Disentangling the wolf-coyote admixture through an ancestry-based approach

Coyote (Canis latrans). Source: Wikimedia Commons/Christopher Bruno, http://www.sxc.hu

Coyote (Canis latrans). Source: Wikimedia Commons/Christopher Bruno, http://www.sxc.hu

Large carnivores like bears and wolves still pose a puzzle for systematics and population genetics. The more data we get, the more complex their evolutionary history seems to be.

In a paper accepted for publication in Molecular Ecology, Bridgett M. vonHoldt and colleagues studied admixture between the grey wolves and coyotes at the North American hybrid zone.
While the grey wolf’s range, which originally included vast parts of North America, is now restricted to Canada, Alaska and the Great Lakes area, the coyote expanded its range to the east. Prior to the expansion, coyotes hybridized with wolves in the Great Lakes region.
vonHoldt and colleagues used a genome-wide SNP dataset from a previous study (vonHoldt et al. 2011), including more than 3,000 ancestry informative sites that were inferred by comparing two non-admixed populations and estimating sites with FST ≥ 0.4.
They took previously-calculated average genome-wide population ancestries (vonHoldt et al. 2011) and subtracted them from the ancestry frequencies to get locus-specific delta ancestry. This way they revealed outlier SNPs with excessive exogenous or endogenous ancestry.
They further used the neighboring SNPs with the same locus-specific delta ancestry direction to identify population-specific differentially introgressed ancestry blocks. In simpler words, they looked at what chunks of wolf genome had above-average coyote ancestry and vice versa.

“Exogenous multi-locus ancestry genotypes were defined as those with ≥50% of the block containing exogenous SNPs. We further focused on multi-locus ancestry genotypes within differentially introgressed blocks that contained the highest degree of exogenous ancestry and chose those loci that fell within the population-specific 85th percentile of exogenous ancestry for subsequent gene ontology analysis.”

vonHoldt et al. found high exogenous multi-locus ancestry genotype frequency in northeastern coyote (0.42-0.53) and Great Lakes wolf populations (0.5-0.71), and lower in midwestern/southern coyotes (0.26-0.40).

“The most intriguing wolf-derived introgressed block that persists in NE coyotes was found on chromosome 4 and harbors >40 annotated genes, some of which may be functionally linked to the intermediate coyote/wolf phenotype typical of the northeastern population. For example, genes functionally linked to skeletal variation are found, including bone morphogenic proteins GDF2 and GDF10, skeletal gene MSX2, growth factor receptor FGFR4, or NSD1 linked to Sotos syndrome, a dominant phenotype characterized by enlarged skull circumference (Kenny et al. 2011).”

Their results indirectly point to a fitness advantage that coyotes gained by hybridization with wolves through enlarged body size. vonHoldt et al. also put their results into the contesxt of recently published updates of the human-Neanderthal admixture:

“Such traces of admixtures in otherwise pure populations are analogous to the persistence of introgressed regions that are suspected to have a role in adaptation. For example, Neanderthal ancestry persists in modern European and Asian populations, which for some genes are hypothesized to be adaptive (e.g. EPAS1, Racimo et al. 2015).”

In the end, vonHoldt and colleagues bring up the question on conservation management of such admixed populations. These topics will need to be reconsidered in the futures, since genome-wide data often show that the species boundaries are not as clear as we like to think.
von Holdt, B. M., Kays, R. W., Pollinger, J. P. and Wayne, R. K. (2016), Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. Accepted Author Manuscript. doi:10.1111/mec.13667

vonHoldt, B. M., Pollinger, J.P., Earl, D.A., Knowles, J.A., Boyko, A.R., et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. doi: 10.1101/gr.116301.110

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