TY  - JOUR
A1  - Deeds, Eric J.
A1  - Hennessey, Hooman
A1  - Shakhnovich, Eugene I.
T1  - Prokaryotic phylogenies inferred from protein structural domains
Y1  - 2005/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 393 
EP  - 402 
DO  - 10.1101/gr.3033805 
VL  - 15 
IS  - 3 
UR  - http://genome.cshlp.org/content/15/3/393.abstract 
N2  - The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole. 
ER  -