scholarly journals Coalescence with background and balancing selection in systems with bi- and uniparental reproduction: contrasting partial asexuality and selfing

2015 ◽  
Author(s):  
Aneil Agrawal ◽  
Matthew Hartfield
Keyword(s):  
Asexual Reproduction ◽  
Balancing Selection ◽  
Stochastic Simulations ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Effective Population ◽  
Sexual And Asexual Reproduction ◽  
Segregation Effect ◽  
Neutral Marker ◽  
Coalescent Time

Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions in Ne via background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescent time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.

scholarly journals Transition from background selection to associative overdominance promotes diversity in regions of low recombination

2019 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Fanny Pouyet ◽  
Laurent Excoffier ◽  
Stephan Peischl
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Locus Model ◽  
Genome Wide ◽  
Linked Selection

SummaryLinked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworth et al. 1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyet et al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.

scholarly journals The pattern of neutral molecular variation under the background selection model.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1619-1632 ◽  
Author(s):  
D Charlesworth ◽  
B Charlesworth ◽  
M T Morgan
Keyword(s):  
Genetic Diversity ◽  
Genomic Region ◽  
Stochastic Simulations ◽  
Background Selection ◽  
Effective Population ◽  
Frequency Spectra ◽  
Low Genetic Diversity ◽  
Neutral Locus ◽  
Large Populations ◽  
Site Diversity

Abstract Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.

scholarly journals Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160471 ◽  
Author(s):  
Josep M. Comeron
Keyword(s):  
Null Hypothesis ◽  
Population Genomics ◽  
Balancing Selection ◽  
Large Fraction ◽  
Null Model ◽  
Rate Variation ◽  
Background Selection ◽  
Effective Population ◽  
Recombination Rates ◽  
Genome Annotations

The consequences of selection at linked sites are multiple and widespread across the genomes of most species. Here, I first review the main concepts behind models of selection and linkage in recombining genomes, present the difficulty in parametrizing these models simply as a reduction in effective population size ( N e ) and discuss the predicted impact of recombination rates on levels of diversity across genomes. Arguments are then put forward in favour of using a model of selection and linkage with neutral and deleterious mutations (i.e. the background selection model, BGS) as a sensible null hypothesis for investigating the presence of other forms of selection, such as balancing or positive. I also describe and compare two studies that have generated high-resolution landscapes of the predicted consequences of selection at linked sites in Drosophila melanogaster . Both studies show that BGS can explain a very large fraction of the observed variation in diversity across the whole genome, thus supporting its use as null model. Finally, I identify and discuss a number of caveats and challenges in studies of genetic hitchhiking that have been often overlooked, with several of them sharing a potential bias towards overestimating the evidence supporting recent selective sweeps to the detriment of a BGS explanation. One potential source of bias is the analysis of non-equilibrium populations: it is precisely because models of selection and linkage predict variation in N e across chromosomes that demographic dynamics are not expected to be equivalent chromosome- or genome-wide. Other challenges include the use of incomplete genome annotations, the assumption of temporally stable recombination landscapes, the presence of genes under balancing selection and the consequences of ignoring non-crossover (gene conversion) recombination events. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations

1997 ◽  
Vol 70 (2) ◽  
pp. 155-174 ◽  
Author(s):  
BRIAN CHARLESWORTH ◽  
MAGNUS NORDBORG ◽  
DEBORAH CHARLESWORTH
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Polymorphic Locus ◽  
Stochastic Simulations ◽  
Population Subdivision ◽  
Background Selection ◽  
Balanced Polymorphism ◽  
Local Selection ◽  
Species Population

Levels of neutral genetic diversity in populations subdivided into two demes were studied by multi-locus stochastic simulations. The model includes deleterious mutations at loci throughout the genome, causing ‘background selection’, as well as a single locus at which a polymorphism is maintained, either by frequency-dependent selection or by local selective differences. These balanced polymorphisms induce long coalescence times at linked neutral loci, so that sequence diversity at these loci is enhanced at statistical equilibrium. We study how equilibrium neutral diversity levels are affected by the degree of population subdivision, the presence or absence of background selection, and the level of inbreeding of the population. The simulation results are compared with approximate analytical formulae, assuming the infinite sites neutral model. We discuss how balancing selection can be distinguished from local selection, by determining whether peaks of diversity in the region of the polymorphic locus are seen within or between demes. The width of such diversity peaks is shown to depend on the total species population size, rather than local deme sizes. We show that, with population subdivision, local selection enhances between-deme diversity even at neutral sites distant from the polymorphic locus, producing higher FST values than with no selection; very high values can be generated at sites close to a selected locus. Background selection also increases FST, mainly because of decreased diversity within populations, which implies that its effects may be distinguishable from those of local selection. Both effects are stronger in selfing than outcrossing populations. Linkage disequilibrium between neutral sites is generated by both balancing and local selection, especially in selfing populations, because of linkage disequilibrium between the neutral sites and the selectively maintained alleles. We discuss how these theoretical results can be related to data on genetic diversity within and between local populations of a species.

scholarly journals Supergene formation is associated with a major shift in genome-wide patterns of diversity in a butterfly

2021 ◽  
Author(s):  
María Ángeles Rodríguez de Cara ◽  
Paul Jay ◽  
Mathieu Chouteau ◽  
Annabel Whibley ◽  
Barbara Huber ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Mate Preferences ◽  
Heterozygote Advantage ◽  
Effective Population ◽  
Adaptive Introgression ◽  
Continental Scale ◽  
Geographic Structure ◽  
Genome Wide ◽  
Genetic Diversity And Structure

AbstractSelection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Adaptive introgression provides a way to assess how adaptive evolution at one locus impacts whole-genome biology. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform subclade. H. numata is known to have evolved a supergene via the introgression of an adaptive inversion about 2.2 million years ago, triggering a polymorphism maintained by balancing selection. This locus controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics, and butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages in a phylogenetic framework. We show that H. numata populations which carry the introgressed inversions in a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest diversity and demographic estimates in the entire clade, as well as a remarkably low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show the lowest effective population sizes and genetic diversity in the clade, and higher levels of geographical structure across the continent. This suggests that the large effective population size of polymorphic populations could be a property associated with harbouring the supergene. Our results are consistent with the hypothesis that the adaptive introgression of the inversion triggered a shift from directional to balancing selection and a change in gene flow due to disassortative mating, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

scholarly journals The Effects of Deleterious Mutations on Linked, Neutral Variation in Small Populations

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 475-483 ◽  
Author(s):  
Snæbjörn Pálsson ◽  
Pekka Pamilo
Keyword(s):  
Small Populations ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Selection Coefficient ◽  
Effective Population ◽  
Strong Reduction ◽  
Tight Linkage ◽  
Neutral Marker ◽  
Population Sizes ◽  
Clear Increase

Abstract The effects of recessive, deleterious mutations on genetic variation at linked neutral loci can be heterozygosity-decreasing because of reduced effective population sizes or heterozygosity-increasing because of associative overdominance. Here we examine the balance between these effects by simulating individual diploid genotypes in small panmictic populations. The haploid genome consists of one linkage group with 1000 loci that can have deleterious mutations and a neutral marker. Combinations of the following parameters are studied: gametic mutation rate to harmful alleles (U), population size (N), recombination rate (r), selection coefficient (s), and dominance (h). Tight linkage (r ≤ 10–4) gives significant associative effects, leading either to strong reduction of heterozygosity when the product Nhs is large or to a clear increase when the product Nhs is small, the boundary between these effects being 1 < Nhs < 4 in our simulations. Associative overdominance can lead to heterozygosities that are larger than predicted by the background selection models and even larger than the neutral expectation.

scholarly journals Resolving the conflict between associative overdominance and background selection

2016 ◽  
Author(s):  
Lei Zhao ◽  
Brian Charlesworth
Keyword(s):  
Selective Advantage ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Effective Population ◽  
Infinite Population ◽  
Recessive Mutations ◽  
Neutral Locus ◽  
Large Populations ◽  
Marker Loci ◽  
Shed Light

In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance), and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical and simulation studies that shed light on the conditions under which retardation versus acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection, with no linkage disequilibrium. With mutation and selection, retardation only occurs when S, the product of twice the effective population size and the selection coefficient, is of order one. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, there is nearly always a retardation of loss of variability. The results shed light on experiments on the loss of variability at marker loci in laboratory populations, and on the results of computer simulations of the effects of multiple selected loci on neutral variability.

scholarly journals Polymorphism and balancing selection at major histocompatibility complex loci.

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 925-938 ◽  
Author(s):  
N Takahata ◽  
Y Satta ◽  
J Klein
Keyword(s):  
Major Histocompatibility Complex ◽  
Dna Sequences ◽  
Balancing Selection ◽  
Heterozygote Advantage ◽  
Nucleotide Substitution Rate ◽  
Major Histocompatibility ◽  
Effective Population ◽  
Nucleotide Substitutions ◽  
Mhc Genes ◽  
Histocompatibility Complex

Abstract Amino acid replacements in the peptide-binding region (PBR) of the functional major histocompatibility complex (Mhc) genes appear to be driven by balancing selection. Of the various types of balancing selection, we have examined a model equivalent to overdominance that confers heterozygote advantage. As discussed by A. Robertson, overdominance selection tends to maintain alleles that have more or less the same degree of heterozygote advantage. Because of this symmetry, the model makes various testable predictions about the genealogical relationships among different alleles and provides ways of analyzing DNA sequences of Mhc alleles. In this paper, we analyze DNA sequences of 85 alleles at the HLA-A, -B, -C, -DRB1 and -DQB1 loci with respect to the number of alleles and extent of nucleotide differences at the PBR, as well as at the synonymous (presumably neutral) sites. Theory suggests that the number of alleles that differ at the sites targeted by selection (presumably the nonsynonymous sites in the PBR) should be equal to the mean number of nucleotide substitutions among pairs of alleles. We also demonstrate that the nucleotide substitution rate at the targeted sites relative to that of neutral sites may be much larger than 1. The predictions of the presented model are in surprisingly good agreement with the actual data and thus provide means for inferring certain population parameters. For overdominance selection in a finite population at equilibrium, the product of selection intensity (s) against homozygotes and the effective population size (N) is estimated to be 350-3000, being largest at the B locus and smallest at the C locus. We argue that N is of the order of 10(5) and s is several percent at most, if the mutation rate per site per generation is 10(-8).

scholarly journals Effective population size of plant species propagating with a mixed sexual and asexual reproduction system

1997 ◽  
Vol 70 (3) ◽  
pp. 251-258 ◽  
Author(s):  
KATSUEI YONEZAWA
Keyword(s):  
Plant Species ◽  
Asexual Reproduction ◽  
Structured Populations ◽  
Effective Size ◽  
Effective Population ◽  
Census Size ◽  
Reproduction System ◽  
Sexual And Asexual Reproduction ◽  
Mean And Variance ◽  
The Mean

The variance effective size (Ne) was formulated for populations of monoecious plant species that are partly asexually propagating with discrete or overlapping generations. It was shown that partly asexually reproducing populations have larger or smaller effective sizes (ratios to the census size N) than fully sexually reproducing populations, according to whether the term Vc/c¯ is smaller or larger than the term (Vk/k¯ +1−β)/2, where c¯ and Vc are the mean and variance of the number of progeny asexually produced per plant per year, respectively, k¯ and Vk are the mean and variance of the number of gametes contributed per plant per year, respectively, and β is the selfing rate of each plant. Asexual reproduction has no effect on Ne when the two terms are equal, as is true when the numbers of both sexually and asexually produced progeny per plant per year are Poisson-distributed (Vc/c¯=1 and Vk/k¯=1+β). Populations with a larger generation length (L) tend to have a smaller effective size: for a population model of age-independent survival and fecundity with an annual rate δ of asexual reproduction, Ne declines asymptotically to N(2−β)/{3−β +Vk/k¯ +(2Vc/c¯ −Vk/k¯ −1+β).δ} as L gets large, which simplifies to N(2−β)/4 under a Poisson-distributed reproductive contribution. The trade-off relation of Ne and L, however, does not always hold: for stage-structured populations, increase in the survival rate of juveniles may act to increase both Ne and L.

Gemmae in Tetralophozia setiformis (Anastrophyllaceae, Marchantiophyta) and their second record in Eurasia

2017 ◽  
Vol 51 ◽  
pp. 242-250
Author(s):  
M. V. Dulin
Keyword(s):  
British Columbia ◽  
Asexual Reproduction ◽  
Leaf Shape ◽  
Leaf Size ◽  
Komi Republic ◽  
The Other ◽  
Widespread Species ◽  
Northern Urals ◽  
Sexual And Asexual Reproduction ◽  
Murmansk Region

Tetralophozia setiformis is a widespread species occurring usually without organs of sexual and asexual reproduction. Gemmae of Tetralophozia setiformis were observed for the second time in Russia and Eurasia in the Northern Urals, Komi Republic. They form compact masses over upper leaves. The compact masses consist largely (70 %) of immature gemmae. Description of gemmae and gemmiparous shoots from the Northern Urals and their comparison with those from the other known localities, namely British Columbia (Canada) and the Murmansk Region (European Russia) were carried out. The gemmiparous plants of T. setiformis from the Northern Urals have approximately the same width as plants without gemmae but they are shorter. The leaves of gemmiparous plants from the Northern Urals are similar to leaves of gemmiparous plants from British Columbia. The leaf shape in upper part of the gemmiparous shoots varies from the typical to ± modified from gemmae production. These leaf shape transitions include reduction of leaf size and lobe number from 4 to 2–3, suppression of development and disappearance of characteristic teeth at the base of sinus. Gemmae size (17 × 22 μm) of plants from the Northern Urals is within variability recorded for plants from the Murmansk Region and British Columbia.

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