An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics

Abstract

Tigers ( Panthera tigris ) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187–353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88–168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.

Ancient DNA Reveals China as a Historical Genetic Melting Pot in Tiger Evolution

“…The population turnover between c. 8,600 BP and c. 1,800 BP suggested possible replacement of the older lineages with more recent lineages showing migratory waves from eastern and northern China. Morphological studies of the Late Pleistocene tiger fossils also supported multiple waves of dispersal from the south to the Far East 33,45 . On the other hand, the evolutionary continuity of RFE tigers from c. 1,800 BP to the present provided evidence for the probable establishment of the current Amur tiger subspecies by approximately 2,000 years ago.…”

“…The past decade has witnessed substantial advances in ancient DNA research, now enabling the retrieval of genomic information from extinct mammals that date back to over one million years ago [22][23][24] , including Felidae such as saber-toothed cats [25][26][27] , the Late Pleistocene Holarctic lions [28][29][30][31] , and the European Late Pleistocene leopards 32 . However, thus far, only one whole genome 33 has been retrieved from Pleistocene/early Holocene tiger specimens, partially due to the foregoing overlap of the tiger distribution with temperate-tropical forest biomes, where specimens are less likely to be preserved than in colder regions.…”

Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China

“…2 and 3 ). Although this ancient woolly rhinoceros clade is solely represented by only one sample in this study, several deeply divergent mitochondrial or nuclear clades have been identified from other Late Pleistocene large herbivores and carnivores in Northern China, e.g., aurochs ( Bos primigenius ) [ 23 ], steppe bison ( Bison priscus ) [ 24 ], cave hyenas ( Crocuta crocuta ultima ) [ 25 , 26 ], and tiger ( Panthera tigris ) [ 27 ]. These distinct ancient clades from different species experienced a long evolutionary history in the same area, which suggests that Northern China might have represented a refugium for some Quaternary mammals.…”

Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey

“…The fossil records and genetic analyses of tigers both show that South China tigers (SCT) play a very important role in tiger evolution [1][2][3]7], which was proved via ancient DNA. A genome-wide monophyly of ancient DNA supported the SCT as a distinct subspecies; eastern China was a genetic melting pot that fostered divergent lineages to merge into the SCT and other subsequent northern subspecies to develop [4].…”