Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

Abstract

Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.

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

“…Lenhert et al, 2019; Miller et al, 2019) and over large geographic distances (e.g. Clucas, Lou, Therkildsen & Kovach, 2019). Arctic Char is expected to use preferred habitats based on temperature, salinity, and prey availability (Spares et al, 2012, 2015; Harris et al 2020).…”

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research

“…The whole-genome analysis provided unprecedented resolution for characterizing geographic differentiation and revealed strong signatures of divergent selection that had not been detectable in prior studies using less dense genome sampling like microsatellites, RAD-seq, and SNP arrays (Clucas et al, 2019). Our raw sequence data amounted to almost 600 Gb and GEOME provided a really useful framework for organizing and archiving the metadata behind our 462 fastq files prior to SRA submission.…”

Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

“…Detection of genetic structure in marine species remains challenging due to the often large effective population sizes and high levels of gene flow facilitated by the scarcity of physical barriers, which lead to genomic homogenization (Danancher & Garcia-Vazquez, 2011;do Prado et al, 2018;Zhao et al, 2018). However, genetic differentiation can be enhanced by oceanic features such as current systems, fronts, gyres and eddies (Nielsen et al, 2004;Blanco-González et al, 2016;Vera et al, 2016;Xuereb et al, 2018), and natural selection in response to environmental variation (Vilas et al, 2015;Clucas et al, 2019;Jiménez-Mena et al, 2020). Distinguishing between neutral and adaptive genetic variation in the marine landscape has become a central issue in conservation biology, allowing for interpreting genetic variation in both historical/demographic and adaptive terms (Nielsen et al, 2009;Bernatchez, 2016).…”