台灣的山椒魚屬於保育類野生動物，近年來全球兩生類下降及氣候的變遷，有關其分類及生態研究是必需進行的。在本博士論文的研究中，嚐試於探討(1)台灣現有山椒魚屬(Hynobius)的種類分類歸屬；(2)以阿里山山椒魚為生態研究對象，討論其微棲息地的需求與偏好；(3)估計阿里山山椒魚於阿里山地區的族群量，並估算其存活率，並以模型預測其族群變動；(4)阿里山山椒魚的族群遺傳結構。
我以形態及分子的資料來分析山椒魚的分類問題。我的結果顯示出在遺傳上有五個明顯的分群，而這五群在形態上亦是有區隔。採用演化種觀點，可以將這五群視為獨立的種類。其中三群分別對應於前人的發現，即台灣山椒魚、楚南氏山椒魚和阿里山山椒魚等三個有效種，另外二種則是新種。
阿里山山椒魚的分布調查共調查了阿里山地區36個林班地中共73個山葵田，在其中9個林班發現山椒魚，而這些地點共有的特色是緩坡及穩定的溪流。山椒魚的微棲地偏好則記錄山椒魚所使用的微棲地及研究地點中適合山椒魚棲息的微棲地的特性。分析顯示阿里山山椒魚偏好使用木塊作為遮蔽物，也偏好遮蔽物上長有苔類者。在遮蔽物下的基質方面，山椒魚偏好碎石基質，但避免使用植物根系組成者。山椒魚偏好使用基質的土壤pH值為中性者、高土壤溼度及適當的土壤硬度。
族群動態的監測以阿里山姐妹潭的阿里山山椒魚族群為標的。使用Jolly-Seber法估算每月的族群量在13至305隻之間。相較於前人的估算數量，此族群在這些年間沒有很大的變化。再以Cormack-Jolly-Seber model來估算此族群的存活機率及捕獲機率，得到成體及亞成體在研究期間的存活率為恆定值，分別是0.996及0.997，皆屬於高存活率。捕獲機率則是隨季節而變，捕獲機率顯著與溫濕度呈正相關。接著再使用族群投影矩陣來分析族群動態及決定此族群的成長率，估計的族群成長率為1.130，代表此族群為穩定且緩慢增長。族群成長率的敏感度及彈性分析都顯示成體的存活率是族群穩定最重要的速率。
阿里山山椒魚遺傳結構研究方面，以AMOVA分析顯示主要遺傳變異分配在山脈之間，但山脈內族群及族群內的遺傳變異也佔相當的比例。以不相合分布(mismatch distribution)分析顯示在阿里山山脈的族群呈現族群數量增加的現象。以Nested Clade Analysis分析顯示幾乎所有的族群都是有限基因交流。再以Bayesian coalescent approach來推論每一個主要clade的分歧時間，並初步推測其親緣地理關係。

The species diversity of Taiwanese Hynobius salamanders has long been debated. In this study, I analyzed morphological and molecular data from these taxonomically problematic salamanders. My results showed that there are five distinct molecular clades of Taiwanese salamanders that match morphological differences and are indicative of specie`s-level recognition. Three species corroborate previous finding, while the other two are described as new species.
The distribution survey of Alishan salamander (Hynobius arisanensis) in Alishan Areas was conducted in 36 forestry areas. We found Alishan salamander in nine of them. Common characters of these localities show a gradual rise slope and with small creeks. Analysis of Hynobius arisanensis microhabitat preferences consisted of two parts: one to record microhabitat use of salamanders, the other one to quantify suitable microhabitat in the study site. Alishan salamanders showed a negative association with rocks, while a positive association with decayed woods. They also like the cover objects of shelters with mosses grown on it. As for substrates, salamanders were found positively to associate with pebbles, and were negatively associated with live plant roots. The Alishan salamander preferred substrates with neutral soil pH, high soil moisture, and suitable soil hardness.
I use the area-constrained method to monitor salamander population dynamic in the Sister Ponds, Chiayi Hsien. I used the Jolly-Seber method to estimate the monthly population size, it ranged between 13 and 305 individuals. It seemed that population size does not decrease as comparing with estimations made by the former researchers. I further used the Cormack-Jolly-Seber model to estimate the survival and capture probability of this population. The survival probabilities for adults and juveniles were 0.996 and 0.997, respectively. Capture probabilities were seasonal-specific, the capture probabilities were significantly positive correlated with rainfalls. Using the population projecting matrix to analyses the population dynamics and to determine population growth rate of this population, it was 1.130, indicating that the population is stable and slow growth. The sensitivity and elasticity of population growth rate both indicate that the adult survival rate was the most important vital rate for the population stability.
In Chapter 5, I use Hynobius arisanensis as a model species to investigate genetic structure of an alpine salamander. AMOVA of three mountain ranges suggested significant genetic differentiation among mountain ranges, among populations within mountain ranges, and within populations. Mismatch distribution analysis showed that populations within Alishan range exhibited a pattern of demographic expansion. Nested clade analysis indicated that study populations showed restricted gene flow or allpartic fragmentation. I also used Bayesian coalescent approach to estimate the divergence time and to inference their phylogeographic relationships.

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