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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 楊瑋誠 | zh_TW |
dc.contributor.advisor | Wei-Cheng Yang | en |
dc.contributor.author | 陳毓蓉 | zh_TW |
dc.contributor.author | Yu-Rong Chen | en |
dc.date.accessioned | 2023-05-18T16:48:08Z | - |
dc.date.available | 2023-11-09 | - |
dc.date.copyright | 2023-05-11 | - |
dc.date.issued | 2023 | - |
dc.date.submitted | 2023-02-16 | - |
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/87279 | - |
dc.description.abstract | 小虎鯨與小抹香鯨科為台灣常見的活體擱淺鯨豚物種。然而台灣以及全球對於這兩類物種的遺傳結構了解甚少,不易評估族群現況以及物種的基本生態資訊。因此本研究利用粒線體控制區以及雙限制酶切位點標定法的方式取得物種遺傳資訊,搭配聚合酶連鎖反應之性別鑒定,對其遺傳結構進行分析。兩類物種在台灣的擱淺模式有所差異,本研究分為小虎鯨與小抹香鯨科兩部分進行分析。
小虎鯨為台灣常見集體擱淺物種,鯨豚集體擱淺事件尤其在黑鯨類(如領航鯨、虎鯨)普遍被認為與緊密且具親緣關係的社群結構有關。然而雖然小虎鯨常發生集體擱淺,但是對於集體擱淺事件內的親緣關係少有研究。本研究分析2009-2022年的50個擱淺樣本(共18次事件,其中8次事件各蒐集到超過三個個體,另外10次事件僅各蒐集到一個個體)。親緣關係是利用限制酶切位點標定法取得單核苷酸多型性分析(取得13377基因座與9286個單核苷酸多型性)。超過三級以上的親緣關係在本研究中定義為沒有親緣關係。我們發現有親緣關係的個體與沒有親緣關係的個體在其中三次集體擱淺事件同時發現。另外三次集體擱淺事件內沒有辨識到有親緣關係的個體存在。此結果與過去認為黑鯨類(包含小虎鯨)與具親緣關係個體組成群體的假說不服,從本研究結果推論小虎鯨的社群結構應由多條支系組成,支系內具有親緣關係但不同支系間沒有緊密的親緣關係。我們認為特殊的覓食策略以及棲地或食性偏好可能是促成這些支系合作組成緊密群體的原因。此外前後時間分布超過十年的樣本中,九成的擱淺個體皆為同一種粒線體單倍型(1045個鹼基對),且此單倍型目前沒有在其他地區被報導,推測台灣擱淺的小虎鯨有區域性族群的可能性,需更進一步研究其他遺傳多樣性指標如第二類主要組織相容性複合物,以評估此族群受威脅程度作為擬定保育政策之參考。 小抹香鯨科通常為單隻擱淺或是母子對擱淺,擱淺全年皆有可能發生。小抹香鯨科下有小抹香鯨以及侏儒抹香鯨兩個現生物種。過去因兩物種型態相似不易辨識,在擱淺分析上多歸在同一類群討論。本研究利用粒線體控制區確認種別後將兩個物種分別進行粒線體分析(小抹香鯨19隻,796個鹼基對;侏儒抹香鯨35隻,798個鹼基對),以及利用限制酶切位點標定法取得單核苷酸多型性進行核基因分析(小抹香鯨8隻,取得29666基因座與27092個單核苷酸多型性;侏儒抹香鯨23隻,取得26937基因座與26121個單核苷酸多型性)。發現兩者在遺傳結構上有差異,小抹香鯨遺傳多樣性高於侏儒抹香鯨,且兩者過去族群變動史有潛在差異。與過去研究發現相同,本研究之粒線體控制區與其他已知地區粒線體控制區序列比較後發現小抹香鯨在印太平洋以及大西洋間沒有明顯族群結構,而侏儒抹香鯨則在兩個洋區有族群分化。本研究更進一步發現印太平洋之侏儒抹香鯨有分成兩個集群的趨勢。雖然兩個物種在生態行為上高度重疊,但食性以及棲地偏好在過去研究中發現有部分差異,可能影響其個體移動狀態,故推測兩物種在族群結構差異可能與食性以及棲地偏好不同有關。 本研究提高小虎鯨以及小抹香鯨科遺傳結構在西太平洋的解析度,且評估兩類群在台灣的遺傳多樣性。儘管兩者皆為台灣常見活體擱淺物種,然而從本研究中發現兩類群物種的遺傳結構有差異,可能在不同族群上面對新興病源引入的承受力有所差異,有待更多遺傳多樣性指標分析,以提供擬定保育政策參考。 | zh_TW |
dc.description.abstract | Pygmy killer whales (Feresa attenuata) and Kogia spp. are the common live stranded cetacean species in Taiwan while the information on their genetic structures in Taiwan and the world is scarce. It is thus difficult to evaluate the population status and ecological information. In the present studies, we use samples collected from stranded F. attenuata and Kogia spp. in Taiwan to analyze the genetic structure by two types of genetic markers: mitochondria control region and nuclear DNA obtained from double digest restriction-site associated DNA (ddRADseq) (Peterson, Weber, Kay, Fisher, & Hoekstra, 2012). The sex was determined by polymerase chain reaction. The stranding patterns of these two species were different in Taiwan and we analyzed the two species separately in the following two parts.
F. attenuata is often reported as mass stranding in Taiwan. Mass stranding events of cetaceans are generally assumed to be associated with tight kinship structures, particularly for the ‘blackfish’ species, such as killer whales (Orcinus orca) and pilot whales (Globicephala spp.) Mass stranding events of F. attenuata are common, but the kinship structure among stranded F. attenuata was little studied. Fifty F. attenuata DNA samples were collected from 18 mass stranding events in Taiwan during 2009-2022. In 8 out of 18 stranding events, more than three individuals were sampled (3-9 individuals) and in each of the rest of the 10 stranding events, only one individual was sampled. The kinship within and between events was analyzed using single nucleotide polymorphisms (SNP) of nuclear DNA obtained from ddRADseq (13377 loci and 9286 SNP). We defined “unrelated” as a kinship being more distant than a third-degree relationship (i.e., first cousins). We found related and unrelated dyads coexisted in 3 mass stranding events, and 3 mass stranding events contained no related within-event dyads. Contradicting the consensus that blackfish species (including F. attenuata) tend to aggregate with kins, our finding alternatively suggested that F. attenuata pods may be composed of multiple unrelated clans. We speculated that the driving forces might be the foraging strategies or prey/habitat preference. The maintenance of a specific foraging strategy needs a tight social bond, which may be the cause of mass stranding. In terms of the mitochondria control region (1045 bp), only three haplotypes were identified, and ninety percent of F. attenuata belonged to the same haplotype. This major haplotype was not reported in another region other than Taiwan, indicating that F. attenuata of this haplotype was the potential to be a regional population. More genetic diversity markers such as class two major histocompatibility complex are needed to evaluate the status of this population to form a better conservation policy. Kogia spp. was mostly stranded solely or with mother/calf dyads and the stranding events happened year around. There are two extant species under the Kogia genus: pygmy sperm whales (Kogia breviceps) and dwarf sperm whales (Kogia sima) (McAlpine, 2018). These two species possessed a similar appearance that is hard to recognize; thus, most stranding research discusses these two species together. In the present study, we identified the individuals at the species level through the mitochondria control region and analyze these two species separately (K. breviceps: n = 19, 796 bp; K. sima: n = 35, 798 bp). The nuclear DNA of both species were also analyzed using single nucleotide polymorphisms (SNP) of nuclear DNA obtained from ddRADseq (K. breviceps: n = 8, 29666 loci and 27092 SNP; K. sima: n = 23, 26937 loci and 26121 SNP). It was found that the genetic structures were different between the two species. The genetic diversity was higher in Kogia breviceps compared to Kogia sima. The historic population changes were also potentially different between the two species. The analysis of the mtDNA control region combining the sequences in the present study with sequences from other countries found that there was population differentiation between Atlantic and Indo-pacific in K. sima while no differentiation was found in K. breviceps, which corresponded with the previous study (Chivers, Leduc, Robertson, Barros, & Dizon, 2005). We further found that the Indo-Pacific population of K. sima was potentially separated into two clusters. Although K. breviceps and K. sima were generally similar in their ecological behavior, some research found that there were some differences existed in prey and habitat preference between the two species (Erwin et al., 2017; McAlpine, 2018; Staudinger, McAlarney, McLellan, & Ann Pabst, 2014; Wang, Walker, Shao, & Chou, 2002). These differences might affect the activity range of an individual. We thus suggest that the difference in population structure between the two species was caused by prey and habitat preference. In the present study, we improved the resolution of the genetic structure of F. attenuata and Kogia spp. in the Western Pacific and evaluate their genetic diversity of them. Although these two species are both common live-stranded species, we found that the genetic structure between them was different This difference might cause different viability when the newly emerged pathogen infects their population. More studies on genetic diversity markers were needed that may provide better evidence to form a conservation policy. | en |
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dc.description.tableofcontents | 口試委員會審定書 i
誌謝 ii 中文摘要 iii ABSTRACT v CONTENTS viii LIST OF FIGURES xi LIST OF TABLES xii Chapter 1 Introduction 1 Chapter 2 Genetic relationship within stranding events in Feresa attenuata 6 2.1 Abstract 6 2.2 Introduction 7 2.3 Materials and methods 10 2.3.1 Samples collection 10 2.3.2 Gender identification 11 2.3.3 Mitochondrial DNA control region amplification 12 2.3.4 Mitochondria haplotypes and genetic diversity 13 2.3.5 Double digest restriction-site associated DNA sequencing (ddRADseq) library building and sequencing. 13 2.3.6 ddRADseq sequencing data processing 13 2.3.7 Kinship analysis estimated by nuclear DNA 14 2.3.8 Genetic diversity and population structure estimated by nuclear DNA 15 2.3.9 Demographic inference and effective population size estimated by nuclear DNA 15 2.4 Results 16 2.4.1 Sample collection and sex determination 16 2.4.2 ddRADseq data cleaning 17 2.4.3 Kinship coefficient 17 2.4.4 Genetic diversity 18 2.4.5 Population structure 18 2.4.6 Demographic inference 19 2.5 Discussion 19 Chapter 3 Genetic structure analysis of stranded Kogia spp. in Taiwan 41 3.1 Abstract 41 3.2 Introduction 42 3.3 Materials and methods 45 3.3.1 Samples collection 45 3.3.2 Gender identification 46 3.3.3 Mitochondrial DNA control region amplification 47 3.3.4 Mitochondria haplotypes and genetic diversity 47 3.3.5 Double digest restriction-site associated DNA sequencing (ddRADseq) library building and sequencing. 48 3.3.6 ddRAD sequencing data processing 48 3.3.7 Kinship analysis estimated by nuclear DNA 49 3.3.8 Genetic diversity and population structure estimated by nuclear DNA 50 3.3.9 Demographic inference and effective population size estimated by nuclear DNA 50 3.4 Results 51 3.4.1 Data collection and sex determination 51 3.4.2 ddRADseq data cleaning 51 3.4.3 Kinship coefficient 52 3.4.4 Genetic diversity 52 3.4.5 Population structure 52 3.4.6 Demographic inference 54 3.5 Discussion 54 Chapter 4 Conclusion 76 REFERENCE 78 | - |
dc.language.iso | en | - |
dc.title | 以粒線體與核基因序列分析臺灣擱淺小虎鯨以及小抹香鯨科之遺傳結構 | zh_TW |
dc.title | Genetic structure analyses of Feresa attenuata and Kogia spp. stranded in Taiwan based on mitochondrial and nuclear DNA sequences | en |
dc.type | Thesis | - |
dc.date.schoolyear | 111-1 | - |
dc.description.degree | 碩士 | - |
dc.contributor.coadvisor | 王弘毅 | zh_TW |
dc.contributor.coadvisor | Hurng-Yi Wang | en |
dc.contributor.oralexamcommittee | 王浩文;沈康寧 | zh_TW |
dc.contributor.oralexamcommittee | Hao-Ven Wang;Kang-Ning Shen | en |
dc.subject.keyword | 集體擱淺,簡化基因組,粒線體控制區,親緣分析,遺傳結構,小虎鯨,小抹香鯨科, | zh_TW |
dc.subject.keyword | Mass stranding events,ddRADseq,mitochondria control region,genetic structure,Kinship,pygmy killer whale,Kogia spp., | en |
dc.relation.page | 92 | - |
dc.identifier.doi | 10.6342/NTU202300533 | - |
dc.rights.note | 同意授權(全球公開) | - |
dc.date.accepted | 2023-02-17 | - |
dc.contributor.author-college | 生命科學院 | - |
dc.contributor.author-dept | 生態學與演化生物學研究所 | - |
dc.date.embargo-lift | 2028-02-15 | - |
顯示於系所單位: | 生態學與演化生物學研究所 |
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