Phylogenetic consequences of symbioses: Eukarya and Eubacteria are not monophyletic taxa

Abstract

In the past systematists have not been concerned with distinguishing the different phylogenetic histories for symbiont taxa that have merged within a composite taxon, or holobiont. I suggest that symbionts can retain their status as discrete taxa and that their independent histories can be included in phylogenetic analyses intending to discover monophyletic groups. Use of reticulate branches to include independent histories for different symbionts, incorporates our improving understanding of evolution and provides greater accuracy in denoting monophyletic groups. In an expanded view, a monophyletic group includes only and all the descendants of the merged-symbionts' common ancestor. Holobiont taxa will have constituent symbionts included in different monophyletic groups and there will be a reduction in the number of monophyletic groups recognized, particularly at higher taxonomic levels. As a consequence of considering symbioses in phylogenetic analyses, the proposed taxa Eubacteria and Eukarya are seen to be non-monophyletic, and, thus, poor indicators of evolutionary history.