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

智力优势。 由于有能力完全描述密切相关的物种和物种内个体的基因组，现在有可能阐明进化在分子水平上进行的机制，通过促进物种内的适应和建立新物种。该项目包括一套完整的隐种草履虫奥雷利亚组合的纤毛原生动物的基因组序列的比较调查。就在这个复合体辐射之前，共同祖先经历了核基因组的完全加倍，初步证据表明，姐妹谱系中替代冗余基因拷贝的沉默导致了可能作为有效生殖隔离屏障的地图变化。复合体相对年轻的年龄，加上其大量的组成物种和相对简单的基因组结构，为理解基因复制在生物多样性产生中的作用提供了强大而前所未有的资源。通过建立所有祖先基因拷贝的完整历史，在一个精细解剖的基因组学上，将评估复制基因的各种功能类别的保存与消亡的模式。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纳入，重复基因进化的几个关键假设将得到检验。借给一个特殊的权力水平的分析是可用性的信息率和完整的分子谱的突变两个奥雷利亚物种。这为破译作用于重复基因的进化力量提供了正式的基础，通过为没有选择的基因的命运提供一个空模型（例如，用于保存的正选择或通过突变降解主动促进基因丢失）。作为在单细胞真核生物的自然组合中进行的第一项此类研究，该项目有可能极大地扩展我们对基因组进化机制的理解，为多细胞物种的更丰富的观察提供补充。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草履虫数据库网络数据系统中，使用户能够随时查询整个物种组合的状态和进化历史的全套旁系同源基因回到祖先的P.奥雷利亚复杂。此外，该数据库将纳入社区一级的努力，将纤毛虫纳入课堂研究。最后，该项目将支持一名研究生和一名博士后研究员的培训，目标是使他们成为草履虫进化遗传学这一新兴领域的领导者。

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.