Dissertation Research: Endogenic Microbial Community Structure and its Influence on Community Assembly and Speciation in Squamate Reptiles

该项目的目标是了解物种群落是如何构成的，以及生活在脊椎动物体内的细菌群落是否会影响新脊椎动物物种的进化。该项目采用了一种新颖的方法，通过探索爬行动物肠道中发现的细菌的进化史和爬行动物宿主的进化史来研究这些问题。通过利用新技术，该项目将揭示脊椎动物体内的细菌群落在多大程度上是由宿主的生态（例如，宿主吃什么，它们住在哪里）或宿主的进化历史（例如，它们与其他物种的关系）构成的。此外，该项目将测试某些细菌群的存在是否通过为宿主创造更多机会（例如帮助消化新食物，在新地区生活）来帮助推动多样化/物种形成。数据将从横跨五个国家和三大洲的各种爬行动物中收集。细菌是最古老的生命形式之一，已经与多细胞生命相互作用了近10亿年。这将是首次对如此多样化的脊椎动物群体的肠道细菌群落进行表征的研究，并为脊椎动物宿主及其体内存在的细菌群落的进化提供综合测试。这项研究将包括来自密西西比州以及巴西、埃塞俄比亚、圭亚那和墨西哥等发展中国家的志愿者和学生。密西西比州的本科生和高中教师将获得有关识别当地两栖动物和爬行动物的实际研究经验和指导。埃塞俄比亚当地的童子军和大学生将获得宝贵的培训，这将提高他们的教育水平，并为他们提供可用于野外生物学家职业的市场技能。本研究旨在探讨脊椎动物内源性微生物组（endogenic microbiome， EM）如何影响多样性的过程，以及这些微生物群落在多大程度上影响宿主群落的组装。鳞片类爬行动物（蛇、蜥蜴）是这类研究的理想系统，因为它们具有良好的系统发育样本，具有广泛的生态特征，并且比其他脊椎动物类群具有更少的分散和破碎性。利用高通量下一代测序，将对Squamata所有主要谱系以及外群爬行动物谱系的内源性细菌群落（EBCs）进行表征（α和β多样性），以获得爬行动物EM的基本信息。关键的预测包括：(i) EBC在Squamata中是系统发育上保守的，（ii）只有拥有适当EBC的谱系才能利用某些生态位，（iii）某些EBC促进宿主物种形成速度的加快，（iv） EBC是一种生态特征，可用于表征宿主生态，并通过限制可利用的生态位空间直接影响宿主组装过程。

The goal of the project is to understand how communities of species are structured and whether bacterial communities living inside vertebrates might influence how new vertebrate species evolve. The project employs a novel approach to investigating these questions by exploring the evolutionary histories of both the bacteria found in the gut of reptiles and the evolutionary history of the reptile hosts. By utilizing novel technologies the project will reveal the extent to which bacterial communities living inside vertebrates are structured by the ecology of the host (e.g. what the host eats, where they live) or the evolutionary histories of the host (e.g. how they are related to other species). Additionally, this project will test whether the presence of certain bacterial groups helps drive diversification/speciation by creating greater opportunity for the host (e.g. help with digesting new foods, live in new areas). Data will be collected from a wide range of reptiles spanning five countries and three continents. Bacteria are some of the oldest forms of life and have interacted with multicellular life for nearly a billion years. This will be the first study to characterize the gut bacterial communities of such a diverse vertebrate group, and provide a synthetic test of evolution in vertebrate hosts and the bacterial communities existing inside them. The study will incorporate volunteers and students from Mississippi and the developing nations of Brazil, Ethiopia, Guyana and Mexico. Undergraduate students and high school teachers in Mississippi will get hands-on research experience and instruction on identifying local amphibians and reptiles. Local scouts and undergraduates in Ethiopia will gain valuable training that will advance their education and provide them with marketable skills they can then apply to their careers as field biologists. This study aims to explore how the vertebrate endogenic microbiome (EM) influences the process of diversification and to what extent these microbial communities affect assembly of host communities. Squamate reptiles (snakes, lizards) present an ideal system for such study as they are well sampled phylogenetically, possess a wide range of ecological traits, and show less dispersal and fragmentation than other vertebrate groups. Using high-throughput next generation sequencing, endogenic bacterial communities (EBCs) for all major lineages of Squamata in addition to outgroup reptilian lineages will be characterized (alpha and beta diversity) to obtain fundamental information on the EM of Reptilia. Key predictions include: (i) EBCs are phylogenetically conserved within Squamata, (ii) only lineages that possess the appropriate EBC will be able to exploit certain niches, (iii) certain EBCs facilitate accelerated speciation rates of the host, (iv) EBCs are ecological traits that can be used to characterize host ecology and directly influence the host assembly process by limiting exploitable niche space.