Relationships among North American deer based on mitochondrial DNA and ultraconserved elements, with comments on mito-nuclear discordance

Despite their economic, cultural, and ecological significance, the phylogenetic relationships among North American deer remain uncertain, due in part to discordance between phylogenies built from mitochondrial DNA (mtDNA) and nuclear markers. Nuclear markers resolve mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus) as reciprocally monophyletic, but mtDNA results in a mixed topology. These two genomic regions have heretofore been analyzed in isolation. We compared phylogenies built from mtDNA cytochrome b and single-nucleotide polymorphisms (SNPs) from the mitogenome and nuclear (ultraconserved elements, UCEs) markers from the same individuals to investigate mito-nuclear discordance within and between taxa in the genus Odocoileus. A Cyt b tree shows haplotype sharing between O. hemionus and O. virginianus. Mitochondrial DNA SNPs separated only O. hemionus and O. virginianus, whereas nuclear SNPs separated O. hemionus, O. virginianus, and the distinct subspecies Coues deer (O. v. couesi), Key deer (O. v. clavium), and Sitka black-tailed deer (O. h. sitkensis) plus Columbian black-tailed deer (O. h. columbianus). We found less support for O. h. columbianus as a distinct taxon, which had signs of introgression with nominate O. h. hemionus. The well-established paraphyly of mtDNA haplotypes from O. virginianus and O. hemionus is confirmed with comparisons of mtDNA and nuclear-encoded SNPs from the same individuals. Our attempts to explain mito-nuclear discordance among Odocoileus deer remain inconclusive. We suspect incomplete lineage sorting of a recent evolutionary split may explain this pattern, although mtDNA capture via ancient hybridization is also a possibility. Niche models suggested allopatric refugia at the Last Glacial Maximum for these taxa except for a parapatric or sympatric distribution estimated for O. virginianus and O. v. clavium and O. hemionus and O. h. columbianus, the latter of which might explain the modern hybrid zone.