Genome-wide insights into the genetic history of human populations

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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The Genetic History of Northern Europe

10.1101/113241 ◽

2017 ◽

Cited By ~ 7

Author(s):

Alissa Mittnik ◽

Chuan-Chao Wang ◽

Saskia Pfrengle ◽

Mantas Daubaras ◽

Gunita Zariņa ◽

...

Keyword(s):

Baltic Sea ◽

Northern Europe ◽

The Baltic Sea ◽

Hunter Gatherers ◽

Glacial Ice ◽

Genetic History ◽

Genome Wide ◽

History Of ◽

Major Shift ◽

The Baltic

Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from ~7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adoption of bronze metallurgy. We show that Scandinavia was settled after the retreat of the glacial ice sheets from a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Western European Mesolithic hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers until around 2,900 calBCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within the Corded Ware Complex.

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A commentary on the history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Journal of Human Genetics ◽

10.1038/jhg.2012.121 ◽

2012 ◽

Vol 57 (12) ◽

pp. 753-754

Author(s):

Jun Gojobori

Keyword(s):

Special Reference ◽

Human Populations ◽

Japanese Archipelago ◽

Snp Data ◽

Genome Wide ◽

History Of ◽

The Japanese Archipelago

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The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Journal of Human Genetics ◽

10.1038/jhg.2012.114 ◽

2012 ◽

Vol 57 (12) ◽

pp. 787-795 ◽

Cited By ~ 77

Author(s):

Keyword(s):

Special Reference ◽

Human Populations ◽

Japanese Archipelago ◽

Snp Data ◽

Genome Wide ◽

History Of ◽

The Japanese Archipelago

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The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity

Genes ◽

10.3390/genes10030222 ◽

2019 ◽

Vol 10 (3) ◽

pp. 222 ◽

Cited By ~ 22

Author(s):

Paolo Abondio ◽

Marco Sazzini ◽

Paolo Garagnani ◽

Alessio Boattini ◽

Daniela Monti ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Human Longevity ◽

Human Populations ◽

Worldwide Distribution ◽

Age Related ◽

Gene Environment ◽

Genome Wide ◽

History Of ◽

Extreme Longevity ◽

Adaptive Role

Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer’s disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.

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Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽

10.3390/genes9070358 ◽

2018 ◽

Vol 9 (7) ◽

pp. 358 ◽

Cited By ~ 10

Author(s):

Olga Dolgova ◽

Oscar Lao

Keyword(s):

Demographic History ◽

Modern Human ◽

Human Populations ◽

Human Genomes ◽

Fitness Consequences ◽

Genome Wide ◽

Anatomically Modern Humans ◽

Genome Wide Data ◽

History Of ◽

Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

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Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip

BMC Genomics ◽

10.1186/s12864-015-1638-6 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 21

Author(s):

Slim Ben Jemaa ◽

Mekki Boussaha ◽

Mondher Ben Mehdi ◽

Jun Heon Lee ◽

Seung-Hwan Lee

Keyword(s):

Population Structure ◽

Genetic History ◽

Genome Wide ◽

History Of

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Coalescent tree recording with selection for fast forward-in-time simulations

10.1101/2021.12.06.470918 ◽

2021 ◽

Author(s):

Remi Matthey-Doret

Keyword(s):

Evolutionary Genetics ◽

Genetic History ◽

Simulation Techniques ◽

Genome Wide ◽

Parental Haplotype ◽

History Of ◽

Speed Up ◽

Coalescent Tree ◽

Fitness Measures ◽

Fitness Calculation

Forward simulations are increasingly important in evolutionary genetics to simulate selection with realistic demography, mating systems and ecology. To reach the performance needed for genome-wide simulations a number of new simulation techniques have been developed recently. Kelleher et al. (2018) introduced a technique consisting in recording the entire genetic history of the population and placing mutations on the coalescent tree. This method cannot model selection. I recently introduced a simulation technique that speed up fitness calculation by assuming that fitness effects among haplotypes are multiplicative (Matthey-Doret, 2021). More precisely, fitness measures are stored for subsets of the genome and, at time of reproduction, if no recombination happen within a given subset, then the fitness for this subset for the offspring haplotype is directly inferred from the parental haplotype. Here, I present a hybrid of the above two techniques. The algorithm records the genetic history of a species, directly places the mutations on the tree and infers fitness of subsets of the genome from parental haplotypes. At recombinant sites, the algorithm explores the tree to reconstruct the genetic data at the recombining segment. I benchmarked this new technique implemented in SimBit and report an important improvement of performance compared to previous techniques to simulate selection. This improvement is particularly drastic at low recombination rate. Such developments of new simulation techniques are pushing the horizon of the realism with which we can simulate species molecular evolution.

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Population-specific sequence and expression differentiation in Europeans

10.1101/749499 ◽

2019 ◽

Author(s):

Xueyuan Jiang ◽

Raquel Assis

Keyword(s):

Target Genes ◽

Demographic History ◽

Copy Number Variations ◽

Human Populations ◽

Rna Seq ◽

Nucleotide Polymorphism ◽

Specific Sequence ◽

Single Nucleotide ◽

Genome Wide ◽

History Of

AbstractMuch of the enormous phenotypic variation observed across human populations is thought to have arisen from events experienced as our ancestors peopled different regions of the world. However, little is known about the genes involved in these population-specific adaptations. Here we explore this problem by simultaneously examining population-specific sequence and expression differentiation in four human populations. In particular, we design a branch-based statistic to estimate population-specific differentiation in four populations, and apply this statistic to single nucleotide polymorphism (SNP) and RNA-seq data from Italian, British, Finish, and Yoruban populations. As expected, genome-wide estimates of sequence and expression differentiation each independently recapitulate the known demographic history of these four human populations, highlighting the utility of our statistic for identifying genic targets of population-specific adaptations. Application of our statistic reveals that genes containing large copy number variations (CNVs) have elevated levels of population-specific sequence and expression differentiation, consistent with the hypothesis that gene turnover is a key reservoir of adaptive variation. Further, European genes displaying population-specific sequence and expression differentiation are enriched for functions related to epigenetic regulation, immunity, and reproduction. Together, our findings illustrate that population-specific sequence and expression differentiation in humans may preferentially target genes with CNVs and play important roles in a diversity of adaptive and disease-related phenotypes.

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