Biology subjects

Merel, V.

Publications and source records attributed to Merel, V..

8 recordsLinked to original sources

bioRxiv2026

Drivers of tandem repeats variation within and between stick insect genomes

Tandemly repeated sequences are noncoding, highly variable, yet integral components of eukaryotic genomes. Empirical research has so far largely focused on a few well-characterized, functional tandem repeats (TRs) or documented the broad diversity and rapid evolution of these repeats without explicitly testing the forces driving their evolution. By characterizing TR abundance and TR sequence composition within and between chromosomes and species in the stick insect genus Timema, we uncover that TR loads are enriched in genomic regions of high recombination but tend to be reduced in species with higher effective population sizes. These results suggest that there is a mutational effect of recombination that generates increased TR loads and that the bulk of TRs experience weak selection, leading to their rapid turnover over short evolutionary timescales. Finally, comparisons of centromere and non-centromere TRs reveal that the rapid divergence of centromeres is best explained by the combination of the fast-evolving nature of TRs per se and centromere-specific evolutionary forces. Overall, this study provides the first in-depth investigation of genome-wide TR evolution, while integrating the effects of recombination, genetic drift, and centromeric position along the genome.

evolutionary biology↗

bioRxiv2026

Alternative splicing shapes sexual dimorphism and erodes following the loss of sex in stick insects

Sexually dimorphic traits emerge from divergent selective pressures acting on males and females and are facilitated by gene regulatory mechanisms. While gene expression differences have been the subject of considerable focus in the evolution of sexual dimorphism, other regulatory processes remain comparatively understudied. One such mechanism is alternative splicing, whereby a single gene can encode multiple distinct transcripts, which can lead to functional diversification of the proteome. Leveraging long-read PacBio Iso-sequencing, we examine patterns of sex differences in gene expression and alternative splicing under different selection regimes. Alternative splicing is widespread in Timema, with the greatest isoform complexity found in the male gonad tissue. We observe similar rates of sex differences in gene expression and splicing, and a core set of genes involved in sexual differentiation and germline development that have conserved differential splicing patterns across the Timema phylogeny. Beyond this, however, differentially spliced genes undergo faster lineage-specific turnover and are subject to greater pleiotropic and purifying constraints than differentially expressed genes. Following the transition from sexual reproduction to asexuality, there is a systematic reduction in isoform diversity and erosion of sex-specific splicing variation. Taken together, our findings suggest a role for sexual selection in maintaining splicing complexity in sexual Timema species.

evolutionary biology↗

bioRxiv2025

Hybridogenesis as an intermediate step between sexual reproduction and parthenogenesis

Many organisms reproduce through non-canonical modes such as parthenogenesis or hybridogenesis (clonal transmission of one parents chromosomes), but whether these arise abruptly or stepwise from each other remains unclear. We address this in the stick-insect genus Bacillus, which harbors several hybrid lineages with diverse reproductive modes. From haplotype-resolved phylogenies of >500 wild-caught individuals, we infer a single, recent ([~]8,000 years) origin of all hybrids. The ancestral hybrid reproduced via hybridogenesis, which subsequently diversified into parthenogenesis and, twice independently, into triploid lineages. Laboratory crosses recapitulate this trajectory, where each step facilitated the next. These findings reveal how a single genomic perturbation can act as a catalyst for evolutionary innovation, turning the loss of sex into a driver of diversification rather than a dead end.

evolutionary biology↗

bioRxiv2024

Functional monocentricity with holocentric characteristics andchromosome-specific centromeres in a stick insect

Centromeres are specialized genomic regions that are critical for chromosome segregation in eukaryotes. However, how the diversity of centromeres evolved, ranging from localized centromeres in monocentric species to complex chromosome-wide distributed centromere regions in holocentric species, remains elusive. Our cellular and genomic analyses in Timema stick insects reveal that within cell variation of the major centromere protein CenH3 recapitulates the variation typically observed across species. While CenH3-containing nucleosomes are distributed in a monocentric fashion on autosomes and bind tandem repeat sequences specific to individual or small groups of chromosomes, they exhibit a holocentric-like distribution on the sex chromosome and bind to more complex intergenic regions. Despite this contrasting distribution, all chromosomes, including the sex chromosome, attach to spindle microtubules at a single location, marking the first instance of a functionally monocentric species with holocentric-like attributes. Together, our findings highlight the potential for gradual transitions towards holocentricity or CenH3-independent centromere determination, and help to understand the rapid centromere sequence divergence between species.

evolutionary biology↗

bioRxiv2024

Recent neo-X and Y sex chromosomes in an ant cricket

In eukaryotes with separate sexes, sex determination often involves heteromorphic sex chromosomes which have diverged as a consequence of recombination suppression. In species with very old heteromorphic sex chromosomes, mechanisms such as dosage compensation and meiotic sex chromosome inactivation adjust for the fact that sex chromosomes occur as a single copy in the heterogametic sex. However, how such mechanisms evolve remains largely unknown because species with young sex chromosomes characterised by recent recombination suppression remain understudied. We discovered such young neo-sex chromosomes in the ant cricket Myrmecophilus myrmecophilus, which displays a neo-XY system. We generated a chromosomal-level assembly of the female genome and compared it to male genomic data and identified four evolutionary strata on the X, with varying degrees of Y chromosome degeneration. Phylogenetic studies and genomic comparisons with closely related species revealed two cases of taxonomic synonymies and that the Myrmecophilus neo-sex chromosomes likely evolved approximately 7 million years ago from an X-autosome fusion. The X strata subsequently emerged as a consequence of two localised events of recombination suppression. Ant crickets thus represent a promising new model for studying the early stages of sex chromosome degeneration and the establishment of processes such as dosage compensation or meiotic sex chromosome inactivation.

evolutionary biology↗

bioRxiv2024

Relaxed purifying selection is associated with an accumulation of transposable elements in flies

Although the mechanisms driving the evolution of genome size are not yet fully understood, one potentially important factor is the dynamics of the accumulation of mobile selfish genetic elements called transposable elements (TEs). Since most of these sequences are neutral or slightly deleterious, a negative correlation between genome size and selection efficacy is expected. However, previous studies based on empirical data from closely related species with contrasting life history traits (thought to result in contrasting levels of selection efficacy) have yielded inconsistent results, leaving this issue controversial. In this study, we perform the first large-scale analysis of the effect of drift on genome size evolution, without any prior assumption about the amount of drift in each sampled species. We reconstructed a phylogeny based on whole-genome data (2,242 genes) for 77 Drosophilid species to examine correlations between genome size, TE content, and measures of selection efficacy (especially using dN/dS ratios of non-synonymous to synonymous divergence). We highlight a strong phylogenetic inertia in genome size and confirm that TEs are the major components of genome size. Using an integrative approach that controls for shared history, we find that genome-wide dN/dS are strongly positively correlated with genome size and TE content, particularly in GC-poor genes. This study highlights the critical importance of controlling for heterogeneity in base composition when testing the controversial correlation between evolutionary rates and genome size. Furthermore, our review of previous studies reveals that the absence of evidence for TE accumulation in association with increased genetic drift may be attributed to a secondary effect of changes in life history traits on TE dynamics. In conclusion, this work provides evidence for TE proliferation in fly genomes when purifying selection is reduced and genetic drift increases, shedding new light on the role of transposable elements and genetic drift in the evolution of genome architecture.

evolutionary biology↗

bioRxiv2020

The worldwide invasion of Drosophila suzukii isaccompanied by a large increase of transposable elementload and a small number of putatively adaptive insertions

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we portrayed the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations (of D. suzukii). We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity [Formula] a proxy of effective population size. We did not find any correlation between TE contents and bio-climatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 5,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.

evolutionary biology↗

bioRxiv2020

Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species

BackgroundAdaptation to rapid environmental changes must occur within a short time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and successfully adapted to novel environmental conditions. Here we investigated how invasive and non-invasive populations of D. suzukii deal with an oxidative stress at both the phenotypic and molecular level. We also investigated the impact of transposable element insertions on the differential gene expression between genotypes in response to oxidative stress. ResultsInvasive populations lived longer in the untreated condition than non-invasive Japanese populations. As expected, lifespan was greatly reduced following exposure to paraquat, but this reduction varied among genotypes (a genotype by environment interaction, GEI) with invasive genotypes appearing more affected by exposure than non-invasive genotypes. We also performed transcriptomic sequencing of selected genotypes upon and without paraquat and detected a large number of genes differentially expressed, distinguishing the genotypes in the untreated environment. While a small core set of genes were differentially expressed by all genotypes following paraquat exposure, much of the response of each population was unique. Interestingly, we identified a set of genes presenting genotype by environment interaction (GEI). Many of these differences may reflect signatures of history of past adaptation. Transposable elements (TEs) were not activated after oxidative stress and differentially expressed (DE) genes were significantly depleted of TEs. ConclusionIn the decade since the invasion from the south of Asia, invasive populations of D. suzukii have diverged from populations in the native area regarding their genetic response to oxidative stress. This suggests that such transcriptomic changes could be involved in the rapid adaptation to local environments.

genomics↗