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

中美：古代纤毛虫草履虫生物多样性的全球模式

• 批准号: 1927159
• 负责人: Michael Lynch
• 金额: $ 200万
• 依托单位: Arizona State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1927159&HistoricalAwards=false
• 关键词: Dimensions; US; China; Global; Patterns

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.

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”的假说，该假说假定全球各地都有大量的微生物物种迁徙。或者，环境因素可以将谱系细分为适应当地的类群。这项研究的重点是一个有魅力但研究很少的属，纤毛虫草履虫，起源于脊椎动物出现之前。这些生物在许多方面都与动物相似，例如拥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，这一组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在多大程度上影响种内和种间变异。研究人员将探索微生物组在推动系统发育和地理分化方面的作用。这项研究将检验形态上神秘的物种在生态/生理特征上是否也相似。两个主要的纤毛虫实验室，一个在美国，一个在中国，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这项研究进行培训。总体而言，这项研究将对研究界广泛感兴趣的微生物的物种形成和适应进行广泛的探索。要了解生物多样性的分布及其相关性，就需要提供有关主要种群遗传参数的信息，如随机遗传漂移和迁徙的力量。综合起来，这些因素可能会限制当地适应的发展。这项研究将在全球范围内调查草履虫及其内生生物种群内和种群之间的遗传变异，获得全基因组序列。来自分子种群遗传学的方法将产生对所有这些物种的全球有效种群规模和迁移率的估计。物种的时间和地理分布将被揭示，神秘物种复合体的存在将正式确立。来自微生物生理学的经典方法将跨温度和资源可获得性的梯度来估计基本代谢需求、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隔离上进行，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。对有和没有内生菌的基因类型的研究将澄清这些细菌是否会对其宿主细胞造成净代谢损失或净收益。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组装和注释，以及在所有遗传位点发现的物种内变异的调查。被测序的菌株将被冷冻保存在可存活的状态，以供未来的研究人员使用。这一奖项反映了NSF的法定使命，并已通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

The divergence of mean phenotypes under persistent directional selection

持续定向选择下平均表型的分歧

• DOI: 10.1093/genetics/iyad091
• 发表时间: 2023
• 期刊: GENETICS
• 影响因子: 3.3
• 作者: Devi, Archana;Speyer, Gil;Lynch, Michael;Roze, ed., D.
• 通讯作者: Roze, ed., D.