Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

Browning, Sharon R.; Browning, Brian L.; Zhou, Ying; Tucci, Serena; Akey, Joshua M.

doi:10.1016/j.cell.2018.02.031

Cited by 326 publications

(558 citation statements)

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“…The age of that peak appears too recent given previous split time estimates of those two Archaic groups from the main human lineage at 550-765 thousand years ago (kya) [14] . However, our simulation with archaic admixture ( Fig 2C), shows that our model tends to underestimate the archaic split time when the migration proportion is low, like the estimated proportions of Neanderthal and Denisovan ancestry in modern humans, which are both below 10% [19][20][21] . We investigated previous observations of potential ancestry from an earlier dispersal out of Africa, present in Papuan and Australian genomes [12,13,22] .…”

Section: Complex Out-of-africamentioning

confidence: 74%

Tracking human population structure through time from whole genome sequences

Wang

Mathieson

O’Connell

et al. 2019

Preprint

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The genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population's history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyse the population separation history. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago. Author SummaryHuman demographic history is reflected in specific patterns of shared mutations between the genomes from different populations. Here we aim to unravel this pattern to infer population structure through time with a new approach, called MSMC-IM. Based on estimates of coalescence rates within and across populations, MSMC-IM fits a time-dependent migration model to the pairwise rate of coalescences. We implemented this approach as an extension to existing software (MSMC2), and tested it with simulations exhibiting different histories of admixture and gene flow. We then applied it to the genomes from 15 worldwide populations to reveal their pairwise separation history ranging from a few thousand up to several million years ago. Among other results, we find evidence for remarkably deep population structure in some African population pairs, suggesting that deep ancestry dating to one million years ago and older is still present in human populations in small amounts today.

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Section: Complex Out-of-africamentioning

confidence: 74%

Tracking human population structure through time from whole genome sequences

Wang

Mathieson

O’Connell

et al. 2019

Preprint

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“…The DNA traces in native Australasians are not identical with those found in the Siberian Denisovans, and recent research indicates that there were at least three separate and varied Denisovan‐like sources of introgression, one of which lived in the same biogeographical zone as H. floresiensis and H. luzonensis (Jacobs et al , ). Populations in southern Asia contain smaller traces of comparable Denisovan‐like DNA, while those in eastern Asia contain traces more similar to the actual Denisova Cave genomes (Browning et al ., ). Specific Denisovan‐like genes linked with high‐altitude adaptation and storage of fats have been recognized in Tibetans and Inuit, respectively (Huerta‐Sánchez et al ., ; Racimo et al ., ).…”

Section: The Impact Of Adna From Neanderthals and Denisovansmentioning

confidence: 97%

Aspects of human physical and behavioural evolution during the last 1 million years

Galway‐Witham

Cole

Stringer

2019

J Quaternary Science

106

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This paper reviews some of the main advances in our understanding of human evolution over the last 1 million years, presenting a holistic overview of a field defined by interdisciplinary approaches to studying the origins of our species. We begin by briefly summarizing the climatic context across the Old World for the last 1 million years before directly addressing the fossil and archaeological records. The main themes in this work explore (i) recent discoveries in the fossil record over the last 15 years, such as Homo naledi and Homo floresiensis; (ii) the implications of palaeogenetics for understanding the evolutionary history of, and relationships between, Neanderthals, Denisovans and Homo sapiens; (iii) the interplay between physiology and metabolic demand, landscape use, and behavioural adaptations in the evolution of morphological and behavioural innovation; and (iv) recent advances in archaeological understanding for the behavioural record, in particular that of the Neanderthals. This paper seeks to provide a broad‐scale, holistic perspective of our current understanding of human evolution for the last 1 Ma, providing a reference point for researchers that can be built upon as new discoveries continue to develop the landscapes of human evolution. © 2019 The Authors. Journal of Quaternary Science Published by Wiley Periodicals, Inc.

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“…Many human lineages coexisted on the African continent, possibly until quite recently (Rightmire, 2009;Harvati et al, 2011;Berger et al, 2017), and genetic evidence points to a history of archaic admixture or deep structure across many modern African populations (Hammer et al, 2011;Lachance et al, 2012;Hsieh et al, 2016;Skoglund et al, 2017;Durvasula and Sankararaman, 2018;Hey et al, 2018). It is likely that modern humans have met and mixed with diverged lineages many times through history, rather than receiving just a single pulse of migrants (Browning et al, 2018;Villanea and Schraiber, 2019). We chose to model the mixing of archaic and modern human branches as continuous and symmetric (Kuhlwilm et al, 2016), parameterizing the migration rate between these branches and the times that migration began and ended.…”

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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Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

Cited by 326 publications

References 50 publications

Tracking human population structure through time from whole genome sequences

Tracking human population structure through time from whole genome sequences

Aspects of human physical and behavioural evolution during the last 1 million years

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

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