Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

Abstract

Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

“…[15,36,[43][44][45][46]), and target enrichment, in which sedaDNA molecules of interest are selectively enriched prior to sequencing (e.g. barcode or mitochondrial loci [16,[47][48][49]). Detailed descriptions of these methods applied to sedaDNA have been recently reviewed elsewhere [50,51].…”

“…With the application of shotgun metagenomics and target enrichment approaches, it is now possible to recover haplotypic and genomic information directly from sedaDNA [43][44][45][47][48][49], which enables the exploration of populationlevel changes and has the potential to detect the arrival or disappearance of alleles and lineages in a region, as recently showcased for Neanderthals from a cave in Spain [48]. This expansion of sedaDNA into environmental palaeogenomics, together with the integration of sedaDNA and traditional palaeogenomic data derived from body fossils [55], will open up new approaches to understanding past biodiversity changes that are inaccessible with other palaeoecological proxies.…”

“…Sampling from multiple comparable locations and using biological replicates and negative controls is essential to ensure proper characterization of a target area and to reduce taxonomic bias and the influence of contamination with modern DNA (e.g. [ 49 , 100 ]). Issues of taxonomic bias and sample heterogeneity are further confounded by a paucity of knowledge on sed aDNA taphonomy (the processes by which DNA is transported from an organism into an environmental archive [ 101 ]) and preservation, although experimental studies are beginning to address these unknowns (e.g.…”

“…[ 36 , 104 ]) and cave systems (e.g. [ 49 ]) do not find evidence of leaching. Furthermore, molecular biology protocols can be impacted by variations in substrate composition and the co-extraction of inhibitors, although new specialist methods, such as the cold-spin DNA extraction method [ 16 ], are beginning to mitigate these issues.…”

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community

“…Ancient metagenomics refers to the analysis of the complex DNA content recovered from degraded, nonliving, biological material (e.g., bones, teeth, dental plaque, paleofeces, sediments), primarily via shotgun high-throughput sequencing. Research often focuses on ancient microbes ( 1 , 2 ) but increasingly also on the simultaneous analysis of numerous (extinct) macroorganisms (see, e.g., references 3 to 5 ). Research questions in the field are often highly interdisciplinary, spanning the humanities and social and natural sciences, adding new perspectives to our understanding of the past, e.g., characterizing causative candidates of historical epidemics ( 6 ), identifying oral microbes in Neanderthals ( 7 ), reconstructing postglacial animal and plant successions in North America ( 8 ), and integrating detailed social and cultural contexts from archaeology and history ( 9 , 10 ).…”