唐鱼养殖种群与广州附近4个野生种群的遗传关系

doi:10.17520/biods.2019290

生物多样性 ›› 2020, Vol. 28 ›› Issue (4): 474-484. DOI: 10.17520/biods.2019290

• 研究报告: 动物多样性 • 上一篇下一篇

唐鱼养殖种群与广州附近4个野生种群的遗传关系

李潮¹,金锦锦¹,罗锦桢^1,²,王春晖^1,³,王俊杰¹,赵俊^1,^*()

1 广东省水产健康安全养殖重点实验室, 广东省水产优质环保养殖工程技术研究中心,广州市亚热带生物多样性与环境生物监测重点实验室, 华南师范大学生命科学学院, 广州 510631
2 佛山南海狮山石门高级中学, 广东佛山 528225
3 广州金域医学检验中心有限公司, 广州 510330

收稿日期:2019-09-17 接受日期:2019-12-24 出版日期:2020-04-20 发布日期:2020-06-15
通讯作者: 赵俊
基金资助:
国家自然科学基金(31372178);国家自然科学基金(31772430);国家科技基础平台项目(2005DKA21402);中国-东盟海上合作基金(CAMC-2018F);国家留学基金(201906750010);广东省高校青年优秀科研人才国际培养计划(2018010162);华南师范大学拔尖研究生联合培养项目

Genetic relationships of hatchery populations and wild populations of Tanichthys albonubes near Guangzhou

Chao Li¹,Jinjin Jin¹,Jinzhen Luo^1,²,Chunhui Wang^1,³,Junjie Wang¹,Jun Zhao^1,^*()

1 Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631
2 Foshan Nanhai Shimen Senior High School, Foshan, Guangdong 528225
3 Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou 510330

Received:2019-09-17 Accepted:2019-12-24 Online:2020-04-20 Published:2020-06-15
Contact: Jun Zhao

摘要/Abstract

摘要：

唐鱼(Tanichthys albonubes)是为数不多的几种原产中国的世界性观赏鱼类之一。自2003年以来, 多个唐鱼野生种群相继被发现, 其濒危状态和等级由野外灭绝降为极危。为研究唐鱼养殖种群与广州附近野生种群之间的遗传关系, 本文分析了唐鱼3个代表性养殖种群和4个野生种群, 共计186个样本的Cyt b基因、2个核基因(ENC1和RAG1)以及13个微卫星位点数据。基于K2P模型的遗传距离结果显示, 唐鱼野生种群间的遗传距离在0.005-0.015之间, 养殖种群间的遗传距离为0.001-0.009。系统发育分析表明, 唐鱼养殖种群包含4个单倍型谱系分支, 其中2个分别与广州附近2个野生种群聚在一起, 另外2个分别独立成支。单倍型网络亲缘关系分析显示, 清远种群只有1个单倍型且与芳村养殖种群共享, 芳村养殖种群拥有最多的单倍型。基于微卫星数据的STRUCTURE分析表明, 所有种群最佳分簇数为2, 清远种群与养殖种群聚为一簇, 良口和石门种群聚为另一簇。主成分分析结果显示, 养殖种群高度重叠并能与野生种群分开, 清远种群与养殖种群存在部分重叠。利用IMa3的基因流分析表明, 存在清远种群至芳村养殖种群的单向基因流。综合本文结果, 作者认为唐鱼养殖种群应起源于广州附近多个野生种群。清远种群来源于养殖种群中的芳村养殖种群。建议在未来唐鱼的保护策略中, 应禁止不规范的放流活动并且禁止将不同野生种群补充至养殖种群, 同时加强唐鱼养殖种群和野生种群的遗传资源管理和持续监测。

关键词: Tanichthys albonubes, 线粒体基因, 核基因, 微卫星, 基因流

Abstract

Tanichthys albonubes is a popular ornamental fish species which had been believed to be extinct in the wild in China. Since 2003, many wild populations have been found on Hainan and Guangxi provinces and therefore the conversation status has been modified to be Critically Endangered. We investigated the genetic relationships of hatchery populations of T. albonubes to their wild populations near Guangzhou. To study these genetic relationships, multilocus data (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) from 186 individuals from three hatchery populations and four wild populations around the city of Guangzhou were analyzed. The K2P genetic distances based on the Cyt b gene among wild populations and hatchery populations of T. albonubes ranged from 0.005 to 0.015, and from 0.001 to 0.009, respectively. Phylogenetic relationships showed hatchery population Fangcun contained four mitochondrial clades, two of which grouped with haplotypes from two wild populations near Guangzhou while the remaining clustered separately. The haplotype networks revealed that the Qingyuan population consisted of one shared haplotype with population Fangcun, which had greater haplotype diversity than all other populations. STRUCTURE analyses from the hatchery and wild populations suggested these populations could be grouped into two clusters (K = 2), one of which was formed by a hatchery population and a Qingyuan population while the other was formed by two wild populations. Principal component analysis showed that hatchery populations and Qingyuan populations overlapped with some degree of genetic variation with these cultured stocks. Directional gene flow was detected from population Qingyuan to population Fangcun using IMa3 programme. Based on these findings, we conclude that population Fangcun originated from multiple wild populations near Guangzhou and subsequently served as the ancestor of cultured populations in Singapore and Canada. We propose that irregular releases of cultured stocks of T. albonubes should be forbidden and captive hatchery using different wild populations should be prevented. At the same time, genetic resources management and sustained monitoring of hatchery and wild populations of T. albonubes should be reinforced in the future.

Key words: Tanichthys albonubes, mitochondrial DNA, nuclear gene, microsatellite, gene flow

李潮,金锦锦,罗锦桢,王春晖,王俊杰,赵俊 (2020) 唐鱼养殖种群与广州附近4个野生种群的遗传关系. 生物多样性, 28, 474-484. DOI: 10.17520/biods.2019290.

Chao Li,Jinjin Jin,Jinzhen Luo,Chunhui Wang,Junjie Wang,Jun Zhao (2020) Genetic relationships of hatchery populations and wild populations of Tanichthys albonubes near Guangzhou. Biodiversity Science, 28, 474-484. DOI: 10.17520/biods.2019290.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019290

https://www.biodiversity-science.net/CN/Y2020/V28/I4/474

图/表 6

图1 本研究中唐鱼4个野生种群的采样地点(种群代号同表1)

Fig. 1 Sampling location of four wild populations of Tanichthys albonubes in this study. Population codes refer to Table 1.

表1 本研究的唐鱼样品信息

Table 1 Sampling information of Tanichthys albonubes of the present study

种群 Population	代号 Code	所属谱系 Lineage*	样本量 Sample size*
种群 Population	代号 Code	所属谱系 Lineage*	mtDNA	nuDNA	Microsatellites
养殖种群 Hatchery populations
广州芳村 Fangcun, Guangzhou, China	FC	A	30	30	30
新加坡 Singapore	SIG	A	24	24	30
加拿大 Canada	CA	A	12	12	12
野生种群 Wild populations
广州从化良口 Liangkou, Conghua, Guangzhou, China	CL	A	30	30	30
广州从化石门 Shimen, Conghua, Guangzhou, China	SM	A	30	30	30
清远 Qingyuan, China	QY	A	30	30	30
外类群
深圳 Shenzhen, China	SZ	A	30	-	-
总计 Total			186	156	162

表2 基于线粒体Cyt b基因的唐鱼种群间K2P遗传距离(种群代号同表1)

Table 2 K2P genetic distance among seven populations of Tanichthys albonubes based on Cyt b gene. Population codes refer to Table 1.

种群Populations	芳村 FC	新加坡SIG	加拿大CA	良口 CL	石门 SM	清远 QY
新加坡 SIG	0.008
加拿大 CA	0.009	0.001
良口 CL	0.006	0.006	0.007
石门 SM	0.009	0.009	0.010	0.007
清远 QY	0.007	0.001	0.002	0.005	0.008
深圳 SZ	0.013	0.014	0.015	0.012	0.015	0.014

图2 基于Cyt b基因的唐鱼系统发育树和单倍型网络图(种群代号同表1)。(A)基于Cyt b基因的贝叶斯树(BI tree)和最大似然树(ML tree)。*号表示后验概率(posterior probabilities, PP) ≥ 0.90和自举值(bootstrap values, BS) ≥ 90; (B)基于Cyt b基因的单倍型网络图(线上短线表示变异步数)。

Fig. 2 Phylogenetic trees and haplotype networks of Tanichthys albonubes based on Cyt b gene. Population codes refer to Table 1. (A) Bayesian inference (BI) and maximum-likelihood (ML) trees of T. albonubes based on Cyt b gene. The asterisks on the branches indicate posterior probabilities (PP) ≥ 0.90 and bootstrap values (BS) ≥ 90. (B) Haplotype networks of T. albonubes based on Cyt b gene (segments above lines indicate the number of mutations).

图3 唐鱼养殖种群和野生种群的种群结构分析(种群代号同表1)。(A)基于13个微卫星位点的STRUCTURE结果图(K = 2); (B) K取不同值时的ΔK值; (C)基于13个微卫星位点的主成分分析。

Fig. 3 Population structure analysis of hatchery and wild populations of Tanichthys albonubes. (A) STRUCTURE plots of K = 2 based on 13 microsatellite loci; (B) ΔK values of the different number of clusters (K); (C) PCA analysis based on 13 microsatellite loci. Population codes refer to Table 1.

图4 唐鱼养殖种群和野生种群间的基因流估算(种群代号同表1)。灰色箭头和方框代表tu的边界值。tu: 种群分开后所经历的时间。绿色箭头代表基因流的方向, 其上数字表示基因流的大小。图中只显示统计上显著的值, 显著性水平: * P < 0.05; ** P < 0.01。

Fig. 4 Gene flow estimation among hatchery and wild populations of Tanichthys albonubes. Grey arrows and boxes were marginal distribution values in demographic units. tu means time since ancestral population splitting. Green arrows and the numbers above them showed the gene flows (2Nm values) and their directions. Only statistically significant cases of gene flow are presented. * P < 0.05, ** P < 0.01. Population codes refer to Table 1.

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唐鱼养殖种群与广州附近4个野生种群的遗传关系

Genetic relationships of hatchery populations and wild populations of Tanichthys albonubes near Guangzhou

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