臺灣博碩士論文加值系統

石首魚科 (Sciaenidae) 的魚種由於會發出聲音，又被稱為 croakers 或drums，包含68屬292個有效種，屬於鱸形目 (Perciformes) 下一個物種數眾多的科。該科的魚類大部分生活在太平洋、印度洋及大西洋的海水、半淡鹹水水域；僅有少數棲息在淡水中。對此全球廣泛分佈的類群而言，其經常引發生物地理學家進一步探討此類群的起源及其在時間、空間上的物種多樣性變化的呈現。然而，如石首魚這些非珊瑚礁魚類類群，我們對其歷史生物地理學的研究卻極為稀少。此外石首魚亦為生態及經濟上的重要海水魚。近幾十年來，石首魚科物種受到近岸漁業、商業性採集及捕撈蝦貨時的混獲威脅，其產量正在逐年減少中。為了制訂並施行有效的保育措施，對於石首魚物種分類知識及其間親緣關係的了解為首要目標。本研究目的為：1) 探討全球石首魚科內的親緣關係；2) 建構石首魚的生物地理，並加以探討其起源，進一步檢視所有可能造成現今石首魚地理分布型式的作用機制； 3) 就印度─西太平洋地區的石首魚之正確分類及種名有效性進行調查。
針對前兩項目的，本研究利用93種、52屬全球採樣的石首魚個體，利用兩個粒線體基因及四個核基因 (粒線體基因COI及Cyt b與核基因RAG1、RH、EGR1及EGR2B，共6619 bp) 重建其親緣關係樹。結果顯示石首魚科為一單系群。在此親緣關係樹中有15個支持度高的主要譜系 (Lineage)，其中有部分關係在先前的研究並未被提出過。其中8個屬為單系群，同時有8個屬非單系群。而8個棲息在淡水的石首魚種 (本研究分析包含5/6個淡水石首魚屬，8/25個種在)，根據其所分布的不同大陸各自形成三個不同的譜系。
利用化石證據輔助，針對歷史生物地理的研究結果呈現：現生種的石首魚起源於晚漸新世 (late Oligocene) 至早中新世 (Early Miocene) 的熱帶美洲。早中新世時經歷了兩次由起源地向外擴張的事件，而其中一次促使石首魚擴張至印度─西太平洋。印度─西太平洋特有的石首魚屬為單一祖先起源，經由區域內的物種分化造成此區為目前石首魚生物多樣性最高的海域。
此外，針對第三個目的，本研究分析了印度─西太平洋特有的18個石首魚屬、51個形態種 (Morpho-species)，包含308個從96個不同地區採集的個體。利用兩種不同的物種界定工具 (ABGD和GMYC) 分析COI基因，並藉由不同物種定義下的各前提 (例如：遺傳相似性、單系群、地理分布及形態特徵) 協助，結果顯示在此分析的印度─西太平洋石首魚包含60個分類單位 (Operational Taxonomic Units; OTUs)，此顯示為可能的新種或隱蔽種。此外，先前所建構之全球石首魚親緣關係樹中顯示的單系群屬亦得到再次的確認。然而由於雙棘原始黃姑魚屬 (Protonibea) 及毛鱨屬 (Megalonibea) 形成一單系群，在此我認為毛鱨屬應為無效的屬。
本研究提供石首魚科在現階段最為全面性的分子親緣關係研究。其貢獻除能有效解決此科魚類在系統分類上的問題，有助於增加我們對全球廣泛分布的非珊瑚礁魚種之歷史生物地理學的了解外，針對印度─西太平洋地區石首魚的親緣關係研究亦為未來石首魚分類研究的基礎。而這些基礎研究在管理石首魚漁業方面也可提供最為基本的觀念。

The family Sciaenidae, also known as croakers or drums, contains approximately 292 species in 68 currently recognized genera and is one of the large perciform families. Members within this family mostly occur in marine and brackish waters of the Atlantic, Indian and Pacific Oceans; only a few inhabit freshwaters. As the worldwide-distributed groups of living animals always attract the attention of biogeographers to document the origins and patterns of diversification in time and space, the knowledge of historical biogeography worldwide within the non-coral marine species is still very limited, such as the Sciaenidae. In addition, most of the sciaenid species are ecologically, economically and recreationally important fish. Since the past decades near-shore fishing, commercial trawling and even by-catch in shrimp fisheries threaten the sciaenid species all over the world. The fishery production has been declining yearly. In order to create and implement effective conservative strategies, taxonomic knowledge of conservative targets and clear phylogenetic relationships within Sciaenidae are essential. The aims of this study are 1) to infer the phylogenetic relationships of the global Sciaenidae; 2) to reconstruct the historical biogeography of the global Sciaenidae to investigate the origin and to test the hypotheses explaining the present-day biogeographic patterns of the global Sciaenidae; 3) to further review and clarify the systematics of the species within the sciaenid genera that are endemic to the Indo-West Pacific (IWP).
For the former two aims, a total of 93 globally sampled sciaenid species from 52 genera were used for reconstructing a molecular phylogeny of the global sciaenids based on two mitochondrial and four nuclear genes (i.e. mitochondrial COI and Cyt b plus nuclear RAG1, RH, EGR1, EGR2B gene; total 6619 bp). The partitioned maximum-likelihood analysis supports the monophyly of the family Sciaenidae. Within the inferred phylogenetic tree, fifteen main and well-supported lineages were identified; some of which have not been recognized previously. Eight genera for which two or more species were examined are monophyletic while eight others are not. The eight strictly freshwater sciaenid species (from five of six described genera) examined herein form three independent freshwater lineages/clades.
In addition, the historical biogeographical analysis concomitant with fossil evidence indicates that the crown group sciaenids originated and diversified in the tropical America during the Oligocene to Early Miocene before undergoing two range expansions. Later eastward dispersal events, subsequent diversification via vicariates (EA vs. IWP), and within region (e.g., IWP) diversification are hypothesized to account for their current global distribution and species diversity patterns.
For the third aim, the present study with the emphasis on the sciaenid genera endemic to the IWP (IWP clade). A total of 308 samples from 51 out of 91 recognized sciaenid morpho-species sampled from 96 different localities within the IWP clade were used in the conducting analyses. Species delimitation analyses conducted by using two different tools (ABGD and GMYC) based on COI gene dataset and other lines of evidence (genetic similarity, monophyly, geographic distribution and morphology) result in 60 OTUs (Operational Taxonomic Units) than expected. This indicates that possible cryptic and/or potential new species are present. The result from the phylogenetic analysis conducted with likelihood method confirms the monophyly of the IWP sciaenid clade. However, the genus Protonibea forms a monophyletic group with genus Megalonibea. This thus suggests that the Megalonibea is an invalid genus.
In summary, I provide the most comprehensive molecular systematic study of the Sciaenidae, which will advantage the future work with the sciaenids, especially to resolve several issues in their systematics, as well as to reliably reconstruct their historical biogeography. Additionally, the advanced phylogenetic study of those IWP endemic sciaenids provides an important framework for the taxonomic study of the family Sciaenidae. Furthermore, the results on DNA-based species delimitation analyses have increased the pace and stringency of our biodiversity assessments that could be served as a guideline for the management and the conservation of the IWP sciaenid species.

口試委員論文審定書 i
致謝 ii
Chapter 1 General Introduction 1
1.1 Croakers and drums, Sciaenidae 1
1.2 Fisheries facts of the Sciaenidae 2
1.3 Taxonomy of the Sciaenidae 3
1.4 Phylogeny of the Sciaenidae 5
1.5 Biogeography of the Sciaenidae 6
1.6 Sciaenids endemic to the Indo-West Pacific 8
1.7 The aims of this dissertation 9
Chapter 2 Phylogeny of the Sciaenidae 14
2.1 Introduction 14
2.2 Materials and Methods 14
2.2.1 Taxonomic sampling 14
2.2.2 Character sampling 15
2.2.3 Analytical methods 17
2.3 Results 18
2.4 Discussion 18
Chapter 3 Historical biogeography of the Sciaenidae 26
3.1 Introduction 26
3.2 Materials and Methods 26
3.2.1 Ethics statement 26
3.2.2 Sampling collection 27
3.2.3 Analytical methods 27
3.3 Results 30
3.3.1 Time-calibrated Phylogenetic 30
3.3.2 Habitat Preference Evolution 31
3.3.3 Ancestral Area Reconstruction 31
3.4 Discussion 32
3.4.1 The origin time of the Sciaenidae 32
3.4.2 Evolutionary Habitat Transitions 33
3.4.3 Region of Origin and Early Diversification of the Sciaenidae 35
3.4.4 Origin of Current Distribution and Diversity Pattern of the Sciaenidae 36
Chapter 4 Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade 46
4.1 Introduction 46
4.2 Materials and Methods 47
4.2.1 Ethics statement 47
4.2.2 Sample collection 47
4.2.3 DNA extraction, PCR amplification and sequencing 48
4.2.4 Analytical methods 49
4.3 Results and Discussions 53
4.3.1 Characteristics of sequence data 53
4.3.2 Inferred phylogenetic trees 54
4.3.3 Species delimitation and diversity 58
4.3.4 Cryptic diversity and necessity for further taxonomic consideration for the species within the IWP clade 60
Chapter 5 Conclusion 99
References 102
Appendix I – Sample list of phylogenetic relationship reconstruction. 122
Appendix II – Primers and PCR protocol used in this study. 132
Appendix III – Sample list of historical biogeography analysis. 133
Appendix IV – Publication 137

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