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

论文研究：测试马来西亚喀斯特壁虎的生态物种形成假说

基本信息

批准号：
1702036
负责人：
Rafe Brown
金额：
$ 1.95万
依托单位：
University of Kansas Center for Research Inc
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-07-01 至 2018-06-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1702036&HistoricalAwards=false
关键词：
DISSERTATION RESEARCH Testing Hypothesis Ecological

项目摘要

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.

石灰岩喀斯特构造是独特的生态系统，其中蕴藏着许多世界上其他地方找不到的物种。不幸的是，由于这些生态系统在水泥工业中的重要性，它们正受到严重威胁。这在东南亚尤其明显，那里的大片喀斯特露头被开采到地面，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公园的重要性。然而，相对较少的研究集中于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来驱动新物种的形成，从而阐明喀斯特适应生物进化的遗传机制。这项研究的结果不仅有助于为世界范围内受威胁的喀斯特栖息地的保护措施提供信息，而且还将有助于了解物种如何适应不断变化的环境。弯趾壁虎属的弯趾壁虎表现出一系列与不同栖息地相关的特殊生态型。其中，喀斯特适应物种在马来西亚的三个远亲分支中独立进化了6次，表明喀斯特谱系的多样化可能是生态驱动的（生态物种形成）。弯趾壁虎喀斯特适应的复制进化代表了一个独特而引人注目的自然系统，可以确定壁虎向喀斯特过渡是否受到最终导致物种形成的基于生态的分歧选择的影响。由于喀斯特生态系统以其独特的地貌特征和物理化学条件为特征，使其与非钙质环境区别开来，因此，在分离但相似的喀斯特环境中发生的独立进化的喀斯特谱系中，预计会发生分歧选择。本研究将使用双消化限制性位点相关DNA （ddRADseq）协议获得的全基因组SNP数据，因为基因组中有大量独立位点，可以检测偏离中性和选择的特征。使用RAD探针方法（hyRAD）的杂交捕获将用于在更远亲的群体中获得可比较和同源的位点。然后，通过使用潜在因素混合模型（LFMM）方法识别与环境变量高度相关的遗传多态性，可以检测基于生态的发散选择的特征。此外，喀斯特和非喀斯特谱系预计将处于生殖隔离的不同阶段，与最近出现分化的谱系相比，较老的谱系在种群中表现出较少（或完全没有）基因流动，在后者中，基因流动可能很常见。