臺灣博碩士論文加值系統

硬皮鰕虎屬(Callogobius Bleeker, 1874)的魚種為棲息於熱帶之底棲隱蔽性鰕虎科魚類，大部分物種棲息於海水中，少數物種可生活於感潮帶。由於本屬物種多棲息於珊瑚礁穴或泥穴中，採集相對困難加上標本保存不易，因此對於本屬魚種之研究多半不甚完整或常有誤鑑的情形產生。臺灣學界以往針對硬皮鰕虎屬有系統的分類研究較為缺乏，但鑒於過往學者曾經發表過兩個世界新種，可見本屬於種在臺灣有一定程度的多樣性，研究價值可見一般。
本研究以臺灣地區所產之硬皮鰕虎屬魚種為研究主角，除在河口與海域的環境採集外也檢視過往典藏和比對文獻，結果呈現臺灣目前有著11個硬皮鰕虎屬物種紀錄，其中包含本研究期間發表的1個新種與確認的3個新物種紀錄。本研究也在文獻查考後建議移除4筆硬皮鰕虎屬的過往物種紀錄。在本研究中也透過檢視典藏的標本確認了一個菲律賓產硬皮鰕虎的有效性。
由於硬皮鰕虎屬的物種型態多樣，本研究挑選25個外部型態特徵進行編碼建立資料矩陣，並且以最大簡約法進行支序分析建構演化樹型，結果顯示本研究中收錄的硬皮鰕虎物種共可被分成3個類群，並且能以感覺乳突列i的狀態作為共裔徵去區分。
分子親緣研究上，本研究以粒線體DNA中ATPase與D-loop片段的序列，配合最大似然法與相鄰連接法分析重建臺灣產硬皮鰕虎屬物種的親緣關係，結果顯示各物種均落在有高bootstrap值支持的單系群外，各物種間的分群也與支序分析結果類似。而在支序分析與分子親緣關係重建上的些許差異或許可解釋為所選擇的外群數量及所涵蓋的分類群範圍差異所致。
本研究也定序組裝了黑鰭緣硬皮鰕虎(Callogobius nigromarginatus Chen & Shao, 2000)的全粒線體基因組，並自其當中提取出12個蛋白質編碼基因，用於重建硬皮鰕虎屬與鰕虎亞目物種的分子親緣關係。結果顯示硬皮鰕虎屬的近親為星鰕虎屬(Asterropteryx Rüppell, 1830)，同時硬皮鰕虎屬的其他近親也可能與星鰕虎同樣具有橫列模式的頭部感覺乳突。
自本研究之系統分類與分子演化結果可知，若如過往僅基於型態相似所建構的硬皮鰕虎屬種間關係與其在鰕虎科中的高階分類關係是遠遠不足且有偏誤的，必須將型態與分子證據整合後才能得到最接近真實演化情況的結果。同時，本研究的結果也呈現出頭部感覺乳突模式對於鰕虎科物種分類的重要性。

Gobies of the genus Callogobius Bleeker, 1874 are a group of tropical bentho-cryptic fishes, with most of the members inhabiting in marine environments and some in brackish waters. Due to their tendency to dwell in coral reef crevices or mud burrows, specimen collections were challenging, leading to incomplete studies or misidentifications. Systematic taxonomic research on this genus were relatively scarce and scattered in Taiwan. However, it is evident that this genus has a certain degree of diversity in Taiwan since previous studies has collected and described two new species, indicating significant research value.
This study focuses on the species of the genus Callogobius found in Taiwan with specimen collections and examinations of museum collections. The results indicate that there are currently 11 recorded species of Callogobius in Taiwan, including one new species described during this study and three newly confirmed species records. Additionally, four previous records were suggested to be removed from the Taiwanese fish fauna and the validity of a Callogobius species from the Philippines was confirmed through examinations of archived specimens.
Due to the morphological diversity of Callogobius, this study selected 25 external morphological characteristics for coding a data matrix, and a cladistic phylogenetic tree was constructed using maximum parsimony analysis. The results indicates that the Callogobius species included in this study can be divided into three groups, which can be distinguished by the synapomorphy of sensory papillae row i.
For the molecular phylogenetic study, sequences of the mitochondrial DNA ATPase and D-loop regions were selected to reconstruct the phylogenetic relationships with maximum likelihood and neighbor-joining methods. The results showed that all species form monophyletic groups with high bootstrap support, and the intraspecific relationships were similar to the results of cladistic analyses. Slight differences between cladistic and molecular phylogenetic analyses might be a result of differences upon outgroup selections.
This study also sequenced and assembled the complete mitochondrial genome of Callogobius nigromarginatus Chen & Shao, 2000, and 12 protein-coding genes were excerpted to reconstruct the molecular phylogenetic relationships of the genus. The results indicates that the closest relatives of Callogobius are species of the genus Asterropteryx Rüppell, 1830, and other close relatives were suggested to possess similar transverse sensory papillae patterns.
From the results of this study, relationships between Callogobius species and their higher taxonomic relationships within Gobiidae, as previously constructed based solely on morphological similarities, are far from sufficient and biased. Integrating morphological and molecular evidence is necessary to obtain results that most closely reflect the true evolutionary situation. Additionally, this study highlights the importance of the head sensory papillae pattern in the taxonomy of Gobiidae.

目錄

壹、前言 1
一、硬皮鰕虎屬簡介 1
二、過往研究回顧 2
三、分子演化研究 9
四、研究目標 10

貳、材料與方法 12
一、標本採集與形態檢視 12
二、分子親緣分析 17

參、結果 23
一、臺灣產硬皮鰕虎屬物種之檢索表與形態描述 23
二、臺灣產硬皮鰕虎屬物種多樣性 79
三、本研究納入比較分析之一種菲律賓產硬皮鰕虎分類描述 80
四、以形態特徵進行硬皮鰕虎之親緣關係重建 84
五、臺灣產硬皮鰕虎屬物種的基因序列片段性質分析 86
六、以基因標記進行臺灣產硬皮鰕虎之親緣關係重建 94
七、黑鰭緣硬皮鰕虎之完整粒線體基因組序列定序 98

肆、討論 101
一、臺灣海域環境特性與硬皮鰕虎屬物種的分布 101
二、臺灣與菲律賓產硬皮鰕虎屬物種的形態支序分析與生態間關係 102
三、臺灣產硬皮鰕虎屬物種的分子親緣研究 103

伍、結論 108
一、臺灣的硬皮鰕虎屬物種多樣性與分布概況 108
二、臺灣產硬皮鰕虎屬物種的形態支序分析 108
三、臺灣產硬皮鰕虎屬物種的分子親緣分析 109
四、硬皮鰕虎屬物種與鰕虎亞科內相關屬別之分子親緣分析 109

陸、參考文獻 110

表目錄
Table 1. Meristic frequencies of the Callogobius species obtained in this study 125
Table 2. Morphometric measurements of Callogobius species from Taiwan 129
Table 3. Morphometric measurements of Callogobius productus collected from the Philippines 135
Table 4. Data matrix for the cladistic analysis of Callogobius species obtained in this study based on 23 selected morphological characters 136
Table 5. The consistency index (CI) and retention index (RI) of all selected morphological characters in the cladistic analysis of this study 137
Table 6. The ATPase sequence base composition of Callogobius species sequenced and outgroup obtained in this study 138
Table 7. Undirectional nucleotide pair frequencies and Ts/Tv ratio of Callogobius species sequenced and outgroup obtained in this study. 139
Table 8. The ATPase 8 sequence pairwise distance of Callogobius species sequenced and outgroup obtained in this study 140
Table 9. The ATPase 6 sequence pairwise distance of Callogobius species sequenced and outgroup obtained in this study 142
Table 10. The ATPase sequence pairwise distance of Callogobius species sequenced and outgroup obtained in this study 144
Table 11. The D-loop sequence base composition of Callogobius species sequenced and outgroup obtained in this study 146
Table 12. The D-loop sequence pairwise distance of Callogobius species sequenced and outgroup obtained in this study 147
Table 13. The concatenate sequence base composition of Callogobius species sequenced and outgroup obtained in this study 149
Table 14. The concatenate sequence pairwise distance of Callogobius species sequenced and outgroup obtained in this study 150
Table 15. Mitogenome organization of Callogobius nigromarginatus 152
Table 16. Base composition and skewness of the mitogenomic components of Callogobius nigromarginatus 153
Table 17. All 36 species selected as OUTs for phylogenetic analysis with their GenBank accession ID 154


圖目錄
Figure 1. Reproduced type specimen sketch of Eleotris hasseltii from Bleeker (1851, Fig. 13) 155
Figure 2. Female urogenital papillae and lateral protrusions of Callogobius sclateri 155
Figure 3. Position of the targeted mtDNA sequence markers in this research with relative position of the primers employed 155
Figure 4. Collection sites of all Callogobius species examined in this study from Taiwan and its adjacent islands 156
Figure 5. Specimen photos of Callogobius species obtained in this study 157
Figure 6. In situ photos of some Callogobius species obtained in this study 160
Figure 7. Specimen photo of “Callogobius liolepis”, a misidentification of Callogobius okinawae 161
Figure 8. Specimen of Callogobius productus collected from Okoy River, Negros, Philipines 161
Figure 9. Head lateral line system and squamation of predorsal and thoracic region of
Callogobius aquilus 162
Figure 10. Head lateral line system of Callogobius clitellus 163
Figure 11. Head lateral line system of Callogobius flavobrunneus 164
Figure 12. Head lateral line system of Callogobius hasseltii 165
Figure 13. Head lateral line system and squamation of predorsal and thoracic region of Callogobius nigromarginatus 166
Figure 14. Head lateral line system of Callogobius okinawae 167
Figure 15. Head lateral line system of Callogobius sclateri 168
Figure 16. Head lateral line system and squamation of predorsal and thoracic region of Callogobius sheni 169
Figure 17. Head lateral line system of Callogobius shunkan 170
Figure 18. Head lateral line system of Callogobius stellatus 171
Figure 19. Head lateral line system of Callogobius tanegasimae 172
Figure 20. Head lateral line system of Callogobius productus 173
Figure 21. The 50% majority-rule consensus tree constructed based upon the most parsimonious tree 174
Figure 22. Transition and transversion versus genetic distance scatter plot of ATPase 8 sequence dataset of Callogobius species sequenced and outgroups obtained 175
Figure 23. Transition and transversion versus genetic distance scatter plot of ATPase 6 sequence dataset of Callogobius species sequenced and outgroups obtained 175
Figure 24. Transition and transversion versus genetic distance scatter plot of ATPase sequence dataset of Callogobius species sequenced and outgroups obtained 176
Figure 25. Transition and transversion versus genetic distance scatter plot of the D-loop sequence dataset of Callogobius species sequenced and outgroups obtained 176
Figure 26. Transition and transversion versus genetic distance scatter plot of the concatenated (ATPase+D-loop) sequence dataset of Callogobius species sequenced and outgroups obtained 177
Figure 27. The maximum likelihood (ML) tree of the ATPase 8 sequence dataset of Callogobius species sequenced and outgroups obtained 178
Figure 28. The neighbor-joining (NJ) tree of the ATPase 8 sequence dataset of Callogobius species sequenced and outgroups obtained 179
Figure 29. The maximum likelihood (ML) tree of the ATPase 6 sequence dataset of Callogobius species sequenced and outgroups obtained 180
Figure 30. The neighbor-joining (NJ) tree of the ATPase 6 sequence dataset of Callogobius species sequenced and outgroups obtained 181
Figure 31. The maximum likelihood (ML) tree of the ATPase sequence dataset of Callogobius species sequenced and outgroups obtained 182
Figure 32. The neighbor-joining (NJ) tree of the ATPase sequence dataset of Callogobius species sequenced and outgroups obtained 183
Figure 33. The maximum likelihood (ML) tree of the D-loop sequence dataset of Callogobius species sequenced and outgroups obtained 184
Figure 34. The neighbor-joining (NJ) tree of the D-loop sequence dataset of Callogobius species sequenced and outgroups obtained 185
Figure 35. The maximum likelihood (ML) tree of the concatenated (ATPase+D-loop) sequence datasets of Callogobius species sequenced and outgroups obtained 186
Figure 36. The neighbor-joining (NJ) tree of the concatenated (ATPase+D-loop) sequence datasets of Callogobius species sequenced and outgroups obtained 187
Figure 37. Mitogenome map of Callogobius nigromarginatus 188
Figure 38. The relative synonymous codon usage in the mitogenome of Callogobius nigromarginatus 188
Figure 39. Putative secondary structures of the 22 tRNA genes of Callogobius nigromarginatus 189
Figure 40. The folded stem-loop structure for the OL of Callogobius nigromarginatus 190
Figure 41. The full sequence of the CR of Callogobius nigromarginatus 190
Figure 42. Phylogenetic tree generated from analysis of concatenated 12 PCG sequences of Callogobius nigromarginatus and other 36 selected OTUs 191

附錄
Appendix 1. Meristic character comparisons and related information upon all nominal species of Callogobius until 2024 192
Appendix 2. Overview of body colorations and markings of all nominal species of Callogobius until 2024. 199
Appendix 3. Previous records of Callogobius from Taiwan with their affiliated publications 207
Appendix 4. Updated records of Taiwanese Callogobius species 209
Appendix 5. Fluid preserved specimens of Callogobius obtained and examined in this study 210
Appendix 6. Genetic materials and sequences assembled in this study with their related information 214
Appendix 7. The ATPase 8 sequence and variable sites of Callogobius species sequenced and outgroup obtained in this study 218
Appendix 8. The ATPase 6 sequence and variable sites of Callogobius species sequenced and outgroup obtained in this study 219
Appendix 9. The D-loop sequence and variable sites of Callogobius species sequenced and outgroup obtained in this study 222
Appendix 10. The complete mtDNA sequence of Callogobius nigromarginatus 227

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