Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
Syst Biol. 2013 Sep;62(5):752-62. doi: 10.1093/sysbio/syt038. Epub 2013 Jun 4.
Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.].
系统发育的根系重建对于理解进化至关重要，但根系重建的重要性、复杂性和困难往往被忽视。对于根系重建，必须比较感兴趣的组（内群）中的多态性特征与在组内最后共同祖先（LCA）之前分化的相对（外群）的特征。如果不存在外群、外群未知或外群距离很远以至于共享的特征很少，则会出现问题，在这种情况下，可以使用起源于 LCA 之前的重复基因作为代理外群来重建多样化的系统发育。在这里，我们描述了这项技术的一个全基因组扩展，可以用于解决进化尺度另一端的问题：内群个体彼此非常密切相关，但下一个最接近的亲缘关系非常遥远。我们使用了来自人类 Q 热病原体柯克斯体的 10 个全基因组序列中的共享直系同源单核苷酸多态性（SNP）来创建一个稳健但无根的系统发育。为了最大限度地增加关于根系重建的信息量特征，我们在整个基因组中搜索多态性重复区域，在每个旁系同源物中都可以识别出直系同源物，以便可以使用旁系同源物来为树系根。由于缺乏内群变异和与已知外群的巨大基因组差异，新兴病原体等最近的辐射通常会带来根系重建挑战。使用系统发育基因组学方法，我们为柯克斯体创建了一个稳健的、有根的系统发育。[柯克斯体；旁系同源 SNP；病原体进化；系统发育；最近辐射；根；使用重复基因进行根系重建。]。
