Biology subjects

Rousselle, M.

Publications and source records attributed to Rousselle, M..

7 recordsLinked to original sources

bioRxiv2026

The dynamics of barrier locus accumulation during speciation with gene flow

Understanding how reproductive isolation (RI) evolves in the context of gene flow is central to explaining how new species arise. Theory predicts that the accumulation of barrier loci depends on the interplay between divergent selection, recombination, and genomic architecture. However, empirical tests that track these processes across multiple stages of divergence within species remain scarce. The pea aphid complex, which comprises sympatric host-specialised biotypes spanning a continuum of divergence, provides a powerful opportunity to examine how ecological adaptation drives reproductive isolation despite ongoing gene flow. Using whole-genome sequencing data from 13 sympatric European biotypes, we constructed a dense, reference-anchored view of genomic divergence that controls for shared genetic background and recombination landscape. Joint analyses of genetic differentiation, absolute divergence, genetic diversity, recombination, and introgression rates reveal a consistent signature of divergence with gene flow and enable robust identification of barrier loci. Across the divergence continuum, RI is highly polygenic, but barrier loci are clustered and enriched in low-recombination regions and large chromosomal rearrangements, which are expected to strengthen linkage disequilibrium and promote the coupling of barrier effects. While genome-wide differentiation and the number of barrier loci increase gradually with divergence, differentiation within barrier loci displays patterns consistent with non-continuous dynamics, which could reflect threshold effects predicted by theory. Barrier loci contain excesses of salivary effector, detoxification and chemosensory genes, highlighting their central role in host plant specialisation and RI. The representation of these gene categories varies across divergence levels, and some loci are shared among independent biotype comparisons, suggesting common functional routes to specialisation via parallel evolution or introgression. Together, our results provide a comprehensive view of the genomic architecture and evolutionary dynamics underlying speciation with gene flow, illustrating how tightly linked, polygenic architectures can facilitate adaptation and diversification in natural populations.

evolutionary biology↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2020

Endemic island songbirds as windows into evolution in small effective population sizes

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation [1,2]. Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (i) lower genetic diversity, (ii) less effective natural selection against slightly deleterious mutations [3,4], and (iii) a lower rate of adaptive evolution [5-8, see also Note S1]. Here, we have used a large set of newly sequenced and published whole genome sequences of Passerida bird species or subspecies (14 insular and 11 continental) to test these predictions. We empirically confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find significantly lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.

evolutionary biology↗

bioRxiv2019

How much does Ne vary among species?

AO_SCPLOWBSTRACTC_SCPLOWGenetic drift is an important evolutionary force of strength inversely proportional to Ne, the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations (DFE). To this aim, we analyze the non-synonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the DFE is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of non-synonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontins paradox while further questioning the meaning of the Ne parameter in population genomics.

evolutionary biology↗

bioRxiv2019

Is adaptation limited by mutation? A timescale dependent effect of genetic diversity on the adaptive substitution rate in animals.

Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with the effective population size Ne. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species.\n\nWe gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate {omega}a, in 50 species from ten distant groups of animals with markedly different population mutation rate {theta}. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between {omega}a and {theta} among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-{theta} taxa. In contrast, we uncover a weak negative correlation between {omega}a and {theta} at a larger taxonomic scale. This result is consistent with Fishers geometrical model predictions and suggests that the proportion of beneficial mutations scales negatively with species long-term Ne.

evolutionary biology↗

bioRxiv2018

Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius

Sex chromosomes have different evolutionary properties as compared to the autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution in the sex chromosomes of a group of tropical butterflies. We first improved the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then we sequenced RNA from male and female whole abdomens and female ovary and gut tissue to identify sex and tissue specific gene expression profiles in H. melpomene. Using these expression profiles we compare sequence divergence and polymorphism, the strength of positive and negative selection and rates of adaptive evolution for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato.\n\nWe show that the rate of adaptive substitutions is higher for Z as compared to autosomal genes, but contrary to expectation it is also higher for male as compared to female biased genes. There is therefore mixed evidence that hemizygosity influences the rate of adaptive substitutions. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic specific tissue. Together our results provide limited support for fast-Z evolution. This contributes to a growing body of literature from other ZW systems that also provide mixed evidence for a fast-Z effect.

evolutionary biology↗

bioRxiv2017

Codon usage bias in animals: disentangling the effects of natural selection, effective population size and GC-biased gene conversion

Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT{leftrightarrow}GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

evolutionary biology↗