印度─西太平洋地區淺水域魚類之族群基因體與生物地理研究

Abstract

印度－西太平洋地區為全球最大的海洋生物地理區，其中心區域具有極高的海洋生物多樣性，並隨著遠離中心的距離逐漸遞減。儘管已有眾多理論試圖解釋形成此物種豐富度高度集中的原因，目前仍難以建立一套普遍適用於所有物種的共識性理論。為了更全面地理解形塑此廣大區域海洋生物多樣性的歷史與生態因素，針對具備不同生態特徵與棲位的物種所進行的每一項生物地理模式與演化歷史研究，皆能提供寶貴的見解。本論文回顧並整理前人對印度－西太平洋地區生物地理的相關研究，並透過兩件針對特定淺海域魚類物種的個案研究，分析歷史環境變遷(如更新世冰期循環)如何影響該區域淺海域物種的分布與演化歷程。 第一個個案探討了更新世冰期循環所引起的海平面變動與生物地理隔離事件，對一種廣泛分布於淺海、且相較於前人研究對象具有較短浮游幼生期之魚類，七帶豆娘魚，族群結構的影響。遺傳分析結果顯示，該物種在印度洋與太平洋之間存在明顯的族群遺傳結構。在太平洋地區，特別是在臺灣，觀察到兩個分布重疊但缺乏基因交流的族群，顯示可能已產生生殖隔離。族群歷史模擬結果顯示，更新世冰期循環期間，印度－太平洋屏障所造成的族群隔離，以及冰期期間族群限縮於庇護所並於間冰期發生的次級接觸皆可能是形塑七帶豆娘魚目前所觀察到之複雜族群遺傳結構的關鍵歷史因素。 第二個個案則聚焦於西南印度洋莫三比克海峽，探討五種淺海域魚類物種的族群動態。這些遠離印度－西太平洋中心區域的島嶼，在氣候變遷劇烈的冰期期間，可能也扮演了庇護所的角色，促使部分族群得以維持存續。遺傳分析結果顯示，這些物種皆在近代經歷過族群擴張，其時間大致落在末次最大冰期（約2萬年前）結束之後。此結果顯示，隨著海平面上升，存活於庇護所的物種得以擴張至新形成的沿海棲地，進而增加族群間的基因交流機會。這一過程可能促成了區域內高物種分化率的形成條件。 綜合而言，本論文有助於更全面理解冰期循環如何形塑印度－西太平洋地區不同淺海域魚類物種的族群演化歷史。研究同時強調整合多種互補性遺傳標記的重要性，並指出部分魚類物種具備成為未來生物地理與演化生物學研究理想模式物種的潛力。

The tropical Indo-West Pacific (IWP) region is the largest marine biogeographical province and harbours the highest concentration of marine biodiversity, particularly in its central area. Despite numerous hypotheses proposed to explain this remarkable species richness, no consensus has been reached. To advance our understanding of the complex evolutionary and ecological processes shaping present-day marine biodiversity patterns in this vast region, it is essential to integrate data from multiple species with diverse ecological traits and ecological niches, as each species may offer unique biogeographical and evolutionary insights. This dissertation presents two case studies on selected shallow-water fish species to investigate the influence of historical and ecological factors on their evolutionary trajectories, using complementary genetic markers. The first case study investigates the impact of Pleistocene glacial cycle-induced biogeographical barriers and isolation in refugia caused by past sea-level fluctuations on Abudefduf septemfasciatus (commonly known as the banded sergeant), a widely distributed shallow-water damselfish characterised by a relatively short pelagic larval duration. Analyses of genome-wide SNPs and mitochondrial DNA reveal the presence of two major genetic clusters across the IWP: one in the Indian Ocean and the other in the Pacific Ocean. Within the Pacific cluster, two subclusters with overlapping distributions in Taiwan suggest potential reproductive isolation. Demographic analyses suggest that recurrent episodes of isolation caused by the Indo-Pacific Barrier and refugial persistence, followed by periods of secondary contact during the Pleistocene glacial cycles, likely shaped the complex population structures observed today. The second case study explores the population dynamics of five shallow-water fish species from the remote islands in the Mozambique Channel. These islands likely served as glacial refugia, preserving marine populations during periods of climatic instability. Mitochondrial and genome-wide SNP analyses reveal signals of recent population expansion, likely occurring after the Last Glacial Maximum (~20,000 years ago). As sea levels rose, species from these refugia recolonised the newly available coastal habitats, fostering increased ecological interactions and potentially promoting diversification. These dynamics may have potentially contributed to the elevated rates of speciation observed in the region. Together, these case studies provide new insights into the historical processes, particularly glacial cycles, that have shaped the population genetic structure and demographic histories of shallow-water fish species in the IWP. The findings underscore the importance of integrating complementary genetic markers and highlight the utility of these fish species as promising models for future research in marine biogeography and evolutionary biology.