Article

Our Paper: The Date of Interbreeding between Neandertals and Modern Humans

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
PLoS Genetics (Impact Factor: 7.53). 10/2012; 8(10):e1002947. DOI: 10.1371/journal.pgen.1002947
Source: PubMed

ABSTRACT

Author Summary
One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans. This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population structure in the ancestors of Neandertals and modern humans. These hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans. We estimate this date by measuring the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

  • Source
    • "Researchers have detected signatures of past hybridization events among these lineages (Green et al. 2010; Fu et al. 2014, 2015; Prufer et al. 2014; Seguin- Orlando et al. 2014). For example, there is evidence for admixture—possibly in the Middle East—between Neanderthals and people expanding from Africa circa 47–65 ka (Sankararaman et al. 2012). In Siberia, this admixture window has been estimated at 50–60 ky (Fu et al. 2014), while in Romania admixture occurred as recently as *40,000 years ago (Fu et al. 2015). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent genomic research has shown that hybridization between substantially diverged lineages is the rule, not the exception, in human evolution. However, the importance of hybridization in shaping the genotype and phenotype of Homo sapiens remains debated. Here we argue that current evidence for hybridization in human evolution suggests not only that it was important, but that it was an essential creative force in the emergence of our variable, adaptable species. We then extend this argument to a reappraisal of the archaeological record, proposing that the exchange of cultural information between divergent groups may have facilitated the emergence of cultural innovation. We discuss the implications of this Divergence and Hybridization Model for considering the taxonomy of our lineage.
    Full-text · Article · Oct 2015 · Evolutionary Biology
  • Source
    • "However, it is also possible at least some of the poor phylogenetic resolution reflects contrasting genealogical histories within loci due to the homogenizing effects of recombination. In particular, individual introgressed regions are expected to be relatively short under a model of ancient hybridization (Sankararaman et al. 2012). To overcome this limitation we used the ABBA-BABA framework to evaluate phylogenetic patterns across SNVs. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The idea that species boundaries can be semipermeable to gene flow is now widely accepted but the evolutionary importance of introgressive hybridization remains unclear. Here we examine the genomic contribution of gene flow between two hybridizing chipmunk species, Tamias ruficaudus and Tamias amoenus. Previous studies have shown that ancient hybridization has resulted in complete fixation of introgressed T. ruficaudus mitochondrial DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear introgression is not known. We used targeted capture to sequence over 10500 gene regions from multiple individuals of both species. We found that most of the nuclear genome is sorted between these species and that overall genealogical patterns do not show evidence for introgression. Our analysis rules out all but very minor levels of interspecific gene flow, indicating that introgressive hybridization has had little impact on the overall genetic composition of these species outside of the mitochondrial genome. Given that much of the evidence for introgression in animals has come from mtDNA, our results underscore that unraveling the importance introgressive hybridization during animal speciation will require a genome-wide perspective that is still absent for many species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Jun 2015 · Evolution
  • Source
    • "This hypothesis of ''ancestral subdivision'' has been seen as an alternative to that of archaic admixture (Durand et al., 2011; Eriksson and Manica, 2012; Blum and Jakobsson, 2011). This issue is still contentious, with some authors arguing that it has been refuted (Yang et al., 2012; Sankararaman et al., 2012; Wall et al., 2013) and others that it has not been properly tested (Eriksson and Manica, 2014). Whatever the outcome of this dispute, there are also other potential biases. "
    [Show abstract] [Hide abstract]
    ABSTRACT: This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to "ghost" admixture, which occurs when a population receives archaic DNA from sources not acknowledged by the statistical model. The effect of ghost admixture depends on two factors: branch-length bias and population-size bias. Branch-length bias occurs because a given amount of admixture has a larger effect if the two populations have been separated for a long time. Population-size bias occurs because differences in population size distort branch lengths in the gene genealogy. In the absence of ghost admixture, these effects are small. They become important, however, in the presence of ghost admixture. Estimators differ in the pattern of response. Increasing a given parameter may inflate one estimator but deflate another. For this reason, comparisons among estimators are informative. Using such comparisons, this article supports previous findings that the archaic population was small and that Europeans received little gene flow from archaic populations other than Neanderthals. It also identifies an inconsistency in estimates of archaic admixture into Melanesia.
    Full-text · Article · Mar 2015 · Theoretical Population Biology
Show more

Questions & Answers about this publication

  • Michael Buchwitz added an answer in Human Evolution:
    Reconstructing neanderthal evolution using modern human DNA?
    I have a very specific question concerning modern human/neanderthal studies. As long as I understand, neanderthal trace in human genome is due to some recombinant loci. That means, neanderthal clonal genes (Y-chromosome, mt-DNA) were completely washed out from the modern human populations due to gene drift, but some recombinant loci still remain in the gene pool. Moreover, they exist in literally any non-African human person.
    Discovering presence of neanderthal alleles in the sapiens genome became possible after scientists sequenced neanderthal genome. Thus, the location of the neanderthal alleles in Eurasian genomes is known and, perhaps, even available. That means, primers can be easily designed for these fragments and the "neanderthal" fragments should be relatively easy to sequence for any modern human.
    That means, by sequencing these fragments for humans from the different parts of Eurasia one can reconstruct the underlining Neanderthal phylogeny, i.e. one can compare the neanderthals from West Europe, Caucasus, Central and East Asia, whose differences may well be much deeper in time than the differences between respective modern human lineages, which are thought to diverge 100 TY or similar. Should the existing differences between modern human populations be completely attributed to the divergence that started 100,000 TY? Or, perhaps, they at least partly root into the time of divergence among neanderthal geographic populations?
    It sounds too simple, that means, most likely is something wrong and stupid in this logic, or evolutionary anthropologists already working on this. Or?
    Would appreciate much for the comment.
    Michael Buchwitz
    Concerning your specific question: The problem might be to recover a large enough sample of fossil neanderthal DNA (not only a single genome but many specimens from different regions, different time slices) to discuss questions of intraspecific variation.

    But see the study of Sankararaman + colleagues (2012): At least some similarity between non-African H. sapiens and H. neanderthalensis can be attributed to interbreeding (in Europe or Asia) between these two in the Late Pleistocene after the divergence of African and non-African H. sapiens.
    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: Author Summary One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans. This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population structure in the ancestors of Neandertals and modern humans. These hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans. We estimate this date by measuring the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.
      Preview · Article · Oct 2012 · PLoS Genetics