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. 2018 May 24;12(8):1994–2010. doi: 10.1038/s41396-018-0150-9

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© International Society for Microbial Ecology 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Phylogenomic tree of Rhodobacteraceae. Maximum-likelihood analysis of concatenated core-genome alignments with 194,215 amino acid positions from 105 sequenced genomes. The tree was inferred with ExaML under the optimal model and 100 bootstrap replicates conducted. Blue branches and labels display the extant distribution of photosynthetic strains, based on the assumption of (i) a photosynthetic ancestry of Rhodobacteraceae and (ii) a strict vertical evolution of the photosynthesis gene cluster (PGC). Red triangles mark independent PGC losses according to this “null-hypothesis”. Plasmid-located PGCs are highlighted in yellow. Rhodobacterales bacterium HTCC2255 was used as a close outgroup based on a preliminary analysis with more distantly related Alphaproteobacteria such as Neomegalonema perideroedes DSM 15528 (color figure online)