Archaic admixture in human history

Wall, Jeffrey D.; Brandt, Débora Y. C.

doi:10.1016/j.gde.2016.07.002

Cited by 25 publications

(21 citation statements)

References 36 publications

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“…All others (15 pairs, all positive controls and putative species pairs) form another group with FST > 0.34 and EGF < 2.5%. Studies of human populations show that maximal FST between human populations is about 0.2 (Nelis et al 2009) and humans have about 1.5-2.1% genes introgressed from Neanderthals (Wall and Yoshihara Caldeira Brandt 2016). Therefore, our criteria for species boundaries are consistent with observations made on human.…”

Section: Genomic Measures To Quantify the Reproductive Barrier And Desupporting

confidence: 83%

Genomic determinants of speciation

Cong

Zhang

Grishin

2019

Preprint

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Studies of life rely on classifying organisms into species. However, since Darwin, there is no agreement about how to separate species from varieties. Contrary to a frequent belief, quantitative standards for species delineation are lacking and overdue, and debates about species delimitation create obstacles for conservation biology, agriculture, legislation, and education. To tackle this key biological question, we have chosen butterflies as model organisms. We sequenced and analyzed transcriptomes of 188 specimens representing pairs of close but clearly distinct species, populations, and taxa that are debated among experts. We find that species are robustly separated from populations by the combination of two measures computed on Z-linked genes: fixation index that detects hiatus between species, and the extent of gene flow that quantifies reproductive isolation. These criteria suggest that all 9 butterfly pairs that caused experts' disagreement are distinct species, not populations. When applied to Homo, our criteria agree that all modern humans are the same species distinct from Neanderthals, suggesting relevance of this study beyond butterflies. Furthermore, we found that proteins involved in interactions with DNA (including proteins encoded by trans-regulatory elements), circadian clock, pheromone sensing, development, and immune response recurrently correlate with speciation. A significant fraction of these proteins is encoded by the Z-chromosome, which appears to be resistant to introgression. Taken together, we find common speciation mechanisms in butterflies, reveal the central role of Zchromosome in speciation, and suggest quantitative criteria for species delimitation using genomic data, which is vital for the exploration of biodiversity.

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Section: Genomic Measures To Quantify the Reproductive Barrier And Desupporting

confidence: 83%

Genomic determinants of speciation

Cong

Zhang

Grishin

2019

Preprint

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“…Given prior genetic evidence for archaic admixture in Eurasia and Africa (reviewed in Wall and Brandt (2016)), we proposed a model that includes two deeply diverged human branches, with one branch mixing with Eurasian ancestors beginning at the OOA event, and the second one mixing with the ancestors of the Yoruba population over a time period that could include the OOA event. In this scenario, this second branch Figure 3(A).…”

Section: Human Expansion Models Underestimate Ld Between Low Frequencmentioning

confidence: 99%

Models of archaic admixture and recent history from two-locus statistics

Ragsdale

Gravel

2018

Preprint

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We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 − 8% genetic ancestry to individuals in world-wide populations. Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and exchanged migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

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“…Comparative analyses of these paleogenomes provided surprising but convincing evidence of reticulate gene flow and admixture between these archaic groups and anatomically modern humans during the Late Pleistocene [103,105]. Additional Neanderthal and Denisovan genome sequence data have been assembled over the past decade, some of which are at sufficiently high depth for functional population genomics investigations of adaptive and maladaptive introgression into modern human populations (for reviews see [129,[192][193][194][195][196]). It is now well established that people outside of sub-Saharan Africa exhibit varying but consistently detectable genomic signatures of admixture with these archaic hominins [82,126,129,192,[194][195][196].…”

Section: Multiple Melting Pots: Reticulate Gene Flow and Admixture Inmentioning

confidence: 99%

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

2019

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Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

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Archaic admixture in human history

Cited by 25 publications

References 36 publications

Genomic determinants of speciation

Genomic determinants of speciation

Models of archaic admixture and recent history from two-locus statistics

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

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