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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 陳韋仁(Wei-Jen Chen) | |
| dc.contributor.author | Pakorn Tongboonkua | en |
| dc.contributor.author | 董木華 | zh_TW |
| dc.date.accessioned | 2021-06-17T06:00:41Z | - |
| dc.date.available | 2019-02-20 | |
| dc.date.copyright | 2019-02-20 | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2019-02-11 | |
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A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869–2876. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/71435 | - |
| dc.description.abstract | 鮃科是鰈形目中的第二大科，目前已知有20屬174物種。該科的成員分佈於熱帶及溫帶海域並從淺海到深海皆有分佈。鮃科在熱帶印度-西太平洋的物種多樣性最高(113種)，其次是和大西洋（30種）再者為東太平洋（20種）。儘管其物種數多，但我們對於鮃科內各個物種之間的親緣關係之認知甚少, 而對其生物多樣性的研究也不完整。因此, 本研究的目的是：1）利用分子生物學的方法重建鮃科魚類的親緣關係; 2）透過Tropical Deep-Sea Benthos (TDSB) program計劃的採集策略及整合性之分折方法(包含物種界定分析)以發掘該科的隱藏性物種多樣性; 3）基於在此建立的鮃科魚類的親緣關係此檢視鮃科魚類的棲息地（深海與淺海）演化。本研究透過TDSB 計劃的15個主要在西太平洋作業的海洋探勘航次和在日本，馬來西亞，泰國，台灣和越南的漁港實地採集活動，共收集了202個標本（60種，14屬）。進行本研究分子分析的兩個資料組 (dataset) 有兩個：多基因資料組包括三個遺傳標記（COI，RH和RAG1）的序列，該資料組用於重建鮃科物種之間的親緣關係; 第二個資料組由來自常用於DNA條碼 (DNA Barcode) 標記的COI基因的序列組成。這資料組包括新獲得的201個序列和從GenBank/Bold數據庫中下載的258個序列; 該資料組主要用於物種界定分析。基於多基因資料組所推衍的親緣關係結果顯示，20個屬中有4個是非單系的，分別是羊舌鮃屬 (Arnoglossus, 4個譜系），左鮃屬（Laeops, 3個譜系），擬鮃屬（Parabothus, 3個譜系）和鰜鮃屬（Psettina 2個譜系）。基於親緣樹（bPTP）和基於遺傳距離（ABGD）方法的物種界定分析結果中, 本研究得到85個彼此互相吻合的OTUs (推定物種)。進一步根據物種的形態證據和其他判定準則，如OTU之水深和地理分佈之考量，最後修訂出108種物。對於棲息地演化，以簡約性（parsimony）和或然率（likelihood）方法所得到關於鮃科魚類是否起源於深海或是淺海的分析結果是不一致的。不過，棲息地轉變在其演化歷史中曾獨立發生了多次。 | zh_TW |
| dc.description.abstract | The sinistral flatfish family Bothidae is the second largest family in the order Pleuronectiformes after the Soleidae (182 species). The Bothidae comprises 175 currently recognized species in 20 genera. The members of this family are distributed in tropical and temperate regions, and from shallow waters to the deep sea (>200 m.). Bothids exhibit their highest species diversity in the tropical Indo-West Pacific (113 species), followed by the Atlantic Ocean (30 species), and eastern Pacific Ocean (20 species). Little is known about the inter-relationships among bothid species and bothid diversity is incompletely studied. Therefore, the aims of this study are to: 1) reconstruct the phylogenetic relationships of bothids using molecular approaches; 2) explore the hidden species diversity within the family through the sampling strategy of the Tropical Deep-Sea Benthos (TDSB) program and the subsequent integrated approach with species delimitation analyses; and 3) examine the habitat evolution of the Bothidae (i.e., transition between deep sea and shallow water) within the established phylogenetic framework. A total of 202 specimens (60 recognized species in 14 genera) were collected from 15 oceanographic expeditions under the TDSB (mainly in the western Pacific Ocean) and fish landings in Japan, Malaysia, Thailand, Taiwan and Vietnam. Molecular analyses were conducted based on two datasets. The multigene dataset included sequences from three genetic markers (COI, RH, and RAG1); this dataset was utilized for reconstructing the phylogeny of the Bothidae. The second dataset was composed of the sequences from a common DNA barcoding marker (COI), in which 201 sequences were newly obtained and 258 sequences were retrieved from the GenBank/Bold databases; this dataset was primarily used for species delimitation analyses. The results from phylogenetic inferences based on the multigene dataset showed that 4 out of 16 genera were not monophyletic: Arnoglossus (4 lineages), Laeops (3 lineages), Parabothus (3 lineages) and Psettina (2 lineages). The results of the species delimitation analyses from the tree-based (bPTP) and genetic distance-based (ABGD) methods were congruent for 85 OTUs (putative species). A total of 108 species were resolved based on the final revision by morphological evidence and other criteria of species delimitation such as the consideration of bathymetrical and geographical distributions of the OTUs. In terms of habitat evolution, while the results from parsimony and likelihood methods were incongruent to each other in inferring whether the Bothidae originated in shallow water habitats or deep-sea habitats, several independent habitat transitions were clearly observed during the species evolution. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T06:00:41Z (GMT). No. of bitstreams: 1 ntu-107-R05241214-1.pdf: 54010593 bytes, checksum: 22f63434159b50cd00ea5d183653c521 (MD5) Previous issue date: 2018 | en |
| dc.description.tableofcontents | Acknowledgement i
Abstract ii 摘要 iv Contents vi Table legend viii Figure legend ix 1. Introduction 1 2. Materials and methods 8 2.1 Specimen collection, preservation, and identification 8 2.2 DNA extraction, PCR amplification, and sequencing 9 2.3 Analytical methods 11 2.3.1 Sequence analysis 11 2.3.2 Species delimitation 11 2.3.2 Phylogenetic analyses 13 2.3.3 Ancestral state reconstruction 14 3. Results 15 3.1 Characteristics of sequence data 15 3.1.1 COI gene dataset 15 3.1.2 Multigene dataset 15 3.2 Species delimitation 16 3.2 Phylogenetic inference 20 3.2.1 COI gene tree 20 3.2.2 Combined gene tree 22 3.2.3 Ancestral trait reconstruction 24 4. Discussion 26 4.1 Species diversity exploration in the global Bothidae 26 4.1.1 Species delimitation 26 4.1.2 Hidden and cryptic diversity within the Bothidae 27 4.2 Phylogenetic relationships of the Bothidae 31 4.3 Habitat evolution 35 5. Conclusion and perspectives 36 6. References 37 Appendix I. Full result of the COI gene tree of the Bothidae A Appendix II. Publication H | |
| dc.language.iso | en | |
| dc.subject | 演化 | zh_TW |
| dc.subject | 隱蔽種 | zh_TW |
| dc.subject | 物種界定 | zh_TW |
| dc.subject | 親緣關係 | zh_TW |
| dc.subject | ?科 | zh_TW |
| dc.subject | 分類學 | zh_TW |
| dc.subject | phylogeny | en |
| dc.subject | taxonomy | en |
| dc.subject | species delimitation | en |
| dc.subject | cryptic species | en |
| dc.subject | Bothidae | en |
| dc.subject | evolution | en |
| dc.title | 西太平洋海域左鮃魚類 (真骨魚類：鮃科) 演化及分類研究 | zh_TW |
| dc.title | Evolution and taxonomy of western Pacific sinistral flatfishes (Teleostei: Bothidae) | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 107-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 柯馬修(Matthew A. Campbell),李欣(Hsin Lee),葉信明(Hsin-Ming Yeh),李茂熒(Mao-Ying Lee) | |
| dc.subject.keyword | ?科,演化,分類學,親緣關係,物種界定,隱蔽種, | zh_TW |
| dc.subject.keyword | Bothidae,evolution,taxonomy,phylogeny,species delimitation,cryptic species, | en |
| dc.relation.page | 96 | |
| dc.identifier.doi | 10.6342/NTU201900454 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2019-02-12 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 海洋研究所 | zh_TW |
| 顯示於系所單位： | 海洋研究所 | |
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