Ancient DNA reveals genetic admixture in China during tiger evolution

The contrast between the oldest fossil presence of tigers 2–3 Mya and
extant tigers’ coalescence approximately 110,000 years ago implies a
complex genomic diversity pattern in ancient tigers that has largely
escaped scientific scrutiny. Here we collected over 60 historical
specimens across mainland Asia and generated whole genome sequences from a
10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8´ coverage), 14
South China tigers (0.1–12´), three Caspian tigers (4–8´), plus 17 new
mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups
and partially derived from an extinct Late Pleistocene lineage. While some
of the 8,000–10,000-year-old RFE mitogenomes are basal to all tigers, one
2,000-year-old specimen resembles present Amur tigers. The Caspian tiger
likely dispersed from an ancestral Northeast Asian population and
experienced gene flow from southern Bengal tigers. Lastly, genome-wide
monophyly supported the South China tiger as a distinct subspecies, albeit
with mitochondrial paraphyly, hence resolving its longstanding taxonomic
controversy. The distribution of mitochondrial haplogroups corroborated by
biogeographical modeling suggested Southwest China was a Late Pleistocene
refugium for a relic basal lineage. As suitable habitat returned, Eastern
China became a genetic melting pot to foster divergent lineages to merge
into South China tigers and other subsequent northern subspecies to
develop. Genomic information retrieved from ancient tigers hence sheds
light on the species’ full evolutionary history leading to nine modern
subspecies and resolves the natural history of surviving tigers.