[Show abstract][Hide abstract] ABSTRACT: Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia). Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ∼12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
[Show abstract][Hide abstract] ABSTRACT: Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
[Show abstract][Hide abstract] ABSTRACT: The discovery of human remains from the Lauricocha cave in the Central Andean highlands
in the 1960
s provided the first direct evidence for human presence in the high altitude Andes.
The skeletons found at this site were ascribed to the Early to Middle Holocene and repre-
sented the oldest known population of Western South America, and thus were used in several
studies addressing the early population history of the continent. However, later excavations
at Lauricocha led to doubts regarding the antiquity of the site. Here, we provide new dating,
craniometric, and genetic evidence for this iconic site. We obtained new radiocarbon dates,
generated complete mitochondrial genomes and nuclear SNP data from five individuals, and
re-analyzed the human remains of Lauricocha to revise the initial morphological and cranio-
metric analysis conducted in the 1960
s. We show that Lauricocha was indeed occupied in
the Early to Middle Holocene but the temporal spread of dates we obtained from the human
remains show that they do not qualify as a single contemporaneous population. However, the
genetic results from five of the individuals fall within the spectrum of genetic diversity ob-
served in pre-Columbian and modern Native Central American populations.
PLoS ONE 06/2015; 10(6):e0127141. DOI:10.1371/journal.pone.0127141 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies1, 2, 3, 4, 5, 6, 7, 8 and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000-year-old Siberian6. By ~6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin9 of at least some of the Indo-European languages of Europe.
[Show abstract][Hide abstract] ABSTRACT: We generated genome-wide data from 69 Europeans who lived between 8,000-3,000
years ago by enriching ancient DNA libraries for a target set of almost four
hundred thousand polymorphisms. Enrichment of these positions decreases the
sequencing required for genome-wide ancient DNA analysis by a median of around
250-fold, allowing us to study an order of magnitude more individuals than
previous studies and to obtain new insights about the past. We show that the
populations of western and far eastern Europe followed opposite trajectories
between 8,000-5,000 years ago. At the beginning of the Neolithic period in
Europe, ~8,000-7,000 years ago, closely related groups of early farmers
appeared in Germany, Hungary, and Spain, different from indigenous
hunter-gatherers, whereas Russia was inhabited by a distinctive population of
hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By
~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred
throughout much of Europe, but in Russia, the Yamnaya steppe herders of this
time were descended not only from the preceding eastern European
hunter-gatherers, but from a population of Near Eastern ancestry. Western and
Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded
Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya,
documenting a massive migration into the heartland of Europe from its eastern
periphery. This steppe ancestry persisted in all sampled central Europeans
until at least ~3,000 years ago, and is ubiquitous in present-day Europeans.
These results provide support for the theory of a steppe origin of at least
some of the Indo-European languages of Europe.
[Show abstract][Hide abstract] ABSTRACT: Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation 5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb develop-ment (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat. Gibbons (Hylobatidae) are critically endangered 1 small apes that inhabit the tropical forests of southeast Asia (Fig. 1) and belong to the super-family Hominoidea along with great apes and humans. In the primate phylogeny, gibbons diverged between Old World monkeys and great apes, providing a unique perspective from which to study the origins of hominoid characteristics. Gibbons have several distinctive traits, the most striking of which is the unusually high number of large-scale chromosomal rearrangements in comparison to the inferred ancestral ape karyotype 2
[Show abstract][Hide abstract] ABSTRACT: Spontaneously arising (de novo) mutations have an important role in medical genetics. For diseases with extensive locus heterogeneity, such as autism spectrum disorders (ASDs), the signal from de novo mutations is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. Here we provide a statistical framework for the analysis of excesses in de novo mutation per gene and gene set by calibrating a model of de novo mutation. We applied this framework to de novo mutations collected from 1,078 ASD family trios, and, whereas we affirmed a significant role for loss-of-function mutations, we found no excess of de novo loss-of-function mutations in cases with IQ above 100, suggesting that the role of de novo mutations in ASDs might reside in fundamental neurodevelopmental processes. We also used our model to identify ∼1,000 genes that are significantly lacking in functional coding variation in non-ASD samples and are enriched for de novo loss-of-function mutations identified in ASD cases.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: We sequenced the genomes of a ~7,000 year old farmer from Germany and eight
~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other
ancient genomes1–4 with 2,345 contemporary humans to show that most
present Europeans derive from at least three highly differentiated populations: West
European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near
Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near
Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but
also harbored WHG-related ancestry. We model these populations’ deep relationships
and show that EEF had ~44% ancestry from a “Basal Eurasian”
population that split prior to the diversification of other non-African lineages.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred, and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses, and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples where they provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present day Basques and Sardinians, and the other related to present day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean 'Iceman'.