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

东南亚是世界上最吸引人、研究最不足的生物多样性热点地区之一。巽他陆架是该地区一个突出的地质特征。巽他陆架目前淹没在南中国海之下，位于马来群岛之下。该地区具有复杂的地质和气候历史，是研究生物多样性驱动因素的良好系统。在这个地区分布的一个群体是石壁虎属的石壁虎。这些壁虎生活在各种基质上，包括不同类型的植被和岩石，包括石灰石，东南亚大量开采石灰石用于生产水泥。采矿和砍伐雨林对该地区独特的生物多样性构成严重威胁。对该地区特有生物的研究可以通过发现隐种和确定高物种多样性的局部区域，为保护规划做出贡献。这类知识对于实施有效的基于科学的保护策略至关重要。这项研究还将进一步加深我们对物种形成和适应独特当地环境的过程的理解，以及使亚洲这一地区拥有如此丰富的特有物种的生物多样性的长期积累。这项研究的部分内容将用于培训本科生，并在杨百翰大学（Brigham Young University）的Bean生命科学博物馆（Bean Life Science Museum）公开展示生物多样性和物种发现。cnemasis属在东南亚广泛分布，是该地区物种最丰富的壁虎属之一，共有54种。这些被认为是低危险性的壁虎生活在各种基质上，生态形态也各不相同；这个分支的特点是有许多微型地方性，这使它成为一个很好的进化研究系统。在这个项目中，我们将：(1)生成一个有良好支持的多位点时间校准的属系统发育，并测试巽他大陆架的时空差异；(2)评估该属的初步系统发育中的多元是“硬”还是“软”，如果是前者，它是一种适应性辐射还是一种非适应性辐射；(3)研究生态形态特征趋同演化对线虫物种多样性的影响（如物种形成率和灭绝率）。目前，一个线粒体基因和三个核基因序列可以解析树的尖端，但无法解析更深的节点。为了测试硬多边形与软多边形假设，将使用“下一代”序列捕获方法来生成数百个位点。从这个数据集将构建一个系统发育树，以明确地测试不同的生物地理学假设，以及通过时间的形态差异（DTT），趋同适应制度转移和生态形态特征的进化。

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.