Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

Mapping Intimacies ◽

10.1101/016626 ◽

2015 ◽

Author(s):

MC Harrison ◽

EB Mallon ◽

D Twell ◽

RL Hammond

Keyword(s):

Arabidopsis Thaliana ◽

Life History ◽

Deleterious Mutation ◽

Rapid Evolution ◽

Relative Strength ◽

Pollen Competition ◽

Deleterious Mutations ◽

Deleterious Alleles ◽

Polymorphism Data ◽

Plant Pollen

AbstractIn many studies sex related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 million years A.thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. In this study we have investigated the relative strength of selection on pollen genes compared to sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible positive selection was stronger on pollen genes than sporophytic genes for A. thaliana; 2) current polymorphism data indicate selection is weaker on pollen genes compared to sporophytic genes. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared to sporophytic genes.

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Deleterious Mutation Accumulation in Arabidopsis thaliana Pollen Genes: A Role for a Recent Relaxation of Selection

Genome Biology and Evolution ◽

10.1093/gbe/evz127 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1939-1951 ◽

Cited By ~ 1

Author(s):

Mark C Harrison ◽

Eamonn B Mallon ◽

Dave Twell ◽

Robert L Hammond

Keyword(s):

Arabidopsis Thaliana ◽

Tissue Specificity ◽

Deleterious Mutation ◽

Rapid Evolution ◽

Relative Strength ◽

Pollen Competition ◽

Deleterious Mutations ◽

Deleterious Alleles ◽

Polymorphism Data ◽

Plant Pollen

Abstract In many studies, sex-related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 Myr, A. thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity, and a dilution of masking in diploid expressed, sporophytic genes. In this study, we have investigated the relative strength of selection on pollen genes compared with sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible, positive selection was stronger on pollen genes than sporophytic genes for A. thaliana and 2) current polymorphism data indicate that selection is weaker on pollen genes compared with sporophytic genes. This weaker selection on pollen genes can in part be explained by their higher tissue specificity, which in outbreeding plants can be outweighed by the effects of haploid expression and pollen competition. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared with sporophytic genes.

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Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

Molecular Biology and Evolution ◽

10.1093/molbev/msaa067 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2192-2196 ◽

Cited By ~ 2

Author(s):

Jonathan Rolland ◽

Dolph Schluter ◽

Jonathan Romiguier

Keyword(s):

Life History ◽

Evolutionary Biology ◽

Life History Traits ◽

Deleterious Mutation ◽

Purifying Selection ◽

Synonymous Substitution ◽

Deleterious Mutations ◽

Data Set ◽

Terrestrial Vertebrates ◽

Genome Data

Abstract Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.

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Vulnerability and life-history traits correlate with the load of deleterious mutations in fish

10.1101/2019.12.29.890038 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jonathan Rolland ◽

Jonathan Romiguier

Keyword(s):

Life History ◽

Evolutionary Biology ◽

Life History Traits ◽

Deleterious Mutation ◽

Purifying Selection ◽

Synonymous Substitution ◽

Life History Strategies ◽

Deleterious Mutations ◽

Terrestrial Vertebrates ◽

Genome Dataset

AbstractUnderstanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome dataset of 76 species of fishes, we show that the rate of deleterious mutation accumulation (measured via dN/dS, i.e. non-synonymous over synonymous substitution rate) is associated to the vulnerability, the life-history strategies, and the latitude of species. Our results, focusing on a large clade of aquatic species, generalizes previous patterns found so far in few clades of terrestrial vertebrates. These results also suggest that vulnerable species accumulate more deleterious substitutions than non-threatened ones, which give insights in how life-history traits, populations sizes and genetic risk of extinction can be tightly interconnected.

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The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽

10.1093/genetics/162.1.395 ◽

2002 ◽

Vol 162 (1) ◽

pp. 395-411 ◽

Cited By ~ 2

Author(s):

Toby Johnson ◽

Nick H Barton

Keyword(s):

Selective Sweep ◽

Deleterious Mutation ◽

Short Interval ◽

Selective Advantage ◽

Asexual Population ◽

Restrictive Assumption ◽

Deleterious Alleles ◽

Fixation Probabilities ◽

Asexual Populations ◽

Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

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Harmful mutation load in the mitochondrial genomes of cattle breeds

BMC Research Notes ◽

10.1186/s13104-021-05664-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Sankar Subramanian

Keyword(s):

Population Size ◽

Artificial Selection ◽

Deleterious Mutation ◽

Genetic Diseases ◽

Mitochondrial Genomes ◽

Deleterious Mutations ◽

Founder Population ◽

Mutation Load ◽

Effective Population ◽

Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

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The mutation load under tetrasomic inheritance and its consequences for the evolution of the selfing rate in autotetraploid species

Genetics Research ◽

10.1017/s0016672399003845 ◽

1999 ◽

Vol 74 (1) ◽

pp. 31-42 ◽

Cited By ~ 59

Author(s):

J. RONFORT

Keyword(s):

Inbreeding Depression ◽

Deleterious Mutation ◽

Stable State ◽

Approximate Solutions ◽

Balance Model ◽

Deleterious Mutations ◽

Selfing Rate ◽

Mutation Load ◽

Mean Fitness ◽

The Mean

Single-locus equilibrium frequencies of a partially recessive deleterious mutation under the mutation–selection balance model are derived for partially selfing autotetraploid populations. Assuming multiplicative fitness interactions among loci, approximate solutions for the mean fitness and inbreeding depression values are also derived for the multiple locus case and compared with expectations for the diploid model. As in diploids, purging of deleterious mutations through consanguineous matings occurs in autotetraploid populations, i.e. the equilibrium mutation load is a decreasing function of the selfing rate. However, the variation of inbreeding depression with the selfing rate depends strongly on the dominance coefficients associated with the three heterozygous genotypes. Inbreeding depression can either increase or decrease with the selfing rate, and does not always vary monotonically. Expected issues for the evolution of the selfing rate consequently differ depending on the dominance coefficients. In some cases, expectations for the evolution of the selfing rate resemble expectations in diploids; but particular sets of dominance coefficients can be found that lead to either complete selfing or intermediate selfing rates as unique evolutionary stable state.

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The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/151.1.119 ◽

1999 ◽

Vol 151 (1) ◽

pp. 119-129 ◽

Cited By ~ 4

Author(s):

Larissa L Vassilieva ◽

Michael Lynch

Keyword(s):

Life History ◽

Caenorhabditis Elegans ◽

Mutation Rate ◽

Life History Traits ◽

Deleterious Mutation ◽

Spontaneous Mutation ◽

Spontaneous Mutations ◽

Homozygous State ◽

Mutational Effect ◽

Biological Differences

Abstract Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of ∼50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability ∼0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

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Sex-dependent dominance maintains migration supergene in rainbow trout

10.1101/504621 ◽

2018 ◽

Cited By ~ 12

Author(s):

Devon E. Pearse ◽

Nicola J. Barson ◽

Torfinn Nome ◽

Guangtu Gao ◽

Matthew A. Campbell ◽

...

Keyword(s):

Rainbow Trout ◽

Sex Chromosomes ◽

Sexual Conflict ◽

Genetic Basis ◽

Deleterious Mutation ◽

Deleterious Mutations ◽

Heteromorphic Sex Chromosomes ◽

Males And Females ◽

Shared Genetic ◽

Environmental Dependence

AbstractTraits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

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Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data

10.1101/062216 ◽

2016 ◽

Cited By ~ 3

Author(s):

Paula Tataru ◽

Maéva Mollion ◽

Sylvain Glemin ◽

Thomas Bataillon

Keyword(s):

Molecular Evolution ◽

Evolutionary Genetics ◽

Deleterious Mutations ◽

Probabilistic Framework ◽

Evolutionary Trajectory ◽

Beneficial Mutations ◽

Fitness Effects ◽

Polymorphism Data ◽

Inference Methods ◽

Biased Estimates

ABSTRACTThe distribution of fitness effects (DFE) encompasses deleterious, neutral and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (α). Inference of DFE and α from patterns of polymorphism (SFS) and divergence data has been a longstanding goal of evolutionary genetics. A widespread assumption shared by numerous methods developed so far to infer DFE and α from such data is that beneficial mutations contribute only negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and α is only predicted by contrasting the SFS with divergence data from an outgroup. Here, we develop a hierarchical probabilistic framework that extends on previous methods and also can infer DFE and α from polymorphism data alone. We use extensive simulations to examine the performance of our method. We show that both a full DFE, comprising both deleterious and beneficial mutations, and α can be inferred without resorting to divergence data. We demonstrate that inference of DFE from polymorphism data alone can in fact provide more reliable estimates, as it does not rely on strong assumptions about a shared DFE between the outgroup and ingroup species used to obtain the SFS and divergence data. We also show that not accounting for the contribution of beneficial mutations to polymorphism data leads to substantially biased estimates of the DFE and α. We illustrate these points using our newly developed framework, while also comparing to one of the most widely used inference methods available.

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