A cold-water fish striving in a warming ocean: Insights from whole-genome sequencing of the Greenland halibut in the Northwest Atlantic

Abstract

Characterizing the extent of genetic differentiation among individuals and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. The Greenland Halibut is one of the main demersal fish species to be commercially exploited in Eastern Canada, and accurate information on geographic population structure and local adaptation is required to ensure the long-term presence of this species. We generated high-quality whole-genome sequencing data for 1,297 Greenland Halibut sampled across 32 locations throughout the Northwest Atlantic (from Arctic Canadian and Greenlandic coasts to the Gulf of St Lawrence). Population genetic structure was analyzed, revealing an absence of population differentiation between Canada and west Greenland but significant genetic differentiation between the Gulf of Saint Lawrence and the remainder of the Northwest Atlantic. Except for Gulf of Saint Lawrence, Greenland Halibut thus appear to be panmictic throughout the Northwest Atlantic. Environmental Association Analyses revealed that the environment explained up to 51 % might be replaced by 51% of the differentiation observed between the two stocks, with both ocean-bottom and surface variables (e.g., temperature and oxygen) involved in the observed genomic differentiation. Altogether, these results indicate that phenotypic differences previously observed between the Gulf of Saint Lawrence and the Northwest Atlantic likely resulted from functional adaptive divergence to their respective environmental conditions. Using coalescent simulations, we also assessed how high levels of migration between the two stocks would allow Greenland Halibut to potentially escape unfavorable environmental conditions in the Gulf of Saint Lawrence. In addition to supporting the management of this important exploited species, this work highlights the utility of using comprehensive genomic datasets to characterize the effects of climate change across a wider range of species.

Connectivity of Greenland halibut in the northwestern Atlantic Ocean inferred from otolith chemistry

“…This study supports the genetic study of Roy et al (2014), demonstrating the existence of a panmixia population of Greenland Halibut from the NWA. Similar results have also been observed through a genomic population assessment based on whole-genome resequencing (SNP) (Ferchaud et al, 2022).…”

Population genomics, life‐history tactics, and mixed‐stock subsistence fisheries in the northernmost American Atlantic salmon populations

“…Demographic inferences based on coalescence should be conducted to estimate current demographic parameters between these two rivers before we can conclude on their demographic independence (e.g. Dorant et al., 2022; Ferchaud et al., 2022). We therefore recommend that, in a management context, it is best to proceed with caution and consider these rivers as two populations at least until more data (e.g., based on coalescence analysis) is available on their demographic independence.…”

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

“…These results support those from Jorde et al (2015) using microsatellites for the presence of a population on Flemish Cap, but also reveal genetic differentiation and complexity along the continental shelf using thousands of genome-wide SNPs. Multiple studies exposed structure using population genomics in marine vertebrates or invertebrates in the Northwest Atlantic, challenging the paradigm of general panmixia for many marine species (e.g., Benestan et al 2015; Van Wyngaarden et al 2017; Kess et al 2021; Dorant et al 2022; Ferchaud et al 2022; Fuentes-Pardo et al 2023; Jones et al 2023). We build on this body of evidence with an uniquely high genomic- and geographic-resolution study for a meroplanktonic species sampled across their northwest Atlantic distribution in addition to samples in the Eastern Arctic.…”

“…Still, environmental gradients can lead to local adaptation and genetic heterogeneity in the ocean, even under conditions of substantial migration and gene flow (Nielsen et al 2009; Tigano and Friesen 2016). Genotype-environment association approaches have revealed candidate adaptive loci among many taxa (e.g., Benestan et al 2016; Jeffery et al 2018; Kess et al 2021; Ferchaud et al 2022), indicating instances of local adaptation (Savolainen et al 2013; Rellstab et al 2015). Thus, while populations might appear homogeneous when assessing neutral loci, the same may not hold true for adaptive regions of their genome (Conover et al 2006; Gagnaire et al 2015).…”