Examining the macroevolutionary trajectories in Amoebozoa, a major lineage of eukaryotes

我们目前对真核生物生命树的看法表明，生命可以分为几个主要的类群，包括变形虫，这是最接近我们自己的主要类群的分支，Obazoa。变形虫主要由生命周期中具有单一的变形虫细胞的有机体组成。这种细胞是动态的，随着被称为伪足的细胞的短暂延伸而移动，形状也会改变。这些细胞也被用来吞噬猎物。阿米巴通常被认为是简单的，因为它们明显缺乏明显的特征。因此，许多生物学家认为这些看起来简单的有机体是“原始的”，并认为它们与最初的真核生物非常相似。初步数据表明，变形虫的复杂性和多样性比人们普遍承认的要多。这个项目旨在找出阿米巴之间的关系，并提出关于这些不同的阿米巴是如何起源于特征被削弱的祖先的想法。鉴于变形虫是与我们最接近的血统，它们的祖先和进化对于更好地理解所有真核生物是如何进化的非常重要。这项研究挑战了阿米巴是原始简单的观点。它使用综合研究，使用整个生命周期的方法，使用基因表达谱和形态数据来解决这一高度多样化的主要真核生物谱系中广泛规模的进化模式。尽管变形虫几乎出现在所有环境中，但令人惊讶的是，人们对它们的进化知之甚少。由于变形虫在基因组水平的数据库中的代表性不足，这一点变得复杂起来，尽管最近已经取得了一些进展，但还需要更多的进展。该项目将首先在系统基因组学框架下，利用广泛采样于变形虫多样性范围的分类群的RNAseq数据，建立一个健壮的变形虫系统发育树。此外，对于显示复杂生活史的分类群，研究人员将使用单细胞RNA测序技术检查不同生命阶段的基因表达谱。这些数据将识别较高级别的阿米巴种群之间的共同点，并通过绘制阿米巴动物树上的特征进化图谱，揭示阿米巴动物的宏观进化轨迹。此外，该项目还将研究变形虫中的基因转移事件、基因创新、基因家族扩张和基因丢失。这是一个研究进化轨迹的独特机会，在这个轨迹中，今天观察到的许多分类群从复杂的祖先进化到更简单的末端分类群。该项目将培训来自基因组学、系统遗传学和变形虫生物学领域中代表性较低的群体的本科生和研究生。

Our current view of the eukaryotic Tree of Life suggests that life can be divided up into several major groups, including the Amoebozoa, the branch closest to our own major group, the Obazoa. The Amoebozoa is composed primarily of organisms that have single, amoeboid cells as part of their life cycles. Such cells are dynamic, changing shape as they move with transient extensions of the cell called pseudopodia. These cells are also used for engulfing prey. Amoebae are often thought to be simple because of their apparent lack of obvious characteristics. Consequently many biologists have the impression that these simple looking organisms are 'primitive' and assume that they are very similar to the first eukaryotes. Preliminary data suggest that there is more complexity and diversity in Amoebozoa than is generally acknowledged. This project is designed to find the relationships among amoebozoans and to develop ideas on how these various amoebae originated from an ancestor whose characteristics were reduced. Given that Amoebozoa is the closest lineage to our own, their ancestry and evolution is important to better understand how all eukaryotes evolved.This research challenges the idea that amoebae are primitively simple. It uses synthetic studies that employ a whole life cycle approach using gene expression profiling and morphological data to address the patterns of broad scale evolution in this highly diverse major eukaryotic lineage. Although amoebozoans occur in nearly every environment, surprisingly little is known about their evolution. This is complicated by the fact that Amoebozoa is under represented in genomic-level databases, and although some recent progress has been made, much more is needed. This project will first develop a robust phylogenetic tree of Amoebozoa under a phylogenomic framework using RNAseq data from taxa broadly sampled across the breadth of the amoebozoan diversity. Additionally, for taxa that display complex life cycles researchers will examine gene expression profiles of various life stages using single cell RNA sequencing techniques. These data will identify commonalties among higher-level amoebozoan groups and by mapping character trait evolution on the tree of Amoebozoa, it will uncover the macroevolutionary trajectories of Amoebozoa. Moreover, this project will examine gene transfer events, gene innovations, gene family expansions and gene losses in Amoebozoa. This represents a unique opportunity to examine the evolution trajectory in which many of the taxa observed today evolved from complex ancestors to more 'simple' terminal taxa. The project will train undergraduate and graduate student training from underrepresented groups in genomics, phylogenetics and Amoebozoa biology.