scholarly journals The effects on neutral variability of recurrent selective sweeps and background selection

2018 ◽  
Author(s):  
José Luis Campos ◽  
Brian Charlesworth
Keyword(s):  
Adaptive Evolution ◽  
Selective Sweep ◽  
Crossing Over ◽  
Background Selection ◽  
Selective Sweeps ◽  
Population Genomic ◽  
Approximate Integral ◽  
Theoretical Predictions ◽  
Site Diversity ◽  
Coalescent Time

ABSTRACTLevels of variability and rates of adaptive evolution may be affected by hitchhiking, the effect of selection on evolution at linked sites. Hitchhiking can be caused either by selective sweeps or by background selection, involving the spread of new favorable alleles or the elimination of deleterious mutations, respectively. Recent analyses of population genomic data have fitted models where both these processes act simultaneously, in order to infer the parameters of selection. Here, we investigate the consequences of relaxing a key assumption of some of these studies – that the time occupied by a selective sweep is negligible compared with the neutral coalescent time. We derive a new expression for the expected level of neutral variability in the presence of recurrent selective sweeps and background selection. We also derive approximate integral expressions for the effects of recurrent selective sweeps. The accuracy of the theoretical predictions was tested against multilocus simulations, with selection, recombination and mutation parameters that are realistic for Drosophila melanogaster. In the presence of crossing over, there is approximate agreement between the theoretical and simulation results. We show that the observed relations between the rate of crossing over and the level of synonymous site diversity and rate of adaptive evolution in Drosophila are probably mainly caused by background selection, whereas selective sweeps and population size changes are needed to produce the observed distortions of the site frequency spectrum.

scholarly journals Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele

2015 ◽  
Author(s):  
Roy Ronen ◽  
Glenn Tesler ◽  
Ali Akbari ◽  
Shay Zakov ◽  
Noah A Rosenberg ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Selective Sweep ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Selective Sweeps ◽  
Evolutionary Trajectory ◽  
Genomic Signatures ◽  
Most Recent Common Ancestor ◽  
Haplotype Allele ◽  
Theoretical Predictions

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory — for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.

scholarly journals Patterns of Genetic Variation at a Chromosome 4 Locus ofDrosophila melanogasterandD. simulans

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 493-507 ◽  
Author(s):  
Mark A Jensen ◽  
Brian Charlesworth ◽  
Martin Kreitman
Keyword(s):  
Selective Sweep ◽  
Theoretical Work ◽  
Strong Positive Correlation ◽  
Selective Sweeps ◽  
Chromosome 4 ◽  
Nucleotide Polymorphism ◽  
Fourth Chromosome ◽  
Frequency Spectra ◽  
Coalescent Simulations ◽  
Site Diversity

AbstractDNA sequence surveys of Drosophila melanogaster populations show a strong positive correlation between the recombination rate experienced by a locus and its level of nucleotide polymorphism. In particular, surveys of the fourth chromosome gene ciD show greatly reduced levels of nucleotide variation; this observation was originally interpreted in terms of selective sweeps occurring on the nonrecombining fourth chromosome. Subsequent theoretical work has, however, uncovered several other selective processes that can reduce variation. In this study, we revisit the Drosophila fourth chromosome, investigating variation in 5–6 kb of the gene ankyrin in D. melanogaster and D. simulans. Silent nucleotide site diversity is ~5 × 10−4 for both species, consistent with the previous observations of low variation at ciD. Given the observed frequency spectra at ankyrin, coalescent simulations indicate that reduced diversity in the region is unlikely to be due to a selective sweep alone. We find evidence for recombinational exchange at this locus, and both species appear to be fixed for an insertion of the transposable element HB in an intron of ankyrin.

scholarly journals Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

2017 ◽  
Vol 114 (24) ◽  
pp. E4762-E4771 ◽  
Author(s):  
José Luis Campos ◽  
Lei Zhao ◽  
Brian Charlesworth
Keyword(s):  
Positive Selection ◽  
Gene Conversion ◽  
Major Effect ◽  
Selective Constraint ◽  
Background Selection ◽  
Selective Sweeps ◽  
Low Levels ◽  
Whole Genome Resequencing ◽  
Site Diversity ◽  
New Mutations

We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (πS) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (KA). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on πS and found that these could account for only part of the observed correlation between πS and KA. We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high KA. Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored.

Chromosomal Patterns of Microsatellite Variability Contrast Sharply in African and Non-African Populations of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 247-256
Author(s):  
M Kauer ◽  
B Zangerl ◽  
D Dieringer ◽  
C Schlötterer
Keyword(s):  
Chromosomal Polymorphism ◽  
Background Selection ◽  
Selective Sweeps ◽  
X Chromosomes ◽  
Evolutionary Forces ◽  
Relative Contribution ◽  
African Populations ◽  
Neutral Variation ◽  
Colonization Process ◽  
The Subject

Abstract Levels of neutral variation are influenced by background selection and hitchhiking. The relative contribution of these evolutionary forces to the distribution of neutral variation is still the subject of ongoing debates. Using 133 microsatellites, we determined levels of variability on X chromosomes and autosomes in African and non-African D. melanogaster populations. In the ancestral African populations microsatellite variability was higher on X chromosomes than on autosomes. In non-African populations X-linked polymorphism is significantly more reduced than autosomal variation. In non-African populations we observed a significant positive correlation between X chromosomal polymorphism and recombination rate. These results are consistent with the interpretation that background selection shapes levels of neutral variability in the ancestral populations, while the pattern in derived populations is determined by multiple selective sweeps during the colonization process. Further research, however, is required to investigate the influence of inversion polymorphisms and unequal sex ratios.

Selection on X-linked Genes During Speciation in the Drosophila athabasca Complex

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 689-703 ◽  
Author(s):  
Michael J Ford ◽  
Charles F Aquadro
Keyword(s):  
Computer Simulation ◽  
Natural Selection ◽  
Molecular Evolution ◽  
Restriction Site ◽  
Neutral Model ◽  
Background Selection ◽  
Selective Sweeps ◽  
Differential Migration ◽  
Site Survey ◽  
Low Levels

Abstract We present the results of a restriction site survey of variation at five loci in Drosophila athabasca, complimenting a previous study of the period locus. There is considerably greater differentiation between the three semispecies of D. athabasca at the period locus and two other X-linked genes (neon-transient-A and E74A) than at three autosomal genes (Xdh, Adh and RC98). Using a modification of the HKA test, which uses fixed differences between the semispecies and a test based on differences in Fst among loci, we show that the greater differentiation of the X-linked loci compared with the autosomal loci is inconsistent with a neutral model of molecular evolution. We explore several evolutionary scenarios by computer simulation, including differential migration of X and autosomal genes, very low levels of migration among the semispecies, selective sweeps, and background selection, and conclude that X-linked selective sweeps in at least two of the semispecies are the best explanation for the data. This evidence that natural selection acted on the X-chromosome suggests that another X-linked trait, mating song differences among the semispecies, may have been the target of selection.

scholarly journals Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanjaya Gyawali ◽  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Chris Kik ◽  
Lindsey J. du Toit
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Selective Sweep ◽  
Spinacia Oleracea ◽  
Genomic Region ◽  
Day Length ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Selective Sweeps ◽  
Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

scholarly journals Diversity patterns and selective sweeps in a Southeast European panel of maize inbred lines as combined with two West European panels

2020 ◽  
Author(s):  
Vlatko Galić ◽  
Violeta Anđelković ◽  
Natalija Kravić ◽  
Nikola Grčić ◽  
Tatjana Ledenčan ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Genetic Material ◽  
Plant Morphology ◽  
Inbred Lines ◽  
Chromosome 2 ◽  
Selective Sweeps ◽  
Phenotypic Analysis ◽  
Maize Breeding ◽  
Favorable Alleles ◽  
Diversity Patterns

AbstractMore than one third of European grain maize is produced in South Eastearn Europe (SEE) and utilization of historical maize material developed in SEE for its favorable alleles and diversity has long been speculated. However, molecular diversity of the SEE maize genetic material is scarce. The objectives of this study were i) to analyze diversity patterns in a large panel of densely genotyped historical accessions from SEE, ii) to compare the data with those obtained from other two European panels, and iii) to identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to SEE conditions. 572 accessions of the historical inbred lines from Maize Research Institute Zemun Polje representing the SEE material were genotyped using the 600k maize genotyping Axiom array. The genotyping results were merged with two European panels DROPS and TUM. Genetic structure and diversity were analyzed using neighbor-joining cladogram, PcoA, Admixture, Structure and sNMF. To detect the selective sweep signals, Tajima’s D statistic and RAiSD were employed. The best number of ancestral populations was K=7, whereby one of them is a subpopulation containing inbreds belong exclusively to the SEE panel. The prevalence of inbreds linked to historical US inbred lines Wf9, Oh43, Pa91 and A374 was detected in SEE. Possible soft selective sweep was detected in chromosome 2 in region harboring a gene linked to promotion of flowering FPF1. Additional scan for selective sweeps using the RAiSD methodology yielded four signals in chromosomes 5 and 6, all in gene-rich regions. Several candidates of selection were identified, influencing the plant morphology and adaptation. Our study provides the first step towards the utilization of the SEE genetic materials for use in maize breeding. Phenotypic analysis is needed for assessment of SEE accessions for favorable alleles, and identification of breeding targets.

Regions of Lower Crossing Over Harbor More Rare Variants in African Populations ofDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 657-665 ◽  
Author(s):  
Peter Andolfatto ◽  
Molly Przeworski
Keyword(s):  
Frequency Spectrum ◽  
Nucleotide Diversity ◽  
Rare Variants ◽  
Purifying Selection ◽  
Crossing Over ◽  
Background Selection ◽  
Deleterious Mutations ◽  
African Populations ◽  
Rapid Fixation ◽  
Parameter Values

AbstractA correlation between diversity levels and rates of recombination is predicted both by models of positive selection, such as hitchhiking associated with the rapid fixation of advantageous mutations, and by models of purifying selection against strongly deleterious mutations (commonly referred to as “background selection”). With parameter values appropriate for Drosophila populations, only the first class of models predicts a marked skew in the frequency spectrum of linked neutral variants, relative to a neutral model. Here, we consider 29 loci scattered throughout the Drosophila melanogaster genome. We show that, in African populations, a summary of the frequency spectrum of polymorphic mutations is positively correlated with the meiotic rate of crossing over. This pattern is demonstrated to be unlikely under a model of background selection. Models of weakly deleterious selection are not expected to produce both the observed correlation and the extent to which nucleotide diversity is reduced in regions of low (but nonzero) recombination. Thus, of existing models, hitchhiking due to the recurrent fixation of advantageous variants is the most plausible explanation for the data.

scholarly journals Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation

2019 ◽  
Vol 59 (4) ◽  
pp. 925-937 ◽  
Author(s):  
Jessica L McKenzie ◽  
Dillon J Chung ◽  
Timothy M Healy ◽  
Reid S Brennan ◽  
Heather J Bryant ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Fundulus Heteroclitus ◽  
Secondary Contact ◽  
Mitochondrial Genomes ◽  
Evolutionary Forces ◽  
Population Genomic ◽  
Genomic Studies

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

scholarly journals Detecting recent selective sweeps while controlling for mutation rate and background selection

2015 ◽  
Vol 25 (1) ◽  
pp. 142-156 ◽  
Author(s):  
Christian D. Huber ◽  
Michael DeGiorgio ◽  
Ines Hellmann ◽  
Rasmus Nielsen
Keyword(s):  
Mutation Rate ◽  
Background Selection ◽  
Selective Sweeps
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