TY - JOUR
T1 - Archaea
T2 - The first domain of diversified life
AU - Caetano-Anollés, Gustavo
AU - Nasir, Arshan
AU - Zhou, Kaiyue
AU - Caetano-Anollés, Derek
AU - Mittenthal, Jay E.
AU - Sun, Feng Jie
AU - Kim, Kyung Mo
PY - 2014
Y1 - 2014
N2 - The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
AB - The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
UR - http://www.scopus.com/inward/record.url?scp=84903515053&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84903515053&partnerID=8YFLogxK
U2 - 10.1155/2014/590214
DO - 10.1155/2014/590214
M3 - Review article
C2 - 24987307
AN - SCOPUS:84903515053
SN - 1472-3646
VL - 2014
JO - Archaea
JF - Archaea
M1 - 590214
ER -