馬口魚族基因體分化之機制：染色體裂變與環境適應

Abstract

馬口魚族（Tribe Opsariichthyini）為一群分布於東亞溪流的小型鯉科魚類，包含異鱲屬（Parazacco）、東瀛鯉屬（Nipponocypris）、鬚鱲屬（Candidia）、鱲屬（Zacco）及馬口魚屬（Opsariichthys）。其中，馬口魚屬物種不僅多樣性極高，亦廣泛分布於整個東亞地區。值得注意的是，相較於其他類群，馬口魚屬的染色體裂變次數顯著偏高，達 14–15 次之多。 本研究組裝了五種馬口魚族物種的染色體層級基因體，並分為兩部分探討不同演化議題。第一部分聚焦於染色體大規模裂變的潛在分子機制。儘管染色體裂變在演化歷程中屢見不鮮，其形成機制與演化意義迄今仍未明朗，且過去多被認為是具破壞性的事件。本研究提出一項可能廣泛存在的機制：大規模裂變與轉座子的大量擴增有關。當轉座子大量插入並累積於著絲點區域，可能導致該區域拓寬，產生額外的著絲點 DNA，進而誘發新的著絲點（kinetochore）形成，產生具雙著絲點的染色體（dicentric chromosome）。這類染色體在裂變後仍可維持減數分裂期間的正常分離。本研究亦觀察到，染色體裂變對物種本身並未造成明顯不良後果，反而可能與加速物種形成相關。 第二部分則探討臺灣特有魚類——臺灣鬚鱲（Candidia barbatus）之族群結構與南北分化的潛在驅動因素。我們分析了 59 個體的全基因體資料，結果顯示臺灣鬚鱲可劃分為北部、中部與南部三個主要族群。與高分化的粒線體基因不同，核基因體呈現相對較低的族群分化程度。根據全基因體資料推論，我們認為傳統的南北分界應往北修正，以涵蓋高屏溪流域。此外，過去被重新命名為屏東鬚鱲之族群，與其他南部族群之間幾無遺傳分化與生殖隔離，顯示其分類地位亟待重新評估。更重要的是，我們發現南北族群的分化並非僅源於地理隔離，亦反映環境適應的結果：北部族群顯示與缺氧與低溫環境相關的適應性基因訊號，而南部族群則呈現與高溫環境相關的遺傳變異。 綜合而言，本研究不僅釐清了轉座子促成染色體大規模裂變的潛在機制，也揭示環境選擇如何塑造臺灣特有淡水魚類的族群結構與適應性演化，對瞭解物種形成與制訂保育策略均具有重要意義。

The tribe Opsariichthyini comprises a group of small cyprinid fishes distributed in East Asian stream habitats, including the genera Parazacco,Nipponocypris, Candidia, Zacco, and Opsariichthys. Among them, species in the genus Opsariichthys exhibit relatively high diversity and are widely distributed throughout East Asia. Notably, compared to other genera, Opsariichthys species have undergone as many as 14–15 chromosomal fission events. In this study, we assembled and analysis chromosome-level genomes for five species of the Opsariichthyini and addressed two distinct questions. The first part focuses on the potential mechanism underlying large-scale chromosomal fission. Although chromosomal fission has repeatedly occurred in evolution, its molecular mechanism remains poorly understood, and it has long been regarded as a harmful event. Here, we identify a potentially widespread mechanism in which large-scale fission is associated with massive transposable element (TE) expansion. TE insertions lead to the expansion of centromeric regions, generating additional centric DNA and potentially inducing the formation of new kinetochores, resulting in dicentric chromosomes. These chromosomes, even after fission, can still maintain proper segregation during meiosis. Importantly, we found no evidence of deleterious effects caused by fission in these species; on the contrary, chromosomal fission may be associated with accelerated speciation. The second part investigates the population structure and potential drivers of north-south divergence in Candidia barbatus, a freshwater fish endemic to Taiwan. We analyzed whole-genome data from 59 individuals and found that C. barbatus can be divided into three major populations: North, Central, and South. In contrast to the highly divergent mitochondrial genome, the nuclear genome shows relatively low levels of differentiation. Based on genome-wide data, we propose that the traditional north-south boundary should be adjusted northward to include the Kaoping River basin. Additionally, the population previously renamed as Candidia pingtungensis shows almost no genetic differentiation or reproductive isolation from other southern populations, suggesting that its taxonomic status requires re-evaluation. More importantly, we found that the north-south divergence is not solely caused by geographic isolation but is also associated with environmental adaptation: the northern population shows selection signals related to hypoxia and cold tolerance, while the southern population exhibits selection signals associated with adaptation to high-temperature environments. This study not only clarifies the potential mechanism of large-scale chromosomal fission but also reveals how environmental selection shapes population structure and local adaptation in a freshwater species endemic to Taiwan. These findings have important implications for understanding evolutionary mechanisms and informing conservation strategies.