Reconstructing Genetic History of Siberian and Northeastern European Populations

Siberia and Western Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups. Yet, genetic variation of peoples from this region is largely uncharacterized. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We combine these datasets with additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees. Our results provide new links between modern and ancient inhabitants of Eurasia. Siberians share 38% of ancestry with descendants of the 45,000-year-old Ust-Ishim people, who were previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to the Ancient North Eurasians, represented by the 24,000-year-old Siberian Malta boy. In addition, Siberians admixtures are present in lineages represented by Eastern European hunter-gatherers from Samara, Karelia, Hungary and Sweden (from 8,000-6,600 years ago), as well as Yamnaya culture people (5,300-4,700 years ago) and modern-day northeastern Europeans. These results provide new evidence of ancient gene flow from Siberia into Europe.

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Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of Schinus molle L.

Biology ◽

10.3390/biology7030043 ◽

2018 ◽

Vol 7 (3) ◽

pp. 43 ◽

Cited By ~ 2

Author(s):

Rafael Lemos ◽

Cristiane Matielo ◽

Dalvan Beise ◽

Vanessa da Rosa ◽

Deise Sarzi ◽

...

Keyword(s):

Genetic Diversity ◽

Invasive Plant ◽

Whole Genome Sequencing Data ◽

Natural Occurrence ◽

Sequencing Data ◽

Dispersal Capacity ◽

Schinus Molle ◽

High Dispersal ◽

History Of

Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree (Schinus molle L.) is a pioneer tree species native from South America which was introduced in North America, Europe and Africa, becoming a threat to these non-native habitats. In this study, we report the discovery and characterization of 17 plastidial (ptSSR) and seven nuclear (nSSR) markers for S. molle based on low-coverage whole-genome sequencing data acquired through next-generation sequencing. The markers were tested in 56 individuals from two natural populations sampled in the Brazilian Caatinga and Pampa biomes. All loci are moderately to highly polymorphic and revealed to be suitable for genetic monitoring of new invasions, for understanding the history of old invasions, as well as for genetic studies of native populations in their natural occurrence range and of orchards established with commercial purposes.

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Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

GigaScience ◽

10.1093/gigascience/giaa014 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 3

Author(s):

Hao Chen ◽

Min Huang ◽

Bin Yang ◽

Zhongping Wu ◽

Zheng Deng ◽

...

Keyword(s):

Geographic Origin ◽

Whole Genome Sequencing Data ◽

Biological Functions ◽

Sequencing Data ◽

Phenotypic Characteristics ◽

Large White ◽

Wild Boars ◽

Domestic Pigs ◽

Southern Chinese ◽

History Of

Abstract Background Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Results Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs. Conclusions This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

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A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population

10.1101/036897 ◽

2016 ◽

Cited By ~ 2

Author(s):

Jayne Y. Hehir-Kwa ◽

Tobias Marschall ◽

Wigard P. Kloosterman ◽

Laurent C. Francioli ◽

Jasmijn A. Baaijens ◽

...

Keyword(s):

Association Studies ◽

Whole Genome Sequencing Data ◽

Strong Linkage Disequilibrium ◽

Genome Wide Association Studies ◽

Sequencing Data ◽

Full Spectrum ◽

Disease Phenotypes ◽

Human Genomes ◽

Genome Wide ◽

Genome Variants

AbstractStructural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation.Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals. Our findings are essential for genome-wide association studies.

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Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People

Molecular Biology and Evolution ◽

10.1093/molbev/msaa276 ◽

2020 ◽

Author(s):

Yun-Hua Lo ◽

Hsueh-Chien Cheng ◽

Chia-Ni Hsiung ◽

Show-Ling Yang ◽

Han-Yu Wang ◽

...

Keyword(s):

Genetic Ancestry ◽

Indigenous Populations ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Single Nucleotide ◽

Homogeneous Population ◽

Taiwanese People ◽

Candidate Loci ◽

Related Trait

Abstract The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.

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The prehistoric peopling of Southeast Asia

Science ◽

10.1126/science.aat3628 ◽

2018 ◽

Vol 361 (6397) ◽

pp. 88-92 ◽

Cited By ~ 103

Author(s):

Hugh McColl ◽

Fernando Racimo ◽

Lasse Vinner ◽

Fabrice Demeter ◽

Takashi Gakuhari ◽

...

Keyword(s):

Southeast Asia ◽

Agricultural Development ◽

East Asian ◽

Southeast Asian ◽

Current Evidence ◽

Human Occupation ◽

Hunter Gatherers ◽

Human Genomes ◽

History Of ◽

Asian History

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

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Three hallmarks of malaria-induced selection in human genomes

10.1101/2020.07.07.170092 ◽

2020 ◽

Author(s):

Jacob A. Tennessen ◽

Manoj T. Duraisingh

Keyword(s):

Statistical Tests ◽

Impact Resistance ◽

Neutral Evolution ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Evolutionary Patterns ◽

Evolutionary Pattern ◽

Human Genomes ◽

Evolutionary Simulations ◽

Host Parasite

AbstractMalaria has plausibly been the single strongest selective pressure on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for non-neutral evolution. Here we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.

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An integrated personal and population-based Egyptian genome reference

Nature Communications ◽

10.1038/s41467-020-17964-1 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Inken Wohlers ◽

Axel Künstner ◽

Matthias Munz ◽

Michael Olbrich ◽

Anke Fähnrich ◽

...

Keyword(s):

Genetic Variation ◽

De Novo ◽

Disease Risk ◽

Population Based ◽

European Ancestry ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Human Genomes ◽

Genome Wide ◽

Polygenic Scores

Abstract A small number of de novo assembled human genomes have been reported to date, and few have been complemented with population-based genetic variation, which is particularly important for North Africa, a region underrepresented in current genome-wide references. Here, we combine long- and short-read whole-genome sequencing data with recent assembly approaches into a de novo assembly of an Egyptian genome. The assembly demonstrates well-balanced quality metrics and is complemented with variant phasing via linked reads into haploblocks, which we associate with gene expression changes in blood. To construct an Egyptian genome reference, we identify genome-wide genetic variation within a cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genome references. Thus, the Egyptian genome reference will be a valuable resource for precision medicine.

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Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes

Molecular Biology and Evolution ◽

10.1093/molbev/msz282 ◽

2019 ◽

Vol 37 (4) ◽

pp. 994-1006 ◽

Cited By ~ 4

Author(s):

María C Ávila-Arcos ◽

Kimberly F McManus ◽

Karla Sandoval ◽

Juan Esteban Rodríguez-Rodríguez ◽

Viridiana Villa-Islas ◽

...

Keyword(s):

Native American ◽

Demographic History ◽

Population History ◽

Indigenous Populations ◽

Physical Endurance ◽

Sequencing Data ◽

Indigenous Group ◽

Native Populations ◽

Human Genome Sequencing ◽

History Of

Abstract Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.

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Population history and gene divergence in Native Mexicans inferred from 76 human exomes

10.1101/534818 ◽

2019 ◽

Author(s):

María C. Ávila-Arcos ◽

Kimberly F. McManus ◽

Karla Sandoval ◽

Juan Esteban Rodríguez-Rodríguez ◽

Alicia R. Martin ◽

...

Keyword(s):

Native American ◽

Demographic History ◽

Population History ◽

Indigenous Populations ◽

Physical Endurance ◽

Sequencing Data ◽

Indigenous Group ◽

Native Populations ◽

Human Genome Sequencing ◽

History Of

AbstractNative American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 kya and subsequently diverging locally 6.5 kya and 5.7 kya, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern indigenous group from Oaxaca whose height is extremely low compared to other native populations.

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Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data

Microbial Genomics ◽

10.1099/mgen.0.000450 ◽

2020 ◽

Vol 6 (11) ◽

Author(s):

Yuanwei Xu ◽

Jessica E. Stockdale ◽

Vijay Naidu ◽

Hollie Hatherell ◽

James Stimson ◽

...

Keyword(s):

Mathematical Modelling ◽

Disease Transmission ◽

Machine Learning Techniques ◽

Whole Genome Sequencing Data ◽

Reconstruction Method ◽

Sequencing Data ◽

Patient Level ◽

Learning Techniques ◽

Level Data ◽

History Of

Outbreaks of tuberculosis (TB) – such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 – provide excellent opportunities to model transmission of this devastating disease. Transmission chains for TB are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine-learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 21 transmission events with reasonable confidence, 9 of which have zero SNP distance, and a maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible TB transmitters.

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