Biology subjects

Mousset, S.

Publications and source records attributed to Mousset, S..

3 recordsLinked to original sources

bioRxiv2022

Modeling the genetic footprint of fluctuating balancing selection: From the local to the genomic scale

Natural selection not only affects the actual loci under selection but also leaves "footprints" in patterns of genetic variation in linked genetic regions. This offers exciting opportunities for inferring selection and for understanding the processes shaping levels of genetic variation in natural populations. Here we develop analytical approximations based on coalescent theory to characterize the genetic footprint of a complex, but potentially common type of natural selection: balancing selection with seasonally fluctuating allele frequencies. We show that seasonal allele frequency fluctuations can have important (and partly unexpected) consequences for the genetic footprint of balancing selection. As also confirmed by stochastic simulations, fluctuating balancing selection generally leads to an increase in genetic diversity close to the selected site, the effect of balancing selection, but reduces diversity further away from the selected site, which is a consequence of the allele-frequency fluctuations effectively producing recurrent bottlenecks of allelic backgrounds. This negative effect usually outweighs the positive effect when averaging diversity levels across the entire chromosome. Strong fluctuating balancing selection even induces a loss of genetic variation in unlinked regions, e.g. on different chromosomes. If many loci in the genome are simultaneously under fluctuating balancing selection this could lead to substantial genome-wide reductions in genetic diversity. This may be the case, even if allele-frequency fluctuations are so small that individual footprints are hard to detect. Thus, together with genetic drift, selective sweeps and background selection, fluctuating selection could be one of the major forces shaping levels of genetic diversity in natural populations. Article summaryIn some species with multiple generations per year, many loci in the genome experience strong seasonally fluctuating selection, in some cases with stable maintenance of polymorphism. Here we investigate the consequences for levels of genetic diversity at linked neutral sites. Using analytical approximations and stochastic simulations, we find a characteristic local genetic footprint with a diversity peak around the selected site and a diversity valley further away and a substantial reduction in diversity levels chromosome-wide and even genome-wide.

evolutionary biology↗

bioRxiv2019

VolcanoFinder: genomic scans for adaptive introgression

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method--VolcanoFinder--to detect recent events of adaptive introgression using polymorphism data from the recipient species only.\n\nVolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity.\n\nUsing coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.\n\nAuthor summaryThe process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.

evolutionary biology↗

bioRxiv2018

Contrasted sex chromosome evolution in primates with and without sexual dimorphism

AO_SCPLOWBSTRACTC_SCPLOWSex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex chromosome biology both from a functional (i.e. number of sex-linked genes) and evolutionary perspective (i.e. extent of Y degeneration and X-Y heteromorphy). The evolution of the pseudoautosomal boundary (PAB) - the limit between the recombining and the non-recombining regions of the sex chromosomes - is well documented in haplorrhines (apes and monkeys) but not in strepsirrhines (lemurs and lorises), which represent almost 30% of all primates. Here we studied the PAB of seven species representing the main strepsirrhine lineages by sequencing a male and a female genome in each species and using sex differences in coverage to identify the PAB. We found that during primate evolution, the PAB has remained unchanged in strepsirrhines whereas several recombination suppression events moved the PAB and shortened the pseudoautosomal region in haplorrhines. Strepsirrhines are well known to have much lower sexual dimorphism than haplorrhines. We suggest that mutations with antagonistic effects between males and females have driven recombination suppression and PAB evolution in haplorrhines. Our work supports the view that sexually antagonistic mutations have influenced the evolution of sex chromosomes in primates.

evolutionary biology↗