Untangling the complex geographic and evolutionary patterns of microbes

微生物的微小尺寸掩盖了它们非凡的复杂性。尽管它们的大小，大多数微生物都有几千个基因，这些基因编码了广泛的代谢和细胞功能，其中一些是通过横向基因转移（LGT）过程从远亲那里获得的。抗生素耐药性的传播和对污染场所等具有挑战性的环境的适应是微生物LGT对社会影响的特别引人注目的例子。LGT的一个结果是，建立一个生命之树来理解微生物的进化可能是不可能的，或者是毫无意义的练习，因为如此多的遗传信息在遥远的谱系之间共享。我提出的研究的第一部分将解决这个问题，通过使用新的标准来组装更能抵抗LGT影响的树，并通过开发可以有效显示垂直（亲代到后代）和横向连接的系统发育网络方法。这项工作的一个关键目标是用一个可以理解的网络取代规范的生命之树，尽管它的复杂性增加了。

The tiny size of microorganisms belies their extraordinary complexity. In spite of their size, most microbes have several thousand genes that encode a wide range of metabolic and cellular functions, some acquired from distant relatives through the process of lateral gene transfer (LGT). The spread of antibiotic resistance and adaptation to challenging environments such as polluted sites are particularly compelling examples of the impact of microbial LGT on society. One consequence of LGT is that building a Tree of Life to understand the evolution of microorganisms may be impossible or a meaningless exercise, since so much genetic information has been shared between distant lineages. The first part of my proposed research will address this question, by using new criteria to assemble trees that are more resistant to the effects of LGT, and by developing phylogenetic network approaches that can effectively show both vertical (parent-to-offspring) and lateral connections. A key objective of this work will be to replace the canonical Tree of Life with a network that is understandable in spite of its increased complexity.