Abstract
Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise FST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.
Highlights
Knowledge on the ecological and evolutionary processes influencing biodiversity and dispersal of marine organisms is fundamental to the understanding of their geneticHow to cite this article Zhang B-D, Xue D-X, Li Y-L, Liu J-X. 2019
To investigate the extent of population structuring in overwintering populations of L. polyactis, DAPC was performed with prior information of sampling locations (K = 4) as the DAPC without prior did not reveal any genetic structure
A similar pattern was evident in the analyses of ADMIXTURE (Fig. 3) and all four populations were split into two groups: the East China Sea group (YD) and an admixed Yellow Sea group consisting of YA, YB, YC, which was consistent with the results revealed using DAPC
Summary
Knowledge on the ecological and evolutionary processes influencing biodiversity and dispersal of marine organisms is fundamental to the understanding of their geneticHow to cite this article Zhang B-D, Xue D-X, Li Y-L, Liu J-X. 2019. Genetic data from putatively neutral markers such as microsatellites, mitochondrial DNA and amplified fragment length polymorphisms (AFLPs) have been extensively used in population genetic studies of marine fishes, these applications have shown the main limitation in reflecting effects of selection or environmental influences (Billington & Hebert, 1990; Jarne & Lagoda, 1996; Campbell, Duchesne & Bernatchez, 2003) Genome scan approaches, such as restriction site-associated DNA sequencing (RAD-seq), present a framework for identifications of genome-wide SNP markers in natural populations and elucidating directional selections by identifying outlier loci with elevated levels of genetic differentiation (Storz, 2005; Miller et al, 2007; Allendorf, Hohenlohe & Luikart, 2010; Etter et al, 2011). Babin et al (2017) evaluated the effects of spatially varying selection in shaping genetic variation across the genome of American Eel (Anguilla rostrata) and outlier loci detected were found to be significantly associated with environmental variables such as latitude, longitude as well as temperature
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