Abstract
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 > 0.05), the outlier panel revealed genetic differentiation between the two regions (global FST = 0.161, p = 0.001; FCT = 0.263, p < 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 and catch volume), but also consider the preservation of adaptive variation.
Highlights
Stocks are the basic unit of management in fisheries and identifying them is a prerequisite to fisheries assessment and other management measures (Kritzer and Liu, 2014)
From a total of 239,995,133 reads obtained from restriction site-associated DNA sequencing (RADseq), the process_radtags program removed 264,906 (0.11%) low quality reads
Since samples with low number of reads tend to decrease the number of loci that can be genotyped from the dataset, we dropped six samples that had read counts
Summary
Stocks are the basic unit of management in fisheries and identifying them is a prerequisite to fisheries assessment and other management measures (Kritzer and Liu, 2014). Neutral markers provide insight on the genome-wide effects of gene flow and genetic drift, whereas non-neutral markers are more likely to reveal locus-specific effects of natural selection and how these change local gene pools (Holderegger et al, 2006; Russello et al, 2012; Mariani and Bekkevold, 2014) These markers have different functionality with regards to stock identification; while neutral markers are used to identify stocks based on the levels of gene flow and demographic independence, non-neutral markers are used to identify genetic groups based on adaptive genetic variation and patterns of local adaptation (Funk et al, 2012; Moore et al, 2014). Genetic assessment using non-neutral markers was difficult most especially for nonmodel organisms; with the advent of next-generation sequencing (NGS), these limitations had been largely overcome (Metzker, 2009; Davey and Blaxter, 2010; Willette et al, 2014; Andrews et al, 2016)
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