scholarly journals Inbreeding depression and genetic load at partially linked loci in a metapopulation

2010 ◽  
Vol 92 (2) ◽  
pp. 127-140 ◽  
Author(s):  
SHU-RONG ZHOU ◽  
JOHN R. PANNELL
Keyword(s):  
Inbreeding Depression ◽  
Random Mating ◽  
Genetic Load ◽  
Minor Effect ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Sexual Systems ◽  
Biological Phenomena ◽  
Population Turnover ◽  
Wide Range

SummaryInbreeding depression has important implications for a wide range of biological phenomena, such as inbreeding avoidance, the evolution and maintenance of sexual systems and extinction rates of small populations. Previous investigations have asked how inbreeding depression evolves in single and subdivided populations through the fixation of deleterious mutations as a result of drift, as well as through the expression of deleterious mutations segregating in a population. These studies have focused on the effects of mutation and selection at single loci, or at unlinked loci. Here, we used simulations to investigate the evolution of genetic load and inbreeding depression due to multiple partially linked loci in metapopulations. Our results indicate that the effect of linkage depends largely on the kinds of deleterious alleles involved. For weakly deleterious and partially recessive mutations, the speed of mutation accumulation at segregating loci in a random-mating subdivided population of a given structure tends to be retarded by increased recombination between adjacent loci – although the highest numbers of fixation of slightly recessive mutant alleles were for low but finite recombination rates. Although linkage had a relatively minor effect on the evolution of metapopulations unless very low values of recombination were assumed, close linkage between adjacent loci tended to enhance population structure and population turnover. Finally, within-deme inbreeding depression, between-deme inbreeding depression and heterosis generally increased with decreased recombination rates. Moreover, increased selfing reduced the effective amount of recombination, and hence the effects of tight linkage on metapopulation genetic structure were decreased with increasing selfing. In contrast, linkage had little effect on the fate of lethal and highly recessive alleles. We compare our simulation results with predictions made by models that ignore the complexities of recombination.

scholarly journals Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter

2000 ◽  
Vol 75 (1) ◽  
pp. 75-81 ◽  
Author(s):  
THOMAS BATAILLON ◽  
MARK KIRKPATRICK
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Large Population ◽  
Genetic Load ◽  
Breeding Systems ◽  
Deleterious Mutations ◽  
Single Locus Analysis ◽  
Population Sizes ◽  
Inbreeding Rate

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

scholarly journals The asexual genome of Drosophila

2017 ◽  
Author(s):  
Stephan Schiffels ◽  
Ville Mustonen ◽  
Michael Lässig
Keyword(s):  
Molecular Evolution ◽  
Genetic Load ◽  
Recombination Rates ◽  
Frequency Spectra ◽  
Ideal System ◽  
Wide Range ◽  
Functional Consequences ◽  
Speed Of Evolution ◽  
Local Interference ◽  
Genomic Regions

AbstractThe rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic segments. Selection under linkage can induce clonal interference, a specific mode of evolution by competition of genetic clades within a population. This mode is well known in asexually evolving microbes, but has not been traced systematically in an obligate sexual organism. Here we show that the Drosophila genome is partitioned into two modes of evolution: a local interference regime with limited effects of genetic linkage, and an interference condensate with clonal competition. We map these modes by differences in mutation frequency spectra, and we show that the transition between them occurs at a threshold recombination rate that is predictable from genomic summary statistics. We find the interference condensate in segments of low-recombining sequence that are located primarily in chromosomal regions flanking the centromeres and cover about 20% of the Drosophila genome. Condensate regions have characteristics of asexual evolution that impact gene function: the efficacy of selection and the speed of evolution are lower and the genetic load is higher than in regions of local interference. Our results suggest that multicellular eukaryotes can harbor heterogeneous modes and tempi of evolution within one genome. We argue that this variation generates selection on genome architecture.Author SummaryThe Drosophila genome is an ideal system to study how the rate of recombination affects molecular evolution. It harbors a wide range of local recombination rates, and its high-recombining parts show broad signatures of adaptive evolution. The low-recombining parts, however, have remained dark genomic matter that has been omitted from most studies on the inference of selection. Here we show that these genomic regions evolve in a different way, which involves clonal competition and is akin to the evolution of asexual systems. This regime shows a lower efficacy of selection, a lower speed of evolution, and a higher genetic load than high-recombining regions. We argue these evolutionary differences have functional consequences: protein stability and protein expression are gene traits likely to be partially compromised by low recombination rates.

Inbreeding depression in a rare deceptive orchid

2001 ◽  
Vol 79 (10) ◽  
pp. 1181-1188 ◽  
Author(s):  
Jean-Baptiste Ferdy ◽  
Sandrine Loriot ◽  
Michel Sandmeier ◽  
Madeleine Lefranc ◽  
Christian Raquin
Keyword(s):  
Inbreeding Depression ◽  
Conservation Biology ◽  
Resource Availability ◽  
Genetic Load ◽  
Outcrossing Rate ◽  
Deleterious Mutations ◽  
Geographic Scale ◽  
Deceptive Pollination ◽  
Inbreeding Level ◽  
Small Geographic Scale

We quantified inbreeding depression for seed maturation and germination in a deceptively pollinated orchid (Dactylorhiza praetermissa (Druce) Soó). Deceptive species do not provide any reward to their pollinators, which thus visit few flowers per plant. Therefore, deceptive species are predicted to experience high outcrossing. In agreement with the prediction that species with high outcrossing rate should possess a heavy genetic load, we demonstrated inbreeding depression in one of the populations we studied. More surprisingly, we found some evidence of inbreeding depression at a small geographic scale. This was not expected, as deceptive orchids generally disperse their pollen and their seeds over long distances. We also demonstrated that the position of a flower within an inflorescence interacts with the type of cross. This indicates that resource availability might modify how severely deleterious mutations affect reproductive success. This could also explain why the intensity of inbreeding depression seems, in the populations we studied, to be determined more by environmental factors than by inbreeding level, as estimated from molecular markers. Inferences in terms of conservation biology are drawn from these results.Key words: inbreeding depression, deceptive pollination, orchid, Dactylorhiza praetermissa.

scholarly journals The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1105-1118 ◽  
Author(s):  
Violaine Llaurens ◽  
Lucy Gonthier ◽  
Sylvain Billiard
Keyword(s):  
Inbreeding Depression ◽  
Balancing Selection ◽  
Genetic Load ◽  
Relative Fitness ◽  
Self Incompatibility ◽  
Deleterious Mutations ◽  
Gas Treatment ◽  
Genomic Inbreeding ◽  
Genomic Regions ◽  
Empirical Approaches

Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individuals are heterozygous at the S locus and recombination is suppressed in the S-locus region, it has been suggested that deleterious mutations could accumulate at genes linked to the S locus, generating a “sheltered load.” In this article, we first theoretically investigate the conditions generating sheltered load in SSI. We show that deleterious mutations can accumulate in linkage with specific S alleles, and particularly if those S alleles are dominant. Second, we looked for the presence of sheltered load in Arabidopsis halleri using CO2 gas treatment to overcome self-incompatibility. By examining the segregation of S alleles and measuring the relative fitness of progeny, we found significant sheltered load associated with the most dominant S allele (S15) of three S alleles tested. This sheltered load seems to be expressed at several stages of the life cycle and to have a larger effect than genomic inbreeding depression.

scholarly journals Deleterious variation mimics signatures of genomic incompatibility and adaptive introgression

2017 ◽  
Author(s):  
Bernard Y. Kim ◽  
Christian D. Huber ◽  
Kirk E. Lohmueller
Keyword(s):  
Population Genetic ◽  
Natural Populations ◽  
Genetic Load ◽  
Population Admixture ◽  
Population Differences ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Adaptive Introgression ◽  
Fitness Effects ◽  
New Mutations

AbstractWhile it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how population admixture affects the dynamics of deleterious variation. Here we use population genetic simulations to examine how admixture impacts deleterious variation under a variety of demographic scenarios, dominance coefficients, and recombination rates. Our results show that gene flow between populations can temporarily reduce the genetic load of smaller populations, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. This can lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30-75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models include both demography and deleterious variation before invoking reproductive incompatibilities or adaptive introgression to explain unusual patterns of genetic variation.

The evolutionary genetics of sexual systems in flowering plants

1979 ◽  
Vol 205 (1161) ◽  
pp. 513-530 ◽  
Keyword(s):  
Inbreeding Depression ◽  
Evolutionary Genetics ◽  
Selective Advantage ◽  
Flowering Plants ◽  
Breeding Systems ◽  
Recombination Rates ◽  
Sexual Systems ◽  
Starting State ◽  
Self Fertilization ◽  
Outcrossing Species

Population genetic studies of the evolution of breeding systems in flowering plants are reviewed. The selective advantage of a gene’s increasing the selfing rate is stressed. In the evolution of outbreeding mechanisms, some strong disadvantage to selfing must therefore be acting; it is suggested that this disadvantage is inbreeding depression. Populations with no absolute barrier to selfing, and with intermediate levels of self-fertilization, appear to be the most likely starting state for the evolution of outbreeding mechanisms. There is some evidence for inbreeding depression in such populations. The evolution of distyly and dioecy are considered in some detail. An explanation for the existence of supergenes controlling these systems is proposed. The breakdown of distyly and tristyly are also considered. The evolution of recombination rates in selfing and outcrossing species is examined briefly.

scholarly journals Genetic load may increase or decrease with selfing depending upon the recombination environment

2021 ◽  
Author(s):  
Shelley A Sianta ◽  
Stephan Peischl ◽  
David A Moeller ◽  
Yaniv Brandvain
Keyword(s):  
Balancing Selection ◽  
Random Mating ◽  
Genetic Load ◽  
Threshold Level ◽  
Mutation Rates ◽  
Selfing Rate ◽  
Effective Population ◽  
Recombination Rates ◽  
Genomic Changes ◽  
Recessive Mutations

Theory predicts that the ability for natural selection to remove deleterious mutations from a population, and prevent the accumulation of genetic load, is a function of the effective population size (Ne). Shifts from random mating to self-fertilization (selfing) are predicted to decrease Ne through a variety of genomic changes - including a reduction in effective recombination and an increase in homozygosity. While a long history of theory suggests that the efficacy of selection, particularly against non-recessive mutations, should decrease with selfing rate, comparisons of genomic-based estimates of the efficacy of selection between related outcrosser-selfer pairs have revealed conflicting results. We address this paradox by simulating the evolution of strongly deleterious recessive and weakly deleterious additive mutations across a range of recombination, mutation and selective parameter combinations. We find that the genetic load of a population can either increase, decrease, or not vary with selfing rate. Genetic load is higher in selfers only when recombination rates are greater than mutation rates. When recombination rates are lower than mutation rates, an accumulation of recessive mutations leads to pseudo-overdominance, a type of balancing selection, in outcrossing populations. Using both simulations and analytical theory, we show that pseudo-overdominance has strong negative effects on the efficacy of selection against linked additive mutations and that a threshold level of selfing prevents pseudo-overdominance. Our results show that selection can be more or less effective in selfers as compared to outcrossers depending on the relationship between the deleterious mutation rate and gene density, and therefore different genomic regions in different taxa could show differing results.

scholarly journals The effect of recombination on background selection

1996 ◽  
Vol 67 (2) ◽  
pp. 159-174 ◽  
Author(s):  
Magnus Nordborg ◽  
Brian Charlesworth ◽  
Deborah Charlesworth
Keyword(s):  
Genetic Recombination ◽  
Random Mating ◽  
Large Population ◽  
Approximate Equation ◽  
Arbitrary Distribution ◽  
Background Selection ◽  
Weak Selection ◽  
Recombination Rates ◽  
Neutral Locus ◽  
Wide Range

SummaryAn approximate equation is derived, which predicts the effect on variability at a neutral locus of background selection due to a set of partly linked deleterious mutations. Random mating, multiplicative fitnesses, and sufficiently large population size that the selected loci are in mutation/selection equilibrium are assumed. Given these assumptions, the equation is valid for an arbitrary genetic map, and for an arbitrary distribution of selection coefficients across loci. Monte Carlo computer simulations show that the formula performs well for small population sizes under a wide range of conditions, and even seems to apply when there are epistatic fitness interactions among the selected loci. Failure occurred only with very weak selection and tight linkage. The formula is shown to imply that weakly selected mutations are more likely than strongly selected mutations to produce regional patterning of variability along a chromosome in response to local variation in recombination rates. Loci at the extreme tip of a chromosome experience a smaller effect of background selection than loci closer to the centre. It is shown that background selection can produce a considerable overall reduction in variation in organisms with small numbers of chromosomes and short maps, such as Drosophila. Large overall effects are less likely in species with higher levels of genetic recombination, such as mammals, although local reductions in regions of reduced recombination might be detectable.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

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