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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，拥有世界上其他地方找不到的许多物种。不幸的是，由于它们在水泥工业中的重要性，这些生态系统受到了严重威胁。这在东南亚尤其明显，那里大片的喀斯特露头正在被采掘到地面上，导致大量动植物物种不可避免地灭绝。因此，保护工作一直着眼于新物种的发现和描述，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上。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，来阐明岩溶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到威胁的喀斯特生境提供保护措施，还将有助于理解物种如何适应不断变化的环境。圆趾壁虎显示出与不同栖息地相关的广泛的专门生态型。其中，适应岩溶的物种在马来西亚的三个远亲支系中独立进化了六次，表明岩溶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种独特的、令人信服的自然系统，用来确定向岩溶过渡的壁虎是否受到基于生态的不同选择，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区别于非钙质环境的物理化学条件，预计不同的选择将作用于独立演化的岩溶谱系，这些岩溶谱系出现在不同但相似的岩溶环境中。这项研究将使用全基因组的SNP数据，这是由于基因组中存在大量独立的基因座，这使得能够检测到偏离中性和选择的签名，因此使用了双酶切限制位点相关DNA(DdRADseq)协议获得的数据。然后，使用RAD探针杂交捕获方法(HyRAD)将被用来在更远的亲缘关系群体中获得可比较的和同源的基因座。然后，通过潜在因子混合模型(LFMM)方法识别与环境变量高度相关的遗传多态，从而检测基于生态的差异选择的特征。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，较老的谱系在种群之间显示出较少(或完全缺乏)基因流动，在这些谱系中，基因流动可能是常见的。