern Ontario cluster with other northeastern US coyote populations; Great Wolves from northern Ontario cluster with those from the Great Lakes states of Wisconsin and Minnesota; western coyotes from the Canadian prairie province of Manitoba cluster with those from western United States; and Gray Wolves from the Northwest Territories cluster with those from Alaska and Yellowstone National Park. So, although more samples would provide more variation for hybrid simulations, it is improbable that further sampling would qualitatively alter the support for the three-species model in both the PCA and hybridization simulations. We suspect that further sampling would only increase the ability of the PCA of all SNP genotypes to more clearly identify two strongly meaningful PCs in the dataset (Fig. S1, S2). As noted in the main text, further sampling may lend itself to tests of alternative evolutionary scenarios (ancient hybridization followed by drift over many generations) and provide more reliable results from sophisticated tests of genomic ancestry. In cases where simulated hybrid genotypes do not overlap with observed genotypes, conclusions may be that either such hybrid genotypes do not exist in the wild because hybridization leading to such genotypes never occurred or that such genotypes were never sampled. We acknowledge that the geographic sampling is incomplete and we cannot rule out the possibility that Gray Wolf x Western Coyote hybrids simply were not sampled in our observed data. However, this does not influence the interpretation that the samples included in the dataset,
coverage of the dataset. In addition, the samples selected for analysis are representative of the larger geographic clustering pattern based analysis on genome-wide SNP data. Based on clustering analysis of 48K SNP data in the program STRUCTURE conducted in [33], coyotes from southern Ontario cluster with other northeastern US coyote populations; Great Wolves from northern Ontario cluster with those from the Great Lakes states of Wisconsin and Minnesota; western coyotes from the Canadian prairie province of Manitoba cluster with those from western United States; and Gray Wolves from the Northwest Territories cluster with those from Alaska and Yellowstone National Park. So, although more samples would provide more variation for hybrid simulations, it is improbable that further sampling would qualitatively alter the support for the three-species model in both the PCA and hybridization simulations. We suspect that further sampling would only increase the ability of the PCA of all SNP genotypes to more clearly identify two strongly meaningful PCs in the dataset (Fig. S1, S2). As noted in the main text, further sampling may lend itself to tests of alternative evolutionary scenarios (ancient hybridization followed by drift over many generations) and provide more reliable results from sophisticated tests of genomic ancestry. In cases where simulated hybrid genotypes do not overlap with observed genotypes, conclusions may be that either such hybrid genotypes do not exist in the wild because hybridization leading to such genotypes never occurred or that such genotypes were never sampled. We acknowledge that the geographic sampling is incomplete and we cannot rule out the possibility that Gray Wolf x Western Coyote hybrids simply were not sampled in our observed data. However, this does not influence the interpretation that the samples included in the dataset,
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