臺灣博碩士論文加值系統

中文摘要

本研究以粒線體細胞色素 b 基因序列作為分子遺傳標誌，試圖瞭解目前臺灣鬚鱲族群的遺傳多樣性、族群間基因交流的程度和可能的族群結構。並利用其結果整合相關的地質事件探討臺灣初級性淡水魚類相之起源模式。我採集自臺灣西部及東北部21條河川的26個樣點，總計337隻個體，並定序粒線體基因組細胞色素 b 基因序列（全長1140 bp）。所有的序列可歸納出23型haplotype (H01-H23)。以最大簡約法（Maximum parsimony，MP)，最大相似法（Maximum likelihood，ML)，貝氏分析（Bayesian inference，BI）和鄰聚法（Neighbor-joining，NJ) 4種方法所重建的親緣關係樹，皆支持將23型haplotype區分成6群不同的系群，分別是 Candidia lineages A~F。系群間的遺傳分化程度相當大，顯示臺灣鬚鱲可能存在不同的隱蔽種。依據分子鐘估計系群間的分歧年代，我推測這六群系群分歧的地點應該在中國大陸，而後陸續藉由更新世內不同的冰期多次入侵至臺灣。由於F系群內haplotype數量明顯多於其他系群，故F系群很可能是最早入侵臺灣的系群。可能的播遷路徑應該侷限在過去臺灣海峽內非深海區（即無海底峽谷地形存在）的範圍內。

臺灣鬚鱲族群內的遺傳變異偏低，但族群間及不同地理區間確存在高度的遺傳分化。26個臺灣鬚鱲族群間的基因交流程度甚小（平均Fst = 0.76），範圍縮小至同一流域內的族群也是相同的現象。北臺灣的淡水河流域8個族群間平均的Fst = 0.44，現今南臺灣的高屏溪流域3個族群間平均的Fst = 0.93。分子變方分析（AMOVA, Analysis of Molecular Variance）結果指出臺灣鬚鱲的族群結構可分為北部、中部，南部（不包括隘寮溪）和屏東地區（包括隘寮溪）。

臺灣鬚鱲在形態上依側線鱗數和側線上鱗數的差異可區分為兩型，分別是北型（northern type，54-56，11-12；包括Candidia A~C系群）和南型（southern type，50-52，9-10；包括Candidia D~F系群）。由形態特徵並不能區別出特定的系群，系群間的形態變異以及是否有生殖隔離存在有待更深入之研究。

Abstract

In the present study, I employed the mitochondrial cytochrome b (mtDNA cyt b) gene as a molecular marker to investigate the phylogeographical patterns and genetic diversity of Candidia barbatus in Taiwan. Integrating the geohistorical events with genetic differentiation within C. barbatus can provide an appropriate model to reconstruct the originating pattern of the primary freshwater ichthyofauna of Taiwan.

MtDNA cyt b sequences of 1140 bp in length were scored from 337 specimens collected from 26 localities covering 21 rivers in western Taiwan from among which 23 different haplotypes were identified. The maximum parsimony (MP), maximum likelihood (ML), neighbor-joining (NJ), and Bayesian inference (BI) revealed similar mtDNA cyt b genealogies designated as Candidia lineages A~F. The deep genetic divergences occurring among lineages A~F suggest that cryptic species may exist within C. barbatus. The approximate molecular dating among lineages A~F indicate differentiations between them occurring earlier on the Asian mainland with subsequent multiple invasions toward Taiwan via a land bridge in the shallow-water zone of the Taiwan Strait during several glacial periods of the Pleistocene (1.6~0.02 million years). Lineage F was probable the first settler of this kind of dispersal toward the southernmost part of Taiwan as evidenced by its possession of more haplotypes.

The low genetic variability within populations resulted in an extremely high genetic divergence between populations and between geographical regions. Moreover, this was associated with a relatively low gene flow among the 26 populations (average Fst = 0.76) or even within the same drainage (average Fst = 0.44 in the Danshui River drainage; average Fst = 0.93 in the Kaoping River drainage). AMOVA could subdivide the likely population structure of C. barbatus into northern, central, southern (excluding the Ailiao tributary), and Pingtung (including the Ailiao tributary) groups.

Pore lateral line scales and transverse scale rows can be used to separate C. barbatus into two morphs: the northern type designated as Candidia A~C, with respective scale formulae of 54-56 and 11-12, and the southern type of Candidia D~F with formulae of 50-52 and 9-10. The northern type is identical with that shown in the original description. In addition to scale counts, other morphological variants could not be used to distinguish Candidia lineages A~F. A more-detailed study of the morphology is necessary, and the“concept of reproductive isolation”should be borne in mind.

Contents

Abstract in Chinese (I)
Abstract (II)
Contents (IV)

1. Introduction (1)

2. Material and Methods
2.1. Sample collection (6)
2.2. DNA extraction, PCR amplification, and direct
sequencing (6)
2.3. Sequence alignment, nucleotide statistics and
saturation analysis (7)
2.4. Phylogenetic analyses (7)
2.5. Relative rate test and Molecular dating (9)
2.6. Neutrality tests (10)
2.7. Population genetic analyses (11)
2.8. Basic methods for the morphological analyses
of fish (14)

3. Result
3.1. Molecular characteristics of the mtDNA cyt b gene in
C. barbatus (15)
3.2. The best model of nucleotide substitutions for the NJ
and ML analyses (16)
3.3. Patterns of phylogeography and pairwise genetic
divergences (16)
3.4. Divergence times among lineages (17)
3.5. Haplotype network and population phylogeny (18)
3.6. Neutrality tests, population structure, and AMOVA (19)
3.7. Morphological variations in C. barbatus (21)

4. Discussion
4.1. Utility of the mitochondrial cytochrome b gene (23)
4.2. A historical biogeographical hypothesis (24)
4.3. Does a cryptic species exist within the C. barbatus
population? (27)
4.4. Patterns of genetic differentiation in C. barbatus (28)
4.5. Conservation management of C. barbatus (30)

5. Conclusions (32)

6. References (33)

Tables (41)

Figures (51)

Appendixes (61)

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