Correlation measures for linkage disequilibrium within and between populations

Ja, Sved

doi:10.1017/s0016672309000159

Cited by 32 publications

(32 citation statements)

References 36 publications

(57 reference statements)

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“…As for admixture among modern populations after the split from Africa, which may certainly affect estimates of their divergence time [ 72 ], the demographic history of large sections of Asia is too complex and elusive to be addressed in a general study, such as this, without detailed modeling of each local process. However, we argue that the impact of modern admixture upon our results cannot be too strong, because geographically intermediate populations were excluded from the final analysis.…”

Section: Discussionmentioning

confidence: 99%

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

et al. 2015

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BackgroundAnthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant.ResultsHere, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes.ConclusionsWe conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from AfricaElectronic supplementary materialThe online version of this article (doi:10.1186/s13323-015-0030-2) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

et al. 2015

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“…Beyond the classical recursions for E[D] and E[D 2 ] (Hill and Robertson, 1968;Rogers, 2014), two-locus statistics are difficult to compute for non-equilibrium, multi-population demographic models. Sved (2009) proposed an IBD based recursion to compute E[r 2 ] across subdivided populations, but its accuracy and interpretation remain debated (Rogers, 2014). The moments-based approach presented here generalizes the recursion for the single-site AFS presented in (Jouganous et al, 2017).…”

Section: Relation To Other Statisticsmentioning

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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“…Compared to alternative measures based on haplotypic or phased data, such correlation methods yield similar results but are computationally very efficient for whole genome data ( Jakobsson et al 2008;Weir 2008;Sved 2009). r LD can be positive or negative.…”

Section: Linkage Disequilibrium Patternsmentioning

confidence: 99%

Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs

McEvoy

Powell²,

Goddard³

et al. 2011

Genome Res.

145

182

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Genetic and fossil evidence supports a single, recent (<200,000 yr) origin of modern Homo sapiens in Africa, followed by later population divergence and dispersal across the globe (the ''Out of Africa'' model). However, there is less agreement on the exact nature of this migration event and dispersal of populations relative to one another. We use the empirically observed genetic correlation structure (or linkage disequilibrium) between 242,000 genome-wide single nucleotide polymorphisms (SNPs) in 17 global populations to reconstruct two key parameters of human evolution: effective population size (N e ) and population divergence times (T). A linkage disequilibrium (LD)-based approach allows changes in human population size to be traced over time and reveals a substantial reduction in N e accompanying the ''Out of Africa'' exodus as well as the dramatic re-expansion of non-Africans as they spread across the globe. Secondly, two parallel estimates of population divergence times provide clear evidence of population dispersal patterns ''Out of Africa'' and subsequent dispersal of proto-European and proto-East Asian populations. Estimates of divergence times between European-African and East Asian-African populations are inconsistent with its simplest manifestation: a single dispersal from the continent followed by a split into Western and Eastern Eurasian branches. Rather, population divergence times are consistent with substantial ancient gene flow to the proto-European population after its divergence with proto-East Asians, suggesting distinct, early dispersals of modern H. sapiens from Africa. We use simulated genetic polymorphism data to demonstrate the validity of our conclusions against alternative population demographic scenarios.

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Correlation measures for linkage disequilibrium within and between populations

Cited by 32 publications

References 36 publications

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

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

Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs

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