scholarly journals Fine-scale population structure reveals high genetic heterogeneity of the Kuwaiti population in the Arabian Peninsula

2020 ◽  
Author(s):  
Muthukrishnan Eaaswarkhanth ◽  
Ajai K Pathak ◽  
Linda Ongaro ◽  
Francesco Montinaro ◽  
Prashantha Hebbar ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Heterogeneity ◽  
Arabian Peninsula ◽  
Genetic Diseases ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Population Movements ◽  
Western Africa ◽  
Scale Population ◽  
Kuwaiti Population

AbstractRecent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.

scholarly journals Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population

2021 ◽  
Author(s):  
Muthukrishnan Eaaswarkhanth ◽  
Ajai K. Pathak ◽  
Linda Ongaro ◽  
Francesco Montinaro ◽  
Prashantha Hebbar ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Arabian Peninsula ◽  
Genetic Diseases ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Population Movements ◽  
Western Africa ◽  
Disease Gene Discovery ◽  
Scale Population ◽  
Sub Saharan

AbstractRecent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

2017 ◽  
Author(s):  
Meghann D Durante ◽  
Iliana B Baums
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Ex Situ ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Acropora Palmata ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Genome Wide ◽  
Scale Population

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, reveal fine-scale population structure and place the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 12 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 12 candidate loci under positive selection. Together, these results suggest that restoration of populations should use local sources and utilize existing functional variation among populations in ex situ crossing experiments to improve stress resistance of this species.

scholarly journals RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

2017 ◽  
Vol 4 (2) ◽  
pp. 160548 ◽  
Author(s):  
David L. J. Vendrami ◽  
Luca Telesca ◽  
Hannah Weigand ◽  
Martina Weiss ◽  
Katie Fawcett ◽  
...  
Keyword(s):  
Population Structure ◽  
Phenotypic Plasticity ◽  
Molecular Ecology ◽  
Natural Populations ◽  
Benthic Invertebrate ◽  
Shell Shape ◽  
Rad Sequencing ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Scale Population

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops ( Pecten maximus ) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher F st values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.

scholarly journals Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4077 ◽  
Author(s):  
Meghann K. Devlin-Durante ◽  
Iliana B. Baums
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Ex Situ ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Acropora Palmata ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Genome Wide ◽  
Scale Population

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

scholarly journals IPCAPS: an R package for iterative pruning to capture population structure

2017 ◽  
Author(s):  
Kridsadakorn Chaichoompu ◽  
Fentaw Abegaz Yazew ◽  
Sissades Tongsima ◽  
Philip James Shaw ◽  
Anavaj Sakuntabhai ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Population Structure ◽  
Principal Component ◽  
R Package ◽  
Component Analysis ◽  
Genomic Variation ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Measurement Scales ◽  
Scale Population

AbstractBackgroundResolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.ResultsThis work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.ConclusionsIPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available from bio3.giga.ulg.ac.be/ipcaps

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