Assembling the Tree of Life: Can Phylogenomics Resolve Deep Phylogeny?

在构建生命树的过程中，解决最深分支的拓扑结构和相对时间安排仍然是最大的挑战之一。然而，了解这一深刻的系统发育对于理解生物学中的基本问题至关重要，例如构成现代生命的复杂网络是如何产生的，以及它们是如何通过与地球的共同进化而塑造的。这项研究项目将开发新的算法来推断一棵生命树，它基于目前可用的数千个完整基因组序列，而不是单个基因或一小部分基因。准确识别和解释水平基因转移是一个将被解决的关键挑战，在水平基因转移过程中，基因在不相关的物种之间交换，可能会模糊系统发育关系。将与早期地球历史和地质年代学专家合作，用地质记录校准生命树上最深分支的时间。该项目将导致更好地了解地球上生命的起源和历史，以及推断基因和物种跨越数十亿年进化时间的进化史的新算法。该项目将汇集不同研究领域的专业知识，并让研究生、本科生和博士后接触跨学科研究。此外，博物馆伙伴关系和播客将使研究成果能够向公众传播。

Resolving the topology and relative timing of the deepest branches remains one of the most significant challenges in Assembling the Tree of Life. Knowledge of this deep phylogeny, however, is critical for understanding foundational questions in biology such as how the complex networks that underlie modern life arose, and how they have been shaped by co-evolution with the Earth. This research project will develop new algorithms to infer a Tree of Life that is based on the thousands of complete genome sequences currently available rather than a single gene or small set of genes. Accurately identifying and accounting for horizontal gene transfer, a process in which genes are exchanged between unrelated species, potentially obscuring phylogenetic relationships, is a key challenge that will be addressed. Calibrating the timing of the deepest branches on the Tree of Life with the geological record will be done in collaboration with experts in early Earth history and geochronology. This project will result in a better understanding of the origin and history of life on Earth, and new algorithms for inferring the evolutionary history of genes and species across billions of years of evolutionary time. The project will bring together expertise from diverse fields of study, and expose graduate, undergraduate, and postdoctoral students to interdisciplinary research. In addition, museum partnerships and podcasts will enable dissemination of research results to the general public.