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      Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution

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          Abstract

          The southern lesser pomfret ( Pampus minor ) is an economically important fish, and its numbers are declining because of overfishing and environmental pollution. In addition, owing to the similarities of its external morphological characteristics to other species in the genus Pampus , it is often mistaken for grey pomfret ( P. cinereus ) or silver pomfret ( P. argenteus ) juveniles. In this study, the genetic diversity and structure of 264 P. minor individuals from 11 populations in China and Malaysia coastal waters were evaluated for the first time, to the best of our knowledge, using mitochondrial cytochrome b fragments. The results showed that P. minor had moderate haplotype diversity and low nucleotide diversity. Furthermore, two divergent lineages were detected within the populations, but the phylogenetic structure corresponded imperfectly with geographical location; thus, the populations may have diverged in different glacial refugia during the Pleistocene low sea levels. Analysis of molecular variation (AMOVA) showed that genetic variation originated primarily from individuals within the population. Pairwise F ST results showed significant differentiation between the Chinese and Malaysian populations. Except for the Xiamen population, which was classified as a marginal population, the genetic differentiation among the other Chinese populations was not significant. During the Late Pleistocene, P. minor experienced a population expansion event starting from the South China Sea refugium that expanded outward, and derivative populations quickly occupied and adapted to the new habitat. The results of this study will provide genetic information for the scientific conservation and management of P. minor resources.

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          Most cited references 29

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          Natural selection shaped regional mtDNA variation in humans.

          Human mtDNA shows striking regional variation, traditionally attributed to genetic drift. However, it is not easy to account for the fact that only two mtDNA lineages (M and N) left Africa to colonize Eurasia and that lineages A, C, D, and G show a 5-fold enrichment from central Asia to Siberia. As an alternative to drift, natural selection might have enriched for certain mtDNA lineages as people migrated north into colder climates. To test this hypothesis we analyzed 104 complete mtDNA sequences from all global regions and lineages. African mtDNA variation did not significantly deviate from the standard neutral model, but European, Asian, and Siberian plus Native American variations did. Analysis of amino acid substitution mutations (nonsynonymous, Ka) versus neutral mutations (synonymous, Ks) (kaks) for all 13 mtDNA protein-coding genes revealed that the ATP6 gene had the highest amino acid sequence variation of any human mtDNA gene, even though ATP6 is one of the more conserved mtDNA proteins. Comparison of the kaks ratios for each mtDNA gene from the tropical, temperate, and arctic zones revealed that ATP6 was highly variable in the mtDNAs from the arctic zone, cytochrome b was particularly variable in the temperate zone, and cytochrome oxidase I was notably more variable in the tropics. Moreover, multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant. From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.
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            THE INTERPRETATION OF POPULATION STRUCTURE BY F-STATISTICS WITH SPECIAL REGARD TO SYSTEMS OF MATING

             Sewall Wright (1965)
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              The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism.

              In order to study the effect of mutation rate heterogeneity on patterns of DNA polymorphism, we simulated samples of DNA sequences with gamma-distributed nucleotide substitution rates in stationary and expanding populations. We find that recent population expansions and mutation rate heterogeneity have similar effects on several polymorphism indicators, like the shape and the mean of the observed pairwise difference distribution, or the number of segregating sites. The inferred size of population expansion thus appears overestimated if nucleotides have dissimilar substitution rates. Interestingly, population expansion and uneven mutation rates have contrasting effects on Tajima's D statistic when acting separately, and the consequence on the associated test of selective neutrality is investigated. The patterns of polymorphism of several human populations analyzed for the mitochondrial control region are examined, mainly showing the difficulty in quantifying the respective contribution of past demographic history and uneven mutation rates from a single sampled evolutionary process. However, substitution rates appear more heterogeneous in the second hypervariable segment of the control region than in the first segment.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                17 August 2020
                : 969
                : 137-154
                Affiliations
                [1 ] Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
                [2 ] College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China
                [3 ] Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia University of Malaya Kuala Lumpur Malaysia
                Author notes
                Corresponding author: Longshan Lin ( lshlin@ 123456tio.org.cn )

                Academic editor: Maria Elina Bichuette

                Article
                52069
                10.3897/zookeys.969.52069
                7515929
                Yuan Li, Cheng Liu, Longshan Lin, Yuanyuan Li, Jiaguang Xiao, Kar-Hoe Loh

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Categories
                Research Article
                Stromateidae
                Population Genetics
                Neogene
                Pacific Ocean

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