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

我们目前对真核生物生命之树的看法表明，生命可以分为几个主要类群，包括阿米巴原虫，这是最接近我们自己的主要类群奥巴索原虫的分支。阿米巴虫主要由具有单个阿米巴细胞的生物体组成，这是其生命周期的一部分。这样的细胞是动态的，当它们移动时形状会随着被称为假足的细胞的短暂延伸而改变。这些细胞也用于吞噬猎物。变形虫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一般认为的要高。这个项目的目的是寻找变形虫之间的关系，并对这些不同的变形虫是如何从一个特征减少的祖先起源的提出想法。鉴于变形虫是与人类最近的谱系，它们的祖先和进化对于更好地理解所有真核生物的进化过程非常重要。这项研究挑战了变形虫是原始简单动物的观点。它使用综合研究，采用全生命周期方法，使用基因表达谱和形态学数据来解决这个高度多样化的主要真核生物谱系的大范围进化模式。尽管变形虫几乎存在于任何环境中，但令人惊讶的是，人们对它们的进化知之甚少。由于阿米巴原虫在基因组水平数据库中的代表性不足，这一事实使情况变得更加复杂，尽管最近取得了一些进展，但还需要做更多的工作。该项目将首先利用在变形虫多样性范围内广泛取样的类群RNAseq数据，在系统基因组框架下建立一个强大的变形虫系统发育树。此外，对于显示复杂生命周期的分类群，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。这些数据将确定高级阿米巴原虫类群之间的共性，并通过在阿米巴原虫树上绘制特征进化图谱，揭示阿米巴原虫的宏观进化轨迹。此外，该项目将研究阿米巴原虫的基因转移事件、基因创新、基因家族扩展和基因损失。这代表了一个独特的机会来研究进化轨迹，其中许多今天观察到的分类群从复杂的祖先进化到更“简单”的终端分类群。该项目将培养来自基因组学、系统遗传学和变形虫生物学等代表性不足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.