RT Journal Article
SR Electronic
T1 What is an archaeon and are the Archaea really unique?
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 256263
DO 10.1101/256263
A1 Ajith Harish
YR 2018
UL http://biorxiv.org/content/early/2018/02/13/256263.abstract
AB The recognition of the group Archaea 40 years ago stimulated research in microbial evolution and molecular systematics that prompted a new classificatory scheme to organize biodiversity. Advances in DNA sequencing techniques have since significantly improved the genomic representation of the archaeal biodiversity. In addition, advances in phylogenetic modeling that facilitate large-scale phylogenomics have resolved many recalcitrant branches of the Tree of Life. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. The issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the Tree of Life. The uncertainty is primarily due to a scarcity of information in standard datasets—the core-genes datasets—to reliably resolve the conflicts. These conflicts can be resolved efficiently by employing complex genomic features and genome-scale evolution models—a distinct class of phylogenomic characters and evolution models—that can be employed routinely to maximize the use of genome sequences as well as to minimize uncertainties in tests of evolutionary hypotheses.