Duplicate Genes and Plant Phylogeny: Phytochromes and the Rooting of Seed Plants, Angiosperms, and Eudicots

关于种子植物、开花植物和开花植物的主要谱系的系统发育树的根的主要进化问题已经引起了进化生物学家的相当大的关注，但一直没有令人信服的解决办法。因此，需要新的方法。pi提出了一种新的策略，他们将分析来自每个群体成员的光敏色素核基因家族的一系列基因复制，以帮助解决这个问题。重复基因生根依赖于基因的同时系统发育分析，这些基因是由基因重复事件引起的，发生在植物类群的分支上。这个过程产生了一个无根的基因网络，其中两个基因树应该由单个分支连接，当网络沿着连接分支扎根时，最好的有根物种树是与两个基因树一致的物种树。光敏色素基因特别适合这种方法，因为基因家族的主要复制显然发生在通向我们感兴趣的三个主要植物群的分支上。此外，我们的初步分析揭示了重复基因树之间的高度一致性，充足的核苷酸变异，以及对一些关键分支事件的相当大的支持。因此，我们有信心，这种方法将提供洞察早期分支事件的每一个系统发育问题。此外，这些研究将阐明植物光敏色素基因家族的进化，并将突出和阐述重复基因生根过程，我们希望这些研究结果将用于解决其他生根难题。

Donoghue DEB 9806937 Major evolutionary questions concerning the root of the phylogenetic tree of seed plants, of flowering plants, and a major lineage within flowering plants (the eudicots) have received considerable attention from evolutionary biologists, but have resisted convincing resolution. New approaches are, therefore, needed. The PIs propose a new strategy in which they will analyze a series of gene duplications in the phytochrome family of nuclear genes from members of each group to help solve this problem. Duplicate gene rooting relies on simultaneous phylogenetic analysis of genes that resulted from a gene duplication event that occurred along the branch subtending the plant group of interest. This procedure yields an unrooted gene network wherein two gene trees should be connected by a single branch, and the best rooted species tree is the one that is congruent with the two gene trees when the network is rooted along the connecting branch. Phytochrome genes are particularly well-suited for this approach because major duplications in the gene family apparently have occurred along the branches leading to each of the three main plant groups that we are interested in. Moreover, our preliminary analyses reveal a high level of agreement among duplicate gene trees, ample nucleotide variation, and considerable support for a number of critical branching events. We therefore are confident that this approach will provide insight into early branching events for each of the phylogenies in question. Additionally, these studies will elucidate the evolution of the phytochrome gene family in plants, and will highlight and elaborate the duplicate gene rooting procedure, which we hope will be of use in solving other difficult rooting problems.