DISSERTATION RESEARCH: Phylogeny, biogeography, and convergent evolution in a radiation of Southeast Asian Rock Geckos (Cnemaspis Strauch, 1887).

东南亚是世界上最耐人寻味、研究最少的生物多样性热点地区之一。这一地区的一个突出的地质特征是舜他陆架，它目前淹没在南中国海之下，位于马来群岛之下。该地区有着复杂的地质和气候历史，是研究生物多样性驱动因素的绝佳系统。在这一地区广泛分布的一种岩壁虎属Cnemaspis。这些壁虎生活在不同的底物上，包括不同类型的植被和岩石，包括石灰岩，在东南亚，石灰岩被大量开采用于生产水泥。开采和清除热带雨林对该地区独特的生物多样性构成严重威胁。对这一区域特有生物的研究可以通过发现神秘物种和确定物种多样性较高的当地地区，为保护规划作出贡献。这种知识对于实施有效的以科学为基础的保护战略至关重要。这项研究也将进一步加深我们对物种形成和适应独特的当地环境的过程的理解，以及生物多样性的长期积累，正是这些因素使亚洲这一地区拥有如此丰富的特有物种。这项研究的一部分将用于培训本科生，并在杨百翰大学的豆类生命科学博物馆开展关于生物多样性和物种发现的公开展示。Cnemaspis属广泛分布于东南亚各地，是该地区物种最丰富的壁虎属之一，已描述的种有54种。这些被认为是低游荡能力的壁虎生活在不同的底物上，生态形态也不同；而支系的特征是一些微小的地方性疾病，使其成为一个很好的进化研究系统。在这个项目中，我们将：(1)建立一个有良好支持的多位点时间校准的该属的系统发育，并测试舜他陆架的空间和时间差异；(2)评估该属的初步系统发育中的多个部分是“硬的”还是“软的”，如果是前者，它是适应性的还是非适应性的辐射；以及(3)调查生态特征的汇聚进化对线虫物种多样性(例如物种形成和灭绝率)的影响。目前，一个线粒体基因和三个核基因序列可以解析树顶端支撑良好的分支，但无法解析更深层次的节点。为了检验硬性和软性多基因分割假说，将使用“下一代”序列捕获方法来生成数百个基因座。根据这一数据集，将构建一棵系统发育树，以明确地测试Sundaland部分地区的可选生物地理假设，以及测试形态随时间的差异(DTT)、收敛的适应制度转变和生态地貌特征的进化。

Southeast Asia is one of the most intriguing and understudied biodiversity hotspots in the world. A prominent geological feature of this area is the Sunda Shelf, which is currently submerged beneath the South China Sea and underlies the Malay Archipelago. This region has a complex geological and climatic history, and serves as an excellent system to study drivers of biotic diversification. One group that occurs throughout this region is the rock gecko genus Cnemaspis. Theses geckos live on various substrates including different types of vegetation and rocks, including limestone, which is heavily mined in Southeast Asia for the production of cement. Mining and clearance of rainforest comprise serious threats to the unique biodiversity of this region. Studies of the endemic organisms of this region can contribute to conservation planning through the discovery of cryptic species and identification of local areas of high species diversity. This kind of knowledge is crucial to the implementation of effective science-based conservation strategies. This study will also further our understanding of the processes of speciation and adaptation to unique local environments, and the long-term accumulation of biodiversity which make this part of Asia so rich in endemic species. Portions of this research will be used to train undergraduates, and to develop a public display about biodiversity and species discovery at the Bean Life Science Museum at Brigham Young University. The genus Cnemaspis is widespread throughout Southeast Asia and is one of the most species-rich gecko genera in the region, with 54 described species. These presumed low vagility geckos live on a variety of substrates and vary in ecomorphology; and the clade is characterized by a number of micro-endemics, making it a great system for evolutionary study. In this project we will: (1) generate a well-supported multilocus time-calibrated phylogeny of the genus and test spatial and temporal divergence across the Sunda Shelf; (2) evaluate whether the polytomy in the preliminary phylogeny for the genus is 'hard' or 'soft', and if the former, whether it is an adaptive or non-adaptive radiation; and (3) investigate the effects on Cnemaspis species diversification (e.g. speciation and extinction rates) derived from the convergent evolution of ecomorphological characters. Currently one mitochondrial gene and three nuclear gene sequences resolve well-supported clades towards the tips of the tree, but fail to resolve deeper nodes. To test the hard vs. soft polytomy hypotheses, a 'Next Generation' sequence-capture method will be used to generate hundreds of loci. From this dataset a phylogenetic tree will be constructed to explicitly test alternative biogeographic hypotheses for colonization of parts of Sundaland, as well as test morphological disparity through time (DTT), convergent adaptive regime shifts, and evolution of ecomorphological characters.