scholarly journals Selective Sweeps in the Presence of Interference Among Partially Linked Loci

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 389-398 ◽  
Author(s):  
Yuseob Kim ◽  
Wolfgang Stephan
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Substantial Reduction ◽  
Natural Populations ◽  
High Rate ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Analytical Approximations ◽  
Fixation Probabilities ◽  
Beneficial Allele

Abstract Recurrent directional selection on a partially recombining chromosome may cause a substantial reduction of standing genetic variation in natural populations. Previous studies of this effect, commonly called selective sweeps, assumed that at most one beneficial allele is on the way to fixation at a given time. However, for a high rate of selected substitutions and a low recombination rate, this assumption can easily be violated. We investigated this problem using full-forward simulations and analytical approximations. We found that interference between linked beneficial alleles causes a reduction of their fixation probabilities. The hitchhiking effect on linked neutral variation for a given substitution also slightly decreases due to interference. As a result, the strength of recurrent selective sweeps is weakened. However, this effect is significant only in chromosomal regions of relatively low recombination rates where the level of variation is greatly reduced. Therefore, previous results on recurrent selective sweeps although derived for a restricted parameter range are still valid. Analytical approximations are obtained for the case of complete linkage for which interference between competing beneficial alleles is maximal.

scholarly journals Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

2019 ◽  
Vol 36 (9) ◽  
pp. 2029-2039 ◽  
Author(s):  
Steven Dreissig ◽  
Martin Mascher ◽  
Stefan Heckmann
Keyword(s):  
Environmental Conditions ◽  
Recombination Rate ◽  
Wild Barley ◽  
Natural Populations ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Positive Linear Correlation ◽  
Short And Long Term ◽  
Underlying Mechanisms ◽  
Chromosome Regions

Abstract Meiotic recombination generates genetic diversity upon which selection can act. Recombination rates are highly variable between species, populations, individuals, sexes, chromosomes, and chromosomal regions. The underlying mechanisms are controlled at the genetic and epigenetic level and show plasticity toward the environment. Environmental plasticity may be divided into short- and long-term responses. We estimated recombination rates in natural populations of wild barley and domesticated landraces using a population genetics approach. We analyzed recombination landscapes in wild barley and domesticated landraces at high resolution. In wild barley, high recombination rates are found in more interstitial chromosome regions in contrast to distal chromosome regions in domesticated barley. Among subpopulations of wild barley, natural variation in effective recombination rate is correlated with temperature, isothermality, and solar radiation in a nonlinear manner. A positive linear correlation was found between effective recombination rate and annual precipitation. We discuss our findings with respect to how the environment might shape effective recombination rates in natural populations. Higher recombination rates in wild barley populations subjected to specific environmental conditions could be a means to maintain fitness in a strictly inbreeding species.

scholarly journals Gene buddies: Linked balanced polymorphisms reinforce each other even in the absence of epistasis

2017 ◽  
Author(s):  
Jacob A Tennessen
Keyword(s):  
Recombination Rate ◽  
Evolutionary Dynamics ◽  
Balancing Selection ◽  
Natural Populations ◽  
Adaptive Variation ◽  
Recombination Rates ◽  
Future Studies ◽  
Close Physical Proximity ◽  
Selection For ◽  
Independent Effects

The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. Such clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon.

scholarly journals A New Model of Genetic Variation and Evolution Evaluates Relative Impacts of Background Selections and Selective Sweeps

2020 ◽  
Author(s):  
Xun Gu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Neutral Theory ◽  
Population Diversity ◽  
Simple Relationship ◽  
Small Contribution ◽  
Background Selection ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
The One

AbstractIntra-population genetic variation and interspecies divergence in chromosome regions can be considerably affected by different local recombination rates. There are two models: (i) the selective sweeps that reduces the genetic diversity at linked sites and elevates the divergence rate; and (ii) the background selection that reduces the genetic diversity at linked sites and divergence rate. An intriguing question, yet highly controversial, is which one is dominant. In this paper, I develop a framework of generalize background selection, formulated by a diffusion model with two killing functions: the one associated with (negative) background selection is the rate to stop a fixation process of a mutation randomly, and the other associated with positive background selection (selective sweep) is the rate to stop a loss process of a mutation randomly. A simple relationship between the level of reduced diversity and the rate of divergence is derived, depending on the strength of generalized background selection (G) and the proportion of positive background selection (β). We analyzed the interspecies divergence and intra-population diversity in low-recombination regions of three organisms (fruitfly, soybean and human). Strikingly, all datasets demonstrated the dominance of (negative) background selection, and the positive background selection (selective sweeps) only has a small contribution (β∼10%). However, our analysis rejects the notion of β=0, namely, a complete negative background selection is unlikely. These findings may shed some lights on the long-term debates around Neutral Theory.

scholarly journals Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii

2020 ◽  
Vol 12 (4) ◽  
pp. 370-380 ◽  
Author(s):  
Ahmed R Hasan ◽  
Rob W Ness
Keyword(s):  
Linkage Disequilibrium ◽  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Effective Rate ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

scholarly journals Sex-specific variation in the genome-wide recombination rate

Genetics ◽  
2020 ◽  
Vol 217 (1) ◽  
pp. 1-11
Author(s):  
April L Peterson ◽  
Bret A Payseur
Keyword(s):  
Sex Differences ◽  
Genetic Variation ◽  
Mus Musculus ◽  
Recombination Rate ◽  
Inbred Strains ◽  
Recombination Rates ◽  
Additional Species ◽  
Male Genome ◽  
Mus Musculus Musculus ◽  
Genome Wide

Abstract In most species that reproduce sexually, successful gametogenesis requires recombination during meiosis. The number and placement of crossovers (COs) vary among individuals, with females and males often presenting the most striking contrasts. Despite the recognition that the sexes recombine at different rates (heterochiasmy), existing data fail to answer the question of whether patterns of genetic variation in recombination rate are similar in the two sexes. To fill this gap, we measured the genome-wide recombination rate in both sexes from a panel of wild-derived inbred strains from multiple subspecies of house mice (Mus musculus) and from a few additional species of Mus. To directly compare recombination rates in females and males from the same genetic backgrounds, we applied established methods based on immunolocalization of recombination proteins to inbred strains. Our results reveal discordant patterns of genetic variation in the two sexes. Whereas male genome-wide recombination rates vary substantially among strains, female recombination rates measured in the same strains are more static. The direction of heterochiasmy varies within two subspecies, Mus musculus molossinus and Mus musculus musculus. The direction of sex differences in the length of the synaptonemal complex and CO positions is consistent across strains and does not track sex differences in genome-wide recombination rate. In males, contrasts between strains with high recombination rate and strains with low recombination rate suggest more recombination is associated with stronger CO interference and more double-strand breaks. The sex-specific patterns of genetic variation we report underscore the importance of incorporating sex differences into recombination research.

scholarly journals Positive Correlation Between Recombination Rates and Levels of Genetic Variation in Natural Populations of Sea Beet (Beta vulgaris subsp. maritima)

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1239-1244 ◽  
Author(s):  
Thomas Kraft ◽  
Torbjörn Säll ◽  
Ingrid Magnusson-Rading ◽  
Nils-Otto Nilsson ◽  
Christer Halldén
Keyword(s):  
Genetic Variation ◽  
Beta Vulgaris ◽  
Significant Positive Correlation ◽  
Natural Populations ◽  
Rflp Markers ◽  
Marker Density ◽  
Recombination Rates ◽  
Positive Correlation ◽  
Physical Unit ◽  
Biological Differences

Abstract The relation between the level of genetic variation and the rate of recombination per physical unit was investigated in sea beet (Beta vulgaris subsp. maritima). The rate of recombination per physical unit was estimated indirectly through marker density in an RFLP linkage map of sugar beet. From this map, we also selected RFLP markers covering two of the nine chromosomes in Beta. The markers were used to estimate the level of genetic variation in three populations of sea beet, two from Italy and one from England. Two estimates of genetic variation were employed, one based on the number of alleles in the sample and the other on heterozygosity. A statistically significant positive correlation was found between recombination rate and genetic variation. Several theoretical explanations for this are discussed, background selection being one. A correlation similar to this has been observed previously in Drosophila, one that was higher than what we obtained for Beta. This is consistent with various biological differences between the two species.

scholarly journals Gene flow biases population genetic inference of recombination rate

2021 ◽  
Author(s):  
Kieran Samuk ◽  
Mohamed A.F. Noor
Keyword(s):  
Gene Flow ◽  
Recombination Rate ◽  
Population Genetic ◽  
Natural Populations ◽  
Recombination Rates ◽  
False Negatives ◽  
Isolation With Migration ◽  
Simplifying Assumptions ◽  
Population Genetic Inference ◽  
Genetic Inference

Accurate estimates of the rate of recombination are key to understanding a host of evolutionary processes as well as the evolution of recombination rate itself. Model-based population genetic methods that infer recombination rates from patterns of linkage disequilibrium (LD) in the genome have become a popular method to estimate rates of recombination. However, these LD-based methods make a variety of simplifying assumptions about the populations of interest that are often not met in natural populations. One such assumption is the absence of gene flow from other populations. Here, we use forward-time population genetic simulations of isolation-with-migration scenarios to explore how gene flow affects the accuracy of LD-based estimators of recombination rate. We find that moderate levels of gene flow can result in either the overestimation or underestimation of recombination rates by up to 20-50% depending on the timing of divergence. We also find that these biases can affect the detection of interpopulation differences in recombination rate, causing both false positive and false negatives depending on the scenario. We discuss future possibilities for mitigating these biases and recommend that investigators exercise caution and confirm that their study populations meet assumptions before deploying these methods.

scholarly journals DNA motifs are not general predictors of recombination in two Drosophila sister species

2018 ◽  
Author(s):  
James M. Howie ◽  
Rupert Mazzucco ◽  
Thomas Taus ◽  
Viola Nolte ◽  
Christian Schlötterer
Keyword(s):  
Recombination Rate ◽  
Large Scale ◽  
Strong Association ◽  
Natural Populations ◽  
Sister Species ◽  
Rate Variation ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
The Difference ◽  
Recombination Rate Variation

ABSTRACTMeiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with dramatic impact on levels of variation in natural populations. Two close sister species, D. simulans and D. mauritiana do not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate that only drops sharply close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination-rate associated sequence motifs. We constructed the first high resolution recombination map for D. simulans, and searched for motifs linked with high recombination in both sister species. We identified five consensus motifs, present in either species. While the association between motif density and recombination is strong and positive in D. melanogaster, the results are equivocal in D. simulans. Despite the strong association in D. melanogaster, we do not find a decreasing density of these repeat motifs towards centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome.

scholarly journals Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

2020 ◽  
Vol 37 (9) ◽  
pp. 2661-2678 ◽  
Author(s):  
Martin Kapun ◽  
Maite G Barrón ◽  
Fabian Staubach ◽  
Darren J Obbard ◽  
R Axel W Wiberg ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Selective Sweeps ◽  
Short Term ◽  
Dna Viruses ◽  
Local Climate ◽  
Term Evolution

Abstract Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

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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