Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia

The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as west-ern Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolu-tionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morpho-logical differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phy-logeny, and Siberian specimens suggest a range contact or overlap between these two groups. Mean-while, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.