scholarly journals The gateway into Remote Oceania: new insights from genome-wide data

2017 ◽  
Author(s):  
Irina Pugach ◽  
Ana T. Duggan ◽  
D. Andrew Merriwether ◽  
Françoise R. Friedlaender ◽  
Jonathan S. Friedlaender ◽  
...  
Keyword(s):  
Solomon Islands ◽  
Population History ◽  
Indigenous Populations ◽  
Autosomal Snps ◽  
Genome Wide ◽  
A Genome ◽  
Bismarck Archipelago ◽  
Genome Wide Data ◽  
Linguistic Divide ◽  
Founder Event

ABSTRACTA widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide dataset of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal SNPs. We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a “leapfrog” fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bi-directional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.

scholarly journals Genomics of end-Pleistocene population replacement in a small mammal

2018 ◽  
Vol 285 (1872) ◽  
pp. 20172624 ◽  
Author(s):  
Petr Kotlík ◽  
Silvia Marková ◽  
Mateusz Konczal ◽  
Wiesław Babik ◽  
Jeremy B. Searle
Keyword(s):  
Small Mammals ◽  
Bank Vole ◽  
Glacial Refugia ◽  
European Population ◽  
Population History ◽  
Clethrionomys Glareolus ◽  
Autosomal Snps ◽  
Genome Wide ◽  
Northern Territories ◽  
Approximate Bayesian

Current species distributions at high latitudes are the product of expansion from glacial refugia into previously uninhabitable areas at the end of the last glaciation. The traditional view of postglacial colonization is that southern populations expanded their ranges into unoccupied northern territories. Recent findings on mitochondrial DNA (mtDNA) of British small mammals have challenged this simple colonization scenario by demonstrating a more complex genetic turnover in Britain during the Pleistocene–Holocene transition where one mtDNA clade of each species was replaced by another mtDNA clade of the same species. Here, we provide evidence from one of those small mammals, the bank vole ( Clethrionomys glareolus ), that the replacement was genome-wide. Using more than 10 000 autosomal SNPs we found that similar to mtDNA, bank vole genomes in Britain form two (north and south) clusters which admix. Therefore, the genome of the original postglacial colonists (the northern cluster) was probably replaced by another wave of migration from a different continental European population (the southern cluster), and we gained support for this by modelling with approximate Bayesian computation. This finding emphasizes the importance of analysis of genome-wide diversity within species under changing climate in creating opportunities for sophisticated testing of population history scenarios.

Associations Between Variants Near a Monoaminergic Pathways Gene (PHOX2B) and Amygdala Reactivity: A Genome-Wide Functional Imaging Study

2012 ◽  
Vol 15 (3) ◽  
pp. 273-285 ◽  
Author(s):  
Olga Therese Ousdal ◽  
Andrew Anand Brown ◽  
Jimmy Jensen ◽  
Per H. Nakstad ◽  
Ingrid Melle ◽  
...  
Keyword(s):  
Individual Differences ◽  
Signaling Pathways ◽  
Functional Imaging ◽  
Genetic Variants ◽  
Regulatory Region ◽  
Phox2b Gene ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Data ◽  
Amygdala Activity

As the amygdala is part of the phylogenetic old brain, and its anatomical and functional properties are conserved across species, it is reasonable to assume genetic influence on its activity. A large corpus of candidate gene studies indicate that individual differences in amygdala activity may be caused by genetic variants within monoaminergic signaling pathways such as dopamine, serotonin, and norepinephrine. However, to our knowledge, the use of genome-wide data to discover genetic variants underlying individual differences in adult amygdala activity is novel. In the present study, the combination of genome-wide data and functional imaging phenotypes from an emotional faces task yielded a significant association between rs10014254 and the amygdala using a region of interest approach. This single nucleotide polymorphism is located in a regulatory region upstream of the Paired-like homeobox 2b (PHOX2B) gene; therefore it could affect the expression of this gene. PHOX2B regulates the expression of enzymes necessary for the synthesis of several monoamines and is essential for the development of the autonomic nervous system. However, an attempt to replicate the finding in an independent sample from North America did not succeed. The synthesis of functional magnetic resonance imaging (fMRI) and genome-wide data takes a hypothesis-free approach as to which genetic variants are of interest. Therefore, we believe that an undirected finding within such a plausible region is of interest, and that our results add further support to the hypothesis that monoaminergic signaling pathways play a central role in regulating amygdala activity.

scholarly journals A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

2020 ◽  
Author(s):  
Choongwon Jeong ◽  
Ke Wang ◽  
Shevan Wilkin ◽  
William Timothy Treal Taylor ◽  
Bryan K. Miller ◽  
...  
Keyword(s):  
Bronze Age ◽  
Population History ◽  
Complex Interplay ◽  
Cultural Changes ◽  
Genetic History ◽  
Nomadic Pastoralists ◽  
Eurasian Steppe ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of

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.

scholarly journals Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mário Vicente ◽  
Edita Priehodová ◽  
Issa Diallo ◽  
Eliška Podgorná ◽  
Estella S. Poloni ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genomic Region ◽  
Population History ◽  
Lactase Persistence ◽  
Control Element ◽  
Genetic Adaptation ◽  
North African ◽  
Life Styles ◽  
Genome Wide ◽  
A Genome

Abstract Background Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Results Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake. Conclusions Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

scholarly journals The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Humberto García-Ortiz ◽  
Francisco Barajas-Olmos ◽  
Cecilia Contreras-Cubas ◽  
Miguel Ángel Cid-Soto ◽  
Emilio J. Córdova ◽  
...  
Keyword(s):  
Demographic History ◽  
Indigenous Populations ◽  
South American ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Genomic Landscape ◽  
A Genome ◽  
Peopling Of The Americas ◽  
History Of ◽  
Genetic Makeup

AbstractThe genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15–30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4–9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.

scholarly journals Using Genome Wide Estimates of Heritability to Examine the Relevance of Gene-Environment Interplay

2016 ◽  
Author(s):  
BENJAMIN W DOMINGUE ◽  
Jason D. Boardman
Keyword(s):  
Genome Wide Association Study ◽  
Environment Interaction ◽  
Education Group ◽  
Gene Environment ◽  
Genome Wide ◽  
Heart Study ◽  
A Genome ◽  
Genome Wide Data ◽  
Higher Educational Attainment ◽  
Family Based

We use genome-wide data from the third generation respondents of the Framingham Heart Study to estimate heritability in body mass index using different quantities of the measured genotype. Heritability decreases rapidly when SNPs implicated by a genome-wide association study are removed but shows essentially no decline when SNPs implicated by a gene-environment interaction in a second genome-wide analysis are removed. This second result is highlighted by our additional finding that the SNPs which explain heritability amongst a subsample defined by higher educational attainment explain no heritability of the heritability in the lower education group, and vice-versa. Finally, we do find consistent heritability estimates when we compare family-based estimates versus those based on measured genotype.

scholarly journals Population Turnover in Remote Oceania Shortly After Initial Settlement

2018 ◽  
Author(s):  
Mark Lipson ◽  
Pontus Skoglund ◽  
Matthew Spriggs ◽  
Frederique Valentin ◽  
Stuart Bedford ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Solomon Islands ◽  
Great Majority ◽  
Long Distance ◽  
Skeletal Morphology ◽  
Fine Grained ◽  
Population Turnover ◽  
Bismarck Archipelago ◽  
Genome Wide Data ◽  
Diverse Groups

SummaryAncient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania (“First Remote Oceanians”) were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.

A genome-wide association study of colorectal cancer in Mexican mestizos suggest novel common tumor-risk variants

2020 ◽  
Author(s):  
AUGUSTO Rojas-Martinez ◽  
Valentina Colistro ◽  
Raquel Cruz ◽  
Clara Ruiz ◽  
Inés Quintela ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Latin American ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Statistical Significance ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Autosomal Snps ◽  
Genome Wide ◽  
A Genome

Abstract Background: Genome-wide association studies (GWAS) for colorectal cancer (CRC) have detected high-risk genetic variants associated with CRC in several ethnic groups, but Latin American communities are still underrepresented. The aim was to identify variants related to CRC in an admixed Latin American population. Methods: The study was performed in 831 cases and 881 controls from Mexico, who were genotyped for 1,006,703 autosomal SNPs. Logistic regression was carried out including covariants, such as sex, age and genetic ancestry. Lastly, we performed a sequence-kernel association test (SKAT) to consider the joint effect of several SNPs lying in genes.Results: Eight chromosomal regions reached genome-wide significance level ( p < 5×10 -8 ): 1p36.22, 1p31.1, 1q42.13, 6p22, 7p14.1, 12q24.32, 16q12.2 and 21q22.2 and 63 variants reached borderline statistical significance ( p < 1×10 − 6 ). SKAT analysis detected 13 loci associated with CRC, none of them previously associated with CRC. Conclusions: We found 8 SNPs and 13 loci associated with CRC. These signals may contribute to enrich the panoply of genes involved with CRC. Further analyses remain to be done to validate the associations in other Latin American populations. This study highlights the importance of conducting GWAS in poorly explored admixed populations.

scholarly journals Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Keyword(s):  
Severe Malaria ◽  
Genome Wide Association Study ◽  
Causal Mechanism ◽  
Chromosome 6 ◽  
Genetic Determinants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Data ◽  
Candidate Loci ◽  
Population Controls

AbstractThe human genetic factors that affect resistance to infectious disease are poorly understood. Here we report a genome-wide association study in 17,000 severe malaria cases and population controls from 11 countries, informed by sequencing of family trios and by direct typing of candidate loci in an additional 15,000 samples. We identify five replicable associations with genome-wide levels of evidence including a newly implicated variant on chromosome 6. Jointly, these variants account for around one-tenth of the heritability of severe malaria, which we estimate as ~23% using genome-wide genotypes. We interrogate available functional data and discover an erythroid-specific transcription start site underlying the known association in ATP2B4, but are unable to identify a likely causal mechanism at the chromosome 6 locus.  Previously reported HLA associations do not replicate in these samples. This large dataset will provide a foundation for further research on the genetic determinants of malaria resistance in diverse populations.

scholarly journals A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0205395 ◽  
Author(s):  
Nathalie Smitz ◽  
Olivia Jouvenet ◽  
Fredrick Ambwene Ligate ◽  
William-George Crosmary ◽  
Dennis Ikanda ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Panthera Leo ◽  
African Lion ◽  
Genome Wide ◽  
A Genome ◽  
Data Assessment ◽  
Genome Wide Data ◽  
Genetic Structure And Diversity
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