Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin

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.

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Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

Molecular Ecology ◽

10.1111/j.1365-294x.2010.04528.x ◽

2010 ◽

Vol 19 (5) ◽

pp. 968-984 ◽

Cited By ~ 103

Author(s):

EVA-MARIA WILLING ◽

PAUL BENTZEN ◽

COCK van OOSTERHOUT ◽

MARGARETE HOFFMANN ◽

JOANNE CABLE ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Population History ◽

Adaptive Divergence ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide

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

10.1101/2020.03.25.008078 ◽

2020 ◽

Cited By ~ 4

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.

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The Multivariate Normal Distribution Framework for Analyzing Association Studies

10.1101/208199 ◽

2017 ◽

Author(s):

Jose A. Lozano ◽

Farhad Hormozdiari ◽

Jong Wha (Joanne) Joo ◽

Buhm Han ◽

Eleazar Eskin

Keyword(s):

Genetic Variants ◽

Statistical Power ◽

Association Studies ◽

Multiple Hypothesis Testing ◽

Population History ◽

Genome Wide Association Studies ◽

Multivariate Normal ◽

Association Testing ◽

Genome Wide ◽

Comprehensive Framework

AbstractGenome-wide association studies (GWAS) have discovered thousands of variants involved in common human diseases. In these studies, frequencies of genetic variants are compared between a cohort of individuals with a disease (cases) and a cohort of healthy individuals (controls). Any variant that has a significantly different frequency between the two cohorts is considered an associated variant. A challenge in the analysis of GWAS studies is the fact that human population history causes nearby genetic variants in the genome to be correlated with each other. In this review, we demonstrate how to utilize the multivariate normal (MVN) distribution to explicitly take into account the correlation between genetic variants in a comprehensive framework for analysis of GWAS. We show how the MVN framework can be applied to perform association testing, correct for multiple hypothesis testing, estimate statistical power, and perform fine mapping and imputation.

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Genes, Psychology and Population History

10.31234/osf.io/kgz2t ◽

2021 ◽

Author(s):

Ken Richardson

Keyword(s):

Social Policy ◽

Genetic Markers ◽

Complex Traits ◽

Population Stratification ◽

Association Studies ◽

Population History ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Historical Dynamics

Genome wide association studies (GWAS) are being increasingly used to identify genetic markers of variation in complex traits such as intelligence and education. However, GWAS are compromised by population stratification (PS) leading to spurious associations, and attempts to correct for them statistically are also proving to be inadequate. This suggests the need for a deeper understanding of the sources of such PS and how its roots in complex social and historical dynamics can seriously mislead interpretations from GWAS/PGS to social policy.

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

BMC Genomics ◽

10.1186/s12864-019-6296-7 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

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.

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Genomic signatures of inbreeding and genetic load in a threatened rattlesnake

10.22541/au.162108650.00989413/v1 ◽

2021 ◽

Author(s):

Alexander Ochoa ◽

H. Lisle Gibbs

Keyword(s):

Threatened Species ◽

Empirical Studies ◽

Genetic Load ◽

Population History ◽

Deleterious Mutations ◽

Genetic Rescue ◽

Isolated Populations ◽

Genome Wide ◽

The Impact

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their negative genetic load but recent work suggests that the impact of load may be minimized by purging resulting from long term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use genome resequencing data to compare levels of inbreeding, levels of genetic load and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus) which exist in small isolated populations and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of genetic load in the form of greater numbers of derived deleterious mutations compared to S. catenatus presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped the “drift sieve” and were polymorphic within S. catenatus populations were more abundant and more often found in homozygote genotypes than in S. tergeminus suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present which impacts implementation of conservation actions such as genetic rescue.

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