scholarly journals Genetic landscapes reveal how human genetic diversity aligns with geography

2017 ◽  
Author(s):  
Benjamin Marco Peter ◽  
Desislava Petkova ◽  
John Novembre
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Rare Variants ◽  
Disease Risk ◽  
Geographic Distance ◽  
Population History ◽  
Human Populations ◽  
Complex Processes ◽  
Scale Population

Geographic patterns in human genetic diversity carry footprints of population history1,2 and provide insights for genetic medicine and its application across human populations3,4. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists5–10, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure11–15 do not incorporate geography directly, and it must be considered post hoc alongside a visual summary. Here, we use a recently developed spatially explicit method to estimate “effective migration” surfaces to visualize how human genetic diversity is geographically structured (the EEMS method16). The resulting surfaces are “rugged”, which indicates the relationship between genetic and geographic distance is heterogenous and distorted as a rule. Most prominently, topographic and marine features regularly align with increased genetic differentiation (e.g. the Sahara desert, Mediterranean Sea or Himalaya at large scales; the Adriatic, interisland straits in near Oceania at smaller scales). In other cases, the locations of historical migrations and boundaries of language families align with migration features. These results provide visualizations of human genetic diversity that reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, there have regularly been factors that subtly distort the underlying relationship across space observed today. The fine-scale population structure depicted here is relevant to understanding complex processes of human population history and may provide insights for geographic patterning in rare variants and heritable disease risk.

scholarly journals Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography

2019 ◽  
Vol 37 (4) ◽  
pp. 943-951 ◽  
Author(s):  
Benjamin M Peter ◽  
Desislava Petkova ◽  
John Novembre
Keyword(s):  
Genetic Diversity ◽  
Geographic Distance ◽  
Population History ◽  
Human Populations ◽  
Geographic Patterns ◽  
Local Patterns ◽  
New Perspective ◽  
Post Hoc ◽  
Genetic Medicine ◽  
The Relationship

Abstract Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate “effective migration” surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Daniel S. Malawsky ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

scholarly journals Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

2018 ◽  
Author(s):  
Clare Bycroft ◽  
Ceres Fernandez-Rozadilla ◽  
Clara Ruiz-Ponte ◽  
Inés Quintela-García ◽  
Ángel Carracedo ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Iberian Peninsula ◽  
Association Studies ◽  
Demographic History ◽  
African Ancestry ◽  
Population History ◽  
Human Populations ◽  
Fine Scale ◽  
The North

Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian Peninsula is linguistically diverse, has a complex demographic history, and is unique among European regions in having a centuries-long period of Muslim rule. Previous genetic studies of Spain have examined either a small fraction of the genome or only a few Spanish regions. Thus, the overall pattern of fine-scale population structure within Spain remains uncharacterised. Here we analyse genome-wide genotyping array data for 1,413 Spanish individuals sampled from all regions of Spain. We identify extensive fine-scale structure, down to unprecedented scales, smaller than 10 Km in some places. We observe a major axis of genetic differentiation that runs from east to west of the peninsula. In contrast, we observe remarkable genetic similarity in the north-south direction, and evidence of historical north-south population movement. Finally, without making particular prior assumptions about source populations, we show that modern Spanish people have regionally varying fractions of ancestry from a group most similar to modern north Moroccans. The north African ancestry results from an admixture event, which we date to 860 - 1120 CE, corresponding to the early half of Muslim rule. Our results indicate that it is possible to discern clear genetic impacts of the Muslim conquest and population movements associated with the subsequent Reconquista.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2020 ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
Qin Qin Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genetic and questionnaire data from >4,000 British Pakistani individuals, mostly with roots in Azad Kashmir and Punjab. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low effective population sizes (Ne) over the last 50 generations, with some showing a decrease in Ne 15-20 generations ago that has resulted in extensive identity-by-descent sharing and increased homozygosity. Using new theory, we show that the footprint of regions of homozygosity in the two largest subgroups is about twice that expected naively based on the self-reported consanguinity rates and the inferred historical Ne trajectory. These results demonstrate the impact of the cultural practices of endogamy and consanguinity on population structure and genomic diversity in British Pakistanis, and have important implications for medical genetic studies.

scholarly journals Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

scholarly journals Dynamic genetic diversity and population structure of Coreius guichenoti

ZooKeys ◽  
2021 ◽  
Vol 1055 ◽  
pp. 135-148
Author(s):  
Dongqi Liu ◽  
Feng Lan ◽  
Sicai Xie ◽  
Yi Diao ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Yangtze River ◽  
Fish Passage ◽  
The Yangtze River ◽  
Artificial Breeding ◽  
Significant Difference ◽  
High Elevations

To investigate the genetic effects on the population of Coreius guichenoti of dam constructions in the upper reaches of the Yangtze River, we analyzed the genetic diversity and population structure of 12 populations collected in 2009 and 2019 using mitochondrial DNA (mtDNA) control regions. There was no significant difference in genetic diversity between 2009 and 2019 (P > 0.05), but the population structure tended to become stronger. Genetic differentiation (FST) among five populations (LX, BB, YB, SF and JA) collected in 2009 was not significant (P > 0.05). However, some populations collected in 2019 were significantly differentiated (P < 0.05), indicating that the population structure has undergone change. A correlation analysis showed that the genetic diversity of the seven populations collected in 2019 was significantly negatively correlated with geographical height (r = −0.808, P = 0.028), indicating that the populations at high elevations were more vulnerable than those at low elevations. In order to prevent the further decrease of genetic diversity and population resources, some conservation and restoration suggestions, such as fish passage and artificial breeding, are put forward.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

scholarly journals Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous FishTenualosa ilisha

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Rashmi Verma ◽  
Mahender Singh ◽  
Sudhir Kumar
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Control Region ◽  
Population Genetic ◽  
Arabian Sea ◽  
Mitochondrial Control Region ◽  
Population Genetic Differentiation ◽  
First Choice ◽  
Scale Population ◽  
And Control

The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure ofHilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (FST  0.0441,p<0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations ofHilsa.

scholarly journals Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5380 ◽  
Author(s):  
Christopher S. Moore ◽  
Matthew J. Ruocchio ◽  
April M.H. Blakeslee
Keyword(s):  
Genetic Diversity ◽  
North Carolina ◽  
Population Structure ◽  
Gene Flow ◽  
Salinity Gradient ◽  
Western Atlantic ◽  
Widespread Species ◽  
Naked Goby ◽  
Gobiosoma Bosc ◽  
Scale Population

Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (∼3 ppt to ∼18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from GenBank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries. Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work. Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population. Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and regional patterns of population connectivity and gene flow.

Genetic diversity and population structure of small yellow croaker (Larimichthys polyactis) in the Yellow and East China seas based on microsatellites

2019 ◽  
Vol 32 ◽  
pp. 16
Author(s):  
Qiqun Cheng ◽  
Wenming Chen ◽  
Li Ma
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
East China ◽  
Rank Test ◽  
Northwestern Pacific ◽  
Allele Frequency Distribution ◽  
China Seas ◽  
Larimichthys Polyactis ◽  
Small Yellow Croaker

Small yellow croaker (Larimichthys polyactis), a member of family Sciaenidae, is mainly distributed in the northwestern Pacific Ocean. To assess the genetic diversity and population structure of this species across its range, we genotyped 150 L. polyactis individuals sampled in five locations along the coast of the Yellow and East China seas using 20 polymorphic microsatellites. A total of 499 alleles were detected at 20 loci across all individuals, and a relatively high level of genetic diversity was observed, with observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) ranging from 0.233 to 1.000, from 0.438 to 0.955, and from 0.367 to 0.953 per locus-location combination, respectively. Analysis of molecular variance (AMOVA) (FST = 0.00915, P < 0.001), pairwise FST, and corrected average pairwise differences indicated that there was extremely low, but statistically significant genetic differentiation among the studied populations. However, Bayesian assignment analysis revealed a high number of immigrants among populations and no obvious genetic differentiation. The Wilcoxon signed-rank test and mode-shift indicator of allele frequency distribution support the inferrence that L. polyactis had not experienced a recent genetic bottleneck. Overall, the results suggest that, despite low genetic differentiation in this species, the small yellow croaker forms a single panmictic population with high genetic variation and gene flow in the studied area. This study will provide useful information for conservation and sustainable exploitation of this important aquatic living resource.

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