Exploring prokaryotic diversity in the genomic era

P Hugenholtz - Genome biology, 2002 - Springer
Our understanding of prokaryote biology from study of pure cultures and genome
sequencing has been limited by a pronounced sampling bias towards four bacterial phyla …

Genome trees and the tree of life

YI Wolf, IB Rogozin, NV Grishin, EV Koonin - TRENDS in Genetics, 2002 - cell.com
Genome comparisons indicate that horizontal gene transfer and differential gene loss are
major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the …

Prokaryotic evolution in light of gene transfer

JP Gogarten, WF Doolittle… - Molecular biology and …, 2002 - academic.oup.com
Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic
information through both homology-dependent recombination and horizontal (lateral) gene …

On the evolution of cells

CR Woese - Proceedings of the National Academy of …, 2002 - National Acad Sciences
A theory for the evolution of cellular organization is presented. The model is based on the
(data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily …

The promise of a DNA taxonomy

ML Blaxter - … Transactions of the Royal Society of …, 2004 - royalsocietypublishing.org
Not only is the number of described species a very small proportion of the estimated extant
number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' …

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

FU Battistuzzi, A Feijao, SB Hedges - BMC evolutionary biology, 2004 - Springer
Background The timescale of prokaryote evolution has been difficult to reconstruct because
of a limited fossil record and complexities associated with molecular clocks and deep …

Highways of gene sharing in prokaryotes

RG Beiko, TJ Harlow… - Proceedings of the …, 2005 - National Acad Sciences
The extent to which lateral genetic transfer has shaped microbial genomes has major
implications for the emergence of community structures. We have performed a rigorous …

From gene trees to organismal phylogeny in prokaryotes: the case of the γ-Proteobacteria

E Lerat, V Daubin, NA Moran - PLoS biology, 2003 - journals.plos.org
The rapid increase in published genomic sequences for bacteria presents the first
opportunity to reconstruct evolutionary events on the scale of entire genomes. However …

Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

A Quaiser, T Ochsenreiter, C Lanz… - Molecular …, 2003 - Wiley Online Library
Acidobacteria have been established as a novel phylum of Bacteria that is consistently
detected in many different habitats around the globe by 16S rDNA‐based molecular …

The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer

O Cohen, U Gophna, T Pupko - Molecular biology and evolution, 2011 - academic.oup.com
Horizontal gene transfer (HGT) is a prevalent and a highly important phenomenon in
microbial species evolution. One of the important challenges in HGT research is to better …