Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote

The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion widespread hybridization with wolves. observation some grey lupus) ancestry within wolves sparked controversy over whether it historically a subspecies its predominant “coyote-like” obtained from post-colonial (2-species hypothesis) versus distinct species closely related that hybridized (3-species hypothesis). We analysed mitogenomes sourced before 20th century bottleneck invasion, along hundreds modern amplicons, led us reject 2-species model investigate broader phylogeographic 3-species suggested fossil record. Our findings broadly support this model, in ranged width American continent prior arrival mid-continent 60–80 ka; subsequently disappeared mid-continent, relegated California forests, ushered emergence their place (50–30 ka); early Holocene (12–10 ka), coyotes had expanded into California, where they admixed phenotypically replaced western process analogous invasion forests. Findings indicate pre-dated not only European colonization but human, possibly coyote, presence North America. These highlight urgency expanding conservation efforts for wolf.