Biology subjects

Derevianko, A. P.

Publications and source records attributed to Derevianko, A. P..

5 recordsLinked to original sources

bioRxiv2025

A high-coverage genome from a 200,000-year-old Denisovan

Denisovans, an extinct sister group of Neandertals who lived in Eastern Eurasia during the Middle and Late Pleistocene, are known only from a handful of skeletal remains and limited genetic data, including the high-coverage genome of a woman who lived [~]65,000 years ago. Here, we present a second high-quality Denisovan genome, reconstructed from a molar found at Denisova Cave. It belonged to a man who lived [~]200,000 years ago in a small Denisovan group. This group mixed with early Neandertals and was then replaced by Denisovans who had mixed with later Neandertals. We show that in addition Denisovans received gene flow from hominins that diverged before the split of the ancestors of Denisovans and modern humans. The two Denisovan genomes allow us to disentangle Denisovan ancestry in present-day humans revealing contributions from at least three distinct Denisovan groups. In particular, Oceanians and South Asians independently inherited DNA from a deeply diverged Denisovan population which was likely isolated in South Asia. This supports an early migration of the ancestors of Oceanians through South Asia followed by the later arrival of the ancestors of present-day South Asians. East Asians do not share this Denisovan component in their genomes, suggesting that their ancestors arrived independently, perhaps by a northerly route. Finally, the two high-quality Denisovan genomes allow us to refine the catalogue of genetic changes that arose on the Denisovan lineage, some of which were contributed to present-day humans.

genomics↗

bioRxiv2023

Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages

The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples. We present genome-wide ancient DNA data for 181 individuals from this region spanning the Mesolithic, Neolithic and Bronze Age. We find that Early to Mid-Holocene hunter-gatherer populations from across the southern forest and forest-steppes of Northern Eurasia can be characterized by a continuous gradient of ancestry that remained stable for millennia, ranging from fully West Eurasian in the Baltic region to fully East Asian in the Transbaikal region. In contrast, cotemporaneous groups in far Northeast Siberia were genetically distinct, retaining high levels of continuity from a population that was the primary source of ancestry for Native Americans. By the mid-Holocene, admixture between this early Northeastern Siberian population and groups from Inland East Asia and the Amur River Basin produced two distinctive populations in eastern Siberia that played an important role in the genetic formation of later people. Ancestry from the first population, Cis-Baikal Late Neolithic-Bronze Age (Cisbaikal_LNBA), is found substantially only among Yeniseian-speaking groups and those known to have admixed with them. Ancestry from the second, Yakutian Late Neolithic-Bronze Age (Yakutia_LNBA), is strongly associated with present-day Uralic speakers. We show how Yakutia_LNBA ancestry spread from an east Siberian origin [~]4.5kya, along with subclades of Y-chromosome haplogroup N occurring at high frequencies among present-day Uralic speakers, into Western and Central Siberia in communities associated with Seima-Turbino metallurgy: a suite of advanced bronze casting techniques that spread explosively across an enormous region of Northern Eurasia [~]4.0kya. However, the ancestry of the 16 Seima-Turbino-period individuals--the first reported from sites with this metallurgy--was otherwise extraordinarily diverse, with partial descent from Indo-Iranian-speaking pastoralists and multiple hunter-gatherer populations from widely separated regions of Eurasia. Our results provide support for theories suggesting that early Uralic speakers at the beginning of their westward dispersal where involved in the expansion of Seima-Turbino metallurgical traditions, and suggests that both cultural transmission and migration were important in the spread of Seima-Turbino material culture.

genomics↗

bioRxiv2020

A high-coverage Neandertal genome from Chagyrskaya Cave

We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We estimate that this individual lived ~80,000 years ago and was more closely related to Neandertals in western Eurasia (1,2) than to Neandertals who lived earlier in Denisova Cave (3), which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a first view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.

genomics↗

bioRxiv2020

The evolutionary history of Neandertal and Denisovan Y chromosomes

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidron 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.

evolutionary biology↗

bioRxiv2019

Mitochondrial Genome Diversity in the Central Siberian Plateau with Particular Reference to Prehistory of Northernmost Eurasia

The Central Siberian Plateau was last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through comprehensive mitochondrial DNA genomes retained in indigenous Siberian populations, the Ket, Tofalar, and Todzhi - we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia over the last 10,000 years. Accordingly, we generated 218 new complete mtDNA sequences and placed them into compound phylogenies along with 7 newly obtained and 70 published ancient mt genomes. Our findings reflect the origins and expansion history of mtDNA lineages that evolved in South-Central Siberia, as well as multiple phases of connections between this region and distant parts of Eurasia. Our result illustrates the importance of jointly sampling modern and prehistoric specimens to fully measure the past genetic diversity and to reconstruct the process of peopling of the high latitudes of the Siberian subcontinent.

genetics↗