DOI: 10.5061/dryad.6djh9w103
title: Supplementary Material for: Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

description: 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 FST 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.
description: 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.
description: # pacific_albacore_ddRADseq<br> Commands and input files
 for population genetic analysis of Pacific Albacore using
 ddRADseq # albacore_STACKS_and_filtering<br>
 Lists input commands used for STACKS and BWA, and subsequent filtering in
 VCFtools, plink, and paralog-finder (HDplot). #
 maps<br> Maps used to select individuals and populations in STACKS
 runs. # excluded_loci<br> Lists used to exclude
 certain loci in STACKS runs. # plink-ld<br> Ped
 and map files used by plink to estimate loci in LD. #
 vcftools-hwe<br> Maps used to select subsets of individuals for
 estimating HWP. # R<br> 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<br> 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<br> 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<br> Available on request from Kathleen O'Malley
 (State Fisheries Genomics Lab, Oregon State University),
 https://agsci.oregonstate.edu/state-fisheries-lab/people
 # Further information<br> See this page:
 https://sites.google.com/view/evauxlution/data