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

杨明柳; 徐岩; 高霆炜; 潘红平; 吴斌; 阎冰

doi:10.12284/hyxb2021026

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

doi: 10.12284/hyxb2021026

杨明柳^1,,
徐岩^{1, 2},
高霆炜¹,
潘红平²,
吴斌¹,
阎冰^1, ,

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

基金项目: 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。

详细信息

作者简介:
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：yangmingliu2010@163.com

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：gxybing@tom.com

中图分类号: Q347
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出版历程
- 收稿日期: 2020-04-23
- 修回日期: 2020-09-28
- 网络出版日期: 2020-12-25
- 刊出日期: 2021-03-02

Genetic diversity of Parasesarma affine from the South China Sea based on mitochondrial DNA COⅠ gene

Yang Mingliu^1
,,
Xu Yan^{1, 2},
Gao Tingwei¹,
Pan Hongping²,
Wu Bin¹,
Yan Bing^{1
, ,}

1.
Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536007, China
2.
College of Animal Science and Technology, Guangxi University, Nanning 530005, China

摘要

摘要: 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H_d为0.508 9，核苷酸多样性水平P_i为0.001 126，表现出中等水平的H_d和低水平的P_i。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(F_st)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
Abstract: 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 (H_d) and nucleotide diversity (P_i) 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 (F_st) 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

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图 1 近亲拟相手蟹的采样点地理位置

Fig. 1 Locations of the sampling stations of P. affine

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图 2 基于近亲拟相手蟹COⅠ基因构建的40个单倍型邻接系统发育树

Fig. 2 Neighbor-joining tree for 40 haplotypes of P. affine based on COⅠ gene

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图 3 近亲拟相手蟹12个群体COⅠ基因单倍型中介网络图

Fig. 3 The median-joining network of COⅠ gene haplotypes in twelve populations of P. affine

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图 4 近亲拟相手蟹COⅠ基因单倍型的核苷酸不配对分布

Fig. 4 Mismatch distributions based on COⅠ gene haplotypes of P. affine

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表 1 中国南部沿海近亲拟相手蟹的采样信息

Tab. 1 The sampling information of P. affine from the South China Sea

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″E	22	2012年9月
YX	福建云霄	23°55′15.3″N，117°25′01.5″E	22	2012年9月
ZH	广东珠海	22°23′45.4″N，113°38′37.8″E	22	2013年6月
YJ	广东阳江	21°46′12.4″N，111°44′49.8″E	14	2013年6月
LF	广东雷州附城镇	20°53′18.2″N，110°10′30.1″E	22	2012年10月
LQ	广东雷州企水镇	20°48′13.2″N，109°44′9.7″E	22	2012年10月
XW	广东徐闻	20°14′47.7″N，110°7′19.3″E	14	2012年10月
SK	广西合浦山口镇	21°29′55.5″N，109°45′41.0″E	10	2012年7月
BH	广西北海	21°24′51.3″N，109°10′25.2″E	21	2012年7月
FCG	广西防城港	21°37′06.2″N，108°14′07.9″E	22	2012年7月
YP	海南洋浦	19°46′08.8″N，109°15′15.0″E	22	2012年10月
DF	海南东方	19°12′58.4″N，108°38′15.2″E	9	2012年10月

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表 2 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

Tab. 2 The base composition and genetic diversity parameters of COⅠ gene fragments among different population of P. affine

群体	碱基组成/%						单倍型多样性（H_d）	核苷酸多样性（P_i）
群体	T	C	A	G	A+T	C+G	单倍型多样性（H_d）	核苷酸多样性（P_i）
LH	37.25	17.16	28.94	16.64	66.19	23.9	0.259 7±0.120 2	0.000 594±0.000 664
YX	37.24	17.18	28.92	16.66	66.16	33.84	0.593 1±0.116 7	0.001 146±0.001 003
ZH	37.25	17.16	28.91	16.67	66.16	33.93	0.545 5±0.127 6	0.001 040±0.000 941
YJ	37.22	17.18	28.94	16.65	66.16	33.83	0.494 5±0.150 6	0.000 898±0.000 880
LF	37.23	17.18	28.91	16.67	66.14	33.85	0.601 7±0.120 6	0.001 174±0.001 019
LQ	37.25	17.16	28.92	16.66	66.17	33.82	0.710 0±0.106 4	0.001 726±0.001 326
XW	37.24	17.17	28.94	16.64	66.18	33.81	0.395 6±0.158 8	0.000 700±0.000 753
SK	37.25	17.16	28.92	16.67	66.17	33.83	0.377 8±0.181 3	0.000 654±0.000 745
BH	37.25	17.17	28.94	16.64	66.19	33.81	0.681 0±0.113 1	0.001 696±0.001 313
FCG	37.28	17.14	18.96	16.62	56.24	33.76	0.541 1±0.125 3	0.001 712±0.001 319
YP	37.24	17.17	28.94	16.65	66.18	33.82	0.411 3±0.130 8	0.000 891±0.000 852
DF	37.27	17.14	28.92	16.67	66.19	33.81	0.222 2±0.166 2	0.000 362±0.000 534
总群体	37.25	17.17	28.93	16.65	66.18	33.82	0.508 9±0.041 9	0.001 126±0.000 951

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表 3 近亲拟相手蟹12个群体单倍型分布情况

Tab. 3 Haplotype distribution of P. affine in twelve populations

单倍型	群体												合计	基因登记号
单倍型	LH	YX	ZH	YJ	LF	LQ	XW	SK	BH	FCG	YP	DF	合计	基因登记号
Hap1	−	−	−	−	−	1	−	−	2	−	−	−	3	MT310974
Hap2	19	14	15	10	14	12	11	8	12	15	17	8	155	MT310975
Hap3	1	3	−	2	2	1	1	1	1	1	1	−	14	MT310976
Hap4	−	−	−	−	−	−	−	−	1	−	−	−	1	MT310977
Hap5	−	−	−	−	−	−	−	−	1	−	−	−	1	MT310978
Hap6	−	−	−	−	−	−	−	−	1	−	−	−	1	MT310979
Hap7	−	−	−	−	−	−	−	−	1	−	1	−	2	MT310980
Hap8	−	−	−	−	−	−	−	−	1	−	−	−	1	MT310981
Hap9	−	−	−	−	−	−	−	−	1	−	−	−	1	MT310982
Hap10	−	−	−	−	−	−	−	−	−	−	−	1	1	MT310983
Hap11	−	−	−	−	−	−	−	−	−	1	−	−	1	MT310984
Hap12	−	−	−	−	−	−	1	−	−	1	−	−	2	MT310985
Hap13	−	−	−	−	−	−	−	−	−	2	−	−	2	MT310986
Hap14	−	−	−	−	−	−	−	−	−	1	−	−	1	MT310987
Hap15	−	−	−	−	−	−	−	−	−	1	−	−	1	MT310988
Hap16	−	−	−	−	−	1	−	−	−	−	−	−	1	MT310989
Hap17	−	−	−	−	−	1	−	−	−	−	−	−	1	MT310990
Hap18	−	1	−	−	−	1	−	−	−	−	−	−	2	MT310991
Hap19	−	−	−	−	−	2	−	−	−	−	−	−	2	MT310992
Hap20	−	−	1	−	−	1	−	−	−	−	−	−	2	MT310993
Hap21	−	−	−	−	−	1	−	−	−	−	−	−	1	MT310994
Hap22	−	−	−	−	1	1	1	−	−	−	1	−	4	MT310995
Hap23	−	−	−	−	1	−	−	−	−	−	−	−	1	MT310996
Hap24	−	−	−	−	1	−	−	−	−	−	−	−	1	MT310997
Hap25	−	−	−	−	1	−	−	−	−	−	−	−	1	MT310998
Hap26	−	−	−	−	1	−	−	−	−	−	−	−	1	MT310999
Hap27	−	−	−	−	1	−	−	−	−	−	−	−	1	MT311000
Hap28	1	−	−	−	−	−	−	−	−	−	−	−	1	MT311001
Hap29	1	−	−	1	−	−	−	−	−	−	−	−	2	MT311002
Hap30	−	1	1	−	−	−	−	1	−	−	−	−	3	MT311003
Hap31	−	−	−	1	−	−	−	−	−	−	−	−	1	MT311004
Hap32	−	−	−	−	−	−	−	−	−	−	1	−	1	MT311005
Hap33	−	−	−	−	−	−	−	−	−	−	1	−	1	MT311006
Hap34	−	1	1	−	−	−	−	−	−	−	−	−	2	MT311007
Hap35	−	1	−	−	−	−	−	−	−	−	−	−	1	MT311008
Hap36	−	1	−	−	−	−	−	−	−	−	−	−	1	MT311009
Hap37	−	−	1	−	−	−	−	−	−	−	−	−	1	MT311010
Hap38	−	−	1	−	−	−	−	−	−	−	−	−	1	MT311011
Hap39	−	−	1	−	−	−	−	−	−	−	−	−	1	MT311012
Hap40	−	−	1	−	−	−	−	−	−	−	−	−	1	MT311013
合计	22	22	22	14	22	22	14	10	21	22	22	9	222	−
注：−代表未检测到单倍型。

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表 4 基于COⅠ基因序列的近亲拟相手蟹群体间遗传分化系数F_st值（对角线下）和群体内（对角线）及群体间（对角线上）遗传距离

Tab. 4 F-statistics (below diagonal) within populations and genetic distance within (diagonal) and between (above diagonal) populations of P. affine based on COⅠ gene

	LH	YX	ZH	YJ	LF	LQ	XW	SK	BH	FCG	YP	DF
LH	0.000 60	0.000 87	0.000 82	0.000 73	0.000 88	0.001 17	0.000 63	0.000 61	0.001 14	0.001 16	0.000 74	0.000 48
YX	−0.006 70	0.001 15	0.001 10	0.001 00	0.001 15	0.001 44	0.000 91	0.000 86	0.001 43	0.001 46	0.001 02	0.000 78
ZH	0.000 00	0.007 01	0.001 04	0.000 99	0.001 12	0.001 41	0.000 87	0.000 83	0.001 37	0.001 41	0.000 96	0.000 70
YJ	−0.014 01	−0.027 17	0.016 03	0.000 90	0.001 02	0.001 32	0.000 79	0.000 75	0.001 30	0.001 34	0.000 89	0.000 65
LF	−0.007 33	−0.010 64	0.006 35	−0.020 15	0.001 18	0.001 45	0.000 91	0.000 89	0.001 44	0.001 48	0.001 02	0.000 78
LQ	0.006 88	0.001 56	0.015 34	−0.005 18	−0.003 56	0.001 73	0.001 21	0.001 19	0.001 72	0.001 70	0.001 32	0.001 08
XW	−0.032 20	−0.017 28	−0.005 01	−0.019 64	−0.032 32	−0.013 10	0.000 70	0.000 65	0.001 20	0.001 22	0.000 78	0.000 53
SK	−0.022 01	−0.055 04	−0.028 66	−0.042 29	−0.038 04	−0.023 05	−0.036 58	0.000 65	0.001 17	0.001 21	0.000 76	0.000 51
BH	−0.004 57	0.000 93	0.001 05	−0.004 57	0.000 90	0.000 39	−0.012 07	−0.026 96	0.001 70	0.001 71	0.001 29	0.001 04
FCG	0.007 20	0.015 73	0.020 38	0.014 93	0.019 66	−0.014 23	0.000 47	−0.006 72	0.000 40	0.001 72	0.001 33	0.001 08
YP	−0.009 17	−0.005 71	−0.007 04	−0.003 57	−0.012 93	0.006 11	−0.029 92	−0.026 99	−0.004 28	0.021 51	0.000 89	0.000 63
DF	−0.015 02	−0.005 80	−0.027 68	0.009 76	−0.022 01	−0.013 50	−0.012 41	−0.003 32	−0.028 18	−0.007 85	−0.024 65	0.000 36

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表 5 近亲拟相手蟹12个群体的AMOVA分析

Tab. 5 Analysis of molecular variance (AMOVA) for the twelve P. affine populations

变异来源	自由度	平方和	变异组成	变异百分比/%	固定值F_ST
组群间	11	3.526	−0.001 38 ^Va	−0.4	−0.004 02 (p=0.757 6)
种群内	210	72.654	0.345 97 $^{{\rm{V_b}}} $	100.4
合计	221	76.18	0.344 59	100
注：V_a 表示组群间方差；V_b 表示组群内群体间方差。

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表 6 近亲拟相手蟹12个群体的中性检验和核苷酸不配对分布

Tab. 6 Neutral testes and mismatch distributions of nucleotide in twelve P. affine populations

群体	Tajima’s D		Fu’s F_s		核苷酸不配对分布
群体	D	p	F_s	p	τ	SSD	Rg
LH	−1.877 63	0.011 00	−2.205 61	0.006 00	3.000 00	0.002 13	0.343 72
YX	−1.778 56	0.019 00	−4.749 13	0.000 00	0.875 00	0.017 16	0.159 63
ZH	−2.139 60	0.001 00	−6.978 93	0.000 00	0.783 20	0.011 77	0.140 50
YJ	−1.278 26	0.085 00	−1.727 37	0.012 00	0.683 59	0.012 90	0.155 30
LF	−2.002 53	0.007 00	−6.347 57	0.000 00	0.894 53	0.016 49	0.156 56
LQ	−1.917 76	0.008 00	−7.818 78	0.000 00	1.166 02	0.005 87	0.092 15
XW	−1.670 53	0.026 00	−2.288 11	0.002 00	0.505 86	0.005 27	0.168 22
SK	−1.400 85	0.077 00	−1.163 94	0.036 00	0.490 23	0.005 79	0.182 72
DG	−2.162 55	0.004 00	−6.321 53	0.000 00	1.115 23	0.001 64	0.067 10
FCG	−1.715 70	0.018 00	−3.162 46	0.007 00	2.312 50	0.055 27	0.243 44
YP	−2.071 98	0.002 00	−4.121 61	0.000 00	0.705 08	0.000 06	0.131 67
DF	−1.088 23	0.191 00	−0.263 48	0.154 00	2.929 69	0.306 72	0.358 02
合计	−2.497 80	0.000 00	−29.929 97	0.000 00	0.714 84	0.000 00	0.950 00

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