scholarly journals A Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese

2018 ◽  
Vol 35 (11) ◽  
pp. 2736-2750 ◽  
Author(s):  
Charleston W K Chiang ◽  
Serghei Mangul ◽  
Christopher Robles ◽  
Sriram Sankararaman
Keyword(s):  
Population Structure ◽  
Ethnic Group ◽  
Chinese Women ◽  
Isolation By Distance ◽  
General Pattern ◽  
Han Chinese ◽  
Data Set ◽  
Novel Variants ◽  
Study Population ◽  
Low Coverage

Abstract As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East–West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world’s largest ethnic group.

scholarly journals A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese

2017 ◽  
Author(s):  
Charleston W. K. Chiang ◽  
Serghei Mangul ◽  
Christopher R. Robles ◽  
Warren W. Kretzschmar ◽  
Na Cai ◽  
...  
Keyword(s):  
Population Structure ◽  
Ethnic Group ◽  
Local Adaptation ◽  
Chinese Women ◽  
Han Chinese ◽  
Data Set ◽  
Novel Variants ◽  
Study Population ◽  
Low Coverage ◽  
Geographical Space

AbstractAs are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world’s largest ethnic group.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

Dietary Choline Intake during Pregnancy and PEMT rs7946 Polymorphism on Risk of Preterm Birth: A Case-Control Study

2021 ◽  
pp. 1-10
Author(s):  
Jie Zhu ◽  
Yu-Hong Liu ◽  
Xiang-Long He ◽  
Martin Kohlmeier ◽  
Li-Li Zhou ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Case Control Study ◽  
Chinese Women ◽  
Case Control ◽  
Han Chinese ◽  
Food Frequency ◽  
Term Delivery ◽  
Choline Intake ◽  
Dietary Choline ◽  
Control Study

<b><i>Introduction and Aims:</i></b> Choline-metabolizing genetic variation may interact with choline intake on fetal programming and pregnancy outcome. This case-control study aims to explore the association of maternal choline consumption and phosphatidylethanolamine N-methyltransferase (PEMT) gene polymorphism rs7946 with preterm birth risk. <b><i>Methods:</i></b> 145 Han Chinese women with preterm delivery and 157 Han Chinese women with term delivery were recruited in Shanghai. Dietary choline intake during pregnancy was assessed using a validated food frequency questionnaire. Additionally, DNA samples were genotyped for PEMT rs7946 (G5465A) with plasma homocysteine (Hcy) levels measured. <b><i>Results:</i></b> Compared with the lowest quartile of choline intake, women within the highest consumption quartile had adjusted odds ratio (aOR) for preterm birth of 0.48 (95% confidence interval, CI [0.24, 0.95]). There was a significant interaction between maternal choline intake and PEMT rs7946 (<i>p</i> for interaction = 0.04), where the AA genotype carriers who consumed the energy-adjusted choline &#x3c;255.01 mg/day had aOR for preterm birth of 3.75 (95% CI [1.24, 11.35]), compared to those with GG genotype and choline intake &#x3e;255.01 mg/day during pregnancy. Additionally, the greatest elevated plasma Hcy was found in the cases with AA genotype and choline consumption &#x3c;255.01 mg/day (<i>p</i> &#x3c; 0.001). <b><i>Conclusion:</i></b> The AA genotype of PEMT rs7946 may be associated with increased preterm birth in these Han Chinese women with low choline intake during pregnancy.

scholarly journals Common variants in MAEA gene contributed the susceptibility to osteoporosis in Han Chinese postmenopausal women

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Xuan Cai ◽  
Jun Dong ◽  
Teng Lu ◽  
Liqiang Zhi ◽  
Xijing He
Keyword(s):  
Postmenopausal Women ◽  
Chinese Women ◽  
Han Chinese ◽  
Blood Levels ◽  
Nucleotide Polymorphisms ◽  
Mineral Density ◽  
Association Analyses ◽  
Metabolism Disorder ◽  
Increased Risk ◽  
Chinese Postmenopausal Women

Abstract Background Osteoporosis (OP) is a complex bone metabolism disorder characterized by the loss of bone minerals and an increased risk of bone fracture. A recent study reported the relationship of the macrophage erythroblast attacher gene (MAEA) with low bone mineral density in postmenopausal Japanese women. Our study aimed to investigate the association of MAEA with postmenopausal osteoporosis (PMOP) in Han Chinese individuals. Methods A total of 968 unrelated postmenopausal Chinese women comprising 484 patients with PMOP and 484 controls were recruited. Four tag single nucleotide polymorphisms (SNPs) that covered the gene region of MAEA were chosen for genotyping. Single SNP and haplotypic association analyses were performed, and analysis of variance was conducted to test the correlation between blood MAEA protein level and genotypes of associated SNPs. Results SNP rs6815464 was significantly associated with the risk of PMOP. The C allele of rs6815464 was strongly correlated with the decreased risk of PMOP in our study subjects (OR[95% CI]=0.75[0.63-0.89], P=0.0015). Significant differences in MAEA protein blood levels among genotypes of SNP rs6815464 were identified in both the PMOP (F=6.82, P=0.0012) and control groups (F=11.5, P=0.00001). The C allele was positively associated with decreased MAEA protein levels in blood. Conclusion This case-control study on Chinese postmenopausal women suggested an association between SNP rs6815464 of MAEA and PMOP. Further analyses showed that genotypes of SNP rs6815464 were also associated with the blood level of MAEA protein.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Empirical Evaluation of Genetic Clustering Methods Using Multilocus Genotypes From 20 Chicken Breeds

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 699-713
Author(s):  
Noah A Rosenberg ◽  
Terry Burke ◽  
Kari Elo ◽  
Marcus W Feldman ◽  
Paul J Freidlin ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Population Structure ◽  
Clustering Algorithm ◽  
Empirical Evaluation ◽  
Unknown Origin ◽  
Clustering Methods ◽  
Genetic Cluster ◽  
Data Set ◽  
Multilocus Genotypes ◽  
Chicken Breeds

Abstract We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently ~98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8–10 highly variable markers from among the 27 markers genotyped also achieved &gt;95% clustering success. When 12–15 highly variable markers and only 15–20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

Genetic isolation by distance and localized fjord population structure in Pacific cod (Gadus macrocephalus): limited effective dispersal in the northeastern Pacific Ocean

2009 ◽  
Vol 66 (1) ◽  
pp. 153-166 ◽  
Author(s):  
Kathryn Maja Cunningham ◽  
Michael Francis Canino ◽  
Ingrid Brigette Spies ◽  
Lorenz Hauser
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Puget Sound ◽  
Pacific Cod ◽  
Genetic Population ◽  
Pacific Cod Gadus Macrocephalus ◽  
Gadus Macrocephalus ◽  
Northeastern Pacific

Genetic population structure of Pacific cod, Gadus macrocephalus , was examined across much of its northeastern Pacific range by screening variation at 11 microsatellite DNA loci. Estimates of FST (0.005 ± 0.002) and RST (0.010 ± 0.003) over all samples suggested that effective dispersal is limited among populations. Genetic divergence was highly correlated with geographic distance in an isolation-by-distance (IBD) pattern along the entire coastal continuum in the northeastern Pacific Ocean (~4000 km; r2 = 0.83), extending from Washington State to the Aleutian Islands, and over smaller geographic distances for three locations in Alaska (~1700 km; r2 = 0.56). Slopes of IBD regressions suggested average dispersal distance between birth and reproduction of less than 30 km. Exceptions to this pattern were found in samples taken from fjord environments in the Georgia Basin (the Strait of Georgia (Canada) and Puget Sound (USA)), where populations were differentiated from coastal cod. Our results showed population structure at spatial scales relevant to fisheries management, both caused by limited dispersal along the coast and by sharp barriers to migration isolating smaller stocks in coastal fjord environments.

scholarly journals Comparative population genetic structure of two Ixodidae ticks (Ixodes ovatus and Haemaphysalis flava) in Niigata Prefecture, Japan

2019 ◽  
Author(s):  
Maria Angenica Fulo Regilme ◽  
Megumi Sato ◽  
Tsutomu Tamura ◽  
Reiko Arai ◽  
Marcello Otake Sato ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Large Scale ◽  
Southern China ◽  
Isolation By Distance ◽  
Mantel Test ◽  
Rrna Gene ◽  
Data Set ◽  
Genetic Groups ◽  
Niigata Prefecture ◽  
Haemaphysalis Flava

AbstractIxodid tick species such as Ixodes ovatus and Haemaphysalis flava are important vector of tick-borne diseases in Japan. In this study, we used genetic structure at two mitochondrial loci (cox1, 16S rRNA gene) to infer gene flow patterns of I. ovatus and H. flava from Niigata Prefecture, Japan. Samples were collected in 29 (I. ovatus) and 17 (H. flava) sampling locations across Niigata Prefecture (12,584.18 km2). For I. ovatus, pairwise FST and analysis of molecular variance (AMOVA) analyses of cox1 sequences indicated significant among-population differentiation. This was in contrast to H. flava, for which there were few cases of low significant pairwise differentiation. A Mantel test revealed isolation by distance and there was positive spatial autocorrelation of haplotypes in I. ovatus cox1 and 16S sequences, but non-significant results were observed in H. flava in both markers. We found three genetic groups (China 1, China 2 and Japan) in the cox1 I. ovatus tree. Newly sampled I. ovatus grouped together with a published I. ovatus sequence from northern Japan and were distinct from two other I. ovatus groups that were reported from southern China. The three genetic groups in our data set suggest the potential for cryptic species among the groups. While many factors can potentially account for the observed differences in genetic structure between the two species, including population persistence and large-scale patterns of range expansion, the differences in the mobility of hosts of tick immature stages (small mammals in I. ovatus; birds in H. flava) is possibly driving the observed patterns.

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