The Evolutionary Consequences of Whole-genome Duplication: the Paramecium Aurelia Complex

智力上的功绩。有了完全描述密切相关物种和物种内个体基因组的能力，现在就有可能通过促进物种内的适应和建立新物种，在分子水平上阐明进化进行的机制。这个项目涉及对纤毛原生动物的草履虫原生动物组合的整套神秘物种的基因组序列的比较调查。就在这个复合体辐射之前，共同的祖先经历了核基因组的完全翻倍，初步证据表明，姐妹系中替代冗余基因拷贝的沉默导致了图谱的变化，这可能是有效的生殖隔离障碍。该复合体相对年轻的年龄，再加上其大量的组成物种和相对简单的基因组结构，为了解基因复制在生物多样性产生中所起的作用提供了一个强大和前所未有的资源。通过在精细解剖的系统发展史上建立所有祖先基因拷贝的完整历史，将评估不同功能类别的重复基因的保存和消亡的模式。这些分析还将揭示基因丢失的时间模式，最终导致在后代分类群中获得新的平衡基因组状态，并澄清基因复活发生的程度。随着基因表达信息的加入，关于重复基因进化的几个关键假说将得到检验。为分析提供特殊能力的是关于两个金黄色葡萄球菌物种突变的速度和完整分子谱的信息。这为破译作用于重复基因的进化力量提供了正式的基础，方法是在没有选择的情况下为基因的命运提供一个零模型(例如，为保存或通过突变退化主动促进基因丢失而进行的正选择)。作为单细胞真核生物自然组合的第一次此类研究，该项目有可能极大地扩展我们对基因组进化机制的理解，为更丰富的多细胞物种观察提供补充。更广泛的影响。这项研究产生的数据将作为草履虫遗传学社区的关键和永久资源，同时也提供了关于在进化上可解释的时间尺度上重复基因动态的第一个详细数据。这些数据将被组织到现有的基于网络的PareciumDB数据系统中，使用户能够方便地查询整个物种组合，以了解整个平行基因集的状态和进化历史，并将其追溯到澳大利亚青霉复合体的祖先。此外，该数据库将被整合到社区一级的努力中，将纤毛虫纳入课堂研究。最后，该项目将支持培训一名研究生和一名博士后研究员，目标是将他们确立为草履虫进化遗传学重新兴起领域的领导者。

Intellectual Merit. With the ability to completely characterize the genomes of closely related species and individuals within species, it is now possible to elucidate the mechanisms by which evolution proceeds at the molecular level, via both the promotion of adaptations within species and the establishment of new species. This project involves a comparative survey of the genome sequences of the complete set of cryptic species of the Paramecium aurelia assemblage of ciliated protozoans. Just prior to the radiation of this complex, the common ancestor experienced a complete doubling of the nuclear genome, and preliminary evidence suggests that silencing of alternative redundant gene copies in sister lineages has led to map changes that may operate as effective reproductive isolating barriers. The relatively young age of the complex, combined with its large number of constituent species and relatively simple genomic architecture, provides a powerful and unprecedented resource for understanding the roles that gene duplication plays in the generation of biodiversity. By establishing the complete history of all ancestral gene copies over a finely dissected phylogeny, the patterns of preservation vs. demise of various functional classes of duplicate genes will be evaluated. The analyses will also reveal the temporal patterns of gene loss that eventually lead to the acquisition of new equilibrium genomic states in the descendant taxa, as well as clarify the extent to which gene resurrections occur. With the inclusion of information on gene expression, several key hypotheses on the evolution of duplicate genes will be tested. Lending an exceptional level of power to the analyses is the availability of information on the rate and complete molecular spectrum of mutations for two aurelia species. This provides a formal basis for deciphering the forces of evolution operating on duplicate genes by providing a null model for the fates of genes in the absence of selection (e.g., positive selection for preservation or active promotion of gene loss by mutational degradation). As the first study of this sort in a natural assemblage of unicellular eukaryotes, this project has the potential to greatly expand our understanding the mechanisms of genome evolution, providing a complement to the much richer set of observations on multicellular species. Broader Impacts. The data generated by this study will serve as a critical and permanent resource for the Paramecium genetics community, while also providing the first detailed data on the dynamics of duplicate genes on an evolutionarily interpretable time scale. The data will be organized into the existing ParameciumDB web-based data system, allowing users to readily query the entire species assemblage for the status and evolutionary history of the full set of paralogous genes back to the ancestor of the P. aurelia complex. In addition, the database will be integrated into a community-level effort at incorporating ciliates in classroom research. Finally, the project will support the training of a graduate student and a postdoctoral fellow, with a goal of establishing them as leaders in the re-emerging field of Paramecium evolutionary genetics.