Horizontal gene transfer and among phyla relationships

在达尔文解释自然进化之前，树就是解释生物之间关系的有组织的形象。然而，通过比较DNA和蛋白质序列来辨别这些关系的现代实践，揭示了人类进化过程中前所未有的复杂性。生物体，特别是微生物，通过水平和垂直遗传的方式进化，不同的有机体群体交换基因，并将它们传递给下一代。这项研究项目解决的问题是：生命之树/网的大规模结构能否被辨别？虽然目前的数据可能被解读为意味着将生命历史描述为一棵单一的分叉树是不完整的，但这不应被视为放弃重建生命历史的理由。这项研究的工作假设是，只要小心防止人工制品，并在分析中加入新的、信息丰富的分子特征，重建生命早期历史确实是可能的。通过对微生物基因组序列的分析，将使用四种互补的方法来解决这个问题。(1)将研究基因组序列数据，以发现创造了有用的分类特征的古代水平基因转移事件。将开发一条自动化的基因组分析管道来发现这些事件，这些特征将被纳入新的进化关系检查中。(2)完整的基因组序列允许将一个生物体的所有基因与其他生物的基因进行比较，以衡量它们在进化上的关联性。然而，基因的水平获取对这些分析的影响尚不清楚。计算机模拟和两组不相关的微生物的基因组序列将被用来衡量不同生物群之间基因共享的高速公路对不同系统基因组方法的影响程度。这两组微生物已经经历了广泛的水平基因转移。(3)将建立一个公共数据库，以存储所有假定已确定的基因转移事件的信息。该数据库将是更广泛的科学界追踪基因转移在新陈代谢途径组装中的作用以及审查生物体对新的生态环境的适应情况的宝贵资源。(4)考虑到进化过程中核苷酸组成的所有变化，所有生物的最后共同祖先--生命树的树干--的性质一直很难辨别。成分分析将被用来检测遗传密码扩展的剩余信号，这些信号发生在生命历史的早期，目的是为生命之树“扎根”。这些对几种原核生物和真核生物基因组的深入分析将有助于深入了解水平基因转移对基因组进化和系统发育重建的影响，以及识别生命树中的自然类群，有助于解决其深层结构。揭开生命之树的结构将在生物学的各个领域产生影响。这项研究计划及其相关的教育活动将为高中、本科生和研究生以及博士后提供一个理想的培训场所，让他们学习基因组和生物进化。计划培养三名博士后研究员，九名研究生，以及大约二十名本科生和高中生，通过计算和实验室研究经验进行培训。其目标是培训计算机科学家和生物学家成为各自学科的专家，并在跨学科交流中变得有效，从而实现成功的跨学科合作。拟议的研究结果将被引入三个校园的相关课程，并将通过一个综合数据库获得，该数据库还包括一个论坛，供公众讨论与基因转移和生物进化有关的主题。

A tree has been the organizing image to explain the relationships among living creatures since before Darwin's explanations for natural descent. The modern practice of comparing DNA and protein sequences to discern these relationships, however, has revealed complexities in the process of descent never before imagined. Organisms, particularly microbes, evolve by horizontal as well as vertical inheritance of traits with different groups of organisms exchanging genes, in addition to passing them down to the next generation. This research project addresses the question: Can the large scale structure of the tree/web of life be discerned? While the current data may be interpreted to mean that the depiction of life's history as a single bifurcating tree is incomplete, this should not be seen as justification to give up on reconstructing life's history. The working hypothesis underlying this research is that a reconstruction of life's early history is indeed possible, provided care is taken to guard against artifacts and that new, informative molecular characters are added to the analyses. Four complementary approaches will be used to address the question through analyses of microbial genome sequences. (1) Genome sequence data will be examined to find ancient horizontal gene transfer events that created useful taxonomic characters. An automated genome analysis pipeline will be developed to find these events, and these characters will be incorporated into new examinations of evolutionary relationships. (2) Complete genome sequences allow comparisons of all the genes of an organism with those of others to measure their evolutionary relatedness. However, the impact of horizontal acquisition of genes on these analyses is unknown. Computer simulations and genome sequences from two unrelated groups of microbes that have undergone extensive horizontal gene transfer, the Haloarchaea and the Thermotogales, will be used to gauge the extent to which different phylogenomic approaches are impacted by highways of gene sharing between different groups of organisms. (3) A public database will be constructed to store information on all putatively identified gene transfer events. This database will be a valuable resource for the wider scientific community to trace the role of gene transfer in the assembly of metabolic pathways and to examine the adaptation of organisms to new ecological niches. (4) The nature of the last common ancestor of all living creatures, the trunk of the tree of life, has been difficult to discern given all the changes in nucleotide composition that have occurred during evolutionary time. A compositional analysis will be used to detect the remaining signal of the genetic code's expansion that occurred early in life's history in order to "root" the tree of life. These in-depth analyses of several prokaryotic and eukaryotic genomes will offer insights into the impacts of horizontal gene transfer on genome evolution and phylogenetic reconstructions, as well as identify natural groups in the tree of life and help to resolve its deep structure. Unraveling the structure of the tree of life will have percussions in all fields of biology.This research program and its associated education activities will provide an ideal training ground in which high school, undergraduate, and graduate students along with postdoctoral fellows can learn about genome and organismal evolution. Plans are for three postdoctoral fellows, nine graduate students, and about twenty undergraduate and high school students to be trained through computational and laboratory research experiences. The goal is to train computer scientists and biologists to become experts in their respective disciplines and to become effective in trans-disciplinary communication; thereby enabling successful interdisciplinary collaborations. Results from the proposed research will be introduced into related courses on three campuses and will be accessible through an integrated database, which also includes a forum for public discussions on topics related to gene transfer and organismal evolution.