scholarly journals A Tutorial of the Poisson Random Field Model in Population Genetics

2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
Praveen Sethupathy ◽  
Sridhar Hannenhalli
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Random Field ◽  
Large Scale ◽  
Genomic Region ◽  
Mathematical Framework ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Bona Fide ◽  
Frequency Changes

Population genetics is the study of allele frequency changes driven by various evolutionary forces such as mutation, natural selection, and random genetic drift. Although natural selection is widely recognized as a bona-fide phenomenon, the extent to which it drives evolution continues to remain unclear and controversial. Various qualitative techniques, or so-called “tests of neutrality”, have been introduced to detect signatures of natural selection. A decade and a half ago, Stanley Sawyer and Daniel Hartl provided a mathematical framework, referred to as the Poisson random field (PRF), with which to determine quantitatively the intensity of selection on a particular gene or genomic region. The recent availability of large-scale genetic polymorphism data has sparked widespread interest in genome-wide investigations of natural selection. To that end, the original PRF model is of particular interest for geneticists and evolutionary genomicists. In this article, we will provide a tutorial of the mathematical derivation of the original Sawyer and Hartl PRF model.

scholarly journals Genome-Wide Natural Selection Signatures Are Linked to Genetic Risk of Modern Phenotypes in the Japanese Population

2020 ◽  
Vol 37 (5) ◽  
pp. 1306-1316 ◽  
Author(s):  
Yoshiaki Yasumizu ◽  
Saori Sakaue ◽  
Takahiro Konuma ◽  
Ken Suzuki ◽  
Koichi Matsuda ◽  
...  
Keyword(s):  
Natural Selection ◽  
Japanese Population ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Enrichment Analysis ◽  
Recent Common Ancestor ◽  
Selection Signatures ◽  
Most Recent Common Ancestor ◽  
Genome Wide ◽  
A Genome

Abstract Elucidation of natural selection signatures and relationships with phenotype spectra is important to understand adaptive evolution of modern humans. Here, we conducted a genome-wide scan of selection signatures of the Japanese population by estimating locus-specific time to the most recent common ancestor using the ascertained sequentially Markovian coalescent (ASMC), from the biobank-based large-scale genome-wide association study data of 170,882 subjects. We identified 29 genetic loci with selection signatures satisfying the genome-wide significance. The signatures were most evident at the alcohol dehydrogenase (ADH) gene cluster locus at 4q23 (PASMC = 2.2 × 10−36), followed by relatively strong selection at the FAM96A (15q22), MYOF (10q23), 13q21, GRIA2 (4q32), and ASAP2 (2p25) loci (PASMC < 1.0 × 10−10). The additional analysis interrogating extended haplotypes (integrated haplotype score) showed robust concordance of the detected signatures, contributing to fine-mapping of the genes, and provided allelic directional insights into selection pressure (e.g., positive selection for ADH1B-Arg48His and HLA-DPB1*04:01). The phenome-wide selection enrichment analysis with the trait-associated variants identified a variety of the modern human phenotypes involved in the adaptation of Japanese. We observed population-specific evidence of enrichment with the alcohol-related phenotypes, anthropometric and biochemical clinical measurements, and immune-related diseases, differently from the findings in Europeans using the UK Biobank resource. Our study demonstrated population-specific features of the selection signatures in Japanese, highlighting a value of the natural selection study using the nation-wide biobank-scale genome and phenotype data.

scholarly journals Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies

2015 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R Street ◽  
Douglas G Scofield ◽  
Pär K Ingvarsson
Keyword(s):  
Natural Selection ◽  
Rate Variation ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Recombination Rates ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Population Sizes ◽  
Wide Scale

AbstractA central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

scholarly journals Models of the population genetics of transposable elements

2005 ◽  
Vol 85 (3) ◽  
pp. 171-181 ◽  
Author(s):  
ARNAUD LE ROUZIC ◽  
GRÉGORY DECELIERE
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Transposable Elements ◽  
Genetic Drift ◽  
Self Regulation ◽  
Evolutionary Forces ◽  
Classical Models

Although transposable elements (TEs) have been found in all organisms in which they have been looked for, the ways in which they invade genomes and populations are still a matter of debate. By extending the classical models of population genetics, several approaches have been developed to account for the dynamics of TEs, especially in Drosophila melanogaster. While the formalism of these models is based on simplifications, they enable us to understand better how TEs invade genomes, as a result of multiple evolutionary forces including duplication, deletion, self-regulation, natural selection and genetic drift. The aim of this paper is to review the assumptions and the predictions of these different models by highlighting the importance of the specific characteristics of both the TEs and the hosts, and the host/TE relationships. Then, perspectives in this domain will be discussed.

scholarly journals Quantifying shifts in natural selection on codon usage between protein regions: A population genetics approach

2020 ◽  
Author(s):  
Alexander L. Cope ◽  
Michael A. Gilchrist
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Protein Structure ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Empirical Studies ◽  
Protein Structures ◽  
Synonymous Codon Usage ◽  
Genome Wide ◽  
Computational Analyses

AbstractEmpirical studies indicate changes to synonymous codon usage can impact protein folding. However, genome-wide computational analyses attempting to establish a more general relationship between codon usage and protein structure have often led to contradictory results. Using a population genetics model, we quantified codon-specific shifts in natural selection across and within protein structures, revealing a complex relationship between codon usage and protein structure. However, these shifts are small, suggesting differences in selection related to protein structure are either very weak or apply to relatively few codons. Using a previously published result, we demonstrate how tests for selection on codon usage can be confounded when failing to account for amino acid biases and gene expression. This work demonstrates the value of using population genetics-based models to quantify and tests for shifts in selection on codon usage. Extensions to this approach are discussed.

scholarly journals Standing covariation between genomic and epigenomic patterns as source for natural selection in wild strawberry plants

2021 ◽  
Author(s):  
Hanne De Kort ◽  
Tuomas Toivainen ◽  
Filip Van Nieuwerburgh ◽  
Bart Panis ◽  
Timo P. Hytonen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Dna Sequence ◽  
Adaptive Evolution ◽  
Epigenetic Inheritance ◽  
Cis Acting ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Polygenic Adaptation ◽  
Wild Strawberry ◽  
Methylation Patterns

Adaptive evolution is generally thought to be the result of natural selection predominantly acting upon pre-existing DNA sequence polymorphisms through gene-environment interactions. Epigenetic inheritance is, however, recently considered an additional molecular force driving adaptive evolution independent of DNA sequence variation. Through comparative analyses of genome-wide genetic (SNPs) and epigenetic (DMCs) variation of wild strawberry plants raised under distinct drought settings, we demonstrate intermediate levels of genome-wide covariation between SNPs and DMCs. Cases of high SNP-DMC covariation were significantly associated with (i) applied stress, (ii) non-adaptive SNPs, and (iii) solitary DMCs (as opposed to DMC islands). We also found that DMCs, drought-responsive DMCs in particular, typically co-vary with hundreds of SNPs, indicating high genomic redundancy as a basis for polygenic adaptation. Our findings suggest that stress-responsive DMCs initially co-vary with many associated SNPs under increased environmental stress (cfr. co-gradient plasticity), and that natural selection acting upon these SNPs subsequently reduce standing covariation with stress-responsive DMCs. In addition, the degree of covariation between SNPs and DMCs appears independent of their respective genomic distance, indicating that trans-acting associations between SNPs and DMCs are as likely as cis-acting associations. Our study is in favor of DNA methylation profiles representing complex quantitative traits rather than independent evolutionary forces, but further research is required to fully rule out SNP-independence of genome-wide DMCs. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns.

scholarly journals Formalizing Darwinism and inclusive fitness theory

2009 ◽  
Vol 364 (1533) ◽  
pp. 3135-3141 ◽  
Author(s):  
Alan Grafen
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Building Block ◽  
Inclusive Fitness ◽  
Theoretical Work ◽  
Mathematical Framework ◽  
Basic Building Block ◽  
Formal Darwinism ◽  
Inclusive Fitness Theory ◽  
Fitness Maximization

Inclusive fitness maximization is a basic building block for biological contributions to any theory of the evolution of society. There is a view in mathematical population genetics that nothing is caused to be maximized in the process of natural selection, but this is explained as arising from a misunderstanding about the meaning of fitness maximization. Current theoretical work on inclusive fitness is discussed, with emphasis on the author's ‘formal Darwinism project’. Generally, favourable conclusions are drawn about the validity of assuming fitness maximization, but the need for continuing work is emphasized, along with the possibility that substantive exceptions may be uncovered. The formal Darwinism project aims more ambitiously to represent in a formal mathematical framework the central point of Darwin's Origin of Species , that the mechanical processes of inheritance and reproduction can give rise to the appearance of design, and it is a fitting ambition in Darwin's bicentenary year to capture his most profound discovery in the lingua franca of science.

scholarly journals Diet unmasks genetic variants that regulate lifespan in outbred Drosophila

2020 ◽  
Author(s):  
Luisa F. Pallares ◽  
Amanda J. Lea ◽  
Clair Han ◽  
Elena V. Filippova ◽  
Peter Andolfatto ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Variants ◽  
Genetic Architecture ◽  
Late Onset ◽  
Evolutionary Forces ◽  
Genotype By Environment ◽  
Genome Wide ◽  
Gxe Interactions ◽  
Frequency Changes ◽  
Insight Into

AbstractSeveral evolutionary forces are thought to maintain genetic variation for fitness-related traits, such as lifespan, but experimental support is limited. Using a powerful experimental design, we identified lifespan-associated variants by exposing outbred Drosophila melanogaster to standard and high-sugar diets and tracking genome-wide allele frequency changes as the flies aged. We mapped alleles associated with early vs late life tradeoffs, late-onset effects, and genotype-by-environment (GxE) interactions – all of which are predicted by long-standing theories to maintain genetic variation for lifespan. We also validated an environmentally-dependent role for nAChRα4 in regulating lifespan; the ortholog of this gene is one of the few lifespan-associated genes in humans (CHRNA3). Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan, as well as the evolutionary processes that shape this key trait.

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