比目魚鮃科魚類親緣關係、物種界定及分類修訂 （真骨魚類：鰺形亞目）

Abstract

鮃科（Bothidae）目前包含 20 個屬、170 個物種，傳統上包含了兩個亞科，分別為線鰭鮃亞科(Taeniopsettinae)及鮃亞科(Bothinae)。該科廣泛分布於熱帶和溫帶海域，由於形態變異性、隱蔽多樣性，以及在系統發育關係上仍存疑慮，故其在系統分類學中存有尚待解決之問題。儘管過去的形態與分子研究支持鮃科為單系群，但各屬之間的親緣關係以及它們的分類有效性及物種界定，仍未獲得充分探討。這些物種分類上的不確定性阻礙了對於該科在演化、生物多樣性與生物地理學的深入探究。本研究旨在透過綜合分類學架構，透過結合分析分子系統發生學、詳細檢視形態與物種界定方法，以解決這些長期存在鮃科的分類學難題。利用兩個粒線體基因（Cytochrome C Oxidase subunit I [COI] 與 12S rRNA）與三個核基因（Early Growth Response protein 3 [EGR3]、Recombination-Activating Gene 1 [RAG1]和Rhodopsin[RH]）建立一個多基因序列矩陣，對鮃科的19 屬、87 個形態物種進行親緣關係演化重建。利用形態檢視了20 個屬中的 147 個命名種，其中包括了122筆正模標本與 682 筆非正模標本。結合重建之親緣關係與其他證據（例如：生物地理），為修訂鮃科在科級與屬級的分類奠定了基礎。親緣結果分析結果顯示Bothinae亞科為並系群，而 Taeniopsettinae 為單系群。此外，Bothinae亞科可進一步分為三個主要分支（Bothinae 1–3）。在屬的層級中，Grammatobothus 被確認為單系群（即Bothinae 1），並與其他屬形成姊妹群關係，而Arnoglossus、Laeops、Parabothus 和 Psettina這四個屬則不是單系群。因此， Taeniopsettinae亞科建議提升為獨立的科，並另外新建立兩個科，分別為Monolenidae（對應Bothinae 2）與Grammatobothidae（對應Bothinae 1），各僅包含一個屬；同時，將鮃科限制於Bothinae 3分支內。本研究建議對現時有效屬名的使用進行修訂，包括：Arnoglossus（對應Arnoglossus V）、Laeops（對應Laeops II）、Parabothus（對應 Parabothus III）、Psettina（對應 Psettina III）。另外，本研究亦建議恢復過去被視為同種異名的屬名並建立新的屬，包括Anticitharus屬、Caulopsetta屬、Psettinella屬與Scidorhombus屬。此外，基於COI 基因資料，利用兩種DNA 物種界定方法 ASAP（Assemble Species by Automatic Partitioning）與 bPTP（Bayesian Poisson Tree Processes），並結合形態特徵、棲息深度及地理分布資訊，對種層級的分類進行探討。透過綜合分類分析共界定出128種假定物種，其中包含 12 種為潛在的新物種，揭示了該科中大量未被發現的隱蔽種。總括而言，本研究是首項結合形態與分子資料，並涵蓋廣泛分類群與地理範圍，對鮃科進行全面性整合分類學修訂的研究。本研究突顯了在鮃科分類學中採用整合性研究方法的重要性，並提供堅實的系統發育架構，作為未來演化、生態與保育研究之依據。

The left-eyed flatfish family Bothidae comprises 170 currently recognized species in 20 genera, traditionally classified under two subfamilies (Bothinae and Taeniopsettinae). Bothids are widely distributed in tropical and temperate oceans, yet their systematics remain highly problematic due to morphological variability, cryptic diversity, and unresolved phylogenetic relationships. Although previous studies based on morphology and molecular data have supported the monophyly of the family, the intrafamilial relationships among its constituent genera, as well as the validity and boundaries of many genera, have not been thoroughly investigated. These taxonomic uncertainties hinder the understanding of bothid evolution, biodiversity, and biogeography. This study aims to address these longstanding systematic issues in Bothidae through an integrated approach that combines molecular phylogeny, detailed morphological examination, and species delimitation. A multigene phylogeny of Bothidae was reconstructed using DNA sequence data from two mitochondrial genes (Cytochrome C Oxidase subunit I [COI] and 12S rRNA) and three nuclear genes (Early Growth Response protein 3 [EGR3], Recombination-Activating Gene 1 [RAG1], and Rhodopsin [RH]) across a comprehensive taxonomic sampling comprising 87 morphospecies representing 19 genera. The morphological examination included 122 type specimens and 682 non-type specimens, representing 147 nominal species in 20 genera. Together with the reconstructed phylogeny and other available evidence (e.g., biogeography), these data formed the basis for revising for the familial- and generic-level taxonomy of Bothidae. The phylogenetic results reveal that the subfamily Bothinae is paraphyletic with respect to monophyletic Taeniopsettinae. Additionally, “Bothinae” can be subdivided into three main clades (Bothinae 1–3). At the generic level, while Grammatobothus is resolved as monophyletic (=Bothinae 1) and as the sister group to the remaining bothids, four other specious genera—Arnoglossus, Laeops, Parabothus, and Psettina—are not. Consequently, the subfamily Taeniopsettinae should be elevated to family status, two new families are newly defined—Monolenelidae (=Bothinae 2) and Grammatobothidae (=Bothinae 1)—each comprising a single genus, and restricting the family Bothidae to Bothinae 3. Revision of the usage of the valid generic names are proposed for Arnoglossus (=Arnoglossus V), Laeops (=Laeops II), Parabothus (=Parabothus III), and Psettina (=Psettina III). In addition, the resurrection of previously synonymized bothid genera (Anticitharus, Caulopsetta, Psettinella, and Scidorhombus ) and the establishment of new genera are recommended. Furthermore, the species-level taxonomy was also investigated using COI gene datasets analysed with two DNA-based species delimitation tools—Assemble Species by Automatic Partitioning (ASAP) and Bayesian Poisson Tree Processes (bPTP)—in conjunction with morphological characteristics, depth distribution, and geographic range data. This integrated approach identified a total of 128 putative species, including 12 potential new species, highlighting substantial unrecognized diversity within the Bothidae. In conclusion, this study presents the first comprehensive taxonomic revision of the Bothidae, integrating extensive morphological and molecular data across broad taxonomic and geographic ranges. The findings highlight the importance of integrative approaches in flatfish taxonomy and establish a robust phylogenetic framework for future evolutionary, ecological, and conservation research.