Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments

Vernot, Benjamin; Zavala, Elena I.; Gómez‐Olivencia, Asier; Jacobs, Zenobia; Slon, Viviane; Mafessoni, Fabrizio; Romagné, Frédéric; Pearson, A. Neil; Petr, Martin; Sala, Nohemi; Pablos, Adrián; Aranburu, Arantza; Castro, José Marı́a Bermúdez de; Carbonell, Eudald; Li, Bo; Krajcarz, Maciej T.; Кривошапкин, А.И.; Колобова, К. А.; Козликин, М.Б.; Shunkov, M.V.; Derevianko, Anatoly P.; Viola, Bence; Grote, Steffi; Essel, Elena; Herráez, David López; Nagel, Sarah; Nickel, Birgit; Richter, Julia; Schmidt, Anna; Peter, Benjamin M.; Kelso, Janet; Roberts, Richard G.; Arsuaga, Juan-Luis; Meyer, Matthias

doi:10.1126/science.abf1667

Cited by 115 publications

(90 citation statements)

References 94 publications

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“…[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].…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

“…[17,52]) and interglacial periods [41], hominin and human sedaDNA has been recovered (e.g. [47,48,53]), LADs have been refined for extinct megafauna (e.g. [36]), and FADs have been established for taxa arriving in a variety of contexts, from newly deglaciated landscapes [15] to island invasions [35].…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

“…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.…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

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

et al. 2021

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Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

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Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

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

et al. 2021

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“…Furthermore, Denny’s Neanderthal ancestry was more closely related to European Neanderthals than to other Siberian Neanderthals, some of which were also found in older fossil layers at Denisova cave. This pattern indicates that the European and Siberian Neanderthal lineages, while genetically distinct, were not always isolated geographically ( Mafessoni et al 2020 ), with further sedimentary aDNA evidence from Galeria de las Estatuas cave in Spain suggesting multiple radiation events of Neanderthal populations ( Vernot et al 2021 ). To add more complexity to this unique finding, at least five long segments (∼1 Mb) of Denny’s genome carry Neanderthal alleles on both chromosomes, suggesting that the Denisovan father’s lineage presented Neanderthal introgression deep in its past.…”

Section: Big Picture Of Archaic Introgressionmentioning

confidence: 98%

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

Ahlquist

Bañuelos

Funk

et al. 2021

Genome Biology and Evolution

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The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: i) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; ii) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; iii) how these novel methods can detect archaic introgression in modern African populations; and iv) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

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“…DNA hybridization capture (a.k.a. target enrichment) has already been successfully applied to enrich low-concentration DNA-fragments of interest from aDNA samples including sediments (Slon et al, 2017;Murchie et al, 2020;Vernot et al, 2021). It relies on the ability of the DNA to hybridize with complementary nucleic acids, the so-called baits.…”

Section: Introduction Paleogenomics Applied To Sediment Samplesmentioning

confidence: 99%

Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

et al. 2021

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Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.

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Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments

Cited by 115 publications

References 94 publications

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

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

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

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