在過去幾十年間，物種生態、分布、與種化之間的連結，一直是演化生物學上的研究重點。近年，具有高度多樣性的蜥蜴，逐漸成為各種時間與空間尺度生態學和演化生物學的研究對象。岩虎（Cnemaspis）是廣布在東南亞的類群，在地理分布和活動時間均呈現很大的種間變異，也使得本屬成為深具價值的研究對象。湄公河三角洲淋溶殘存的花崗岩石洞中，就分布著四種當地特有的岩虎，分別是坎山岩虎（C. nuicamensis）、鐸山岩虎（C. tucdupensis）、橙肢岩虎（C. aurantiacopes）、與雪尾岩虎（C. caudanivea）。這些洞穴壁虎極為狹窄的分布區域，以及特化的生態現象，成為我珍貴的研究題材。我利用次世代定序技術之中的限制酶基因組測序技術（RAD-seq），以瞭解這四個特有物種的演化過程。由於壁虎並沒有可供參考比對的基因組序列，因此我們利用不同的參數設定，嘗試對定序獲得的大量序列進行組裝，最後將相關的參數M設置為4，而n設置為7；相關的運算與評估過程描述於第一章。
在第二章之中，我則是利用第一章獲得的參數和組裝的序列進行溯祖運算，以估計種化過程的時間、遺傳交流、有效族群量的變動等等。結果發現這四種岩虎在地質年代中均呈現有效族群量的劇烈縮減，而受限的遺傳交流也證明逐漸消失的花崗石洞對它們的族群分化有重大的影響。壁虎對棲地的高度特化雖然促進牠們的種化，但是也導致牠們在演化過程中受困於原棲息地，而邁向演化的死胡同。我的研究強調這種對棲地極度專一的物種，在保育上有其重要性與急迫性。
從第二章的研究顯示近緣物種受到地形的阻隔，而呈現劇烈的遺傳分化。但是坎山岩虎與鐸山岩虎的地理位置相隔非常近，在過去的歷史之中，卻無法入侵對方的領域。因此在第三章之中，我試著對這兩個姊妹種的生態棲位進行量化，以了解牠們無法共域存在的原因。結果顯示這兩個物種在棲地偏好上雖然有細微的差異，但是不足以讓牠們存在明顯的生態分化。除了地理分隔的效應之外，生態棲位的保守性也解釋了牠們無法共存的原因。
在第四章，我試圖將研究角度延伸到整個岩虎屬在活動時間的生態區隔。有別於其他的壁虎，岩虎最特殊的現象就是牠們有極高比例日行性的物種。而在岩虎分布的範圍之中，彎趾虎（Cyrtodactylus）是一個分布和岩虎高度重疊的類群，在東南亞形成極高的物種多樣性。我們懷疑岩虎的日夜行性演化可能與牠們和彎趾虎的競爭有高度的相關。分析岩虎的演化樹，我發現岩虎在棲地的使用上具有高度的保守性，但是在時間的使用上具有高度的變異性，顯示對岩虎而言，時間棲位的改變是一個解決棲位競爭較為彈性的作法。雖然從模型上來說，雨量和濕度是一個影響日夜行性更為顯著的環境因子；但是加入彎趾虎之後，可以顯著改善模型的可信度。在彎趾虎不存在的地區，岩虎有較高的機會回復大部分壁虎正常的夜行性棲位。

For decades, the link among ecology, distribution and speciation has been the focus for evolutionary biologist. Recently, lizards as a widely distributed and highly diverse group, have emerged as new model organisms for ecological and evolutionary studies from various community levels at a variety of spatial and temporal scales. Rock geckos – genus Cnemaspis, are widely distributed in Southeast Asia and have diverse spatial ranges and temporal activity pattern among its species. This makes this genus a suitable model to study the relationship among ecology, distribution and speciation. The monophyletic group of four Cnemaspis species (C. nuicamensis, C. tucdupensis, C. caudanivea and C. aurantiacopes) are endemic to southern Mekong Delta and are isolated to multiple neighbor rocky areas. This distributional pattern provides an excellent chance to study genetic and ecological differentiation within a minute geographic scale. Therefore, I focused on investigation on the speciation and niche of these four species, especially the two sister species C. nuicamensis and C. tucdupensis.
In order to understand the speciation of these species, I inferred the historical demography by estimating the population parameters (population size, divergence time and gene flow) of these species. I utilized one of the powerful of Next Generation Sequencing tools, the Restriction site associated DNA sequencing, which can generate large genetic data to fill the necessity of data analyses. In order to overcome the caveat of RAD-seq without reference genome, I explored the influence of parameters on the output loci dataset in Chapter 1. By using the most recommended program for RAD-seq – STAKCS, I conducted the optimization of a de novo assembly for my downstream population genetics analyses. After iterating values of the main parameter of STACKS and comparing the resultants from multiple de novo loci assembly, the most optimized parameters for my RAD-seq dataset were selected as M = 4 and n = 7. Using the optimized parameter for my dataset from Chapter 1, I applied several coalescence-based approaches to estimate divergence times, gene flow and demographic fluctuations during speciation processes in Chapter 2. The results showed long-term population shrinkage in the four geckos and limited gene flow during their divergence, suggesting that the erosion and fragmentation of the granite boulder hills have had great impacts on these populations’ divergences and population declines. These results also showed that the specialist gecko’s habitat specialization has facilitated the fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. My study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
The results from Chapter 2 showed the limited dispersal ability of C. nuicamensis. And it was confirmed when the recent described Cyrtodactylus species, which occurs in similar habitat, can cross the range of both Cnemaspis sister species. Therefore, there is a question why C. nuicamensis did not cross to its sister species’ range. In Chapter 3, I investigate the realized niche of the two sister species to see if there is enough divergence in their habitat use for them to coexist. The results showed that there is somewhat difference in the habitat preference of the sister species but is unlikely enough to use distinct resource and be sympatric. This suggest that there is strong niche conservatism in Cnemaspis species which promoted speciation and prevent sympatry afterward.
In Chapter 4, I attempted to infer the link between the pattern of temporal activity among Cnemaspis species and the existence of sympatric Cyrtodactylus species. Diel activity and habitat use pattern across the phylogeny of Cnemaspis genus were analyzed. And the relationship between the temporal activity pattern of Cnemaspis species with the existence of sympatric Cyrtodactylus species along with other ecological factors was tested. I found strong phylogenetic signal in habitat use trait but not in temporal activity, showing that the temporal niche of this genus is more labile compare to microhabitat niche. Further, the absent of the competitor as Cyrtodactylus species may create an opportunity for Cnemaspis species to shift back to nocturnality.

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