Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.