Soria-Carrasco Victor, Castresana Jose
Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.
Mol Biol Evol. 2008 Nov;25(11):2319-29. doi: 10.1093/molbev/msn176. Epub 2008 Aug 12.
Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsistencies in trees of prokaryotes in comparison with those of higher eukaryotes, where no lateral gene transfer is expected. To test this, we used 21 proteomes each of eukaryotes (mainly opisthokonts), proteobacteria, and archaea that spanned equivalent levels of genetic divergence. In each domain of life, we defined a set of putative orthologous sequences using a phylogenetic-based orthology protocol and, as a reference topology, we used a tree constructed with concatenated genes of each domain. Our results show, for most of the tests performed, that the magnitude of topological inconsistencies with respect to the reference tree was very similar in the trees of proteobacteria and eukaryotes. When clade support was taken into account, prokaryotes showed some more inconsistencies, but then all values were very low. Discrepancies were only consistently higher in archaea but, as shown by simulation analysis, this is likely due to the particular tree of the archaeal species used here being more difficult to reconstruct, whereas the trees of proteobacteria and eukaryotes were of similar difficulty. Although these results are based on a relatively small number of genes, it seems that phylogenetic reconstruction problems, including orthology assignment problems, have a similar overall effect over prokaryotic and eukaryotic trees based on single genes. Consequently, lateral gene transfer between distant prokaryotic species may have been more rare than previously thought, which opens the way to obtain the tree of life of bacterial and archaeal species using genomic data and the concatenation of adequate genes, in the same way as it is usually done in eukaryotes.
细菌和古菌系统发育树中的差异通常被解释为横向基因转移事件。然而，这种差异也可能是由于系统发育假象或直系同源物分配问题。有助于解决这一困境的第一步可能是估计原核生物树与高等真核生物树中系统发育不一致的程度，因为高等真核生物中预计不存在横向基因转移。为了验证这一点，我们使用了21个真核生物（主要是后鞭毛生物）、变形菌和古菌的蛋白质组，它们涵盖了相当水平的遗传差异。在生命的每个领域，我们使用基于系统发育的直系同源物协议定义了一组假定的直系同源序列，并以每个领域串联基因构建的树作为参考拓扑结构。我们的结果表明，在大多数测试中，变形菌和真核生物树中相对于参考树的拓扑不一致程度非常相似。当考虑分支支持时，原核生物显示出更多的不一致，但所有值都非常低。古菌中的差异仅始终较高，但如模拟分析所示，这可能是由于此处使用的古菌物种的特定树更难重建，而变形菌和真核生物的树重建难度相似。尽管这些结果基于相对较少的基因，但似乎包括直系同源物分配问题在内的系统发育重建问题对基于单个基因的原核生物和真核生物树具有相似的总体影响。因此，远距离原核生物物种之间的横向基因转移可能比以前认为的更为罕见，这为利用基因组数据和适当基因的串联来获得细菌和古菌物种的生命树开辟了道路，就像在真核生物中通常所做的那样。
