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.

Genetic data was generated using double digest restriction site-associated DNA sequencing (ddRADseq). Full methods are provided in the main text and Appendix S2 contained within this repository.

# pacific_albacore_ddRADseq
Commands and input files for population genetic analysis of Pacific Albacore using ddRADseq

# albacore_STACKS_and_filtering
Lists input commands used for STACKS and BWA, and subsequent filtering in VCFtools, plink, and paralog-finder (HDplot).

# maps
Maps used to select individuals and populations in STACKS runs.

# excluded_loci
Lists used to exclude certain loci in STACKS runs.

# plink-ld
Ped and map files used by plink to estimate loci in LD.

# vcftools-hwe
Maps used to select subsets of individuals for estimating HWP.

# R
R files for running loci filtering and population genetic analyses (e.g. whoa, adegenet, fsthet). I recommend viewing original source GitHub pages and tutorials noted in each R file credits.

# Sampling, and genotype and loci fasta files
Sampling and sequence spreadsheets, genetic data (vcf, genepop, and structure genotype files, and the fasta consensus file for the 84 putatively adaptive loci), and full results for genome scan program and Fst analyses are available in this Dryad repository.

# Demultiplexed reads
Demultiplexed forward and reverse DNA sequence reads for the albacore sequenced in this study are openly available on the NCBI sequence read archive (SRA) under: PRJNA579774, http://www.ncbi.nlm.nih.gov/bioproject/579774

# Raw Illumina reads
Available on request from Kathleen O'Malley (State Fisheries Genomics Lab, Oregon State University), https://agsci.oregonstate.edu/state-fisheries-lab/people

# Further information
See this page: https://sites.google.com/view/evauxlution/data