多基因联合揭示海南鲌的遗传结构与遗传多样性

doi:10.17520/biods.2021166

生物多样性 ›› 2021, Vol. 29 ›› Issue (11): 1505-1512. DOI: 10.17520/biods.2021166

• 研究报告: 动物多样性 • 上一篇下一篇

多基因联合揭示海南鲌的遗传结构与遗传多样性

向登高¹^,², 李跃飞², 李新辉², 陈蔚涛²^,^*(), 马秀慧¹^,^*()

1.贵州大学动物科学学院, 贵阳 550025
2.中国水产科学研究院珠江水产研究所, 广州 510380

收稿日期:2021-04-29 接受日期:2021-07-05 出版日期:2021-11-20 发布日期:2021-07-27
通讯作者: 陈蔚涛,马秀慧
作者简介:E-mail: lovemxh@126.com
*E-mail: ncuskchenweitao@163.com;
基金资助:
珠江渔业资源调查与评估创新团队项目(2020TD-10)

Population structure and genetic diversity of Culter recurviceps revealed by multi-loci

Denggao Xiang¹^,², Yuefei Li², Xinhui Li², Weitao Chen²^,^*(), Xiuhui Ma¹^,^*()

1 College of Animal Science, Guizhou University, Guiyang 550025
2 Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380

Received:2021-04-29 Accepted:2021-07-05 Online:2021-11-20 Published:2021-07-27
Contact: Weitao Chen,Xiuhui Ma

1. 附录1 本研究使用的引物信息.pdf(373KB)

摘要/Abstract

摘要：

海南鲌(Culter recurviceps)是我国华南地区重要经济鱼类, 由于受到近些年水利开发、过度捕捞、环境污染等诸多因素的影响, 其资源量快速下降, 亟需得到更多的关注和保护。为保护和合理开发海南鲌种质资源, 本研究采集了华南地区23个地理群体207尾海南鲌样本, 测定了2个线粒体基因(Cytb和ND2)并从Barcode of Life Data System数据库获得相对应线粒体COI基因, 结合多种分析方法(系统发育分析、分化时间估算、单倍型网状图、群体遗传分析和Mantel检验)对海南鲌的遗传结构和遗传多样性展开研究。系统发育分析和单倍型网状图表明华南地区海南鲌群体被分成3个谱系(I、II和III), 其中谱系I和III由珠江的群体组成, 谱系II由海南岛的群体组成。分化时间估算发现3个谱系之间的分化时间介于0.028-0.251 Ma之间, 表明华南地区更新世气候变化可能是造成海南鲌谱系分化的重要原因。群体遗传分析发现海南鲌群体之间存在极显著的遗传分化(F_ST = 0.511, P < 0.001), 并且符合距离隔离模式(R = 0.348, P = 0.0010)。群体动态历史分析表明, 海南鲌群体可能在0.010-0.025 Ma经历了群体扩张, 表明更新世的气候波动也影响了海南鲌的群体大小和分布。综上所述, 海南鲌群体由3个谱系组成, 更新世气候变化是导致3个谱系分化和影响海南鲌群体动态历史的重要因素。此外, 海南鲌群体之间的遗传分化也可能受到了空间距离的影响。

关键词: 海南鲌, 遗传结构, 遗传多样性, 多基因

Abstract

Aim: Culter recurviceps (Cypriniformes: Cyprinidae) is an economic fish species in South China. Nevertheless, the resources of this species declined rapidly during recent years due to water conservancy, overfishing, and environmental pollution. Therefore, more attention and conservation measure are needed for this species. Population genetic analyses can both reveal genetic diversity and population structure of particular species and provide implications for management and conservation of these species. The aim of this study is to investigate the population genetic structure and genetic diversity of C. recurviceps and further provide implications for the preservation and reasonable development of its resources.
Methods: We collected 207 individuals from 23 populations in the drainages in Southern China. With respect to the 207 individuals, two mitochondrial genes (Cytb and ND2) were sequenced and the corresponding mitochondrial COI gene was obtained from the Barcode of Life Data System (BOLD) database. We then combined the three genes to study the genetic structure and genetic diversity of C. recurviceps populations. Multiple analyses including phylogenetic analysis, divergence time estimates, haplotype network, population genetic analyses, and Mantel tests were employed.
Results: Phylogenetic analysis and haplotype network revealed that C. recurviceps populations contained three lineages (I, II and III). The members of lineages I and III contained populations from the Pearl River and the representatives of lineage II comprised of populations from the Hainan Island. Divergence time estimates indicated the three lineages were split between 0.028 and 0.251 million years ago (Ma), suggesting that Pleistocene climate change may have triggered the divergence of the three lineages. Population genetic analyses showed significant genetic differentiation (F_ST = 0.511, P < 0.001) and isolation by distance pattern (R = 0.348, P = 0.0010) was observed among C. recurviceps populations. Demographic analyses revealed that C. recurviceps populations might experience population expansion during 0.010-0.025 Ma, implying that Pleistocene climatic fluctuations have influenced the population size and distribution of C.recurviceps populations.
Conclusion: We observed that C. recurviceps populations in South China consisted of three mitochondrial lineages. Pleistocene climate changes have not only triggered the divergences of the three lineages, but also influenced the demographic history of C. recurviceps populations. Furthermore, spatial distance acted as a key factor that improved the population differentiation among C. recurviceps populations.

Key words: Culter recurviceps, population structure, genetic diversity, multi-loci

向登高, 李跃飞, 李新辉, 陈蔚涛, 马秀慧 (2021) 多基因联合揭示海南鲌的遗传结构与遗传多样性. 生物多样性, 29, 1505-1512. DOI: 10.17520/biods.2021166.

Denggao Xiang, Yuefei Li, Xinhui Li, Weitao Chen, Xiuhui Ma (2021) Population structure and genetic diversity of Culter recurviceps revealed by multi-loci. Biodiversity Science, 29, 1505-1512. DOI: 10.17520/biods.2021166.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2021166

https://www.biodiversity-science.net/CN/Y2021/V29/I11/1505

图/表 6

参考文献 28

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群体 Population	样本量 Sample size	经纬度 Locality
海南岛水系 Hainan Island drainage
白沙 Baisha (BS)	33	19˚13′ N/109˚26′ E
南丰 Nanfeng (NF)	15	19˚25′ N/109˚33′ E
定安 Dingan (DA)	4	19˚40′ N/110˚21′ E
珠江水系 Pearl River drainage
从江 Congjiang (CJ)	9	25˚44′ N/108˚55′ E
崇左 Chongzuo (CZ)	14	22˚16′ N/107˚22′ E
桂平 Guiping (GP)	14	23˚23′ N/110˚04′ E
武宣 Wuxuan (WX)	2	23˚35′ N/109˚40′ E
古竹 Guzhu (GZ)	16	23˚30′ N/114˚42′ E
惠州 Huizhou (HZ)	11	23˚06′ N/114˚24′ E
江门 Jiangmen (JM)	4	22˚34′ N/113˚07′ E
横沥 Hengli (HL)	1	22˚43′ N/113˚29′ E
开平 Kaiping (KP)	5	22˚22′ N/112˚41′ E
柳州 Liuzhou (LZ)	5	24˚18′ N/109˚23′ E
柳城 Liucheng (LC)	8	24˚38′ N/109˚14′ E
南宁 Nanning (NN)	7	22˚46′ N/108˚21′ E
清远 Qingyuan (QY)	5	23˚37′ N/113˚03′ E
梧州 Wuzhou (WZ)	13	23˚25′ N/111˚16′ E
濛江 Mengjiang (MJ)	1	23˚27′ N/110˚44′ E
永福 Yongfu (YF)	12	24˚59′ N/109˚59′ E
郁南 Yunan (YN)	11	23˚14′ N/111˚31′ E
思林 Silin (SL)	12	23˚30′ N/107˚20′ E
韶关 Shaoguan (SG)	2	24˚47′ N/113˚35′ E
平乐 Pingle (PL)	3	24˚37′ N/110˚38′ E
总计 Total	207

群体 Population	样本量 Sample size	经纬度 Locality
海南岛水系 Hainan Island drainage
白沙 Baisha (BS)	33	19˚13′ N/109˚26′ E
南丰 Nanfeng (NF)	15	19˚25′ N/109˚33′ E
定安 Dingan (DA)	4	19˚40′ N/110˚21′ E
珠江水系 Pearl River drainage
从江 Congjiang (CJ)	9	25˚44′ N/108˚55′ E
崇左 Chongzuo (CZ)	14	22˚16′ N/107˚22′ E
桂平 Guiping (GP)	14	23˚23′ N/110˚04′ E
武宣 Wuxuan (WX)	2	23˚35′ N/109˚40′ E
古竹 Guzhu (GZ)	16	23˚30′ N/114˚42′ E
惠州 Huizhou (HZ)	11	23˚06′ N/114˚24′ E
江门 Jiangmen (JM)	4	22˚34′ N/113˚07′ E
横沥 Hengli (HL)	1	22˚43′ N/113˚29′ E
开平 Kaiping (KP)	5	22˚22′ N/112˚41′ E
柳州 Liuzhou (LZ)	5	24˚18′ N/109˚23′ E
柳城 Liucheng (LC)	8	24˚38′ N/109˚14′ E
南宁 Nanning (NN)	7	22˚46′ N/108˚21′ E
清远 Qingyuan (QY)	5	23˚37′ N/113˚03′ E
梧州 Wuzhou (WZ)	13	23˚25′ N/111˚16′ E
濛江 Mengjiang (MJ)	1	23˚27′ N/110˚44′ E
永福 Yongfu (YF)	12	24˚59′ N/109˚59′ E
郁南 Yunan (YN)	11	23˚14′ N/111˚31′ E
思林 Silin (SL)	12	23˚30′ N/107˚20′ E
韶关 Shaoguan (SG)	2	24˚47′ N/113˚35′ E
平乐 Pingle (PL)	3	24˚37′ N/110˚38′ E
总计 Total	207

群体 Population	单倍型数 Number of haplotype	单倍型多样性 Haplotype diversity	核苷酸多样性 Nucleotide diversity	中性检测 Neutrality tests
群体 Population	单倍型数 Number of haplotype	单倍型多样性 Haplotype diversity	核苷酸多样性 Nucleotide diversity	Tajima’s D	Fu’s Fs
BS	7	0.383 (± 0.107)	0.0002 (±0.0001)	-1.75856**	-6.19981***
CJ	4	0.806 (± 0.089)	0.0021 (±0.0003)	1.29983	2.70828
CZ	7	0.879 (± 0.058)	0.0009 (±0.0001)	0.01278	-1.77070
GP	10	0.923 (± 0.060)	0.0011 (±0.0001)	-0.27622	-5.21979***
GZ	10	0.917 (± 0.049)	0.0013 (±0.0003)	-1.10830	-3.75174*
HZ	7	0.891 (± 0.074)	0.0014 (±0.0002)	-1.41142	-1.25974
KP	4	0.900 (± 0.161)	0.0019 (±0.0008)	-0.92693	0.35685
LZ	3	0.800 (± 0.164)	0.0026 (±0.0006)	1.25408	2.74649
LC	5	0.893 (± 0.086)	0.0018 (±0.0005)	-0.66317	0.49798
NF	2	0.133 (± 0.112)	0.0001 (±0.0001)	-1.15945	-0.64899
NN	3	0.762 (± 0.115)	0.0006 (±0.0002)	1.10686	0.78880
QY	5	1.000 (± 0.126)	0.0031 (±0.0006)	0.40617	-0.71434
WZ	12	0.987 (± 0.035)	0.0022 (±0.0004)	-1.15138	-6.16071***
YF	2	0.485 (± 0.106)	0.0004 (±0.0001)	1.35640	2.32787
YN	5	0.782 (± 0.107)	0.0011 (±0.0004)	-1.13653	0.36244
SL	9	0.909 (± 0.079)	0.0020 (±0.0004)	-0.32946	-2.27867
DA	1	NA	NA	NA	NA
SG	2	NA	NA	NA	NA
PL	1	NA	NA	NA	NA
WX	2	NA	NA	NA	NA
JM	4	NA	NA	NA	NA
MJ	1	NA	NA	NA	NA
HL	1	NA	NA	NA	NA
总计 Total	52	0.912 (± 0.012)	0.0023 (±0.0001)	-0.91788	-24.88587***

群体 Population	单倍型数 Number of haplotype	单倍型多样性 Haplotype diversity	核苷酸多样性 Nucleotide diversity	中性检测 Neutrality tests
群体 Population	单倍型数 Number of haplotype	单倍型多样性 Haplotype diversity	核苷酸多样性 Nucleotide diversity	Tajima’s D	Fu’s Fs
BS	7	0.383 (± 0.107)	0.0002 (±0.0001)	-1.75856**	-6.19981***
CJ	4	0.806 (± 0.089)	0.0021 (±0.0003)	1.29983	2.70828
CZ	7	0.879 (± 0.058)	0.0009 (±0.0001)	0.01278	-1.77070
GP	10	0.923 (± 0.060)	0.0011 (±0.0001)	-0.27622	-5.21979***
GZ	10	0.917 (± 0.049)	0.0013 (±0.0003)	-1.10830	-3.75174*
HZ	7	0.891 (± 0.074)	0.0014 (±0.0002)	-1.41142	-1.25974
KP	4	0.900 (± 0.161)	0.0019 (±0.0008)	-0.92693	0.35685
LZ	3	0.800 (± 0.164)	0.0026 (±0.0006)	1.25408	2.74649
LC	5	0.893 (± 0.086)	0.0018 (±0.0005)	-0.66317	0.49798
NF	2	0.133 (± 0.112)	0.0001 (±0.0001)	-1.15945	-0.64899
NN	3	0.762 (± 0.115)	0.0006 (±0.0002)	1.10686	0.78880
QY	5	1.000 (± 0.126)	0.0031 (±0.0006)	0.40617	-0.71434
WZ	12	0.987 (± 0.035)	0.0022 (±0.0004)	-1.15138	-6.16071***
YF	2	0.485 (± 0.106)	0.0004 (±0.0001)	1.35640	2.32787
YN	5	0.782 (± 0.107)	0.0011 (±0.0004)	-1.13653	0.36244
SL	9	0.909 (± 0.079)	0.0020 (±0.0004)	-0.32946	-2.27867
DA	1	NA	NA	NA	NA
SG	2	NA	NA	NA	NA
PL	1	NA	NA	NA	NA
WX	2	NA	NA	NA	NA
JM	4	NA	NA	NA	NA
MJ	1	NA	NA	NA	NA
HL	1	NA	NA	NA	NA
总计 Total	52	0.912 (± 0.012)	0.0023 (±0.0001)	-0.91788	-24.88587***

	BS	CJ	CZ	WG	GZ	JH	NF	HZ	KP	ZC	MZ	NN	QY	SL	YF	YN
BS	0.000	***	***	***	***	***	NS	***	***	***	***	***	***	***	***	***
CJ	0.816	0.000	*	*	**	NS	***	NS	NS	NS	NS	NS	NS	NS	*	NS
CZ	0.859	0.160	0.000	NS	***	NS	***	***	NS	*	NS	NS	***	NS	NS	NS
WG	0.838	0.157	0.000	0.000	**	*	***	**	NS	NS	NS	NS	*	*	NS	NS
GZ	0.842	0.260	0.211	0.111	0.000	*	***	NS	*	*	NS	***	***	**	***	***
JH	0.849	0.000	0.237	0.234	0.307	0.000	***	*	NS	NS	NS	NS	NS	NS	*	*
NF	0.000	0.753	0.834	0.802	0.803	0.795	0.000	***	***	***	***	***	***	***	***	***
HZ	0.868	0.264	0.288	0.175	0.025	0.292	0.830	0.000	NS	*	NS	***	**	*	***	***
KP	0.876	0.000	0.021	0.021	0.142	0.000	0.847	0.150	0.000	NS	NS	NS	NS	NS	NS	NS
ZC	0.747	0.000	0.091	0.043	0.103	0.000	0.664	0.119	0.000	0.000	NS	NS	NS	NS	*	NS
MZ	0.765	0.050	0.010	0.000	0.036	0.058	0.691	0.057	0.000	0.000	0.000	NS	*	NS	NS	NS
NN	0.899	0.100	0.083	0.061	0.290	0.192	0.906	0.372	0.136	0.020	0.078	0.000	*	NS	NS	NS
QY	0.841	0.007	0.351	0.344	0.373	0.000	0.779	0.361	0.046	0.062	0.146	0.299	0.000	NS	**	*
SL	0.800	0.000	0.068	0.085	0.168	0.000	0.735	0.185	0.000	0.003	0.000	0.105	0.102	0.000	NS	NS
YF	0.913	0.211	0.000	0.024	0.209	0.324	0.921	0.314	0.053	0.113	0.028	0.227	0.429	0.066	0.000	NS
YN	0.854	0.093	0.000	0.000	0.161	0.146	0.821	0.228	0.000	0.043	0.000	0.107	0.218	0.013	0.000	0.000

多基因联合揭示海南鲌的遗传结构与遗传多样性

Population structure and genetic diversity of Culter recurviceps revealed by multi-loci

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