Recent demography drives changes in linked selection across the maize genome

AbstractGenetic diversity is shaped by the interaction of drift and selection, but the details of this interaction are not well understood. The impact of genetic drift in a population is largely determined by its demographic history, typically summarized by its long-term effective population size (Ne). Rapidly changing population demographics complicate this relationship, however. To better understand how changing demography impacts selection, we used whole-genome sequencing data to investigate patterns of linked selection in domesticated and wild maize (teosinte). We produce the first whole-genome estimate of the demography of maize domestication, showing that maize was reduced to approximately 5% the population size of teosinte before it experienced rapid expansion post-domestication to population sizes much larger than its ancestor. Evaluation of patterns of nucleotide diversity in and near genes shows little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. Young alleles, however, show evidence of much stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Our results demonstrate that recent demographic change — a hallmark of many species including both humans and crops — can have immediate and wide-ranging impacts on diversity that conflict with would-be expectations based on Ne alone.

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Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽

10.3390/genes12020258 ◽

2021 ◽

Vol 12 (2) ◽

pp. 258

Author(s):

Karim Karimi ◽

Duy Ngoc Do ◽

Mehdi Sargolzaei ◽

Younes Miar

Keyword(s):

Population Genomics ◽

Association Studies ◽

American Mink ◽

Population History ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Effective Population ◽

Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

International Journal of Molecular Sciences ◽

10.3390/ijms21155585 ◽

2020 ◽

Vol 21 (15) ◽

pp. 5585

Author(s):

Mathieu Gand ◽

Kevin Vanneste ◽

Isabelle Thomas ◽

Steven Van Gucht ◽

Arnaud Capron ◽

...

Keyword(s):

In Silico ◽

Protein S ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Viral Genomes ◽

Genome Data ◽

Gene Coding ◽

Control And Prevention ◽

The Impact

The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus’ genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.

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Purifying Selection in Corvids Is Less Efficient on Islands

Molecular Biology and Evolution ◽

10.1093/molbev/msz233 ◽

2019 ◽

Vol 37 (2) ◽

pp. 469-474 ◽

Cited By ~ 3

Author(s):

Verena E Kutschera ◽

Jelmer W Poelstra ◽

Fidel Botero-Castro ◽

Nicolas Dussex ◽

Neil J Gemmell ◽

...

Keyword(s):

Purifying Selection ◽

Life History Strategies ◽

Whole Genome Sequencing Data ◽

Small Populations ◽

Deleterious Mutations ◽

Mutation Load ◽

Sequencing Data ◽

Effective Population ◽

Extinction Rates ◽

Island Species

Abstract Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size Ne. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.

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Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

10.1101/805903 ◽

2019 ◽

Author(s):

Xi Wang ◽

Carolina Bernhardsson ◽

Pär K. Ingvarsson

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Picea Abies ◽

Population Size ◽

Effective Population Size ◽

Norway Spruce ◽

Demographic History ◽

Sequencing Data ◽

Effective Population ◽

Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

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Population Stratification at the Phenotypic Variance level and Implication for the Analysis of Whole Genome Sequencing Data from Multiple Studies

10.1101/2020.03.03.973420 ◽

2020 ◽

Author(s):

Tamar Sofer ◽

Xiuwen Zheng ◽

Cecelia A. Laurie ◽

Stephanie M. Gogarten ◽

Jennifer A. Brody ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Statistical Power ◽

Epidemiological Studies ◽

Whole Genome Sequencing Data ◽

Phenotypic Variance ◽

Whole Genome ◽

Sequencing Data ◽

Level Data ◽

The Impact

SummaryIn modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term ‘variance stratification’. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We describe a WGS-appropriate analysis approach, implemented in freely-available software, which allows study-specific variances and thereby improves performance in practice. We also illustrate the variance stratification problem, its solutions, and a corresponding diagnostic procedure in data from the Trans-Omics for Precision Medicine Whole Genome Sequencing Program (TOPMed), used in association tests for hemoglobin concentrations and BMI.

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Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions

10.1101/390369 ◽

2018 ◽

Author(s):

Melak Weldenegodguad ◽

Ruslan Popov ◽

Kisun Pokharel ◽

Innokentyi Ammosov ◽

Ming Yao ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Artificial Selection ◽

Demographic History ◽

Population Variation ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Taurine Cattle ◽

Cattle Farming

AbstractNorthern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome resequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.

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The demographic history and mutational load of African hunter-gatherers and farmers

10.1101/131219 ◽

2017 ◽

Author(s):

Marie Lopez ◽

Athanasios Kousathanas ◽

Hélène Quach ◽

Christine Harmant ◽

Patrick Mouguiama-Daouda ◽

...

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Demographic History ◽

Purifying Selection ◽

Human Populations ◽

Mutational Load ◽

Sequencing Data ◽

Hunter Gatherers ◽

African Populations ◽

The Impact

AbstractThe distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

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