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

PRJEB108287 Original Paper / DOI2026-03-231 samples (study)

AI interpretationAI-generated

An 110,000-year-old Altai Neandertal genome reveals early population structure and Denisovan gene flow.

Researchers sequenced a ~110,000-year-old male Neandertal from Denisova Cave to high coverage. Comparing it with other Neandertal genomes, they found it was closer to an older Denisova Cave Neandertal than to European or later Altai Neandertals. Both Denisova Cave Neandertals show gene flow from Denisovans, unlike later Neandertals. They also lived in smaller, more isolated groups, and early eastern and later western Neandertals were as genetically distinct as today's most differentiated human populations.

Sample interpretation

This study analyzes a single high-coverage genome from a ~110,000-year-old male Neandertal from Denisova Cave, alongside previously published high-quality Neandertal genomes. No Y-chromosome or mitochondrial haplogroup data are provided in the abstract. The sample is key for understanding early Neandertal population structure in the Altai region.

For genealogy enthusiasts

For ancestry enthusiasts, this shows Neandertals were not a single homogeneous group. Early eastern and later western Neandertals were deeply structured, and some early Neandertals interbred with Denisovans. This helps refine models of archaic admixture in modern human ancestry.

Abstract

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.

Samples & Data on TheYtree

1samples on site
1Y haplogroup resolved
1archaeological sites

Sample Map

Map tiles by TheYtree · dot size = number of samples

Paternal (Y-DNA) Haplogroups

HaplogroupSamples
A000b 1

Sample Highlights More samples →

SampleY-DNAmtDNACulture / Period
Denisova A000b — · 110,000 BP