Research Article

Low Rates of Lateral Gene Transfer among Metabolic Genes Define the Evolving Biogeochemical Niches of Archaea through Deep Time

Figure 1

Genome phylogeny and node ages. Node ages (scale at bottom, in millions of years before present) were inferred using relaxed molecular clock method penalized likelihood. The presence of a cytochrome oxidase (subunit I or subunit I+III from either Heme-copper oxygen reductase family A1 or B) was coded in Mesquite as in the genome or in the genome. The maximum likelihood method (implementing the Mk1 model) was used to estimate the probability that each ancestral genome in the tree (each node) contained a cytochrome oxidase gene. A completely white circle indicates zero likelihood of a cytochrome oxidase gene; a completely black circle indicates a 100% likelihood, while intermediate shading of the pie indicates an intermediate likelihood. The corresponding geologic age of the nodes in the tree can be determined using the age diagram at the bottom. The archaeal tree was split into two figures, (a) one showing the Euryarchaeota and the other (b) showing the Crenarchaeota, for ease of viewing. Major archaeal clades are indicated using colored boxes, with the appropriate family names shown.
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(a) Genome phylogeny and node ages, Euryarchaeota
843539.fig.001b
(b) Genome phylogeny and node ages, Crenarchaeota