Biology subjects

Desmarais, E.

Publications and source records attributed to Desmarais, E..

3 recordsLinked to original sources

bioRxiv2023

Divergence and gene flow history at two large chromosomal inversions involved in long-snouted seahorse ecotype formation

Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations over time until one arrangement becomes fixed. Many questions remain about how these different inversion polymorphisms arise, how the mechanisms responsible for their long-term maintenance interact, and ultimately how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is known to be subdivided into partially isolated lineages and marine-lagoon ecotypes differentiated by structural variation. Here, we aim to characterise these differences along the entire genome, and to reconstruct their history and role in ecotype formation. We generated a near chromosome-level reference genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. Combined with linked-read sequencing data, we found evidence for two megabase-scale chromosomal inversions showing contrasted allele frequency patterns across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one being likely maintained by divergent selection, and the other by associative overdominance. Haplotype combinations characterising Mediterranean ecotypes also suggest the existence of potential interactions between the two inversions, possibly driven by environment-dependent fitness effects. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels between the two inversions, with a likely impact on their long-term dynamics.

genomics↗

bioRxiv2018

Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by ancestry tracts

Understanding the evolutionary consequences of human-mediated introductions of domestic strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. In the brown trout Salmo trutta, decades of stocking practices have profoundly impacted the genetic makeup of wild populations. Small local Mediterranean populations in the Orb River watershed (Southern France) have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. However, the genomic impacts of two distinct sources of stocking (locally-derived vs divergent) on the genetic integrity of wild populations remain poorly understood. Here, we evaluate the extent of admixture from both domestic strains within three wild populations of this watershed, using 75,684 mapped SNPs obtained from double-digest restriction-site-associated DNA sequencing (dd-RADseq). Using a local ancestry inference approach, we provide a detailed picture of admixture patterns across the brown trout genome at the haplotype level. By analysing the chromosomal ancestry profiles of admixed individuals, we reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigree. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.

genomics↗

bioRxiv2016

A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species Salmo salar revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3,721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity ({pi}) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high density linkage map provides a useful genomic resource for future aquaculture, conservation and eco-evolutionary studies in brown trout.

genomics↗