Dimensions US-China: Global Patterns of Biodiversity in the Ancient Ciliate Paramecium

微生物是否表现出与多细胞物种相似的地理分布模式？一种观点是“万物无处不在”的假设，该假设假设微生物物种在地球仪中的高水平迁移。或者，环境因素可以细分为适应当地的类群谱系。这项研究的重点是一个魅力，但研究甚少属，纤毛虫草履虫，它起源于脊椎动物的外观之前。这些生物在许多方面与动物相似，例如具有独立的生殖系和体细胞基因组，并携带细菌微生物组。然而，与动物不同的是，这一组中的所有物种在形态上都很相似，这简化了许多分析。种群基因组研究将揭示种群细分和迁移对种内和种间变异的影响程度。研究人员将探索微生物组在推动系统发育和地理分歧中的作用。该研究将检查形态上隐藏的物种是否在生态/生理特征上也相似。两个主要纤毛虫实验室（一个在美国，一个在中国）的共同努力将产生一个全球分子多样性的公共数据库。研究生和博士后研究员将通过本研究进行培训。总的来说，这项研究将为研究界提供广泛兴趣的微生物物种形成和适应的广泛探索。 要了解生物多样性的分布情况及其相关性，就需要了解关键的种群遗传参数，如随机遗传漂变和迁移的能力。这些因素结合在一起，可能会限制地方适应的发展。本研究将在全球范围内对草履虫属30种物种及其内吞生物种群内和种群间的遗传变异进行调查，获得全基因组序列。从分子种群遗传学的方法将产生全球有效的人口规模和所有这些物种的迁移率的估计。物种的时间和地理分布将被揭示，并正式建立神秘物种复合体的存在。来自微生物生理学的经典方法将在温度和资源可用性的梯度上估计基础代谢需求、生长和细胞大小的关键参数。这项工作将在所有物种的广泛的地理隔离，以确定是否发生了当地的适应，或者如果这样的模式是一致的表型可塑性反应。对有和没有内吞生物体的基因型的研究将澄清这些细菌是否对其宿主细胞施加净代谢损失或增益。由此产生的数据将编入门户网站，向用户提供所有物种基因组的可访问汇编和注释，同时沿着调查在所有遗传位点发现的物种内变异。测序菌株将被冷冻保存在一个可行的状态，供未来的研究人员使用。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

Do microbes exhibit patterns of biogeographic distribution similar to those of multicellular species? One idea is the 'everything is everywhere' hypothesis, which postulates high levels of migration scattering microbial species throughout the globe. Alternatively, environmental factors could be subdividing lineages into locally adapted taxa. This study focuses on a charismatic but poorly studied genus, the ciliate Paramecium, which originated prior to the appearance of vertebrates. These creatures are animal-like in many ways, such as having separate germline and somatic genomes and carrying a bacterial microbiome. Unlike animals, however, all species in this groups are similar in morphology, which simplifies many analyses. The population-genomic studies will reveal the extent to which intra- and interspecific variation is shaped by the population subdivision and migration. The researchers will explore the role of the microbiome in driving phylogenetic and geographic divergence. The study will examine if morphologically cryptic species are also similar in ecological/physiological traits. The combined efforts of two major ciliate labs, one in the US and one in China, will yield a public database of global molecular diversity. Graduate students and postdoctoral fellows will be trained by this research. Overall, this study will provide a wide-ranging exploration of speciation and adaptation in microbes of broad interest to the research community. An understanding of the distribution of biodiversity and its relevance requires information on key population-genetic parameters such as the power of random genetic drift and migration. Combined, these can constrain the development of local adaptations. This study will acquire whole-genome sequences in a worldwide survey of genetic variation within and among populations of 30 Paramecium species and their endocytobionts. Methods from molecular population genetics will yield estimates of global effective population sizes and migration rates for all such species. The temporal and geographic distributions of species will be revealed, and the existence of cryptic species complexes formally established. Classical methods from microbial physiology will estimate key parameters of basal metabolic requirements, growth, and cell size across gradients of temperature and resource availability. This work will be done on a wide range of geographic isolates of all species to determine whether local adaptation has occurred, or if such patterns are consistent with phenotypic-plasticity responses. Study of genotypes with and without endocytobionts will clarify whether such bacteria impose net metabolic losses or gains for their host cells. The resultant data will be organized into web portals to provide users with accessible assemblies and annotations of the genomes of all species, along with the survey of within-species variants found at all genetic loci. Sequenced strains will be cryopreserved in a viable state for use by future researchers.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.