Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria
James A. Lake 1,*, Joseph Larsen 1, Brooke Sarna 1, Rafael R. de la Haba 1,5, Yiyi Pu 1,3, HyunMin Koo 1,4, Jun Zhao 1,2 and Janet S. Sinsheimer 1
1University of California, Los Angeles;
2Peking University;
3Zhejiang University;
4University of Alabama, Birmingham,
5University of Sevilla.
↵Author for correspondence: James A. Lake, MCD Biology and Human Genetics, 232 Boyer Hall, University of California, Los Angeles 90095, USA. E-mail: Lake{at}mbi.ucla.edu
Received December 21, 2014.
Revision received August 12, 2015.
Revision received October 30, 2015.
Accepted November 9, 2015.
Source/Fonte:
James A. Lake and Janet S. Sinsheimer (2013) The deep roots of the Rings of Life. Genome Biology and Evolution 5: 2440-2448.
James A. Lake and Janet S. Sinsheimer (2013) The deep roots of the Rings of Life. Genome Biology and Evolution 5: 2440-2448.
Abstract
Although prokaryotes are usually classified using molecular phylogenies instead of phenotypes after the advent of gene-sequencing, neither of these methods is satisfactory because the phenotypes cannot explain the molecular trees and the trees do not fit the phenotypes. This scientific crisis still exists and the profound disconnection between these two pillars of evolutionary biology - genotypes and phenotypes - grows larger. We use rings and a genomic form of goods thinking to resolve this conundrum (McInerney, J et al., 2011; Nelson-Sathi, S et al. 2015).
The Proteobacteria is the most speciose prokaryotic phylum known. It is an ideal phylogenetic model for reconstructing Earth's evolutionary history. It contains diverse free living-, pathogenic-, photosynthetic-, sulfur metabolizing- and symbiotic species. Due to its large number of species (Whitman et al. 1998) it was initially expected to provide strong phylogenetic support for a proteobacterial tree of life. But despite its many species, sequence-based tree analyses are unable to resolve its topology.
Here we develop new rooted ring analyses and study Proteobacterial evolution. Using protein family data and new genome-based outgroup rooting procedures, we reconstruct the complex evolutionary history of the Proteobacterial Rings (combinations of tree-like divergences and endosymbiotic-like convergences). We identify and map the origins of major gene flows within the Rooted Proteobacterial Rings (P < 3.6 x 10-6) and find that the evolution of the Alpha-, Beta-, and Gamma- proteobacteria is represented by a unique set of Rings. Using new techniques presented here we also root these rings using outgroups. We also map the independent flows of genes involved in DNA-, RNA-, ATP-, and membrane- related processes within the Proteobacteria and thereby demonstrate that these large gene flows are consistent with endosymbioses (Probability < 3.6 x 10-9).
Our analyses illustrate what it means to find that a gene is present, or absent, within a gene flow, and thereby clarify the origin of the apparent conflicts between genotypes and phenotypes. Here we identify the gene flows that introduced photosynthesis into the Alpha-, Beta- and Gammaproteobacteria from the common ancestor of the Actinobacteria and the Firmicutes. Our results also explain why Rooted Rings, unlike trees, are consistent with the observed genotypic- and phenotypic- relationships observed among the various proteobacterial classes. We find that Ring phylogenies can explain the genotypes and the phenotypes of biological processes within large and complex groups like the Proteobacteria.
Key words: Phylogenetic Classification Genotypes Phenotypes Rooting Rings Endosymbioses Chlorophylls Gene Losses/Gains
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