Sex and recombination purge the genome of deleterious alleles: An Individual Based Modeling Approach

MacPherson, Brian; Scott, Ryan; Gras, Régis

doi:10.1016/j.ecocom.2021.100910

Cited by 9 publications

(7 citation statements)

References 69 publications

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“…We observed strong correlations (R 2 range = 0.938 -0.955, p<0.001, except again for MSL, with R 2 = 0.252) between levels of GC3 and π N /π S ratio among all Coho salmon populations (Fig 4A). An Moreover, this also highlights the effect of recombination on the efficiency of purifying selection [50]. The samples at the expansion front (Mile Slough R., Porcupine R., Snake R.) in Alaska were the populations with the lowest correlations between GC3 and π N /π S .…”

Section: Recombination Rates Shape the Deleterious Mutational Landscapementioning

confidence: 76%

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Allele surfing causes maladaptation in a Pacific salmon of conservation concern

Rougemont

Leroy

Rondeau

et al. 2022

Preprint

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The Anthropocene threatens worldwide biodiversity, with a potential to induce species decline and range contraction. In this context, it is important to quantify species adaptive potential and how demographic changes may impact selection efficacy and the burden of deleterious mutations in different populations. Here we show that key evolutionary processes, including variation in effective population size through postglacial change in demography and recombination rates have affected the efficacy of selection and impacted the load in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing (30x coverage) data from populations at different latitudinal distances from their southern glacial refugium, we found support for postglacial gene surfing, with reduced Ne at the range recolonization front, thus inducing both a reduction of the adaptive potential and a surf of deleterious alleles in populations evolving at low Ne. This inference was robust to various proxy of the load, namely ratios of non-synonymous to synonymous diversity, the number of missense and loss of function mutations. In addition, comparing residual tetrasomic and re-diploidizing regions of the salmon genome, we found support for a prime role of recombination rates in shaping the within-genome variation of the load. Overall, our empirical results are remarkably consistent with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.

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Section: Recombination Rates Shape the Deleterious Mutational Landscapementioning

confidence: 76%

“…Moreover, this also highlights the effect of recombination on the efficiency of purifying selection [50]. The samples at the expansion front (Mile Slough R., Porcupine R., Snake R.) in Alaska were the populations with the lowest correlations between GC3 and π N /π S .…”

Section: Resultsmentioning

confidence: 94%

Allele surfing causes maladaptation in a Pacific salmon of conservation concern

Rougemont

Leroy

Rondeau

et al. 2022

Preprint

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“…For Tetrahymena, whose meiotic products are not long lasting, we can only suppose that they adjourn meiosis until an otherwise unproductive period when vegetative reproduction is halted, anyway. Alternatively, cells might perceive nutritional stress as dwindling vigor owing to the accumulation of mutations and respond by genome rejuvenation via sex (see [10,11]).…”

Section: Tetrahymena Sexual Reproductionmentioning

confidence: 99%

Tetrahymena meiosis: Simple yet ingenious

Loidl

2021

PLoS Genet

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The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial feature of eukaryotes. However, extant meiotic structures and processes can vary considerably between organisms. The ciliated protist Tetrahymena thermophila, which diverged from animals, plants, and fungi early in evolution, provides one example of a rather unconventional meiosis. Tetrahymena has a simpler meiosis compared with most other organisms: It lacks both a synaptonemal complex (SC) and specialized meiotic machinery for chromosome cohesion and has a reduced capacity to regulate meiotic recombination. Despite this, it also features several unique mechanisms, including elongation of the nucleus to twice the cell length to promote homologous pairing and prevent recombination between sister chromatids. Comparison of the meiotic programs of Tetrahymena and higher multicellular organisms may reveal how extant meiosis evolved from proto-meiosis.

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“…Sexual organisms also have the benefit of segregation and recombination to facilitate efficient purifying selection, purging deleterious mutations from the population (Felsenstein 1974; MacPherson et al 2021; Kondrashov 1994; Hartfield & Keightley 2012; Hollister et al 2015). Recombination is especially effective at purging such mutations as it not only prevents disadvantageous mutations from becoming established in a population, but it also makes it more likely for favorable mutations to become fixed within a population (Felsenstein 1974).…”

Section: Introductionmentioning

confidence: 99%

“…Sexual organisms also have the benefit of segregation and recombination to facilitate efficient purifying selection, purging deleterious mutations from the population (Felsenstein 1974;MacPherson et al 2021;Kondrashov 1994;Hartfield & Keightley 2012;Hollister et al 2015). Recombination is especially effective at purging such mutations as it not only prevents disadvantageous mutations from becoming established in a population, but it also makes it more likely for favorable mutations to become fixed within a population (Felsenstein 1974).…”

Section: Introductionmentioning

confidence: 99%

Reduced effectiveness of purifying selection on new mutations in a parthenogenic terrestrial isopod (Trichoniscus pusillus)

Yarbrough

Chandler

2023

Preprint

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The "paradox of sex" refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one would suspect nature would select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in the closely related terrestrial isopod species Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all wild-caught T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin for this population, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius, suggesting this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonyous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs support the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but that this only becomes apparent over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature.

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Sex and recombination purge the genome of deleterious alleles: An Individual Based Modeling Approach

Cited by 9 publications

References 69 publications

Allele surfing causes maladaptation in a Pacific salmon of conservation concern

Allele surfing causes maladaptation in a Pacific salmon of conservation concern

Tetrahymena meiosis: Simple yet ingenious

Reduced effectiveness of purifying selection on new mutations in a parthenogenic terrestrial isopod (Trichoniscus pusillus)

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