利用基因組單核苷酸變異探討台灣山羌的族群結構與變動

Exploring Population Structure and Demography of the Taiwan Reeves's Muntjac (Muntiacus reevesi micrurus, Sclater, 1875) Using Genome-Wide Single Nucleotide Variations

彭翊倫(Yi-Lun Peng)

指導教授 ： 王弘毅

國立臺灣大學/生命科學院/生態學與演化生物學研究所/碩士(2025年)

https://doi.org/10.6342/NTU202500507

摘要

台灣山羌Muntiacus reevesi micrurus (Sclater, 1875)是廣泛分布於台灣全島的小型鹿科動物。過去曾因過度獵捕被列為保育類，目前雖已脫離保育名錄，但其族群動態及遺傳多樣性仍需關注。以往研究多集中於粒線體DNA，缺乏基因體層級(genome-wide)的族群遺傳分析。本研究基於71個台灣各地山羌樣本，應用ddRADseq (Double Digest Restriction Associated DNA Sequencing)技術進行全基因組單核苷酸多態性(SNPs)分析，並結合資料庫中60隻中國山羌的全基因組資料，探討其族群結構、遺傳多樣性及歷史動態。台灣山羌在倒數第二次冰期(Penultimate glacial period)與中國山羌分化。台灣山羌族群結構可分為北部與南部兩大群，濁水溪與烏溪之間有混合群出現。台灣山羌南北族群基因交流仍存在，遺傳距離主要受到最小成本路徑影響。棲位分析顯示，南北族群棲息在不同環境中，進一步促成遺傳分化。環境變因分析指出，平均日溫差、年溫差和季節性降水是影響族群分布的可能因子。富集分析指出磷脂質酶A2活性(Phospholipase A2)受到選擇，影響毛披型態、神經發展、生殖系統以及離子穩態。近年來，人類活動導致族群數量下降，儘管遺傳多樣性在中性演化範疇內未見顯著變化，但台灣山羌的核苷酸多樣性相較於其他鹿科動物低。雖然台灣山羌已脫離保育名錄，但氣候變遷與人類活動仍可能威脅其族群穩定。族群動態與遺傳結構的研究有助於揭示其演化歷程與適應潛力。

關鍵字

遺傳多樣性 ； 族群結構 ； ddRADseq ； 保育遺傳

並列摘要

The Formosan Reeves’ muntjac (Muntiacus reevesi micrurus, Sclater, 1875) is a small cervid widely distributed across the entire Taiwan. Previously classified as a protected species due to overhunting, it has since been removed from the list of protected wildlife. However, its population dynamics and genetic diversity remain critical concerns. Previous studies have predominantly focused on mitochondrial DNA, lacking genome-wide population genetic analyses. In this study, we analyzed 71 Formosan muntjac samples using double digest restriction-site associated DNA sequencing (ddRADseq) to generate genome-wide single nucleotide polymorphism (SNP) data. We then combined these data with 60 whole genome sequences from Chinese muntjac to examined population structure, genetic diversity, and demographic history of this species. Our results indicate that Formosan muntjac diverged from Chinese muntjac during the Penultimate Glacial Period. Within Taiwan, the species exhibits a north-south population structure, with a contact zone identified between the Jhuoshuei River and Wu River. Despite this differentiation, gene flow persists between northern and southern populations, with genetic distance primarily shaped by least-cost path connectivity. Ecological niche analyses reveal that the northern and southern populations inhabit distinct environments, further promoting genetic differentiation. Environmental association analyses suggest that mean diurnal range, temperature annual range, and precipitation seasonality are key factors influencing population distribution. Functional enrichment analysis highlights Phospholipase A2 activity as a candidate under selection, potentially impacting coat morphology, neural development, reproductive physiology, and ion homeostasis. In recent years, human activities have contributed to population decline. While genetic diversity remains within the range expected under neutral evolution, nucleotide diversity in Formosan muntjac is relatively low compared to other cervids. While the Formosan muntjac is no longer listed as a protected species, ongoing climate change and anthropogenic disturbances may still impact its population stability. Research on population dynamics and genetic structure reveals its evolutionary history and adaptive potential.

並列關鍵字

genetic diversity ； population structure ； ddRADseq ； conservation genetics

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