Data from: Admixture mapping identifies introgressed genomic regions in North American canids

Hybrid zones typically contain novel gene combinations that can be tested
by natural selection in a unique genetic context. Parental haplotypes that
increase fitness can introgress beyond the hybrid zone, into the range of
parental species. We used the Affymetrix canine SNP genotyping array to
identify genomic regions tagged by multiple ancestry informative markers
that are more frequent in an admixed population than expected. We surveyed
a hybrid zone formed in the last 100 years as coyotes expanded their range
into eastern North America. Concomitant with expansion, coyotes hybridized
with wolves and some populations became more wolflike, such that coyotes
in the northeast have the largest body size of any coyote population.
Using a set of 3102 ancestry informative markers, we identified 60
differentially introgressed regions in 44 canines across this admixture
zone. These regions are characterized by an excess of exogenous ancestry
and, in northeastern coyotes, are enriched for genes affecting body size
and skeletal proportions. Further, introgressed wolf-derived alleles have
penetrated into Southern US coyote populations. Because no wolves
currently exist in this area, these alleles are unlikely to have
originated from recent hybridization. Instead, they probably originated
from intraspecific gene flow or ancient admixture. We show that grey wolf
and coyote admixture has far-reaching effects and, in addition to
phenotypically transforming admixed populations, allows for the
differential movement of alleles from different parental species to be
tested in new genomic backgrounds.