scholarly journals Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Guang Yao Fan ◽  
Yi Ye ◽  
Yi Ping Hou
Keyword(s):  
Population Structure ◽  
X Chromosome ◽  
Cost Effective ◽  
Genetic Distances ◽  
Ancestry Informative Marker ◽  
Genetic Population ◽  
Single Nucleotide ◽  
Chinese Populations ◽  
Population Structures ◽  
Biogeographical Ancestry

Abstract Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.

scholarly journals New kinship and FST estimates reveal higher levels of differentiation in the global human population

2019 ◽  
Author(s):  
Alejandro Ochoa ◽  
John D. Storey
Keyword(s):  
Population Structure ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Population Genetic Analysis ◽  
Most Recent Common Ancestor ◽  
Complex Population ◽  
Population Structures ◽  
Modern Population

Kinship coefficients and FST, which measure genetic relatedness and the overall population structure, respectively, have important biomedical applications. However, existing estimators are only accurate under restrictive conditions that most natural population structures do not satisfy. We recently derived new kinship and FST estimators for arbitrary population structures [1, 2]. Our estimates on human datasets reveal a complex population structure driven by founder effects due to dispersal from Africa and admixture. Notably, our new approach estimates larger FST values of 26% for native worldwide human populations and 23% for admixed Hispanic individuals, whereas the existing approach estimates 9.8% and 2.6%, respectively. While previous work correctly measured FST between subpopulation pairs, our generalized FST measures genetic distances among all individuals and their most recent common ancestor (MRCA) population, revealing that genetic differentiation is greater than previously appreciated. This analysis demonstrates that estimating kinship and FST under more realistic assumptions is important for modern population genetic analysis.

scholarly journals Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0247815
Author(s):  
Bo-Hye Nam ◽  
Hyaekang Kim ◽  
Donghyeok Seol ◽  
Heebal Kim ◽  
Eun Soo Noh ◽  
...  
Keyword(s):  
Population Structure ◽  
Genotyping By Sequencing ◽  
Population Genetic Study ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Pacific Abalone ◽  
Genome Region ◽  
Population Structures ◽  
Haliotis Discus ◽  
Abalone Haliotis Discus

Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.

scholarly journals Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management

2020 ◽  
Vol 21 (13) ◽  
pp. 4805
Author(s):  
Angelina Nunziata ◽  
Valentino Ruggieri ◽  
Milena Petriccione ◽  
Luigi De Masi
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Cost Effective ◽  
Agroforestry Systems ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
European Chestnut ◽  
Wide Variability ◽  
Necessary And Sufficient

European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterized to evaluate the range of genetic diversity using random amplified polymorphic DNA (RAPD) markers. The genetic distances indicated a sufficiently wide variability range among tested genotypes and confirmed they were suitable for our goal. A single nucleotide polymorphism (SNP) mining within 64 expressed sequence tags (EST), covering all the linkage groups, was performed by high-resolution melting (HRM) and validated by target resequencing. Fifty-six SNPs were retrieved by monitoring the variability present on the whole set of considered cultivars in loci uniformly distributed on the genome. A subset of 37 SNPs was finally transformed into kompetitive allele-specific PCR (KASP) markers that were successfully evaluated for varietal discrimination. Three assays (C1083, G0115 and A5096) were identified as necessary and sufficient for distinguishing among the tested cultivars. The developed tools can be effectively exploited by stakeholders for improving the management of the European chestnut genetic resources.

Spatial genetic subdivision among populations of the highly migratory black marlin Istiompax indica within the central Indo-Pacific

2016 ◽  
Vol 67 (8) ◽  
pp. 1205 ◽  
Author(s):  
Samuel M. Williams ◽  
Michael B. Bennett ◽  
Julian G. Pepperell ◽  
Jess A. T. Morgan ◽  
Jennifer R. Ovenden
Keyword(s):  
Population Structure ◽  
Nuclear Dna ◽  
Mitochondrial Control Region ◽  
Genetic Population Structure ◽  
Secondary Contact ◽  
Nuclear Markers ◽  
Genetic Population ◽  
Tissue Samples ◽  
Spatial Subdivision ◽  
Population Structures

The black marlin Istiompax indica is a highly migratory species and as a result is expected to show little genetic population structure throughout its broad geographic range. Tissue samples from 183 I. indica were collected from three geographic regions within the central Indo-Pacific and analysed using mitochondrial and nuclear DNA markers. Nuclear genetic heterogeneity was found among populations in the south-western Pacific Ocean, eastern Indian Ocean and South China Sea (significant FST values of 0.013–0.037). Combining information from nuclear markers with published movement and reproductive data suggests that reproductive philopatry plays a role in maintaining contemporary I. indica population structure. Analyses of the mitochondrial control region did not reflect this pattern; however, it identified historical population structure. Differing patterns of genetic population structure revealed by mitochondrial and nuclear markers demonstrated that a transition must have occurred between historical and contemporary population structures. This restructuring presumably reflects a species whose populations have become genetically isolated before experiencing a period of secondary contact. The spatial subdivision evident among populations indicates that I. indica in this central Indo-Pacific region should be managed as three independent stocks, to guide the sustainability of this fisheries resource.

scholarly journals Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 625 ◽  
Author(s):  
Umberto Esposito ◽  
Ranajit Das ◽  
Syakir Syed ◽  
Mehdi Pirooznia ◽  
Eran Elhaik
Keyword(s):  
Population Structure ◽  
Principal Component ◽  
Population History ◽  
Ancestry Informative Markers ◽  
Single Nucleotide ◽  
Ancient Population ◽  
Human Genomes ◽  
Snp Microarrays ◽  
Population Structures ◽  
Wide Testing

The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient—and oftentimes haploid—DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.

scholarly journals Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach

2021 ◽  
Vol 12 ◽  
Author(s):  
Rachel P. Naegele ◽  
Jeff DeLong ◽  
Safa A. Alzohairy ◽  
Seiya Saito ◽  
Noor Abdelsamad ◽  
...  
Keyword(s):  
Population Structure ◽  
Botrytis Cinerea ◽  
Fungicide Resistance ◽  
Cost Effective ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Pathogen Diversity ◽  
Snp Panels ◽  
The Individual ◽  
Population Genetic Analyses

As sequencing costs continue to decrease, new tools are being developed for assessing pathogen diversity and population structure. Traditional marker types, such as microsatellites, are often more cost effective than single-nucleotide polymorphism (SNP) panels when working with small numbers of individuals, but may not allow for fine scale evaluation of low or moderate structure in populations. Botrytis cinerea is a necrotrophic plant pathogen with high genetic variability that can infect more than 200 plant species worldwide. A panel of 52 amplicons were sequenced for 82 isolates collected from four Michigan vineyards representing 2 years of collection and varying fungicide resistance. A panel of nine microsatellite markers previously described was also tested across 74 isolates from the same population. A microsatellite and SNP marker analysis of B. cinerea populations was performed to assess the genetic diversity and population structure of Michigan vineyards, and the results from both marker types were compared. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and multiple fungicide resistance (MFR). Microsatellites were also able to differentiate population structure associated with another fungicide, fluopyram, while SNPs were able to additionally differentiate structure based on year. For both methods, AMOVA results were similar, with microsatellite results explaining a smaller portion of the variation compared with the SNP results. The SNP-based markers presented here were able to successfully differentiate population structure similar to microsatellite results. These SNP markers represent new tools to discriminate B. cinerea isolates within closely related populations using multiple targeted sequences.

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.

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