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.

石灰岩喀斯特地层是独特的生态系统，拥有许多世界上其他地方找不到的物种。不幸的是，这些生态系统由于其在水泥行业的重要性而受到严重威胁。这在东南亚尤其值得注意，那里大片的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，保护工作已转向新物种的发现和描述，以强调该生态系统作为生物多样性濒临灭绝的方舟的重要性。然而，相对较少的研究关注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全球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。Cyrtodactylus 属的弯趾守宫表现出多种专门的生态型与不同的栖息地相关。其中，适应喀斯特的物种在马来西亚的三个远缘分支中独立进化了六次，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且引人注目的自然系统，可以确定向喀斯特过渡的壁虎是否受到基于生态的发散选择，最终导致物种形成。由于喀斯特生态系统具有独特的地貌特征和理化条件，使其与非钙质环境区分开来，因此不同的选择预计将作用于独立演化的喀斯特谱系，这些谱系发生在独立但相似的喀斯特环境中。本研究将使用通过双消化限制位点相关 DNA (ddRADseq) 方案获得的全基因组 SNP 数据，因为整个基因组中存在大量独立基因座，这使得能够检测中性偏离和选择特征。然后使用 RAD 探针方法 (hyRAD) 进行杂交捕获，以获得更远缘相关群体之间的可比较的直系同源基因座。然后，可以通过使用潜在因子混合模型（LFMM）方法识别与环境变量表现出高度相关性的遗传多态性来检测基于生态的趋异选择的特征。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，与最近分化的谱系相比，较古老的谱系显示出较少（或完全缺乏）的种群间基因流，其中基因流可能是常见的。