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 w..., , , # Ancient DNA reveals genetic admixture in China during tiger evolution

[https://doi.org/10.5061/dryad.73n5tb324](https://doi.org/10.5061/dryad.73n5tb324)

## Description of the data and file structure

| File | Description |
| ---- | ----------- |
| 11th\_hard\_no\_old.bcf.gz | hard filtered vcf file |
| auto\_neutral\_psdo\_gt\_psdo\_miss10\_info\_11th\_hard\_no\_old.bcf.gz | Pseudohaploid vcf file. NB: don't use any field in INFO |
| auto\_neutral\_hqc\_miss4\_meanDP5\_info\_11th\_hard\_no\_old.bcf.gz | Strictly filtered vcf file. NB: don't use any field in INFO |
| gl\_tv\_mafF\_misF.dp1.beagle.gz | Genotype likelihood file. |
| file.md5 | MD5 |

## Code/Software

Github link
https://github.com/xinsun1/Xin\_etal\_2023\_NEE\_TigerPopGen