Physiology, phylogeny, and LUCA.

William Martin,Madeline Weiss,Filipa Sousa,Sinje Neukirchen,Shijulal Nelson-Sathi

doi:10.15698/mic2016.12.545

William Martin, Madeline Weiss + Show 3 more

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https://doi.org/10.15698/mic2016.12.545

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Abstract

Genomes record their own history. But if we want to look all the way back to life's beginnings some 4 billion years ago, the record of microbial evolution that is preserved in prokaryotic genomes is not easy to read. Microbiology has a lot in common with geology in that regard. Geologists know that plate tectonics and erosion have erased much of the geological record, with ancient rocks being truly rare. The same is true of microbes. Lateral gene transfer (LGT) and sequence divergence have erased much of the evolutionary record that was once written in genomes, and it is not obvious which genes among sequenced genomes are genuinely ancient. Which genes trace to the last universal ancestor, LUCA? The classical approach has been to look for genes that are universally distributed. Another approach is to make all trees for all genes, and sift out the trees where signals have been overwritten by LGT. What is left ought to be ancient. If we do that, what do we find?

Highlights

Evolution and the nature of the very first kinds of life are interesting topics
One might interject that methanogenesis is restricted to a particular phylogenetic group, the methanogens, but new phylogenetic depictions of the 'tree of life' have methanogens basal among the archaea, with loss of methanogenesis in many independent groups [9,10], those losses corresponding to gene acquisitions from bacteria in some cases [11], thereby decoupling phylogeny from physiology in the methanogens, too, which no longer appear as a monophyletic group
We found that the trees of genes that trace to LUCA implicate clostridia and methanogens as the earliest-branching forms of bacteria and archaea respectively

Summary

Introduction

Evolution and the nature of the very first kinds of life are interesting topics. An important concept in very early evolution is the last universal common ancestor, LUCA for short, because it represents the organism, cell, thing, or chemical reaction, depending on one's concept of LUCA, from which all life forms we know are descended.

Results

Conclusion