重新評估刺尾鯛目的演化歷史：基於時間校準框架探討笛鯛科、龍占魚科以及金線魚科的親緣關係與生態多樣化

Abstract

刺尾鯛目(Acanthuriformes)是棘鰭類 (Acanthomorpha)中一群多樣性極高的魚類類群，包含 54 科、超過 2,300 個物種。儘管該目的多樣性與演化已在部分科別中受到廣泛研究，但對於三個具重要生態及經濟價值的科:笛鯛科(Lutjanidae)、龍占魚科(Lethrinidae)及金線魚科(Nemipteridae)的探索仍不足。本研究使用三個粒線體基因(COI、12S、CYTB)及兩個核基因(RAG1、RH)建立新的多基因之序列資料矩陣，以重新評估三科內物種的親緣關係。接著利用五個單拷貝核蛋白編碼基因(EGR1、EGR2B、EGR3、RAG1、RH)重建刺尾鯛目主要譜系的時間校準親緣樹，以推估刺尾鯛目主要譜系的分歧時間，並探討三個關鍵的生態特徵:水深分布、棲地異質性及體型是如何影響該目及三個科別的演化。此外，本研究也應用幾何形態計量分析(geometric morphometrics)量化三科內物種間的體型差異，並視覺化其與親緣關係推論、水深及棲地的關聯。親緣關係分析結果支持三個科皆為單系群，但指出笛鯛科內有四個現行所認定的屬為多系群。在科間關係方面，笛鯛科與蓋刺魚科(Pomacanthidae)呈姊妹群關係，但支持度弱，而龍占魚科、金線魚科與鯛科(Sparidae)則形成一個高支持度的單系群，即先前所提出的 Sparoidea 超科。於生態多樣化及演化之探究上，笛鯛科中兩個亞科(Apsilinae 和Etelinae)內的物種，於始新世期間自淺海擴展至較深的水層，而金線魚科的部分譜系在中新世後擴張深度範圍至深水層。三科均多次獨立發生由非礁區向礁區的棲地轉變，而部分笛鯛科與金線魚科的部分譜系則演化出更為細長的體型。幾何形態計量分析結果顯示，體型變異主要受到親緣關係之連動，而非水深分布或棲地因子而衍生之差異。綜合而言，本研究提供了一個整合親緣關係、形態與生態的分析框架，揭示三科經歷了各自獨立的生態轉變，但棲息水深及棲地類型並非為驅動體型演化的主要因素。

Acanthuriformes comprising over 2,300 species across 54 families is a diverse order of acanthomorph fishes. While the remarkable diversity and evolution of this order have been widely investigated in several families, studies focusing on three ecologically and economically important families—Lutjanidae, Lethrinidae, and Nemipteridae—remain limited. This study constructed three multi-gene datasets to re-evaluate the phylogenetic hypothesis of the three families. The datasets include DNA sequences from three mitochondrial (COI, 12S, CYTB) and two nuclear (RAG1, RH) markers. Furthermore, using a newly reconstructed time-calibrated phylogeny of Acanthuriformes based on five single-copy nuclear protein-coding gene (EGR1, EGR2B, EGR3, RAG1, RH) sequences, I intend to re-evaluate the divergence times of major acanthuriform lineages and to examine how the three key ecological traits—depth distribution, habitat association, and body shape—have evolved within the order and the three focal families. Additionally, the geometric morphometric analyses were employed to quantify body shape variation within each of the three families and to visualize its associations with the inferred phylogenies, as well as with depth and habitat. Phylogenetic results of the three focal families are consistent with previous studies, confirming their monophyly; however, four of the currently recognized genera in Lutjanidae are resolved as polyphyletic. As to the inter-familial relationship, Lutjanidae is weakly supported as the sister group of the Pomacanthidae. Lethrinidae, Nemipteridae, and Sparidae form a strongly supported clade, previously known as superfamily Sparoidea. Within the Lutjanidae, the most recent common ancestor of two subfamilies (Apsilinae and Etelinae) was inferred to expand its depth ranges from shallow to deep water during the Eocene, whereas several lineages in Nemipteridae underwent depth expansions to deeper waters after the Miocene. Transitions from non-reef to reef-associated habitats occurred independently across all three families. Additionally, some lineages in Lutjanidae and Nemipteridae evolved more slender body forms. Geometric morphometric analyses indicate that body shape variation is more associated with inferred phylogenies than with depth distribution or habitats. Together, this study provides an integrative framework that links phylogeny, ecology, and morphology in acanthuriform fishes with focus on the Lutjanidae, Lethrinidae, and Nemipteridae. These families have undergone lineage-specific ecological transitions; however, the expansion of depth range and the transition to complex habitats do not appear to be the primary drivers of body shape evolution within these families.