IOCAS-IR  > 海洋生物分类与系统演化实验室
印度-西太平洋鲳属鱼类 系统分类、起源与演化研究
韦杰鸿
Subtype博士
Thesis Advisor徐奎栋
2024-05-17
Degree Grantor中国科学院大学
Place of Conferral中国科学院海洋研究所
Degree Name理学博士
Keyword鲳属 物种多样性 分布格局 起源演化 本地适应
Abstract

鲳属隶属于辐鳍鱼纲、远洋鱼系、鲭形目、鲳科,是印度-西太平洋海域沿岸国家重要的海洋渔业资源和经济鱼类。我国是鲳属渔业资源捕捞和利用大国,以银鲳为主的鲳属鱼类年捕捞量达30万吨,年捕捞量和外贸进出口总量分别约占全球鲳科产值的75%和80%。由于过度捕捞和环境变迁,该物种的渔业资源近年来出现了明显的衰退。鲳属物种由于形态近似,多个物种的有效性和地理分布依然存在争议,相关研究经常发生种名误用或误鉴定,厘清鲳属物种分类和分布格局势在必行。目前亟待解决的科学问题包括:①全球鲳属物种的有效性及鉴定标准如何确定?②全球鲳属物种多样性分布格局如何?其起源中心和主要驱动因素是什么?③银鲳种群遗传多样性形成和维持机制如何?与古地质气候事件和现代海洋环境的存在何种关系?

本研究针对上述科学问题,基于中国科学院海洋生物标本馆收藏的鲳属4个有效物种(银鲳、灰鲳、珍鲳和刘氏鲳)的模式标本,以及课题组自2009-2021年间自我国、马来西亚、印度、伊拉克、科威特和巴林6国收集的209个鲳属肌肉样品及其凭证标本,结合形态分类学和分子系统发育学研究方法,开展了印度-西太平洋鲳属鱼类系统分类、起源与演化研究。本研究获取了准确鉴定的209个鲳属物种样本的Cox1Cytb基因序列,评估了其作为鲳属物种鉴定DNA条形码的可行性。研究结果显示,Cytb序列拥有更多的种间变异位点,更适用于鲳属物种鉴定。基于Cox1Cytb串联数据进行的系统发育和物种界定分析结果均显示,209个鲳属肌肉样本共包含7个鲳属物种,分别为银鲳Pampus argenteus (Euphrasen, 1788)、素鲳P. candidus (Cuvier, 1829)、中国鲳P. chinensis (Euphrasen, 1788)、灰鲳P. cinereus (Bloch, 1795)、刘氏鲳P. liuourum Liu & Li, 2013、珍鲳P. minor Liu & Li, 1998和翎鲳P. punctatissimus (Temminck & Schlegel, 1845)。使用这些DNA条形码资料进一步鉴定和分析了全球数据库的全部鲳属线粒体序列,证明了全球目前仅存在上述7种鲳属物种。过往研究报道的“镰鲳”序列实际上均为银鲳,镰鲳是银鲳的同物异名。秀鲳P. griseus (Cuvier, 1833)灰鲳的序列数据在系统发育树中聚为1个单系群,二者的分化程度极低,物种界定分析显示二者为同一物种,因此秀鲳应视为后者的同物异名。刘氏鲳与其近似种——灰鲳和素鲳在形态和分子遗传上均存在明确差异,应视为有效物种。

为认识鲳属物种的分布格局,本研究基于全球序列的采集样点信息,绘制了全球鲳属物种的分布图。结果显示,银鲳实际上广泛分布于西太平洋,北至日本和俄罗斯沿岸海域,而非仅局限于台湾海峡以南的南海北部海域;灰鲳不仅分布于孟加拉湾和阿拉伯海东岸,阿拉伯湾亦存在其野生群体;刘氏鲳仅分布于东南亚至我国长江口以南海域,在印度洋没有分布,因此刘氏鲳与模式产地位于印度南部沿海的灰鲳应为不同物种。

利用线粒体全基因组的分歧时间和祖先分布的推断分析表明,鲳属起源于大约8.35-11.33百万年前(晚中新世,late Miocene)的印度-太平洋的中部海域,可能意味着鲳属起源与印澳群岛生物多样性热点的崛起有关。姊妹种灰鲳刘氏鲳的分化可追溯至1.20-1.72百万年前,可能与中更新世过渡期(Mid Pleistocene Transition)的冰川隔离有关。

使用重测序技术获取了我国沿海不同纬度的6个地理群体共计117尾银鲳的基因组草图(draft genome)。邻接树、主成分分析和Admixture分析均显示6个群体间无明显谱系分化,且大部分基因位点分化与地理距离无关,表q明6个群体共同构成1个遗传种群。然而,经过Mantel检验却发现有21个100 Kb基因组滑窗存在显著的Isolation by distance现象(p < 0.05),其中亦包含了1,607个存在Isolation by distance现象的核苷酸多态位点,意味着这些位点与基因组区域可能在不同地理群体间发生了本地适应。基于功能注释发现这些滑窗内包含了18个参与神经元信号传导、突触可塑性调节的基因(如Dlgap1Cacng2Pten等)和7个参与生物钟核心基因表达调控的重要基因(Crtc1Paip2JunPtenPde4bPlcl1Grm1),分析显示不同纬度海域的生境差异(如光周期、温度和盐度)可能驱动了银鲳群体神经活动和昼夜节律的本地适应。同时,1,607个存在Isolation by distance现象的位点中,96.02%为非编码位点,仅有28个位点为非同义突变位点,表明银鲳群体的本地适应可能主要通过基因表达调控实现,而非蛋白功能改变。

本研究基于馆藏模式标本、新鲜标本和全球线粒体序列数据,综合运用多种分子系统学分析方法,澄清了银鲳、镰鲳、灰鲳、素鲳、刘氏鲳和秀鲳等多个物种的有效性问题,确定了世界鲳属包含7个有效物种,即银鲳、素鲳、中国鲳、灰鲳、刘氏鲳、珍鲳和翎鲳,揭示了世界鲳属物种多样性分布格局。研究发现鲳属起源、分化与历史重大地质和气候事件存在着时空联系。以银鲳为例,探讨了鲳属物种潜在的跨纬度本地适应现象及其可能形成机制。研究结果为鲳属相关研究提供了坚实的分类学依据,对查清鲳属渔业资源现状,促进鲳属渔业资源保护和可持续利用研究具有重要意义。

Other Abstract

The Pampus species (pomfrets), which belong to Actinopterygii, Pelagiaria, Scombriformes, and Stromateidae, are commercially important species for coastal countries in the Indo-Pacific region. China is one of the major countries that consume the stromateid fishery resources, with its annual catch and total foreign trade value accounted for about 75% and 80% of the global value, respectively. Recently, the annual catch of pomfrets mainly Pampus argenteus (Euphrasen, 1788) in China has been over 300,000 tons. Due to overfishing and environmental changes, fishery resource of P. argenteus is now facing obvious decline. It is imperative to perform in-depth investigation on their current fishery resources and develop specific aquacultural technology to promote the sustainable utilization of the Pampus fishery resources. However, due to their highly similar external morphology, misidentification and taxonomic issues frequently occur in the Pampus researches, seriously affecting the reliability and repeatability of the researches.

The Institute of Oceanography, Chinese Academy of Sciences preserves type specimens for P. argenteus, P. cinereus (Bloch, 1795), P. minor Liu & Li, 1998 and P. liuorum Liu & Li, 2013, and has published a series of taxonomic works on the genus, which laid a solid foundation for clarifying the species diversity and classification of the genus Pampus. From 2009 to 2021, the Institute has established a sample bank for genus Pampus, including 209 pieces of muscle samples and their voucher specimens collected from China, Malaysia, India, Iraq, Kuwait and Bahrain. Based on these materials, this research carried out a study on the systematic classification, origin and evolution of the Pampus species in the Indo-West Pacific, with an emphasis the following three dimensions: (1) Validities and diagnoses for the Pampus species; (2) The global species diversity and geographical distributions of genus Pampus, and the driving factor for their evolution; (3) Population structures of P. argenteus and its relation to geographic events and modern ocean environment.

Based on the significant taxonomic works, type specimens of the Pampus species, and phylogenetic methods, 74 muscle samples were accurately identified in this study, with their Cox1 and Cytb sequences amplified as the DNA barcodes identification of the Pampus species. The results show that the Cytb sequence with more interspecific variations is a suitable barcoding marker to identify the Pampus species. Phylogenetic analyses and species delimitations based on Cox1 and Cytb data showed that all the 74 muscle samples had been divided into seven species. They are, based on their morphologies, P. argenteus, P. candidus (Cuvier, 1829), P. chinensis (Euphrasen, 1788), P. cinereus, P. liuorum, P. minor and P. punctatissimus (Temminck & Schlegel, 1845). The mitochondrial sequences from the global database were further identified and analyzed based on the obtained barcodes, which firmly supported that there are only seven Pampus species reported around the world. Sequences of P. echinogaster Basilewsky, 1855 reported in previous studies are actually P. argenteus, and P. echinogaster should be thus treated as a junior synonym of P. argenteus. The sequence of P. griseus (Cuvier, 1833) is identical to that of P. cinereus and therefore should be considered as a synonym for the latter. In contrast, the geographic distributions, morphology and genetic characters of P. liuorum are clearly distinct from its close-related species P. candidus and P. cinereus, which thus should be treated as a valid species.

A map indicating the global species diversity and distributions of genus Pampus has been plotted based on the sample information of the global mitochondrial sequences, which revealed the new boundaries for the Pampus species. The results show that silver pomfret is actually widely distributed in the West Pacific, from the northern South China Sea to coastal Japan and Russia, rather than just limited to the waters south to the Taiwan Strait; P. cinereus is widely distributed in the Indian Ocean, including the Arabian Sea and Arabian Gulf. P. liuorum is only distributed from coastal Southeast Asia to the Yangtze River estuary, and thus could not be treated as P. cinereus, which typed in India.

Divergence time inference and ancestral distribution reconstruction based on mitogenomic data suggests that the most common ancestor of genus Pampus is originated in the central Indo-Pacific waters about 8.35-11.33 million years ago (late Miocene), associated with the rise of the Indo-Australian Archipelago Biodiversity Hotspots. The divergence of the two closely related species, P. cinereus and P. liuorum can be traced back to 1.20-1.72 million years ago, which might be related to the glacial isolation during the Mid Pleistocene Transition.

Analyses on the whole genome resequencing data revealed absence of population differentiation of P. argenteus along the coast of China. Neighbour-joing tree, principal component analysis and Admixture analysis showed that there is no obvious lineage differentiation among the six populations, and correlation between geographic distance and genetic differentiations among most gene loci was insignificant, supporting that the six populations constituted a single population among sampling sites. However, Mantel test discovered significant isolation by distance pattern in 21 100-Kb sliding windows (p < 0.05), including 1,607 single nucleotide polymorphic sites with significant isolation by distance. The functional annotations revealed that these sliding windows contained 17 genes involved in neuronal signal transduction and synaptic plasticity (such as Dlgap1, Cacng2, and Pten, etc.) and 6 important genes involved in the expression regulations of the core circadian clock genes (Crtc1, Paip2, Jun, Pde4b, plcl1 and Grm1). This suggests that latitude cline of environmental factors, such as photoperiod, temperature, and salinity, may drive local adaptations in neural activity and circadian rhythms among individuals among sites. Meanwhile, 96.02% of 1,607 isolated by distance loci belongs to non-coding regions, whereas only 28 loci were non-synonymous mutations, suggesting that the local adaptation of the fish population may be mainly achieved by transcriptional and translational regulations rather than changes in protein functions.

Based on type materials and molecular methods, we verified validities of numerous important species names in the genus Pampus, clarified their species diversity and distributions. It is revealed that evolutionary events in the genus Pampus were, to a certain extent, closed to the key palaeogeographical events. The potential local adaptations of P. argenteus and their association with latitude cline was uncovered. The results produced in this study could provide a reliable taxonomic basis for the related researches on genus Pampus, which are of great significance for further conservation and sustainable utilization of the Pampus fishery resources.

MOST Discipline Catalogue理学 ; 理学::海洋科学
Language中文
Table of Contents

第1章 绪论... 1

1.1 鲳属分类学研究进展及存在问题... 1

1.1.1 鲳属的分类地位和鉴别特征... 1

1.1.2 鲳属亟待解决的物种分类问题... 4

1.2 鲳属物种的地理分布问题... 9

1.3 鲳属物种起源中心与驱动物种分化的可能因素... 12

1.4 现代海洋生物种群遗传多样性格局及其可能形成机制... 13

1.5 论文选题的意义和科学问题... 18

第2章 基于DNA条形码技术的鲳属系统分类学研究... 20

2.1 引言... 20

2.2 材料与方法... 21

2.2.1 样品采集与物种鉴定... 21

2.2.2 DNA提取、扩增和测序... 25

2.2.3 系统发育和条形码间隙分析... 26

2.2.4 物种界定分析... 27

2.3 结果... 28

2.3.1 Cox1和Cytb 的序列变异指数和条形码间隙... 28

2.3.2 系统发育分析... 28

2.3.3 物种界定... 28

2.4 讨论... 32

2.4.1 灰鲳、刘氏鲳和素鲳的有效性问题... 32

2.4.2 Liu et al.(2013a)重新描述的银鲳及其新模标本的有效性... 33

2.4.3 Cox1和Cytb条形码在鲳属物种鉴定中的适用性评估... 33

2.5 小结... 34

第3章 基于全球线粒体序列数据揭示鲳属物种多样性和地理分布格局... 35

3.1 引言... 35

3.2 材料与方法... 35

3.2.1 技术路线... 35

3.2.2 馆藏鲳属鱼类标本线粒体序列数据... 36

3.2.3 全球鲳属鱼类线粒体序列数据... 39

3.2.4 数据整理、筛选和比对... 39

3.2.5 物种鉴定、系统发育学分析和物种界定... 39

3.2.6 分化时间推估... 40

3.2.7 祖先分布格局重建... 41

3.3 结果... 41

3.3.1 鲳属全球线粒体数据集... 41

3.3.2 物种鉴定、系统发育学分析和物种界定分析... 42

3.3.3 鲳属物种分布格局... 43

3.3.4 鲳属物种分化时间... 47

3.4 讨论... 47

3.4.1 全球线粒体大数据分析揭示鲳属分类新证据... 47

3.4.2 鲳属的起源与演化... 50

3.4.3 全球数据在解决生物多样性和分布问题上的优缺点... 50

3.5 小结... 51

第4章 我国沿岸银鲳地理群体遗传结构与本地适应现象... 52

4.1 引言... 52

4.2 材料与方法... 52

4.2.1 样品采集... 52

4.2.2 DNA测序和SNP检测... 52

4.2.3 种群结构与多样性分析... 53

4.2.4 种群动态历史分析... 53

4.2.5 基于IBD筛选银鲳种群的受选择滑窗及SNP位点... 54

4.3 结果... 54

4.3.1 测序和SNP检测结果... 54

4.3.2 多样性指数、pairwise Fst和pairwise XP-CLR.. 56

4.3.3 种群结构、基因流和种群动态历史... 57

4.3.4 各样点环境差异... 57

4.3.5 基于IBD筛选的受选择滑窗和SNP位点... 63

4.4 讨论... 67

4.4.1 种群起源与洄游习性对我国沿岸银鲳地理群体遗传结构的可能影响... 67

4.4.2 基因表达调控可能是银鲳地理种群本地适应的重要方式... 68

4.4.3 纬度梯度可能驱动银鲳神经活动的本地适应... 69

4.4.4 光周期差异可能驱动银鲳生物钟调控的本地适应... 71

4.4.5 温度差异可能驱动银鲳群体胁迫响应相关基因的分化... 73

4.5 小结... 73

第5章 结论与展望... 75

参考文献... 78

附录一 鲳属全球线粒体序列数据和鉴定结果... 97

附录二 银鲳染色体水平高质量基因组测定... 168

附录三 缩写与全称... 185

致 谢... 191

作者简历及攻读学位期间发表的学术论文与其他相关学术成果... 193

Document Type学位论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/185216
Collection海洋生物分类与系统演化实验室
Recommended Citation
GB/T 7714
韦杰鸿. 印度-西太平洋鲳属鱼类 系统分类、起源与演化研究[D]. 中国科学院海洋研究所. 中国科学院大学,2024.
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