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      Spatial Genetic Structure and Diversity of Large Yellow Croaker (Larimichthys crocea) from the Southern Yellow Sea and North-Central East China Sea: Implications for Conservation and Stock Enhancement

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      MDPI AG

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          Abstract

          As a wild resource, the large yellow croaker Larimichthys crocea has been seriously threatened since the mid-1980s. Owing to the implementation of protection measures, such as the establishment of a protection zone, fishing prohibitions, restocking programs and successful mariculture, its resources have gradually recovered year by year. Limited by the low spatial resolution and incomplete spatial coverage of sampling stations, the spatial genetic structure and diversity of large yellow croakers from the southern Yellow Sea and north-central East China Sea remains unclear. In order to evaluate the genetic diversity status of this wild stock, 22 wild sites were collected from the southern Yellow Sea and north-central East China Sea and analyzed by investigating genetic variability and its population structure using mitochondrial COI sequence in this study. Among the 662 sequences, a total of 71 different haplotypes were defined. The haplotype diversity (h) and nucleotide diversity (π) values were 0.644~1.000 and 0.00220~0.00473 respectively. The highest h and π occurred in the southern Yellow Sea (YS). AMOVA analysis showed no genetic differentiation among those 22 sites after Bonferroni correction. By comparing with previous studies, the croaker has maintained relatively steady genetic diversity in recent years. Our result also suggested that the croakers in the South Yellow Sea and north-central East China Sea belonged to the same group. Thus, they can be released as a management unit without regard for heterogenicity among those in the sea area. The YS populations can serve as parents for released fish fries in the South Yellow Sea and north-central East China Sea.

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          MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

          Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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            Arlequin (version 3.0): An integrated software package for population genetics data analysis

            Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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              Molecular Evolutionary Genetics

                Author and article information

                Journal
                WATEGH
                Water
                Water
                MDPI AG
                2073-4441
                January 2023
                January 13 2023
                : 15
                : 2
                : 338
                Article
                10.3390/w15020338
                caa394bc-9638-4f6d-a482-638a8ac572de
                © 2023

                https://creativecommons.org/licenses/by/4.0/

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