利用粒線體D-loop序列探討臺灣長鬃山羊親緣地理關係與歷史族群波動

Abstract

親緣地理學為探討生物族群之遺傳與地理結構的學科，透過親緣地理分析將生物現今的系譜資訊結合地理分布，能夠進一步推論生物過去所受到如氣候變遷影響其分布的演化歷史。臺灣是高山型島嶼，擁有約三分之一面積為海拔1,000 m以上的高山地形，並且已證實多處山區過去曾經歷冰河期。如此崎嶇的地形與劇烈的氣候變化是否會對臺灣高海拔大型哺乳類動物的族群遺傳結構造成影響，尚有待研究。臺灣長鬃山羊（Capricornis swinhoei）為臺灣唯一野生的牛科動物，且為珍貴保育的臺灣特有種，廣泛分布於臺灣各地山區。由於臺灣長鬃山羊之親緣地理分析研究尚不完整，本研究以粒線體DNA D-loop序列作為分子遺傳標記欲探討其遺傳多樣性、親緣關係、族群數量波動及族群遺傳結構。 本研究從全臺灣36個採樣點、342個樣本中成功定序得342條D-loop序列全長（1,122-1,125 bp），並從中獲得126個基因單套型。以單套型重建親緣關係樹結果顯示有100的支持度將臺灣長鬃山羊分為兩個主要類群，分別分布於太魯閣與雪霸山區、以及臺灣全島山區，依其分布將之命為太魯閣雪霸主要類群及臺灣主要類群。兩大主要類群在12.5至13.4萬年前分岐，大約落在里斯冰河期。根據AMOVA分析結果顯示臺灣長鬃山羊的遺傳結構在奇萊山區與丹大之間、玉山國家公園以東南存在顯著的遺傳分化（ΦCT = 0.26525; P < 0.001），並且與地理距離顯著相關（r = 0.6690; P < 0.001）。依據中性檢測、核苷酸變異分布、貝氏天際線圖分析結果顯示，約在沃姆冰河期結束時臺灣主要類群曾經歷族群擴張的事件。總結分析結果，地理距離為造成臺灣長鬃山羊基因交流的阻礙可能因素之一，此外過去所經歷之多次冰河週期帶來的氣候變遷亦為造就現今遺傳結構的重要因子。此篇研究提供臺灣長鬃山羊及其他臺灣高海拔生物的親緣地理研究的參考資訊。

Phylogeography is the study of the genetic and geographic structure of populations and species. Phylogeographic analysis provides an insight into historical factors, such as climate change, by examining current patterns of genealogy and geographic distribution. Taiwan is a mountainous island, which contains one third area of mountains that are up to 1,000 meters of elevations and has experienced several glacial cycles. Whether the geological history and the past glacial periods affected the alpine large mammals’ genetic population structures and diversities in Taiwan hasn’t been extensively studied. Formosan serow（Capricornis swinhoei）is the only endemic wild bovidae animal that protected by law in Taiwan, and widely distributed in the mountainous regions（400-3,952 m elevation）throughout the island. Due to lacking of phylogeographic studies, the phylogeographic relationships and historical demography of Formosan serow remains unclear. In this study, we examined the mitochondria DNA D-loop regions (1) to assess the genetic diversity and phylogenetic relationship, (2) to investigate the differentiation and phylogeographic relationships, and (3) to infer the historical evolutionary processes of Formosan serow in Taiwan. In total, 342 samples（feces, blood and tissue）collected from 36 localities throughout Taiwan was examined. We obtained 126 haplotypes from D-loop region（1,122-1,125 bp）. Two major clades with 100% supported bootstrap values were identified in D-loop sequences analysis. Furthermore, the two major clades were defined as Taroko and Sheipa major clade and Taiwan major clade because they were mainly distributed to the Taroko and Sheipa Mountain Area, and the entire mountainous area of Taiwan, respectively. The divergence time between these two phylogroups were examined at approximately 0.125 to 0.134 mya（million years ago）during Riss glaciation（0.2-0.13 mya）. According to AMOVA and mantel test, the Formosan serow population can be divided into three genetic units that existed significant genetic differentiation correlated to geographical distances（ΦCT = 0.26525; P < 0.001）（r = 0.6690; P < 0.001）. Mismatch distribution analysis, Neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the population of Taiwan major clade, with horizons dated to approximately 0.02 mya during the end of Würm glaciation（0.11-0.012 mya）. In conclusion, the geographical distance with restriction of gene flow was one of the factors that shaped current genetic differentiation and variant geographical distribution of haplotypes. In addition, past climate change caused by multiple glacial periods also played an important role in shaping the current phylogeographic structure. This study will provide usefully information for further phylogeographic study of Formosan serow, and other alpine species in Taiwan.