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Journal ArticleDOI

Higher levels of neanderthal ancestry in East Asians than in Europeans.

TL;DR: The results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations.
Abstract: Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from ∼30,000 to 300,000 years ago (KYA). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 KYA. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

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Citations
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Journal ArticleDOI
02 Jan 2014-Nature
TL;DR: It is shown that interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene and a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans is established.
Abstract: We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

1,691 citations

Journal ArticleDOI
Swapan Mallick1, Swapan Mallick2, Swapan Mallick3, Heng Li3, Mark Lipson2, Iain Mathieson2, Melissa Gymrek, Fernando Racimo4, Mengyao Zhao1, Mengyao Zhao2, Mengyao Zhao3, Niru Chennagiri2, Niru Chennagiri3, Niru Chennagiri1, Susanne Nordenfelt3, Susanne Nordenfelt2, Susanne Nordenfelt1, Arti Tandon2, Arti Tandon3, Pontus Skoglund2, Pontus Skoglund3, Iosif Lazaridis3, Iosif Lazaridis2, Sriram Sankararaman3, Sriram Sankararaman2, Sriram Sankararaman5, Qiaomei Fu3, Qiaomei Fu6, Qiaomei Fu2, Nadin Rohland3, Nadin Rohland2, Gabriel Renaud7, Yaniv Erlich8, Thomas Willems9, Carla Gallo10, Jeffrey P. Spence4, Yun S. Song4, Yun S. Song11, Giovanni Poletti10, Francois Balloux12, George van Driem13, Peter de Knijff14, Irene Gallego Romero15, Aashish R. Jha16, Doron M. Behar17, Claudio M. Bravi18, Cristian Capelli19, Tor Hervig20, Andrés Moreno-Estrada, Olga L. Posukh21, Elena Balanovska, Oleg Balanovsky22, Sena Karachanak-Yankova23, Hovhannes Sahakyan17, Hovhannes Sahakyan24, Draga Toncheva23, Levon Yepiskoposyan24, Chris Tyler-Smith25, Yali Xue25, M. Syafiq Abdullah26, Andres Ruiz-Linares12, Cynthia M. Beall27, Anna Di Rienzo16, Choongwon Jeong16, Elena B. Starikovskaya, Ene Metspalu17, Ene Metspalu28, Jüri Parik17, Richard Villems29, Richard Villems28, Richard Villems17, Brenna M. Henn30, Ugur Hodoglugil31, Robert W. Mahley32, Antti Sajantila33, George Stamatoyannopoulos34, Joseph Wee, Rita Khusainova35, Elza Khusnutdinova35, Sergey Litvinov35, Sergey Litvinov17, George Ayodo36, David Comas37, Michael F. Hammer38, Toomas Kivisild17, Toomas Kivisild39, William Klitz, Cheryl A. Winkler40, Damian Labuda41, Michael J. Bamshad34, Lynn B. Jorde42, Sarah A. Tishkoff11, W. Scott Watkins42, Mait Metspalu17, Stanislav Dryomov, Rem I. Sukernik43, Lalji Singh5, Lalji Singh44, Kumarasamy Thangaraj44, Svante Pääbo7, Janet Kelso7, Nick Patterson3, David Reich3, David Reich2, David Reich1 
13 Oct 2016-Nature
TL;DR: It is demonstrated that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Abstract: Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

1,133 citations

Journal ArticleDOI
20 Mar 2014-Nature
TL;DR: The results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
Abstract: Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

810 citations

Journal ArticleDOI
25 Aug 2016-Nature
TL;DR: This paper reported genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers, showing that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other.
Abstract: We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

695 citations

Journal ArticleDOI
21 Aug 2014-Nature
TL;DR: Improved accelerator mass spectrometry 14C techniques are applied to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, showing that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.
Abstract: The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

605 citations

References
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Journal ArticleDOI
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

45,957 citations


"Higher levels of neanderthal ancest..." refers methods in this paper

  • ...Samtools 0.1.18 (Li et al. 2009) was used to convert the BAM files into a pileup alignment (mpileup arguments: -...

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Journal ArticleDOI
07 May 2010-Science
TL;DR: The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

3,575 citations


"Higher levels of neanderthal ancest..." refers background or methods or result in this paper

  • ...Our results and those of Meyer et al. (2012) imply that the relatively simple admixture scenario proposed by Green et al. (2010) needs to be altered....

    [...]

  • ...Green et al. noted that another potential explanation is ancient population subdivision within Africa before both Neanderthals and modern humans left Africa (cf. Green et al. 2010, figure 6)....

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  • ...D-statistics and estimates of admixture rates D-statistics, introduced by Green et al. (2010), are summary statistics for genome sequences from four populations....

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  • ...This method is similar to the one used by Green et al. (2010) but is less restrictive and allows quantification of the differences in the number of admixed segments in different populations....

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  • ...A detailed analysis of a draft Neanderthal genome and five low-coverage (4X) human sequences estimated that Neanderthals made a 1 – 4 % contribution to the gene pool of modern non-African populations (GREEN et al. 2010)....

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Journal ArticleDOI
20 Dec 2002-Science
TL;DR: General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.
Abstract: We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.

2,661 citations


"Higher levels of neanderthal ancest..." refers result in this paper

  • ...If this scenario is correct, the time of separation of the ancestors of modern European and East Asian populations is Neanderthal Ancestry in Eurasians 207 constrained....

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  • ...For analysis B, we redownloaded the genomic data from the Complete Genomics website (ftp://ftp2.completegenomics. com/, software version 2.0.2.15, file format version 2.0, Neanderthal Ancestry in Eurasians 201 February 2012)....

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  • ...Communicating editor: A. Di Rienzo Neanderthal Ancestry in Eurasians 209 GENETICS Supporting Information http://www.genetics.org/lookup/suppl/doi:10.1534/genetics.112.148213/-/DC1 Higher Levels of Neanderthal Ancestry in East Asians than in Europeans Jeffrey D. Wall, Melinda A. Yang, Flora Jay, Sung K. Kim, Eric Y. Durand, Laurie S. Stevison, Christopher Gignoux, August Woerner, Michael F. Hammer, and Montgomery Slatkin Copyright © 2013 by the Genetics Society of America DOI: 10.1534/genetics.112.148213 J. D. Wall et al. 2 SI File S1 Additional D-statistic results We computed D(P1, P2, Neanderthal, Outgroup) for all pair of individuals (P1,P2) from the Complete Genomics data, as described in the Materials and Methods....

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  • ...The relative frequencies of Neanderthal Ancestry in Eurasians 205 these putative Neanderthal haplotypes in the 42 sampled modern human individuals then provide estimates of the relative contributions of Neanderthal DNA to the gene pools of contemporary human populations....

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  • ...We define two SNPs to be “congruent” if their diploid allele counts (i.e., zero, one, or two counts of a particular allele) across individuals are Neanderthal Ancestry in Eurasians 203 completely correlated (i.e., r2 = 1)....

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Journal ArticleDOI
12 Oct 2012-Science
TL;DR: The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Abstract: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

1,690 citations


"Higher levels of neanderthal ancest..." refers background or methods or result in this paper

  • ...We also obtained the high-coverage Denisova genome from Meyer et al. (2012)....

    [...]

  • ...Because we have analyzed more modern human sequences than Meyer et al. (2012) did, we are able to show the extent of variation within both Asian and African populations....

    [...]

  • ...Our results and those of Meyer et al. (2012) imply that the relatively simple admixture scenario proposed by Green et al. (2010) needs to be altered....

    [...]

  • ...This conclusion is consistent with that of Meyer et al. (2012), which was based on the analysis of a smaller number of modern human sequences....

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  • ...In this study, we revisit the question of Neanderthal admixture, using an expanded data set of 42 high-coverage (.45·) modern human genomic sequences, and we take advantage of the recent high-coverage Denisova genome (Meyer et al. 2012) to obtain more refined estimates of admixture proportions....

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Journal ArticleDOI
TL;DR: Combining the demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).
Abstract: Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).

1,636 citations


"Higher levels of neanderthal ancest..." refers background in this paper

  • ...Consequently, estimates of East Asian–European population divergence of ,30 KYA (Gutenkunst et al. 2009; Gravel et al. 2011) are unlikely to be correct....

    [...]

  • ...NEANDERTHALS were a group of archaic hominins thatoccupied large parts of Europe and West Asia from 30,000 to 300,000 years ago (KYA) (Stringer and Hublin 1999; Hublin 2009)....

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  • ...This timeframe is also supported by a 40- to 50- KYA modern human fossil recently found in China (Fu et al. 2013)....

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  • ...Rather than have two distinct episodes of admixture, it seems more plausible that admixture took place over a protracted period 50–80 KYA....

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  • ...Genetics, Vol. 194, 199–209 May 2013 199 50–80 KYA, prior to the divergence of modern-day European and Asian populations....

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Is there a race or culture that is more closely related to neanderthals?

The paper states that Neanderthals contributed more DNA to modern East Asians than to modern Europeans, suggesting that East Asians have a higher level of Neanderthal ancestry.