%A Caetano-Anollés,Gustavo %A Mittenthal,Jay E. %A Caetano-Anollés,Derek %A Kim,Kyung Mo %D 2014 %J Frontiers in Genetics %C %F %G English %K Structure,phylogenetic analysis,molecular clock,protein folds,protein evolution %Q %R 10.3389/fgene.2014.00306 %W %L %M %P %7 %8 2014-September-11 %9 Perspective %+ Prof Gustavo Caetano-Anollés,Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois,Urbana, IL, USA,gca@illinois.edu %# %! A time-calibrated history of biochemistry %* %< %T A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity %U https://www.frontiersin.org/articles/10.3389/fgene.2014.00306 %V 5 %0 JOURNAL ARTICLE %@ 1664-8021 %X Time-calibrated phylogenomic trees of protein domain structure produce powerful chronologies describing the evolution of biochemistry and life. These timetrees are built from a genomic census of millions of encoded proteins using models of nested accumulation of molecules in evolving proteomes. Here we show that a primordial stem line of descent, a propagating series of pluripotent cellular entities, populates the deeper branches of the timetrees. The stem line produced for the first time cellular grades ~2.9 billion years (Gy)-ago, which slowly turned into lineages of superkingdom Archaea. Prompted by the rise of planetary oxygen and aerobic metabolism, the stem line also produced bacterial and eukaryal lineages. Superkingdom-specific domain repertoires emerged ~2.1 Gy-ago delimiting fully diversified Bacteria. Repertoires specific to Eukarya and Archaea appeared 300 millions years later. Results reconcile reductive evolutionary processes leading to the early emergence of Archaea to superkingdom-specific innovations compatible with a tree of life rooted in Bacteria.