Louis Bernatchez

From tropical rainforests to scorching deserts: biogeography shapes climate-change plasticity in Australian rainbowfishes

This study examines how biogeographic history influences thermal tolerance and gene expression plasticity in Australian rainbowfishes across different climatic ecotypes.

Tropical rainforest versus savannah: Biome-specific landscape structure mediates adaptive strategies and resilience to environmental change

This study examines how biome-specific landscape structure influences adaptive strategies and resilience in tropical rainbowfish across rainforest and savannah ecosystems.

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback

The paper characterizes sex-biased gene expression in liver, gills, and brain of threespine sticklebacks, finding high differentiation in gills and liver but not brain, and links sex bias to dosage compensation and Y chromosome degeneration.

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

The paper identifies structural variants, SNPs, and indels in Atlantic salmon populations to explore their role in local adaptation.

Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements and duplication

The paper identifies deviant SNPs in whole-genome sequencing data from four species, showing their prevalence and impact on population genomic analyses.

Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

The paper uses genome-wide data to infer isolation-by-distance and population size history in coho salmon, identifying genes associated with latitude and potential osmoregulation roles.

A compendium of novel genomics technologies provides a chromosome-scale assembly and insights into the sex determining system of the Greenland Halibut

This study provides a chromosome-scale genome assembly for Greenland Halibut and identifies a nascent XY sex determination system with a putative Y-autosomal fusion.

Population structure and genomic evidence for local adaptation to freshwater and marine environments in anadromous Arctic Char (Salvelinus alpinus) throughout Nunavik, Quebec, Canada

This study identifies neutral and adaptive genomic variation in Arctic Char populations across Nunavik, revealing genetic structure and local adaptation to environmental factors like temperature and salinity.

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

The paper investigates how copy number variants (CNVs) drive genetic structure in capelin, finding associations with fitness traits, temperature, and population divergence, contrasting with SNP-based results.

The structural variation landscape in 492 Atlantic salmon genomes

This study identifies 15,483 high-confidence structural variants in 492 Atlantic salmon genomes, revealing their role in population structure, functional impact, and domestication traits.

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

This study shows that copy number variants (CNVs) better reveal genotype-temperature associations than SNPs in American lobster populations.

Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish

This study shows that standing genetic variation and chromosomal rearrangements contribute to local adaptation in capelin despite high gene flow.

Sex-specific co-expression networks and sex-biased gene expression in the salmonid Brook Charr Salvelinus fontinalis

The paper characterizes sex-specific co-expression networks and sex-biased gene expression in Brook Charr, identifying modules associated with growth, reproduction, and stress, and finding more transcripts in female networks with higher variation.

Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon

The paper investigates chromosomal fusions and genomic variation in Atlantic salmon to understand their role in local adaptation within a river system.

Intestinal microbiota of whitefish (Coregonus sp.) species pairs and their hybrids in natural and controlled environment.

This study compares the intestinal microbiota of wild and captive whitefish species pairs and their hybrids to assess microbiota variation and transmission patterns.

Parallel epigenetic modifications induced by hatchery rearing in a Pacific Salmon

This study identifies parallel epigenetic modifications in hatchery-reared Coho Salmon that may explain rapid fitness changes upon release, using RRBS to detect methylation differences.

Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

The paper shows that unbalanced sex ratios and sex-linked markers can cause false genetic differentiation signals in population studies, highlighting the need for sex information in genomic analyses.

Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

The paper introduces FAASG, an initiative to study salmonid genomes to understand phenotypic variation and improve aquaculture and conservation.

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook Charr Salvelinus fontinalis

This study identifies the sex chromosome in Brook Charr, characterizes heterochiasmy, and identifies QTL for growth, reproductive, and stress-related traits in salmonids.