Biology subjects

Brazier, T.

Publications and source records attributed to Brazier, T..

4 recordsLinked to original sources

bioRxiv2024

Leveraging whole genomes, mitochondrial DNA, and haploblocks to decipher complex demographic histories: an example from a broadly admixed arctic fish

The study of phylogeography has transitioned from mitochondrial haplotypes to genome-wide analyses, blurring the line between this field and population genomics. Whole-genome sequencing offers the opportunity to join use both and provides the density of markers necessary to investigate genetic linkage and recombination along the genome. This facilitates the unraveling of complex demographic histories of admixture between divergent lineages, as is often the case in species evolving in recently deglaciated habitats. In this study, we sequenced 1120 Arctic Char genomes from 33 populations across Canada and Western Greenland to characterize patterns of genetic variation and diversity, and how they are shaped by hybridization between the Arctic and Atlantic glacial lineages. Several lines of evidence supported mito-nuclear discordance in lineage distribution, with all Canadian populations under the 66th parallel being characterized by introgression from the Atlantic lineage, leading to higher nuclear genetic diversity. By scanning the genome using local PCAs, we identified putative low-recombining haploblocks as local ancestry tracts from either lineage and described the impacts of recombination on the introgression landscape in admixed populations. Finally, we inferred conflicting origins of recolonization using whole genomes vs. ancestry tracts for the Arctic lineage, suggesting that haplotypes sheltered from introgression by low recombination could enlighten complex post-glacial histories. Overall, we argue that Whole-Genome Sequencing, even at low depths of coverage, provides a versatile approach to the study of phylogeographic dynamics.

evolutionary biology↗

bioRxiv2024

The geometry of gametic dispersal in a flying mammal, Rhinolophus hipposideros

Dispersal influences population and evolutionary dynamics, with effects that depend on the dispersal strategies through which gene flow occurs. In some species, mating partners move exclusively for mating, dispersing genes but not individuals. This is the case in many bat species, of which the lesser horseshoe bat (Rhinolophus hipposideros) shows a genetic structure at a fine spatial scale suggesting restricted dispersal. We investigated how natal and mating dispersal shape gene flow in this species in two metapopulations using paternity and population assignments. Half of the inferred paternities were intra-colonial and gave an estimate of the mean mating dispersal distance of around 11 km, explaining the observed genetic structure. Complete gametic dispersal distances were further estimated by combining natal with mating dispersal distances. The resulting gametic dispersal kernels showed a mean distance of around 20 km and a fat-tailed distribution typical of an excess of long-distance dispersal movements. It is the first time that natal and mating dispersal distances have been separately estimated and then combined in animals, documenting quantitatively how mating dispersal decorrelates gene and individual flows. It is important to consider this mechanism to explain dispersal evolution.

evolutionary biology↗

bioRxiv2023

Ubiquitous recombination gradients within plant genic regions shaped by recombination hotspots

During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5-3 untranslated regions, are enriched in hotspots, but this has been characterized in a handful of species only. We also lack a clear description of fine-scale variation in recombination rates within genic regions and little is known about hotspot position and intensity in plants. To address this question we constructed fine-scale recombination maps from genetic polymorphism data and inferred recombination hotspots in eleven plant species. We detected gradients of recombination both in 5 and 3 of genic regions in most species, yet gradients varied in intensity and shape depending on specific hotspot locations and gene structure. To further characterize recombination gradients, we decomposed them according to gene structure by rank and number of exons. We generalized the previously observed pattern that recombination hotspots are organized around the boundaries of coding sequences, especially 5 promoters. However, our results also provided new insight into the relative importance of the 3 end of genes in some species and the possible location of hotspots away from genic regions in some species. Variation among species seemed driven more by hotspot location among and within genes than by differences in size or intensity among species. Our results shed light on the variation in recombination rates at a very fine scale, more detailed than whole genome averaged estimates used so far, revealing the diversity and complexity of genic recombination gradients emerging from the interaction between hotspot location and gene structure.

genomics↗

bioRxiv2022

Diversity and determinants of recombination landscapes in flowering plants

During meiosis, crossover rates are not randomly distributed along the chromosome and therefore they locally influence the creation of novel genotypes and the efficacy of selection. To date, the broad diversity of recombination landscapes among plants has rarely been investigated, undermining the overall understanding of the constraints driving the evolution of crossover frequency and distribution. The determinants that shape the local crossover rate and the diversity of the resulting landscapes among species and chromosomes still need to be assessed in a formal comparative genomic approach. We gathered genetic maps and genomes for 57 flowering plant species, corresponding to 665 chromosomes, for which we estimated large-scale recombination landscapes. Chromosome length drives the basal recombination rate for each species, but within species we were intrigued to notice that the chromosome-wide recombination rate is proportional to the relative size of the chromosome. Moreover, for larger chromosomes, crossovers tend to accumulate at the ends of the chromosome leaving the central regions as recombination-free regions. Based on identified crossover patterns and testable predictions, we proposed a conceptual model explaining the broad-scale distribution of crossovers where both telomeres and centromeres are important. Finally, we qualitatively identified two recurrent crossover patterns among species and highlighted that these patterns globally correspond to the underlying gene distribution. In addition to the positive correlation between recombination and gene density, we argue that crossover patterns are essential for the efficiency of chromosomal genetic shuffling, even though the ultimate evolutionary potential forged by the diversity of recombination landscapes remains an open question.

evolutionary biology↗