本研究探討了南海 (SCS) 地區石首魚科叫姑魚屬(Johnius)的分類學、動物地理學和演化史。首先，利用形態學和COI分子的方法對臺灣水域進行分類重新整理，成功辨識分出七種的叫姑魚屬的種類。其中，大多數的魚種分布在臺灣的西部海域，介於高雄的興達港 (22.4° N) 和新竹 (24.8° N) 之間，其中臺灣叫姑魚 J. taiwanensis、鱗鰭叫姑魚 J. distinctus 和皮氏叫姑魚 J. belangerii 全年都有捕獲紀錄。鈍頭叫姑魚 J. amblycephalus 和婆羅洲叫姑魚 J. borneensis 僅在夏季被捕獲，而屈氏叫姑魚 J. trewavasae則較罕見。此外，在南海海域成功鑑定出 17 種有效的叫姑魚屬魚種，其中包括一個新發現物種-佐氏叫姑魚 Johnius sasakii sp. nov. ，並對其進行了全面的描述。從南海叫姑魚屬的動物地理學得知，叫姑魚屬可分為三群，分別是廣佈群3種(鈍頭叫姑魚 J. amblycephalus，皮氏叫姑魚 J. belangerii 和 婆羅洲叫姑魚 J. borneensis)、北方群4種(鱗鰭叫姑魚 J. distinctus，叫姑魚 J. grypotus，臺灣叫姑魚 J. taiwanensis 和屈氏叫姑魚 J. trewavasae)和南方群10種(卡氏叫姑魚 J. carouna、突吻叫姑魚 J. coitor、異鱗叫姑魚 J. heterolepis、寬眼叫姑魚 J. latifrons、大鼻孔叫姑魚 J. macorhynus、菲律賓叫姑魚 J. philippinus、斜口叫姑魚 J. plagiostoma、佐氏叫姑魚 J. sasakii、尖尾叫姑魚 J. trachycephalus 和韋氏叫姑魚 J. weberi) 所組成。南海南部擁有最大的物種豐富度和特有種，達13種，而南海北部較低，僅有8種(包括卡氏叫姑魚)。南海北部和南部範圍交疊了兩個動物區：前者從臺灣到中國南部的海南島，後者從南越到馬來西亞半島南部。根據三個粒線體標記基因(16S、COI、Cyt b) 和兩個核標記基因(S7、視紫質)分子序列數據，構建了叫姑魚屬的親緣關係樹。利用時間校準推斷叫姑魚屬起源於中新世晚期。由祖先系統發育的研究顯示，叫姑魚屬的祖先可能起源於南海，然後擴展為兩條途徑：一個分支在南海北部發生分化，形成亞熱帶地區群，另一個分支則向南海南部擴散，在熱帶地區群呈現高度的物種多樣性的熱帶地區群。推測叫姑魚屬在上新世-更新世時期可能由於週期性冰川的作用和海平面波動而迅速種化。
關鍵詞：形態學、空間分佈、動物地理學分佈、特徵演化歷史重建、分隔事件。

This study examined the taxonomy, zoogeography, and evolutionary history of the genus Johnius in the South China Sea (SCS) region. Firstly, a taxonomic review in Taiwanese waters successfully identified and separated seven legitimate Johnius species based on morphology and the COI molecular approach. The majority were found in the western coast of Taiwan between Xingda (22.4° N) and Hsinchu (24.8° N), with J. taiwanensis, J. distinctus, and J. belangerii being caught throughout the year. Johnius amblycephalus and J. borneensis only caught in summer, and J. trewavasae was rarely encountered. A total of 17 valid Johnius species successfully identified in the SCS waters, including a newly discovered species, Johnius sasakii sp. nov., are fully described. Thus, a zoogeographical inference of Johnius in the SCS concludes that this genus is comprised of widely distributed (3 species, J. amblycephalus, J. belangerii, and J. borneensis), northern (4 species, J. distinctus, J. grypotus, J. taiwanensis, and J. trewavasae), and southern (10 species, J. carouna, J. coitor, J. heterolepis, J. latifrons, J. macorhynus, J. philippinus, J. plagiostoma, J. sasakii, J. trachycephalus, and J. weberi) species that mostly occur in this region. The southern SCS has the largest species richness and endemism number, with 13 species distributed, compared with the northern SCS which has the lowest, with 8 species dispersed. The northern and southern SCS range bounds overlap two faunas: the former from Taiwan to Hainan, southern China, and the latter from southern Vietnam to south Peninsular Malaysia. Lastly, a phylogenetic tree was constructed based on concatenated sequence data from a partial set of three mitochondrial (16S, COI, Cyt b) and two nuclear (S7, Rhodopsin) marker genes to infer Johnius relationships. An origin in the late Miocene was inferred for Johnius by using time calibrations. The ancestral phylogeny suggests that ancestral Johnius likely originated in the SCS, then expanded into two pathways: divergence at the northern SCS as a subtropical region, and at the southern SCS with high diversification in the tropics. It was suggested this genus speciated rapidly during the Pliocene-Pleistocene epoch, likely due to cyclical glaciations and sea level fluctuations.

Thesis validation letter……………………………………………………………………....
Acknowledgments……………………………………………………………………..….....ii
Abstract Chinese…………………………………………………………………….……...iii
Abstract English……………………………………………………………………….…….v
Table of contents……………………………………………………………………….…..vii
Table of figures…………………………………………………………………………….xii
Table of tables………………………………………………………………………..…..xviii
Chapter 1: General introduction…………………………………………………………….1
1.1Diversification of marine fishes in the South China Sea……….……….………….1
1.2Dispersal and diversity of Johnius………………………………………………….3
1.3Systematics of genus Johnius……………………...……………………………….5
1.4Biogeography and evolutionary dispersal in Johnius…………………….........…...6
1.5Objectives…………………………………………………………………………..7
Chapter 2: Taxonomic review of the genus Johnius (Perciformes: Sciaenidae) in Taiwanese waters, with their geographical distribution.……………………….……………….9
2.1 Introduction………………………………………………………………...……….9
2.2 Material and methods……………………………………………………………...10
2.2.1 Sampling and examination of specimens……… ……..…………………….10
2.2.2 Integrated approach to verifying Johnius species…………………………..11
2.3 Result…………………………………………………………………………..….13
2.3.1 Genus Wak Lin, 1938, accepted as a junior synonym of Johnius Bloch, 1793………………………………………………………………………...13
2.3.2 Synonyms and invalid names of nominal species of Johnius, 1793………….14
2.3.3 Integrated identification of Taiwan Johnius species…………………..…….15
2.3.4. Spatial distribution and seasonal abundance of Taiwan Johnius…………….16
2.4 Systematics……………………………………………………………...…………16
2.4.1. Johnius amblycephalus (Bleeker, 1855)…………………………...………18
2.4.2. Johnius belangerii (Cuvier, 1830)…………………………...……...……..18
2.4.3. Johnius borneensis (Bleeker, 1851)..………………………...…………….19
2.4.4. Johnius distinctus (Tanaka, 1916)...………………………...……………...20
2.4.5. Johnius grypotus (Richardson, 1846)...………………………...…….…...20
2.4.6. Johnius taiwanensis Chao et al., 2019……..………….…….…...………..21
2.4.7. Johnius trewavasae Sasaki, 1992..………...…………………...…….…...22
2.4.8. Key to the species of Johnius occurring in Taiwan waters…………….….23
2.5 Discussion…………………………………………………………….…………...24
2.6 Conclusions………………………………………………………………….…….26
2.7 Summary of chapter 2…………………………………………..…………….…...27
Chapter 3: Taxonomic revision of the genus Johnius (Perciformes: Sciaenidae) from South China Sea and a new species description of with note on zoogeographical distribution……………………………………………………………………41
3.1 Introduction……………………………………………………………………….41
3.2 Material and methods……………………………………………………………..43
3.2.1 Sampling survey and collection……… ……………………..……………..43
3.2.2 Meristic and morphometric characters examined…………………………..44
3.2.3 Molecular data………………………………………………………………45
3.3 Result……………………………………………………………………………...46
3.3.1 Genus Bola Hamilton, 1822 and Wak Lin, 1938 as a junior synonym of Johnius Bloch, 1793......……………...………………………….………….………46
3.3.2 Synonyms and invalid names of nominal species of Johnius Bloch, 1793…………………………………………..……………………………46
3.3.3. Integrated identification of South China Sea Johnius species…………….47
3.4 Systematics………………….…………………………………………………….48
3.4.1 Key to the species of Johnius in the South China Sea waters………………49
3.4.2 Johnius coitor (Hamilton, 1822) ....………………………...……………….51
3.4.3 Johnius plagiostoma (Bleeker, 1849) ……………………………………….53
3.4.4 Johnius weberi Hardenberg, 1936..………...………………...……………...55
3.4.5 Johnius trachycephalus (Bleeker, 1851)..………………….…......…………57
3.4.6 Johnius latifrons Sasaki, 1992……..…..……………………..……………..59
3.4.4 Johnius philippinus Sasaki, 1999……….………………….…...…………...60
3.4.5 Johnius sasakii sp. nov. Hanafi, Chen, Seah, Chang, Liu & Chao, 2022……62
3.5 Discussion……………………………………………………………..…..………66
3.5.1 Biodiversity of Johnius in the SCS…………………………………………..66
3.5.2 Johnius in Taiwan with the SCS boundary CYR…………………………….68
3.5.3 Geographic groups and the SCS circulation currents………………………...70
3.5.4 Reproduction of Johnius and the seasonal variation…………………………71
3.6 Conclusions……………………………………………………………………......72
3.7 Supplementary material examined…………..…………………………………….73
3.7.1 Johnius amblycephalus (Bleeker, 1855) …………………………………….73
3.7.2 Johnius belangerii (Cuvier, 1830) ………………………………………......74
3.7.3 Johnius borneensis (Bleeker, 1851) …………………………………………75
3.7.4 Johnius carouna (Cuvier, 1930) …………………………………………….76
3.7.5 Johnius heterolepis Bleeker, 1873………………………………………......78
3.7.6 Johnius macrorhynus (Mohan, 1976) ………………………………………79
3.7.7 Johnius sasakii Hanafi, Chen, Seah, Chang, Liu & Chao, 2022……….…....80
3.7.8 Johnius trewavasae Sasaki, 1992……………………………………………80
3.7.9 Johnius macropterus (Bleeker, 1853) ………………………………………80
3.8 Summary of chapter 3………………………………………………………..……81
Chapter 4: Phylogeny systematics and evolutionary history of the genus Johnius in the South China Sea inferred by multilocus sequence data…………………….……….114
4.1 Introduction………………………………………………………….…………...114
4.2 Materials and methods……………………………………………………….…...116
4.2.1 Sampling procedure...……………………………………………….…......116
4.2.2 DNA extraction, PCR and sequencing analysis….………………………..117
4.2.3 Sequence, alignments, data exploration, model and outgroup selection…...117
4.2.4 Sequence analysis and reconstruction of phylogeny…………………..…..118
4.2.5 Divergence time estimation……………………………………………..…119
4.2.6 Reconstruction of ancestral distribution …………………………….…..…119
4.3 Results………………………………………………………………...………….120
4.3.1 Sequence analyses…………………..………………….......…………...…120
4.3.2 Phylogenetic reconstructions………………..……………………………..120
4.3.3 Divergence time estimation……. ………...…………………...…………..121
4.3.4 The potential origin of genus Johnius………...……………………………122
4.4 Discussion…………………………………………………………..……………123
4.4.1 Phylogeny of the genus Johnius in the SCS………………………………..123
4.4.2 Phylogeography of the genus Johnius in the SCS ………………………....124
4.4.3 Potential origin and evolutionary history of Johnius ……………………....125
4.5 Conclusions……………………………………………………………..………..128
4.6 Summary of chapter 4……………………………………...……………..……....128
Chapter 5: Future studies……………………………………………………….…………154
5.1 Future studies of Johnius in the Indo-West Pacific region………………….…...154
References……………………………………………………………………….………..156
Autobiography/Curriculum Vitae (CV)…………………………………………….…….172
Appendices……………………………...………………………………………………..180
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