Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock

Abstract

Amino acid sequence data from 57 different enzymes were used to determine the divergence times of the major biological groupings. Deuterostomes and protostomes split about 670 million years ago and plants, animals, and fungi last shared a common ancestor about a billion years ago. With regard to these protein sequences, plants are slightly more similar to animals than are the fungi. In contrast, phylogenetic analysis of the same sequences indicates that fungi and animals shared a common ancestor more recently than either did with plants, the greater difference resulting from the fungal lineage changing faster than the animal and plant lines over the last 965 million years. The major protist lineages have been changing at a somewhat faster rate than other eukaryotes and split off about 1230 million years ago. If the rate of change has been approximately constant, then prokaryotes and eukaryotes last shared a common ancestor about 2 billion years ago, archaebacterial sequences being measurably more similar to eukaryotic ones than are eubacterial ones.

Steroid receptor phylogeny and vertebrate origins

“…This assumption has proven reasonable for analyses of sequence changes over the last billion years (Doolittle et al, 1996;Wray et al, 1996). It appears to be valid for the overall evolution of the human nuclear receptors, which are about the same distance from the deepest branch (Fig.…”

A novel transcription factor, ELF5, belongs to the ELF subfamily of ETS genes and maps to human chromosome 11p13–15, a region subject to LOH and rearrangement in human carcinoma cell lines

“…Given that these ETS domains occur in three taxa, we can infer at least four gene duplications (A, B, C and D in Figure 2c). The ®rst two gene duplications (A and B) involves both protostome and deuterostome taxa (Drosophila and mammals, respectively) and therefore must have occurred before the origin of the deuterostome lineage 550 ± 750 Myr ago (Doolittle et al, 1996). A third gene duplication (C) involves two mammalian lineages (Rodenta and Primata) and therefore must have occurred 115 ± 129 Myr ago (Easteal and Herbert, 1997).…”

The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module

“…The diversification of the proteasomal regulatory proteins into subgroups apparently occurred after the divergence of the archaebacteria from the eukaryotes 1.7 billion years ago, but prior to the split of plants, animals, and fungi (Doolittle et al 1996). The divergence of eukaryotic proteasomal regulatory proteins into distinct subgroups may have accompanied the diversification of the core 20S subunits of the proteasome.…”