Fig. 3.

Evolutionary heterogeneity in rates of environmental adaptation in terrestrial Thaumarchaeota inferred from the amoA 370-sequence tree within the BAMM framework. There is evidence that diversification (Fig. 2) is coupled to pH adaptation at two levels: (A) comparing the global rate of pH adaptation through time (green line) to the equivalent data for diversification rates (orange dotted line; taken from Fig. 2B) and (B) comparing the most probable phenotypic rate-shift configurations with equivalent diversification rate-shift data (Fig. 2C). (C) Equivalent analyses were performed for eight additional environmental factors on a smaller amoA tree of 181 sequences. (D) Ancestral pH preferences are shown for the 370-sequence amoA tree based on a ridge regression approach (28), with estimates of ancestral pH provided at key nodes.