Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus

Abstract

Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole‐genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range‐wide pattern of isolation‐by‐distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long‐term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble beeBombus vosnesenskii

“…WGR data is a powerful tool for detecting adaptation and can overcome potential shortcomings of previously used approaches such as reduced representation sequencing (e.g., RADseq) (Jackson et al 2020), which may not detect all possible targets of selection when linkage blocks are small (Fuentes-Pardo & Ruzzante, 2017), as in bumble bees (Stolle et al, 2011). Whole genome data enables analyses that infer species’ demographic histories which can complement contemporary landscape genomics (Beichman, Huerta-Sanchez, & Lohmueller, 2018; de Greef et al, 2022; Iannucci et al, 2021). First, based on prior results of near-panmixia from other genetic markers, we examine population structure and test for any influence of spatial-environmental variation that may not have been apparent in earlier studies.…”

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

“…RADseq) (Jackson et al, 2020), which may not detect all possible targets of selection when linkage blocks are small (Fuentes‐Pardo & Ruzzante, 2017), as in bumble bees (Stolle et al, 2011). Whole genome data enable analyses that infer species' demographic histories, which can complement contemporary landscape genomics (Beichman et al, 2018; de Greef et al, 2022; Iannucci et al, 2021). First, we examine population structure, and based on previous studies using other markers (Jackson et al, 2018; Lozier et al, 2011), we expect to detect high levels of gene flow in B. vosnesenskii .…”

Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters

“…After all filtering steps, one BES individual (Figure S1C) kept a small fraction of the raw reads (6.65%, 2.73X coverage) and was discarded from further analysis. Mean sequencing depth was 10.11X (Figure S1B), which is considered an intermediate coverage level (Bourgeouis & Warren, 2021;Fuentes-Pardo & Ruzzante, 2017), and similar depth levels were used in other population genomic studies on cetaceans based on whole genome resequencing (Cerca et al, 2022;de Greef et al, 2022;Zhou et al, 2018). Scaffold coverage comparisons between male and female sequencing data (Figure S2) identified 47 sex associated scaffolds (122.3 Mb), which were subsequently removed from downstream analysis.…”