Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
Highlights
The Alphaproteobacteria is an extraordinarily diverse and disparate group of bacteria and wellknown to most biologists for encompassing the mitochondrial lineage (Williams et al, 2007; Roger et al, 2017)
Comparisons of their rRNA genes show that these genomes are truly novel, being considerably divergent from other described alphaproteobacteria
UWC8, which is only 92% identical. Phylogenetic analysis of both the 16S rRNA gene and a dataset that comprises 200 single-copy conserved marker genes confirm that each species belongs to different families and orders within the Alphaproteobacteria (Supplementary file 1 and Figure 2—figure supplement 1)
Summary
The Alphaproteobacteria is an extraordinarily diverse and disparate group of bacteria and wellknown to most biologists for encompassing the mitochondrial lineage (Williams et al, 2007; Roger et al, 2017). Eight major orders are well recognized, namely the Caulobacterales, Rhizobiales, Rhodobacterales, Pelagibacterales, Sphingomonadales, Rhodospirillales, Holosporales and Rickettsiales (the latter two formerly grouped into the Rickettsiales sensu lato), and their interrelationships have recently become better understood (Viklund et al, 2012; Viklund et al, 2013; Rodrıguez-Ezpeleta and Embley, 2012; Wang and Wu, 2014). These eight orders were grouped into two subclasses by Ferla et al (2013): the subclass
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