DOI: 10.5061/dryad.4qrfj6qbx
title: Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines

description: Stock identification and delineation are important in the management and
 conservation of marine resources. These were highlighted as priority
 research areas for Bali sardinella (Sardinella lemuru) which is among the
 most commercially important fishery resources in the Philippines. Previous
 studies have already assessed the stocks of S. lemuru between Northern
 Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding
 conflicting results. Phenotypic variation suggests distinct stocks between
 the two regions, while mitochondrial DNA did not detect evidence of
 genetic differentiation for this high gene flow species. This paper tested
 the hypothesis of regional structuring using genome-wide single nucleotide
 polymorphisms (SNPs) acquired through restriction-site associated DNA
 sequencing (RADseq). We examined patterns of population genomic structure
 using a full panel of 3,573 loci, which was then partitioned into a
 neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar
 inferences were obtained from the full and neutral panels, which were
 contrary to the inferences from the outlier panel. While the full and
 neutral panels suggested a panmictic population (global FST ~ 0, p
 &gt; 0.05), the outlier panel revealed genetic differentiation between
 the two regions (global FST = 0.161, p = 0.001; FCT = 0.263, p &lt;
 0.05). This indicated that while gene flow is apparent, selective forces
 due to environmental heterogeneity between the two regions play a role in
 maintaining adaptive variation. Annotation of the outlier loci returned
 five genes that were mostly involved in organismal development. Meanwhile,
 three unannotated loci had allele frequencies that correlated with sea
 surface temperature. Overall, our results provided support for local
 adaptation despite high levels of gene flow in S. lemuru. Management
 therefore should not only focus on demographic parameters (e.g., stock
 size, catch volume), but also consider the preservation of adaptive
 variation.
description: <em>Sardinella lemuru</em> samples were collected
 from embayments found along the northern coast of Mindanao covering two
 geopolitical regions, Northern Mindanao Region (NMR) and Northern
 Zamboanga Peninsula (NZP). Dorsal muscle tissue was excised from each
 sample, preserved in a nucleotide stabilization solution, and then sent to
 Beijing Genomics Institute (BGI) for DNA extraction, library preparation,
 and restriction site-associated DNA sequencing (RADseq).
 The genomic data was processed using the STACKS bioinformatics
 pipeline. Optimization was first performed on a subset of samples wherein
 the optimal genotyping parameters were determined following several
 criteria. These parameters were then used on the full dataset to obtain
 the single nucleotide polymoprhisms (SNPs) for population genomics
 analyses. The SNPs were subjected to additional filters
 (e.g., missing data, Hardy-Weinberg Equilibrium, Linkage Disequilibrium),
 resulting to the full panel. This was then subjected to several outlier
 screening methods (Arlequin, BayeScan, fstHet, OutFLANK, and pcadapt);
 loci that were identified as outliers by at least one method were removed
 from the full panel to generate the neutral panel, while loci that were
 detected as outliers by at least two screening methods were used to
 generate the outlier panel. The three SNP panels (full,
 neutral, outlier) were then subjected to population genomics analyses,
 such as the calculation of genetic diversity (e.g., no. of alleles,
 observed and expected heterozygosity), determination of spatial pattern of
 genetic structure using ordination methods (e.g., PCA, DAPC), calculation
 of the magnitude of genetic differentiation using pairwise
 F<sub>ST</sub>, and testing hypotheses of genetic structure
 using AMOVA. Loci under the outlier panel were also
 extracted from the STACKS catalog and were identified using NCBI-BLAST.
 Functional annotation of the identified sequences was done using the
 UniProt database. Moreover, the association between the outlier loci and
 environmental parameters were elucidated by correlating the allele
 frequencies with remotely sensed oceanographic parameters, namely sea
 surface temperature (SST), chlorophyll-a (chl-a), and particulate organic
 carbon (POC).
description: A. DATA_Sample_Metadata.csv - contains the sampling location and
 collection date B. DATA_Stacks_Optimization - contains
 all the files used for visual diagnostics to guide selection of the
 optimal genotyping parameters in STACKS<br>      
  /1_FilteredReadCount.csv<br>        /2_STACKS_m.csv<br>      
  /3_STACKS_Mn.csv<br>        <br>C. DATA_SNP_Panels - contains
 the SNP panels (in GENEPOP format) used in the analyses <br>      
  /1_Raw_Panel.gen    <br>        /2_Full_Panel.gen<br>      
  /3_Neutral_Panel.gen<br>        /4_Outlier_Panel.gen
 D. SCRIPT_PopSNPs - Contains all information pertinent to the
 analyses done.<br>        /1_PopSNPs.Rmd - the R Markdown
 file<br>        /2_PopSNPs.html - output of the markdown file in
 .html format