| Summary: | 碩士 === 國立臺灣大學 === 海洋研究所 === 107 === 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.
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