Beyond broad strokes: sociocultural insights from the study of ancient genomes

Racimo, Fernando; Sikora, Martin; Linden, Marc Vander; Schroeder, Hannes; Lalueza-Fox, Carles

doi:10.1038/s41576-020-0218-z

Cited by 56 publications

(38 citation statements)

References 142 publications

(120 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Future work analyzing the rapidly growing aDNA record will help to resolve additional details of other social and cultural factors operating at finer scales (e.g., leveraging more precise timings of shifts and more subtle shifts in ROH patterns). In particular, future studies focusing on specific localized questions can combine archaeological and genetic evidence such as the one provided by the new methodology presented here (Racimo et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, ROH have been identified in ancient DNA (aDNA, e.g. Broushaki et al, 2016;Sikora et al, 2017;Schroeder et al, 2018;Racimo et al, 2020;Mafessoni et al, 2020;Cassidy et al, 2020), that is, genetic material extracted from ancient human remains. This advance is especially promising, as large datasets of aDNA have been generated in the last decade (Skoglund and Mathieson, 2018).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

Ringbauer

Novembre

Steinrücken

2020

Preprint

View full text Add to dashboard Cite

We present a novel method to detect runs of homozygosity (ROH) from low-coverage genotype data typical for ancient human DNA. ROH are the genetic signature of matings between related parents, and as such, the frequency and length distribution of these blocks can give insight into recent population history and mating patterns. Existing methods identify ROH by scanning for regions that lack heterozygote genotypes, but this strategy frequently fails for ancient individuals: The vast majority of ancient DNA data has low read depth (ă3ˆ), which makes reliable diploid genotype calling infeasible. To overcome this limitation, we make use of linkage disequilibrium information from a panel of modern reference haplotypes using a Hidden Markov Model. Our method scans for long stretches where the read data are consistent with only a single haplotype. When tested on simulated and down-sampled pseudo-haploid data from a targeted set of 1.24 million single nucleotide polymorphisms ("1240k SNPs") widely used in ancient DNA, our implementation robustly works for coverage down to 0.5ˆand can tolerate error rates up to 3%, with high power and low false positive rate for blocks longer than 4 centiMorgans. Therefore, the method can screen a substantial fraction of human genome-wide ancient DNA data for parental relatedness, which will yield new evidence for questions regarding past demography and social organization.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

Ringbauer

Novembre

Steinrücken

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…With the current level of productivity in ancient genomic research, many more individuals from the recent historical past will be sequenced to high genomic coverage in the near future. This will allow us to extend this methodological framework to an increasingly large genomic population dataset of ancient and modern people 33 . This approach will serve not only to uncover individual ancestry links, but it could also unravel the origins and the spread of mutations subjected to positive selection, because this process should preserve longer genomic blocks than expected under a process of random recombination 34 .…”

Section: Discussionmentioning

confidence: 99%

Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans

Ferrando-Bernal

Morcillo-Suárez

de-Dios

et al. 2020

Sci Rep

Self Cite

View full text Add to dashboard Cite

Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual-that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.Many studies have demonstrated that human population genetic structuring in Europe correlates with geography; for instance, a two dimensional representation of the genetic variation with principal component analysis (PCA) essentially mirrors a geographical map of Europe 1,2 . Several ancient DNA (aDNA) studies have shown that the overall genetic structure was shaped by three ancestral and over-imposed genomic components respectively deriving from the Mesolithic hunter-gatherers, the Early Neolithic farmers, and the steppe nomads that entered Europe from the East around 5,000 years ago 3-7 . However, it is expected that the genetic homogenisation of the European populations during the last two millennia complicates our ability to discern subtle changes in ancestry by using some common population genetic tools.Complementary to these analyses, the distribution of so-called identity by descent (IBD) genomic stretches, which are co-inherited genetic segments delimited by recombination events, can provide information on more recently shared ancestry among individuals [8][9][10] . Such genomic block characterization in current populations has demonstrated the presence of co-ancestry across geographically distant Europeans shared over the last few thousand years, and revealed more recently shared co-ancestry in neighboring populations 11 . Nevertheless, most IBD blocks are not expected to be recognizable after a few hundreds of years because they are being broken by recombination during meiosis. Since the far majority of ancient human genomes sequenced to date are >2,...

show abstract

“…Ancient genome sequencing from bone (Hagelberg et al, 1989) , teeth (Höss et al, 1996) and hair (Gilbert et al, 2007) has revolutionised our understanding of natural history and the human past (Hofreiter et al, 2001;Racimo et al, 2020) . When skeletal material is not available, sediment ancient DNA has sometimes been used to determine the presence or absence of different species.…”

Section: Introductionmentioning

confidence: 99%

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Gelabert

Sawyer

Bergström

et al. 2021

Preprint

View full text Add to dashboard Cite

SummaryArchaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.HighlightsWe demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remainsA single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomesWe show that sediment ancient DNA can reveal important aspects of the human and faunal pastEvidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum∼0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species

show abstract

Beyond broad strokes: sociocultural insights from the study of ancient genomes

Cited by 56 publications

References 142 publications

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Contact Info

Product

Resources

About