Supplementary Material for: Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

Supplementary Material for: Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

Files include a spreadsheet of samples and sequencing success (Appendix S1), a document containing supplementary methods, references, tables and figures (Appendix S2), lists of identified outlier loci per genome scan program (Appendix S3), full pairwise F_ST results for the 12 sample areas (Appendix S4), and genetic data files (genepop and vcf genotype files, and fasta consensus files for outlier loci). Commands used for stacks and other software, and required input files (e.g. population maps, lists of excluded loci) are included as well, and these are also hosted on GitHub: https://github.com/fvaux/pacific_albacore_ddRADseq

Paper 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, 2 individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, 4 or 5 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 and 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.