# A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals

## TL;DR

A high-quality Neandertal genome from the Altai Mountains shows that early Neandertals were more genetically diverse and lived in smaller, isolated groups compared to later ones.

## Contribution

The study reveals population structure and genetic differentiation among Neandertals using a high-coverage genome from Denisova Cave.

## Key findings

- Older Neandertals from the Altai region mixed with Denisovans, unlike later Neandertals.
- Eastern and Western Neandertal populations were as genetically differentiated as modern human populations.
- Neandertals from 120,000 to 80,000 years ago lived in smaller and more isolated groups than later European Neandertals.

## Abstract

We present a high-quality genome of a ~110,000-y-old male Neandertal from Denisova Cave in the Altai Mountains. He as well as a ~120,000-y-old Neandertal from the same cave lived in smaller and more isolated groups than later Neandertals in Europe and the ancestors of both individuals mixed with Denisovans. The older Eastern and younger Western Neandertals were as differentiated in terms of the frequencies of genetic variants as the most differentiated present-day human populations worldwide, suggesting that present-day humans exhibit relatively low levels of population differentiation compared to Neandertals.

We present a genome sequenced to ~37-fold genomic coverage from an approximately 110,000-y-old male Neandertal from Denisova Cave in the Altai Mountains and analyze it together with previously published Neandertal genomes of high quality. We show that he belonged to a population more closely related to a ~120,000-y-old Neandertal from Denisova Cave than to Neandertals in Europe or to a ~80,000-y-old Neandertal from Chagyrskaya Cave in the Altai Mountains. Both Neandertals from Denisova Cave show evidence of gene flow from Denisovans, a pattern not seen in later Neandertals from the Altai region or from Western Europe. The extent of chromosomal regions of homozygosity in Neandertals from the Altai region between 120,000 and 80,000 y ago indicates that they lived in smaller and more isolated groups than later Neandertals in Europe (54,000 to 40,000 y ago). We estimate the extent of allele frequency differentiation among Neandertal populations and find that the older Eastern Neandertals in the Altai region and younger Western Neandertals in Europe were as differentiated as the most differentiated present-day human populations worldwide.