Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

Abstract

Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double‐digest restriction site‐associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross‐hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.

The genic view of hybridization in the Anthropocene

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Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of fine-scale adaptation and a temperature-associated cline amid panmixia

“…Even when populations display little to no neutral genomic differentiation, adaptive population structure can be detected through outlier-based methods (e.g. albacore (Vaux et al, 2021)) or environment association methods (e.g. American lobster (Benestan et al, 2016), summer flounder (Hoey and Pinsky, 2018), or greenlip abalone (Sandoval-Castillo et al, 2018)).…”

Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish

“…Additionally, RADseq has proven to be an effective tool in identifying and assessing intraspecific differentiation, especially in 1 Vermilion and sunset rockfish are scheduled for a stock assessment in 2021 under the auspices of the PFMC where the two species will be assessed collectively as a complex. cases where traditional markers (i.e., mtDNA and microsatellites) failed to detect signals of structure (Bohling et al 2019;Gaither et al 2020;Longo et al 2020;Morgan et al 2018;Vaux et al 2021;Vendrami et al 2019). Although distinguishing between clear taxonomic units at the level of species is paramount, the identification of significant intraspecific population genetic structure is also important for species-specific management (Bernatchez et al 2017;Hauser and Seeb 2008;Spies and Punt 2015;Waples et al 2008).…”