The tree of one percent

Abstract

Two significant evolutionary processes are fundamentally not tree-like in nature--lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.

Figure 1

Five different current views of the general shape of microbial evolution. (a) The 'classical' tree derived from comparison of rRNA sequence and rooted with ancient paralogs. It is thought to arise from a collection of non-cellular supramolecular aggregates in the primordial soup, between which there is lateral gene transfer (LGT). A process dubbed genetic annealing gives rise to cells. In this scenario, the three domains of life - Eubacteria, Archaebacteria and Eukaryotes - branch off in that order. (b) The introns-early tree. This proposes that the ancestor of all three domains contained introns, which were lost in the Archaebacteria and Euacteria. (c) The neomuran tree. This introduces an ancestral group of organisms from which Archaeabacteria and Eukaryotes arose after the loss of the eubacterial-type cell wall in one lineage (the neomuran revolution). (d) The symbiotic tree. This proposes that the ancestor of eukaryotes originated by the endosymbiosis of one prokaryote (X) in another prokaryote host (Y), giving rise to nucleated (n) eukaryotic cells. The different groups of eukaryotes arose by subsequent separate endosymbiotic events involving various prokaryotes - the ancestors of plastids (p) and mitochondria (m) - in host cells of this lineage. (e) The prokaryote-host tree. This also incorporates endosymbiosis as the origin of mitochondria and plastids, but proposes that the endosymbiotic event that gave rise to a cell containing nucleus and mitochondria occurred in a prokaryotic host. This leads to a ring-like relationship between the ancestral organisms rather than a tree (see inset 2). This model also invokes extensive LGT throughout microbial evolution (see inset 1). See text for further details.

Figure 2

As a representative eukaryote example, the non-redundant set of human proteins (NCBI's Refseq database [70]) was compared using BLAST to a data set containing all proteins from 224 prokaryotic genomes: (a) 24 archaebacteria and (b) 200 eubacteria. In each panel, individual genomes are represented by columns and individual proteins by rows; numbers of proteins are indicated on the left and percentage amino-acid identity by the color scale shown on the right. BLAST hits with an e-value ≤ 10^-20 and ≥ 20% amino-acid identity were recorded. The percent identity of the best blast hit for each human protein in each prokaryote was color coded as shown on the right and plotted with MATLAB^©. The 31 proteins that were used in the recent tree of life [9] are marked with ticks in column (c). A table containing the numbers, genes, and species underlying the figure is available as additional data file 1.