DISSERTATION RESEARCH: Testing the Hypothesis of Ecological Speciation in Malaysia's Karst Geckos

石灰岩喀斯特地貌是一种独特的生态系统，孕育着世界上其他地方找不到的许多物种。不幸的是，这些生态系统由于在水泥工业中的重要性而受到严重威胁。这在东南亚尤其明显，那里大片的岩溶露头被开采到地面，导致许多动植物物种不可避免地灭绝。因此，保护工作已经转向发现和描述新物种，以突出这一生态系统作为生物多样性濒危方舟的重要性。然而，相对较少的研究集中在了解产生这种生物多样性的机制。该项目旨在通过研究基因如何与环境相互作用以驱动新物种的形成，阐明适应岩溶的生物进化的遗传机制。这项研究的结果不仅有助于为全球受威胁的喀斯特栖息地的保护措施提供信息，而且还有助于了解物种如何适应不断变化的环境。其中，喀斯特适应物种独立进化了6次在三个遥远的相关分支在马来西亚，表明喀斯特谱系的多样性可能是生态驱动（生态物种形成）。在弯趾壁虎的岩溶适应复制进化代表了一个独特的和令人信服的自然系统，以确定是否壁虎过渡到岩溶受到生态为基础的分歧选择，最终导致物种形成。由于岩溶生态系统的特点是独特的地貌特征和理化条件，使它们除了非石灰质环境，不同的选择预计将作用于独立发展的岩溶谱系发生在单独的，但类似的岩溶环境。本研究将使用全基因组SNP数据，该数据是使用双消化限制性位点相关DNA（ddRADseq）方案获得的，因为整个基因组中存在大量独立的基因座，这使得能够检测偏离中性和选择特征。然后使用RAD探针法（hyRAD）进行杂交捕获，以获得更远的亲缘关系组中的可比和直系同源基因座。基于生态的分歧选择的签名，然后可以通过识别遗传多态性，表现出与环境变量的潜在因素混合模型（LFMM）方法的高度相关性进行检测。此外，喀斯特和非喀斯特血统预计将在不同阶段的生殖隔离，与较老的血统显示较少（或完全缺乏）人口之间的基因流相比，最近已经分化的血统，其中基因流可能是常见的。

Limestone karst formations are unique ecosystems that harbor many species found nowhere else in the world. Unfortunately, these ecosystems are severely threatened due to their importance in the cement industry. This is especially notable in Southeast Asia where extensive tracts of karst outcrops are being quarried to the ground, resulting in the inevitable extinction of numerous species of plants and animals. Consequently, conservation efforts have been geared towards the discovery and description of new species to highlight the importance of this ecosystem as imperiled arks of biodiversity. However, relatively little research has focused on understanding the mechanisms that have generated this biodiversity. This project aims to elucidate the genetic mechanisms responsible for the evolution of karst-adapted organisms by investigating how genes interact with the environment to drive the formation of new species. Results from this study will not only aid in informing conservation measures in threatened karst habitats worldwide, but will also contribute towards the understanding of how species adapt to an ever changing environment.Bent-toed Geckos of the genus Cyrtodactylus exhibit a wide array of specialized ecotypes that are associated with different habitats. Among these, karst-adapted species have evolved independently six times in three distantly related clades in Malaysia, indicating that the diversification of karst lineages may be ecologically driven (ecological speciation). The replicated evolution of karst adaptation in Bent-toed Geckos represents a unique and compelling natural system to determine whether geckos transitioning to karsts are subjected to ecologically-based divergent selection that ultimately leads to speciation. Because karst ecosystems are characterized by unique geomorphological features and physiochemical conditions that set them apart from non-calcareous environments, divergent selection is expected to act on independently evolving karst lineages that occur in separate but similar karst environments. This study will use genome-wide SNP data obtained using a double-digest restriction-site associated DNA (ddRADseq) protocol due to the availability of large numbers of independent loci across the genome, which enable the detection of departure from neutrality and signatures of selection. A hybridization capture using RAD probes method (hyRAD) will then be used to obtain comparable and orthologous loci among more distantly related groups. Signatures of ecologically-based divergent selection can then be detected by identifying genetic polymorphisms that exhibit high correlation with environmental variables using a latent factor mixed model (LFMM) method. Additionally, karst and non-karst lineages are expected to be in different stages of reproductive isolation, with older lineages showing less (or a complete lack of) gene flow among populations compared to lineages that have diverged more recently, in which gene flow may be common.