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生物地理分布模式？一种观点是“万物无处不在”假说，该假说假设微生物物种在全球范围内的高水平迁移。或者，环境因素可以将谱系细分为局部适应的分类群。这项研究的重点是一个有魅力但研究很少的属，纤毛草履虫，它起源于脊椎动物出现之前。这些生物在很多方面与动物相似，比如有独立的生殖系和体细胞基因组，并携带细菌微生物群。然而，与动物不同的是，这一群体中的所有物种在形态上都是相似的，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驱动系统发育和地理差异中的作用。该研究将检验形态上隐种是否在生态/生理特征上也相似。两个主要的纤毛虫实验室，一个在美国，一个在中国，将共同努力，产生一个全球分子多样性的公共数据库。本研究将培养研究生和博士后。总的来说，这项研究将为研究界广泛关注的微生物的物种形成和适应提供广泛的探索。要了解生物多样性的分布及其相关性，就需要掌握诸如随机遗传漂变和迁移的力量等关键种群遗传参数的信息。综合起来，这些因素会限制当地适应性的发展。本研究将在全球范围内对30种草履虫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。分子群体遗传学的方法将产生所有这些物种的全球有效种群规模和迁移率的估计。揭示了物种的时空分布，并正式确立了隐种复合体的存在。微生物生理学的经典方法将估算温度和资源可用性梯度下基础代谢需求、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地理分离上进行，以确定是否发生了局部适应，或者这种模式是否与表型可塑性反应一致。对含有和不含内吞菌的基因型的研究将阐明这些细菌是否对其宿主细胞造成净代谢损失或收益。由此产生的数据将被组织到门户网站中，为用户提供所有物种基因组的可访问汇编和注释，以及在所有遗传位点上发现的物种内变异的调查。测序后的菌株将在可行状态下冷冻保存，以供未来的研究人员使用。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.