Article(id=1233732361872003741, tenantId=1146029695717560320, journalId=1149651085930835976, issueId=1233732360236225173, articleNumber=null, orderNo=null, doi=10.12284/hyxb2021026, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1587571200000, receivedDateStr=2020-04-23, revisedDate=1601222400000, revisedDateStr=2020-09-28, acceptedDate=null, acceptedDateStr=null, onlineDate=1772074316708, onlineDateStr=2026-02-26, pubDate=1614182400000, pubDateStr=2021-02-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1772074316708, onlineIssueDateStr=2026-02-26, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1772074316708, creator=13701087609, updateTime=1772074316708, updator=13701087609, issue=Issue{id=1233732360236225173, tenantId=1146029695717560320, journalId=1149651085930835976, year='2021', volume='43', issue='2', pageStart='1', pageEnd='140', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1772074316317, creator=13701087609, updateTime=1772074316317, updator=13701087609, preIssue=null, nextIssue=null, ext=null, issueFiles=null}, startPage=105, endPage=115, ext={EN=ArticleExt(id=1233732363579085476, articleId=1233732361872003741, tenantId=1146029695717560320, journalId=1149651085930835976, language=EN, title=Genetic diversity of Parasesarma affine from the South China Sea based on mitochondrial DNA COⅠ gene, columnId=1194652708754920165, journalTitle=Haiyang Xuebao, columnName=Research Note, runingTitle=null, highlight=null, articleAbstract=

In this study, the population genetic diversity and structure of Parasesarma affine in the South China Sea were analyzed based on 222 individuals of twelve populations using Cytochrome Oxidase Ⅰ (COⅠ) sequence. A 612 bp fragment of COⅠ gene were sequenced, from which 34 polymorphic sites were tested and 40 haplotypes were defined. The most frequent haplotype was Hap2 with the highest frequency of 69.81%, which was shared in all twelve populations. Total haplotype diversity (Hd) and nucleotide diversity (Pi) were 0.508 9, 0.001 126, respectively, which represented a moderate level of haplotype diversity and a low level of nucleotide diversity. No clustering corresponding to sampling localities was found in neighbor-joining tree and haplotype network. The genetic distance ranged from 0.000 36 to 0.001 73 within populations and from 0.000 48 to 0.001 72 between populations. Genetic fixation index (Fst) and analysis of molecular variance (AMOVA) indicated that the genetic variance mainly came from individuals within populations, and a low level of genetic differentiation among twelve populations. Both neutral test and mismatch-distribution analysis implied that the populations of P. affine had a recent population expansion event that occurred in about 51 000 years ago in the late Pleistocene epoch. In summary, the longer time of the planktonic larval phase and the lack of evident geographical barriers in the marine realm might be major reasons for that P. affine could carry out extensive gene flow and possessed a low level of genetic differentiation among all twelve populations. In addition, the severe climate change of pleistocene epoch might also have important effects on the genetic structure and patterns of distribution of P. affine populations. The research results could provide a theoretical basis for the conservation and utilization of P. affine.

, correspAuthors=Bing Yan, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright © 2021 Pratacultural Science. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Mingliu Yang, Yan Xu, Tingwei Gao, Hongping Pan, Bin Wu, Bing Yan), CN=ArticleExt(id=1233732364736713434, articleId=1233732361872003741, tenantId=1146029695717560320, journalId=1149651085930835976, language=CN, title=基于COⅠ基因片段的中国南部沿海近亲拟相手蟹的群体遗传多样性研究, columnId=1194652708993995497, journalTitle=海洋学报, columnName=研究报道, runingTitle=null, highlight=null, articleAbstract=

为了研究我国南部沿海近亲拟相手蟹(Parasesarma affine)的群体遗传结构,本研究对12个地理群体共222个个体的线粒体DNA的细胞色素氧化酶亚基Ⅰ (COⅠ)基因片段进行了分析。结果表明,612 bp的COⅠ基因片段检测到34个变异位点,共定义了40个单倍型,其中Hap2为12个群体的共享单倍型,占个体总数的69.81%。总群体的单倍型多样性水平Hd为0.508 9,核苷酸多样性水平Pi为0.001 126,表现出中等水平的Hd和低水平的Pi。单倍型邻接发育树和单倍型中介网络图没有形成明显的地理系谱结构。近亲拟相手蟹群体内的遗传距离为0.000 36~0.001 73,群体间的遗传距离为0.000 48~0.001 72。群体间的遗传分化系数(Fst)和分子方差分析(AMOVA)结果表明,近亲拟相手蟹群体遗传分化水平低,其变异主要来自群体内。中性检验和核苷酸不配对分布结果提示,近亲拟相手蟹近期经历了群体扩张事件,扩张时间大约发生于5.1万年前的更新世晚期。研究表明,较长的幼虫浮游期以及海洋环境中缺少影响群体扩散的屏障可能是近亲拟相手蟹各地理群体间能进行广泛的基因交流,从而表现出较低的遗传分化水平的重要原因,更新世的剧烈气候变迁亦可能对其群体的遗传结构和分布格局产生影响。研究结果为近亲拟相手蟹自然资源的保护及合理开发利用提供了一定理论依据。

, correspAuthors=阎冰, authorNote=null, correspAuthorsNote=
阎冰(1966—),男,研究员,主要从事红树林污染生态研究。E-mail:
, copyrightStatement=版权所有©《海洋学报》编辑部 2021, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=A8cs3/RbZwn2Zw/zoJnHYQ==, magXml=cXNdHQ+OvfcUQb1u8Ab5HQ==, pdfUrl=null, pdf=cYvlXWXP7b01DRMRH+rUNg==, pdfFileSize=986584, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=6qsHPwZbrOgbifCHm/Um5g==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=gmFzAx+Fu1GrrE/0im5Lvg==, mapNumber=null, authorCompany=null, fund=null, authors=

杨明柳(1988—),女,广西省桂林市人,助理研究员,主要从事海洋生物研究。E-mail:

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杨明柳(1988—),女,广西省桂林市人,助理研究员,主要从事海洋生物研究。E-mail:

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The sampling information of P. affine from the South China Sea

, figureFileSmall=null, figureFileBig=null, tableContent=
群体采样地点经纬度样本数采集时间
LH福建龙海24°28′06.4″N,117°54′19.5″E222012年9月
YX福建云霄23°55′15.3″N,117°25′01.5″E222012年9月
ZH广东珠海22°23′45.4″N,113°38′37.8″E222013年6月
YJ广东阳江21°46′12.4″N,111°44′49.8″E142013年6月
LF广东雷州附城镇20°53′18.2″N,110°10′30.1″E222012年10月
LQ广东雷州企水镇20°48′13.2″N,109°44′9.7″E222012年10月
XW广东徐闻20°14′47.7″N,110°7′19.3″E142012年10月
SK广西合浦山口镇21°29′55.5″N,109°45′41.0″E102012年7月
BH广西北海21°24′51.3″N,109°10′25.2″E212012年7月
FCG广西防城港21°37′06.2″N,108°14′07.9″E222012年7月
YP海南洋浦19°46′08.8″N,109°15′15.0″E222012年10月
DF海南东方19°12′58.4″N,108°38′15.2″E92012年10月
), ArticleFig(id=1233800600803144459, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=CN, label=表1, caption=

中国南部沿海近亲拟相手蟹的采样信息

, figureFileSmall=null, figureFileBig=null, tableContent=
群体采样地点经纬度样本数采集时间
LH福建龙海24°28′06.4″N,117°54′19.5″E222012年9月
YX福建云霄23°55′15.3″N,117°25′01.5″E222012年9月
ZH广东珠海22°23′45.4″N,113°38′37.8″E222013年6月
YJ广东阳江21°46′12.4″N,111°44′49.8″E142013年6月
LF广东雷州附城镇20°53′18.2″N,110°10′30.1″E222012年10月
LQ广东雷州企水镇20°48′13.2″N,109°44′9.7″E222012年10月
XW广东徐闻20°14′47.7″N,110°7′19.3″E142012年10月
SK广西合浦山口镇21°29′55.5″N,109°45′41.0″E102012年7月
BH广西北海21°24′51.3″N,109°10′25.2″E212012年7月
FCG广西防城港21°37′06.2″N,108°14′07.9″E222012年7月
YP海南洋浦19°46′08.8″N,109°15′15.0″E222012年10月
DF海南东方19°12′58.4″N,108°38′15.2″E92012年10月
), ArticleFig(id=1233800600916390668, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=EN, label=Table 2, caption=

The base composition and genetic diversity parameters of COⅠ gene fragments among different population of P. affine

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群体碱基组成/%单倍型多样性(Hd核苷酸多样性(Pi
TCAGA+TC+G
LH37.2517.1628.9416.6466.1923.90.259 7±0.120 20.000 594±0.000 664
YX37.2417.1828.9216.6666.1633.840.593 1±0.116 70.001 146±0.001 003
ZH37.2517.1628.9116.6766.1633.930.545 5±0.127 60.001 040±0.000 941
YJ37.2217.1828.9416.6566.1633.830.494 5±0.150 60.000 898±0.000 880
LF37.2317.1828.9116.6766.1433.850.601 7±0.120 60.001 174±0.001 019
LQ37.2517.1628.9216.6666.1733.820.710 0±0.106 40.001 726±0.001 326
XW37.2417.1728.9416.6466.1833.810.395 6±0.158 80.000 700±0.000 753
SK37.2517.1628.9216.6766.1733.830.377 8±0.181 30.000 654±0.000 745
BH37.2517.1728.9416.6466.1933.810.681 0±0.113 10.001 696±0.001 313
FCG37.2817.1418.9616.6256.2433.760.541 1±0.125 30.001 712±0.001 319
YP37.2417.1728.9416.6566.1833.820.411 3±0.130 80.000 891±0.000 852
DF37.2717.1428.9216.6766.1933.810.222 2±0.166 20.000 362±0.000 534
总群体37.2517.1728.9316.6566.1833.820.508 9±0.041 90.001 126±0.000 951
), ArticleFig(id=1233800601071579923, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=CN, label=表2, caption=

近亲拟相手蟹不同群体COⅠ基因片段的碱基组成和遗传多样性

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群体碱基组成/%单倍型多样性(Hd核苷酸多样性(Pi
TCAGA+TC+G
LH37.2517.1628.9416.6466.1923.90.259 7±0.120 20.000 594±0.000 664
YX37.2417.1828.9216.6666.1633.840.593 1±0.116 70.001 146±0.001 003
ZH37.2517.1628.9116.6766.1633.930.545 5±0.127 60.001 040±0.000 941
YJ37.2217.1828.9416.6566.1633.830.494 5±0.150 60.000 898±0.000 880
LF37.2317.1828.9116.6766.1433.850.601 7±0.120 60.001 174±0.001 019
LQ37.2517.1628.9216.6666.1733.820.710 0±0.106 40.001 726±0.001 326
XW37.2417.1728.9416.6466.1833.810.395 6±0.158 80.000 700±0.000 753
SK37.2517.1628.9216.6766.1733.830.377 8±0.181 30.000 654±0.000 745
BH37.2517.1728.9416.6466.1933.810.681 0±0.113 10.001 696±0.001 313
FCG37.2817.1418.9616.6256.2433.760.541 1±0.125 30.001 712±0.001 319
YP37.2417.1728.9416.6566.1833.820.411 3±0.130 80.000 891±0.000 852
DF37.2717.1428.9216.6766.1933.810.222 2±0.166 20.000 362±0.000 534
总群体37.2517.1728.9316.6566.1833.820.508 9±0.041 90.001 126±0.000 951
), ArticleFig(id=1233800601184826134, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=EN, label=Table 3, caption=

Haplotype distribution of P. affine in twelve populations

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单倍型群体合计基因登记号
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Hap3611MT311009
Hap3711MT311010
Hap3811MT311011
Hap3911MT311012
Hap4011MT311013
合计22222214222214102122229222
), ArticleFig(id=1233800601310655260, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=CN, label=表3, caption=

近亲拟相手蟹12个群体单倍型分布情况

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单倍型群体合计基因登记号
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), ArticleFig(id=1233800601440678689, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=EN, label=Table 4, caption=

F-statistics (below diagonal) within populations and genetic distance within (diagonal) and between (above diagonal) populations of P. affine based on COⅠ gene

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LHYXZHYJLFLQXWSKBHFCGYPDF
LH0.000 600.000 870.000 820.000 730.000 880.001 170.000 630.000 610.001 140.001 160.000 740.000 48
YX−0.006 700.001 150.001 100.001 000.001 150.001 440.000 910.000 860.001 430.001 460.001 020.000 78
ZH0.000 000.007 010.001 040.000 990.001 120.001 410.000 870.000 830.001 370.001 410.000 960.000 70
YJ−0.014 01−0.027 170.016 030.000 900.001 020.001 320.000 790.000 750.001 300.001 340.000 890.000 65
LF−0.007 33−0.010 640.006 35−0.020 150.001 180.001 450.000 910.000 890.001 440.001 480.001 020.000 78
LQ0.006 880.001 560.015 34−0.005 18−0.003 560.001 730.001 210.001 190.001 720.001 700.001 320.001 08
XW−0.032 20−0.017 28−0.005 01−0.019 64−0.032 32−0.013 100.000 700.000 650.001 200.001 220.000 780.000 53
SK−0.022 01−0.055 04−0.028 66−0.042 29−0.038 04−0.023 05−0.036 580.000 650.001 170.001 210.000 760.000 51
BH−0.004 570.000 930.001 05−0.004 570.000 900.000 39−0.012 07−0.026 960.001 700.001 710.001 290.001 04
FCG0.007 200.015 730.020 380.014 930.019 66−0.014 230.000 47−0.006 720.000 400.001 720.001 330.001 08
YP−0.009 17−0.005 71−0.007 04−0.003 57−0.012 930.006 11−0.029 92−0.026 99−0.004 280.021 510.000 890.000 63
DF−0.015 02−0.005 80−0.027 680.009 76−0.022 01−0.013 50−0.012 41−0.003 32−0.028 18−0.007 85−0.024 650.000 36
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基于COⅠ基因序列的近亲拟相手蟹群体间遗传分化系数Fst值(对角线下)和群体内(对角线) 及群体间(对角线上)遗传距离

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LHYXZHYJLFLQXWSKBHFCGYPDF
LH0.000 600.000 870.000 820.000 730.000 880.001 170.000 630.000 610.001 140.001 160.000 740.000 48
YX−0.006 700.001 150.001 100.001 000.001 150.001 440.000 910.000 860.001 430.001 460.001 020.000 78
ZH0.000 000.007 010.001 040.000 990.001 120.001 410.000 870.000 830.001 370.001 410.000 960.000 70
YJ−0.014 01−0.027 170.016 030.000 900.001 020.001 320.000 790.000 750.001 300.001 340.000 890.000 65
LF−0.007 33−0.010 640.006 35−0.020 150.001 180.001 450.000 910.000 890.001 440.001 480.001 020.000 78
LQ0.006 880.001 560.015 34−0.005 18−0.003 560.001 730.001 210.001 190.001 720.001 700.001 320.001 08
XW−0.032 20−0.017 28−0.005 01−0.019 64−0.032 32−0.013 100.000 700.000 650.001 200.001 220.000 780.000 53
SK−0.022 01−0.055 04−0.028 66−0.042 29−0.038 04−0.023 05−0.036 580.000 650.001 170.001 210.000 760.000 51
BH−0.004 570.000 930.001 05−0.004 570.000 900.000 39−0.012 07−0.026 960.001 700.001 710.001 290.001 04
FCG0.007 200.015 730.020 380.014 930.019 66−0.014 230.000 47−0.006 720.000 400.001 720.001 330.001 08
YP−0.009 17−0.005 71−0.007 04−0.003 57−0.012 930.006 11−0.029 92−0.026 99−0.004 280.021 510.000 890.000 63
DF−0.015 02−0.005 80−0.027 680.009 76−0.022 01−0.013 50−0.012 41−0.003 32−0.028 18−0.007 85−0.024 650.000 36
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Analysis of molecular variance (AMOVA) for the twelve P. affine populations

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变异来源自由度平方和变异组成变异百分比/%固定值FST
组群间113.526−0.001 38 Va−0.4−0.004 02 (p=0.757 6)
种群内21072.6540.345 97 $^{{\rm{V_b}}} $100.4
合计22176.180.344 59100
), ArticleFig(id=1233800601818166060, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=CN, label=表5, caption=

近亲拟相手蟹12个群体的AMOVA分析

, figureFileSmall=null, figureFileBig=null, tableContent=
变异来源自由度平方和变异组成变异百分比/%固定值FST
组群间113.526−0.001 38 Va−0.4−0.004 02 (p=0.757 6)
种群内21072.6540.345 97 $^{{\rm{V_b}}} $100.4
合计22176.180.344 59100
), ArticleFig(id=1233800601956578098, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1233732361872003741, language=EN, label=Table 6, caption=

Neutral testes and mismatch distributions of nucleotide in twelve P. affine populations

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群体Tajima’s DFu’s Fs核苷酸不配对分布
DpFspτSSDRg
LH−1.877 630.011 00−2.205 610.006 003.000 000.002 130.343 72
YX−1.778 560.019 00−4.749 130.000 000.875 000.017 160.159 63
ZH−2.139 600.001 00−6.978 930.000 000.783 200.011 770.140 50
YJ−1.278 260.085 00−1.727 370.012 000.683 590.012 900.155 30
LF−2.002 530.007 00−6.347 570.000 000.894 530.016 490.156 56
LQ−1.917 760.008 00−7.818 780.000 001.166 020.005 870.092 15
XW−1.670 530.026 00−2.288 110.002 000.505 860.005 270.168 22
SK−1.400 850.077 00−1.163 940.036 000.490 230.005 790.182 72
DG−2.162 550.004 00−6.321 530.000 001.115 230.001 640.067 10
FCG−1.715 700.018 00−3.162 460.007 002.312 500.055 270.243 44
YP−2.071 980.002 00−4.121 610.000 000.705 080.000 060.131 67
DF−1.088 230.191 00−0.263 480.154 002.929 690.306 720.358 02
合计−2.497 800.000 00−29.929 970.000 000.714 840.000 000.950 00
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近亲拟相手蟹12个群体的中性检验和核苷酸不配对分布

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群体Tajima’s DFu’s Fs核苷酸不配对分布
DpFspτSSDRg
LH−1.877 630.011 00−2.205 610.006 003.000 000.002 130.343 72
YX−1.778 560.019 00−4.749 130.000 000.875 000.017 160.159 63
ZH−2.139 600.001 00−6.978 930.000 000.783 200.011 770.140 50
YJ−1.278 260.085 00−1.727 370.012 000.683 590.012 900.155 30
LF−2.002 530.007 00−6.347 570.000 000.894 530.016 490.156 56
LQ−1.917 760.008 00−7.818 780.000 001.166 020.005 870.092 15
XW−1.670 530.026 00−2.288 110.002 000.505 860.005 270.168 22
SK−1.400 850.077 00−1.163 940.036 000.490 230.005 790.182 72
DG−2.162 550.004 00−6.321 530.000 001.115 230.001 640.067 10
FCG−1.715 700.018 00−3.162 460.007 002.312 500.055 270.243 44
YP−2.071 980.002 00−4.121 610.000 000.705 080.000 060.131 67
DF−1.088 230.191 00−0.263 480.154 002.929 690.306 720.358 02
合计−2.497 800.000 00−29.929 970.000 000.714 840.000 000.950 00
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基于COⅠ基因片段的中国南部沿海近亲拟相手蟹的群体遗传多样性研究
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杨明柳 1 , 徐岩 1, 2 , 高霆炜 1 , 潘红平 2 , 吴斌 1 , 阎冰 1, *
海洋学报 | 研究报道 2021,43(2): 105-115
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海洋学报 | 研究报道 2021, 43(2): 105-115
基于COⅠ基因片段的中国南部沿海近亲拟相手蟹的群体遗传多样性研究
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杨明柳1 , 徐岩1, 2, 高霆炜1, 潘红平2, 吴斌1, 阎冰1, *
作者信息
  • 1广西科学院 广西红树林研究中心 广西红树林保护与利用重点实验室,广西 北海 536007
  • 2广西大学 动物科学技术学院,广西 南宁 530005
  • 杨明柳(1988—),女,广西省桂林市人,助理研究员,主要从事海洋生物研究。E-mail:

通讯作者:

阎冰(1966—),男,研究员,主要从事红树林污染生态研究。E-mail:
Genetic diversity of Parasesarma affine from the South China Sea based on mitochondrial DNA COⅠ gene
Mingliu Yang1 , Yan Xu1, 2, Tingwei Gao1, Hongping Pan2, Bin Wu1, Bing Yan1, *
Affiliations
  • 1Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536007, China
  • 2College of Animal Science and Technology, Guangxi University, Nanning 530005, China
出版时间: 2021-02-25 doi: 10.12284/hyxb2021026
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为了研究我国南部沿海近亲拟相手蟹(Parasesarma affine)的群体遗传结构,本研究对12个地理群体共222个个体的线粒体DNA的细胞色素氧化酶亚基Ⅰ (COⅠ)基因片段进行了分析。结果表明,612 bp的COⅠ基因片段检测到34个变异位点,共定义了40个单倍型,其中Hap2为12个群体的共享单倍型,占个体总数的69.81%。总群体的单倍型多样性水平Hd为0.508 9,核苷酸多样性水平Pi为0.001 126,表现出中等水平的Hd和低水平的Pi。单倍型邻接发育树和单倍型中介网络图没有形成明显的地理系谱结构。近亲拟相手蟹群体内的遗传距离为0.000 36~0.001 73,群体间的遗传距离为0.000 48~0.001 72。群体间的遗传分化系数(Fst)和分子方差分析(AMOVA)结果表明,近亲拟相手蟹群体遗传分化水平低,其变异主要来自群体内。中性检验和核苷酸不配对分布结果提示,近亲拟相手蟹近期经历了群体扩张事件,扩张时间大约发生于5.1万年前的更新世晚期。研究表明,较长的幼虫浮游期以及海洋环境中缺少影响群体扩散的屏障可能是近亲拟相手蟹各地理群体间能进行广泛的基因交流,从而表现出较低的遗传分化水平的重要原因,更新世的剧烈气候变迁亦可能对其群体的遗传结构和分布格局产生影响。研究结果为近亲拟相手蟹自然资源的保护及合理开发利用提供了一定理论依据。

近亲拟相手蟹  /  COⅠ基因  /  遗传多样性  /  遗传结构

In this study, the population genetic diversity and structure of Parasesarma affine in the South China Sea were analyzed based on 222 individuals of twelve populations using Cytochrome Oxidase Ⅰ (COⅠ) sequence. A 612 bp fragment of COⅠ gene were sequenced, from which 34 polymorphic sites were tested and 40 haplotypes were defined. The most frequent haplotype was Hap2 with the highest frequency of 69.81%, which was shared in all twelve populations. Total haplotype diversity (Hd) and nucleotide diversity (Pi) were 0.508 9, 0.001 126, respectively, which represented a moderate level of haplotype diversity and a low level of nucleotide diversity. No clustering corresponding to sampling localities was found in neighbor-joining tree and haplotype network. The genetic distance ranged from 0.000 36 to 0.001 73 within populations and from 0.000 48 to 0.001 72 between populations. Genetic fixation index (Fst) and analysis of molecular variance (AMOVA) indicated that the genetic variance mainly came from individuals within populations, and a low level of genetic differentiation among twelve populations. Both neutral test and mismatch-distribution analysis implied that the populations of P. affine had a recent population expansion event that occurred in about 51 000 years ago in the late Pleistocene epoch. In summary, the longer time of the planktonic larval phase and the lack of evident geographical barriers in the marine realm might be major reasons for that P. affine could carry out extensive gene flow and possessed a low level of genetic differentiation among all twelve populations. In addition, the severe climate change of pleistocene epoch might also have important effects on the genetic structure and patterns of distribution of P. affine populations. The research results could provide a theoretical basis for the conservation and utilization of P. affine.

Parasesarma affine  /  COⅠ gene  /  genetic diversity  /  genetic structure
杨明柳, 徐岩, 高霆炜, 潘红平, 吴斌, 阎冰. 基于COⅠ基因片段的中国南部沿海近亲拟相手蟹的群体遗传多样性研究. 海洋学报, 2021 , 43 (2) : 105 -115 . DOI: 10.12284/hyxb2021026
Mingliu Yang, Yan Xu, Tingwei Gao, Hongping Pan, Bin Wu, Bing Yan. Genetic diversity of Parasesarma affine from the South China Sea based on mitochondrial DNA COⅠ gene[J]. Haiyang Xuebao, 2021 , 43 (2) : 105 -115 . DOI: 10.12284/hyxb2021026
近亲拟相手蟹(Parasesarma affine)隶属于方蟹总科(Grapsoidea),相手蟹科(Sesarmidae),拟相手蟹属(Parasesarma),广泛分布于东海、南海、印度−西太平洋[1],栖息于红树林湿地中,以红树植物凋落物、沉积物、藻类等为食,是一种活动能力和适应能力均很强的常见种与优势种[2-3]。近亲拟相手蟹是红树林蟹类中重要种类之一,在红树林生态系统的结构和功能中扮演着非常重要的角色[4]。目前,国内外有关于近亲拟相手蟹的研究已涉及生物学、摄食行为、形态分类、线粒体DNA全基因组等方面[5-8],但未见其群体遗传相关的研究报道。近年来,我国红树林遭到了不同程度的破坏,天然红树林植被的退化和生境的破碎化对红树林蟹类群落造成了一定影响,环境污染、围塘养殖、港口建设等人为活动也使得蟹类资源面临着巨大威胁[2, 9-10]。因此,开展近亲拟相手蟹群体遗传的研究,对全面了解近亲拟相手蟹群体遗传多样性现状及加强红树林蟹类资源保护工作具有重要意义。
线粒体DNA具有分子结构稳定、母系遗传、进化速度快、核苷酸替代速率高等特征,是研究动物分子系统发育和群体遗传的重要遗传标记[11]。细胞色素氧化酶Ⅰ(COⅠ)基因是线粒体DNA中最常用的标记之一,可用于揭示种群之间遗传结构,目前已被广泛地应用于蟹类的群体遗传研究中[1215]。本研究采用线粒体COⅠ基因对我国南部沿海12个近亲拟相手蟹群体进行群体遗传学研究,分析近亲拟相手蟹群体的遗传结构和历史动态,以期为红树林蟹类的资源保护与利用提供基础资料。
本研究所用的近亲拟相手蟹于2012年7月至2013年6月采集于福建龙海、福建云霄、广东珠海、广东阳江、广东雷州、广东徐闻、广西合浦山口、广西北海、广西防城港、海南洋浦、海南东方等12个采样地,共计222个个体(表1图1)。所有个体置于95%酒精中固定,并保存于−20℃冰箱。
取近亲拟相手蟹步足肌肉10 mg左右,采用E. Z. N. A.TMSQ Tissue DNA Kit 试剂盒(Omega公司) 提取总DNA,于−20℃分管保存备用。使用无脊椎动物通用引物COILl490:5’-GGTCAACAAATCATAAAGATATTGG-3’;COIH2198:5’-TAAACTTCAGGGTGACCAAAAAATCA-3’[16]扩增COⅠ基因片段,引物由广州英潍捷基测序公司合成。PCR反应体系为50 µL,其中包含2×Taq10 MasterMix (北京奥赛博公司)25 µL,模板 DNA 2 µL,引物各2 µL,其余用 Milli-Q-Water 补足到50 µL。PCR反应条件为94℃预变性2 min,94℃变性45 s,47℃退火50 s,72℃延伸1 min,35个循环,最后72℃再延伸8 min。PCR产物经1%的琼脂糖凝胶电泳检测确认为目的片段后,将样品送至广州英潍捷基测测公司进行纯化,并用ABI3730XL测序仪进行正反链双向测序。
所获得的序列均由DNAstar 7.1[17]软件包中的SeqMan、MegAlign进行校对、编辑、排序。Dnasp v5.0[18]统计单倍型数目、多态位点数、简约信息位点数,Arlequin3.1[19]计算单倍型多样性和核苷酸多样性。采用MEGA7.0[20]软件计算近亲拟相手蟹群体内和群体间平均遗传距离,并基于Kimura 2-parameter模型构建单倍型邻接树(1 000次自展重复)。使用Network 4.51[21]软件包中介邻接网络法(Median Joining, MJ)构建单倍型中介网络图。利用Arlequin 3.1[19]软件进行分子方差分析(Analysis of Molecular Variance, AMOVA),来评估近亲拟相手蟹群体间的遗传变异,计算群体间的遗传分化指数Fst值,并用Tajima's D和Fu's Fs中性检验及核苷酸不配对分布,来进行群体的历史动态评估[2223]。采用公式τ=2ut估算群体扩张发生的大致时间,其中t为群体发生扩张的时间,u为所研究的整个序列的进化速率,u采用2.3%每百万年的核苷酸分歧速率[2425]
本研究的近亲拟相手蟹12个群体共222条序列经比对分析后,获得长度为612 bp的COⅠ基因片段,其A、T、C、G的平均含量分别为28.93%、37.25%、17.17%、16.65%,A+T含量(66.18%)明显大于C+G含量(33.82%),碱基存在明显的偏向性(表2)。共检测到34个变异位点,包括19个单核苷酸变异位点,15个简约信息位点,无插入或缺失位点。34个变异位点共发生了35次核苷酸替换,其中有30次转换,5次颠换,转换和颠换之比为6.0。
近亲拟相手蟹总群体的单倍型多样性指数Hd为0.508 9,核苷酸多样性指数Pi为0.001 126。各群体间的单倍型多样性指数Hd在0.222 2~0.710 0之间,核苷酸多样性指数Pi在0.000 362~0.001 726之间,其中雷州企水群体的单倍型多样性和核苷酸多样性最高,海南东方群体的单倍型多样性和核苷酸多样性相对较低。
在222个个体中,COⅠ基因片段检测到的34个变异位点共定义了40个单倍型,由表3可知,有29个独有单倍型和11个共享单倍型。其中单倍型Hap2在12个群体中均有分布,在群体中所占比例高达69.82%,为主体单倍型。Hap3为10个群体共享,在群体中所占比例为6.31%;Hap22为4个群体共享,Hap30为3个群体共享,Hap7、Hap12、Hap18、Hap20、Hap29、Hap34各为2个群体共享。在12个群体中,雷州企水群体的单倍型数量最多(10个),其次为广西北海群体(9个),海南东方群体的单倍型最少(2个)。由于部分群体的样本个体数量较少,这可能会在一定程度上影响单倍型数量、单倍型多样性和核苷酸多样性的统计结果。
为了更好地了解近亲拟相手蟹各单倍型之间的关系,以弧边招潮(Uca arcua,基因登陆号:LC053370)为外群,构建了单倍型邻接发育树(图2)。从系统发育树可以看出,40个单倍型没有分成明显的支系,不同地理群体的单倍型并没有出现明显的地域分群。利用中介网络邻接法构建的单倍型网络中介图呈星状散射分布,主体单倍型为Hap2,其他单倍型与主体单倍型Hap2仅保留一步或两步突变。中介网络图中近亲拟相手蟹各群体的单倍型呈零散分布,没有明显的地理系谱结构,其结果进一步支持了系统发育树的分析(图3)。
表4可以看出,12个近亲拟相手蟹群体内的遗传距离在0.000 36~0.001 73之间,海南东方群体内的遗传距离最小,为0.000 36;雷州企水群体内的遗传距离最大,为0.001 73。在不同地理群体间的遗传距离范围为0.000 48~0.001 72,其中雷州企水群体与广西北海群体遗传距离最大,为0.001 72,而海南东方群体与福建龙海群体之间的遗传距离最小,为0.000 48。这表明群体内和群体间的遗传分化程度均很低,各群体间没有形成地理隔离现象。遗传分化系数Fst结果显示,12个群体间的Fst值均较小,范围为−0.055 04~0.021 51,且统计学差异不显著(p>0.05),表明各群体间没有发生明显的遗传分化。绝大多数群体间的Fst值为负值,表明大部分群体内的遗传差异水平大于群体间的遗传差异水平。
根据群体间遗传距离及遗传分化情况,将12个群体作为一个整体进行分子方差分析,结果显示,群体间的变异百分比为−0.4%,而组群内的变异百分比为100.4%,这亦表明了群体间的遗传分化程度低,且群体的遗传变异主要来自群体内,而不是群体间。总的固定指数(FST)为−0.004 02,表明来自同一个群体的两个随机个体比来自不同群体的两个随机个体有更大的遗传差异(表5)。
由于近亲拟相手蟹群体间没有显著的遗传分化,因此将12个群体合并为一个大群体进行历史动态分析。中性检验显示(表6),总群体的Tajima’s D检验(Tajima’s D=−2.497 80,p<0.05)和Fu’s Fs检验(Fu’s Fs=−29.929 97,p<0.05)结果均为负值,差异显著,并且Fu’s Fs检验的绝对值大于Tajima’s D检验绝对值,提示近亲拟相手蟹曾经发生过群体扩张事件。此外,核苷酸不配对分析结果表明,偏离方差(SSD)和Rg(Raggedness index)均较小,统计结果不显著(p>0.05),表明未显著偏离群体扩张模型,进一步暗示了近亲拟相手蟹可能经历过群体扩张。并且,近亲拟相手蟹的单倍型核苷酸不配对分布图呈明显的单峰泊松分布,且观测值不明显偏离模拟值(图4)。由此可见,中性检验和核苷酸不配对结果一致,均提示近亲拟相手蟹群体在历史上可能发生过群体扩张。基于核苷酸不配对分布得到的总群体扩张参数τ值为0.714 84,估算得出中国南部沿海近亲拟相手蟹群体发生扩张时间大约在5.1万年前。
本研究中,我国南部沿海12个近亲拟相手蟹群体222个个体的COⅠ碱基组成中A+T含量占总碱基的66.18%,表现出较强的AT偏向性,与已经报道的相手蟹科的双齿近相手蟹(Perisesarma bidens[14]、迈纳新胀蟹(Neosarmatium meinerti[26]、其他软体动物(疣荔枝螺Reishia clavigera[27]、星虫动物(可口革囊星虫Phascolosoma esculenta[28]等的COⅠ碱基组成特点相似,符合无脊椎动物线粒体DNA的碱基组成特征。
单倍型多样性指数和核苷酸多样性指数是衡量群体遗传多样性的一项重要指标[29]。根据单倍型多样性指数和核苷酸多样性指数的特征,Grant和Bowen[30]对遗传多样性划分为低Hd和低PiHd<0.5,Pi<0.5%)、高Hd和低Pi、低Hd和高Pi、高Hd和高Pi等4种遗传特征类型。近亲拟相手蟹12个群体的单倍型多样性指数为0.508 9,核苷酸多样性指数为0.001 126,符合高Hd和低Pi类型,暗示其群体近期可能经历了快速扩张事件[30]。这种高Hd和低Pi的遗传多样性特征不仅存在于蟹类等甲壳动物中[13, 31],许多种海洋无脊椎动物,尤其是具有浮游幼体阶段和高繁殖潜力的海洋无脊椎动物也存在这种特征[2728, 32]。此外,近亲拟相手蟹群体较低的核苷酸多样性可能是由于新形成的单倍型存在的时间较短,其累积的核苷酸突变很快就随之消失而造成[33],瓶颈效应及随后的群体扩张也可能会导致这种遗传多样性格局。
单倍型中介网络图中单倍型呈星状散射分布,Hap2位于网络中介图中心,其广泛分布于各个群体,占总个体数的69.81%,这暗示着Hap2为祖先单倍型。本研究检测到40种单倍型中有11个共享单倍型和29个独有单倍型,独有单倍型仅在1个群体中的1个个体表现,并且其他单倍型与主体单倍型Hap2仅保留一步或两步突变,这种现象通常可以认为是群体瓶颈效应后,少量有效群体近期迅速扩张事件引起[34],进一步表明近亲拟相手蟹可能经历过群体快速爆发事件。
遗传分化系数Fst结果显示,近亲拟相手蟹12个群体间的Fst值范围为−0.055 04~0.021 51,统计学差异不显著(p>0.05),群体间的遗传分化水平很低。基于遗传距离分析的结果发现,群体间的遗传距离接近甚至小于群体内的遗传距离,各群体间没有形成地理隔离,AMOVA分析结果也表明,群体间的遗传分化程度低,群体的遗传变异主要来自群体内。这些结果暗示着近亲拟相手蟹各群体间存在广泛的基因交流,并且不同地理群体可以以随机交配的方式进行基因交流[29],推测中国南部沿海可能缺少能明显影响近亲拟相手蟹群体扩散的地理屏障。
许多具有浮游阶段且有较强潜在扩散能力的海洋生物,在非常广阔的范围内通常会表现出很低的遗传分化[35]。在大多数海洋无脊椎动物中,浮游性幼虫发育是它们繁殖策略中很重要的一部分,浮游幼虫期持续的时间越长,它们可能在洋流的作用下扩散得越远,不同地理群体在较大的地理范围内潜在的基因流就越高,从而导致遗传同质性[36]。近亲拟相手蟹是一种广泛分布于红树林中的常见种类,与大多数红树林蟹类一样,会与潮汐同步释放幼虫,这些浮游幼虫可能会借助潮汐和洋流运输作用跨越数十千米至数百千米进行扩散[3738]。相手蟹的幼虫发育通常经过4~5个溞状幼体期和1个大眼幼体期,幼虫期持续将近1个月,有的甚至超过1个月[26, 31, 39]。较长的幼虫浮游期以及海洋环境中缺少影响群体扩散的屏障可能是近亲拟相手蟹群体能进行频繁的基因交流,从而在较大地理范围内表现出较低的遗传分化水平的重要原因。类似的结果在双齿近相手蟹[14]、环纹招潮(Uca annulipes[40]的群体遗传研究中也有报道。
本研究中单倍型中介网络图呈星状结构、中性检验和核苷酸不配对分析的结果均暗示着近亲拟相手蟹近期发生过群体扩张事件,根据核苷酸不配对τ值估算群体扩张时间大约发生在5.1万年前的更新世晚期。更新世的剧烈气候波动,冰期和间冰期变化频繁,冰川不断进退消融,由此引起的海平面的升降对地球上的动植物地理空间分布格局和遗传结构均产生了重大影响[4142]。更新世海平面周期性的波动使海洋生物经历了栖息地的反复收缩和扩张,尤其是末次冰盛期,大部分地区为巨大的冰原所覆盖,西太平洋边缘海平面下降,栖息地急剧收缩,迫使众多海洋生物进入生物避难所,随着冰川消退和气温回升,海平面上升,栖息地范围扩大,幸存物种开始重新扩散并快速增长[41, 43]。近亲拟相手蟹的群体扩张时间大约发生在5.1万年前,推测近亲拟相手蟹在更新世冰盛期经历了栖息地剧烈收缩和种群数量的减少,随着气温回升,海平面的上升和栖息地范围的扩大,适宜的环境让近亲拟相手蟹幸存种群开始迅速扩张。不少研究也发现蟹类在更新世发生过群体扩张事件[12, 14, 40],海平面和温度的变化可能导致了其群体遗传结构的变化。由此可见,更新世的剧烈气候变迁对海洋蟹类群体的遗传结构和分布格局产生了巨大影响。
综上所述,近亲拟相手蟹12个地理群体内和群体间的遗传距离小,不同地理群体的单倍型没有明显的地理系谱结构,群体间的遗传分化程度低,群体的遗传变异主要来自群体内,这些暗示着近亲拟相手蟹不同地理群体间存在着广泛的基因交流。幼虫浮游期长和较强的潜在扩散能力,海洋环境中缺少影响群体扩散的屏障以及近期的群体扩张事件,可能是近亲拟相手蟹不同地理群体间存在着广泛的基因交流,没有形成显著遗传结构的重要原因,研究结果为近亲拟相手蟹自然资源的保护及合理开发利用提供了一定理论依据。然而,浮游幼虫的扩散是非常复杂的过程,易受到生活史特征、洋流、地理屏障等生物和非生物因素的影响,也有越来越多研究证明,海洋区域中存在着边界和屏障,导致一些蟹类群体的基因交流受限和出现遗传分化[26, 4445]。此外,近年来中国沿海环境不断发生变化,特别是人为干扰的加剧,可能会对近亲拟相手蟹这种生活于潮间带区域的蟹类种群动态产生较大影响。本研究的样品采集于2012−2013年,至于这几年的沿海环境变化和人为活动是否会导致近亲拟相手蟹群体的遗传结构在不同时间尺度上出现差异尚不明确。稳定的遗传变异对群体的演化及适应环境变化有重要作用,不同区域动物群体遗传变异在时间尺度上具有一定的稳定性[46],但也有研究发现在不同的年份中,人为干扰严重的区域一些动物群体的遗传结构出现分化,而远离人为干扰环境中的群体,在不同年份中群体之间遗传结构不存在差异[47]。由于本研究的采样时间、地点和样品量存在一定局限性,至于近亲拟相手蟹群体在更大的地理范围内是否存基因交流限制和显著遗传结构,以及在不同的时间尺度上群体遗传结构是否存在差异,还需扩大研究范围,深入研究群体遗传变异的时空动态变化,并运用多种分子标记手段,以得出更全面和客观的结论。
  • 国家重点研发计划科技基础资源调查专项(2017FY100704);广西自然科学基金项目(2017GXNSFBA198163);广西“红树林和海草系统保育与生态监测”特聘专家岗基金资助。
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doi: 10.12284/hyxb2021026
  • 接收时间:2020-04-23
  • 首发时间:2026-02-26
  • 出版时间:2021-02-25
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  • 收稿日期:2020-04-23
  • 修回日期:2020-09-28
基金
国家重点研发计划科技基础资源调查专项(2017FY100704);广西自然科学基金项目(2017GXNSFBA198163);广西“红树林和海草系统保育与生态监测”特聘专家岗基金资助。
作者信息
    1广西科学院 广西红树林研究中心 广西红树林保护与利用重点实验室,广西 北海 536007
    2广西大学 动物科学技术学院,广西 南宁 530005

通讯作者:

阎冰(1966—),男,研究员,主要从事红树林污染生态研究。E-mail:
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https://castjournals.cast.org.cn/joweb/hyxb/CN/10.12284/hyxb2021026
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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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