scholarly journals Impacts of Recurrent Hitchhiking on Divergence and Demographic Inference in Drosophila

2017 ◽  
Author(s):  
Jeremy D. Lange ◽  
John E. Pool
Keyword(s):  
Natural Selection ◽  
Population Genetic ◽  
Large Population ◽  
Selective Sweeps ◽  
Demographic Parameter ◽  
Genome Wide ◽  
Standard Population ◽  
Population Sizes ◽  
The Common ◽  
Demographic Inference

AbstractIn species with large population sizes such as Drosophila, natural selection may have substantial effects on genetic diversity and divergence. However, the implications of this widespread nonneutrality for standard population genetic assumptions and practices remain poorly resolved. Here, we assess the consequences of recurrent hitchhiking (RHH), in which selective sweeps occur at a given rate randomly across the genome. We use forward simulations to examine two published RHH models for D. melanogaster, reflecting relatively common/weak and rare/strong selection. We find that unlike the rare/strong RHH model, the common/weak model entails a slight degree of Hill-Robertson interference in high recombination regions. We also find that the common/weak RHH model is more consistent with our genome-wide estimate of the proportion of substitutions fixed by natural selection between D. melanogaster and D. simulans (19%). Finally, we examine how these models of RHH might bias demographic inference. We find that these RHH scenarios can bias demographic parameter estimation, but such biases are weaker for parameters relating recently-diverged populations, and for the common/weak RHH model in general. Thus, even for species with important genome-wide impacts of selective sweeps, neutralist demographic inference can have some utility in understanding the histories of recently-diverged populations.

scholarly journals Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data

2019 ◽  
Author(s):  
C.J. Battey ◽  
Peter L. Ralph ◽  
Andrew D. Kern
Keyword(s):  
Population Genetic ◽  
Isolation By Distance ◽  
Association Studies ◽  
Genetic Data ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Summary Statistics ◽  
Genome Wide ◽  
Mixed Populations ◽  
Demographic Inference

ABSTRACTReal geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies. We find that most common summary statistics have distributions that differ substantially from that seen in well-mixed populations, especially when Wright’s neighborhood size is less than 100 and sampling is spatially clustered. Stepping-stone models reproduce some of these effects, but discretizing the landscape introduces artifacts which in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations were surprisingly robust to isolation by distance. We also show that the combination of spatially autocorrelated environments and limited dispersal causes genome-wide association studies to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.

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 Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

2019 ◽  
Vol 11 (10) ◽  
pp. 2875-2886 ◽  
Author(s):  
Venkat Talla ◽  
Lucile Soler ◽  
Takeshi Kawakami ◽  
Vlad Dincă ◽  
Roger Vila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Nucleotide Diversity ◽  
Gene Annotation ◽  
Rate Variation ◽  
Butterfly Species ◽  
Relative Role ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes

Abstract The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

scholarly journals When good mutations go bad: how population size can change the direction of natural selection

2021 ◽  
Author(s):  
Yevgeniy Raynes ◽  
Christina L Burch ◽  
Daniel M Weinreich
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Underlying Mechanism ◽  
Deleterious Mutations ◽  
Fitness Costs ◽  
Sign Inversion ◽  
Population Sizes ◽  
The Common ◽  
Fitness Benefits ◽  
The Cost

Classical evolutionary theory holds that the efficiency, but not the direction, of natural selection depends on population size. In small populations, drift overwhelms selection, rendering all fitness-affecting mutations selectively neutral. Yet, beneficial mutations never become deleterious and deleterious mutations never become beneficial. Remarkably, several mutations, including in modifiers of recombination and mutation rate, have now been shown to be favored at some population sizes but disfavored at others, challenging established theory. Previously, we have designated this phenomenon sign inversion. Here we show that, unlike selected mutations in the classical framework, mutations susceptible to sign inversion confer both fitness costs and fitness benefits, that vary among their carriers. Furthermore, all such mutations can be classified based on whether their effects differ between or within mutant lineages. Using computer simulations, we demonstrate that both between-lineage and within-lineage variability can cause sign inversion and elucidate the common underlying mechanism. Our results confirm that variability in the sign of selective effects is necessary for sign inversion, which occurs because drift overwhelms selection on carriers bearing the cost and carriers enjoying the benefit at different population sizes.

scholarly journals POLYALLELIC MUTATIONAL EQUILIBRIA

Genetics ◽  
1975 ◽  
Vol 79 (4) ◽  
pp. 681-691
Author(s):  
Jack Lester King ◽  
Tomoko Ohta
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Mutation Rate ◽  
Large Population ◽  
Electrophoretic Mobilities ◽  
Mutational Step ◽  
Order Of Magnitude ◽  
Population Sizes ◽  
Mean And Variance ◽  
Allelic Mutation

ABSTRACT A new deterministic formulation is derived of the equilibrium between mutation and natural selection, which takes into account (a) the possibility of many allelic mutation states, (b) selection coefficients of the order of magnitude of the mutation rate and (c) the possibility of further mutation of already mutant alleles. The frequencies of classes of alleles 0, 1, 2, n mutant steps removed from the type allele are shown to form a Poisson distribution, with a mean and variance of the mutation rate divided by the coefficient of selection against each incremental mutational step. — This formulation is interpreted in terms of the expected frequencies of electromorphs, defined as classes of alleles characterized by common electrophoretic mobilities of their protein products. Electromorph frequencies are predicted to form stable unimodal distributions of relatively few phenotypic classes. Common electromorph frequencies found throughout the ranges of species with large population sizes are interpreted as being a uniquely electrophoretic phenomenon; band patterns on starch and acrylamide gels are phenotypes, not genotypes. It is predicted that individual electromorphs are highly heterogeneous with regard to amino acid sequence.

scholarly journals Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

2015 ◽  
Vol 113 (1) ◽  
pp. 152-157 ◽  
Author(s):  
Clare D. Marsden ◽  
Diego Ortega-Del Vecchyo ◽  
Dennis P. O’Brien ◽  
Jeremy F. Taylor ◽  
Oscar Ramirez ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Amino Acid ◽  
Artificial Selection ◽  
Selective Breeding ◽  
Large Population ◽  
Disease Genes ◽  
Mendelian Disease ◽  
Selective Sweeps ◽  
Gray Wolves ◽  
Genome Wide

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

scholarly journals Conflicting genomes, the demic theory & biodiversity

1997 ◽  
Vol 20 (1) ◽  
pp. 129-140
Author(s):  
H.F. Hoenigsberg
Keyword(s):  
Natural Selection ◽  
Suicidal Behavior ◽  
Large Population ◽  
Pleiotropic Effects ◽  
P Elements ◽  
Selfish Genes ◽  
Y Chromosomes ◽  
Population Sizes ◽  
Phenotypic Manipulation ◽  
The Individual

Organismic-centered Darwinism, in order to use direct phenotypes to measure natural selection's effect, necessitates genome's harmony and uniform coherence plus large population sizes. However, modern gene-centered Darwinism has found new interpretations to data that speak of genomic incoherence and disharmony. As a result of these two conflicting positions a conceptual crisis in Biology has arisen. My position is that the presence of small, even pocket-size, demes is instrumental in generating divergence and phenotypic crisis. Moreover, the presence of parasitic genomes as in acanthocephalan worms, which even manipulate suicidal behavior in their hosts; segregation distorters that change meiosis and Mendelian ratios; selfish genes and selfish whole chromosomes, such as the case of B-chromosomes in grasshoppers; P-elements in Drosophila; driving Y-chromosomes that manipulate sex ratios making males more frequent, as in Hamilton's X-linked drive; male strategists and outlaw genes, are eloquent examples of the presence of real conflicting genomes and of a non-uniform phenotypic coherence and genome harmony. Thus, we are proposing that overall incoherence and disharmony generate disorder but also more biodiversity and creativeness. Finally, if genes can manipulate natural selection, they can multiply mutations or undesirable characteristics and even lethal or detrimental ones, hence the accumulation of genetic loads. Outlaw genes can change what is adaptively convenient even in the direction of the trait that is away from the optimum. The optimum can be "negotiated" among the variants, not only because pleiotropic effects demand it, but also, in some cases, because selfish, outlaw, P-elements or extended phenotypic manipulation require it. With organismic Darwinism the genome in the population and in the individual was thought to act harmoniously without conflicts, and genotypes were thought to march towards greater adaptability. Modern Darwinism has a gene-centered vision in which genes, as natural selection's objects can move in dissonance in the direction which benefits their multiplication. Thus, we have greater opportunities for genomes in permanent conflict.

scholarly journals Effects of linked selective sweeps on demographic inference and model selection

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Alexander G. Shanku ◽  
Andrew D. Kern
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Positive Selection ◽  
Population Size ◽  
Natural Populations ◽  
Parameter Estimates ◽  
Selective Sweeps ◽  
Recent Positive Selection ◽  
Demographic Inference ◽  
The Impact

AbstractThe availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of datasets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models—often severely. Moreover, we find that selection can lead to incorrect inferences of population size changes when none have occurred. We argue that the amount of recent positive selection required to skew inferences may often be acting in natural populations. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.

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