DOI: 10.5061/dryad.0nv00
title: Data from: Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

description: The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that
 plays a major role in the global nitrogen cycle. Previous analyses of the
 ammonia monooxygenase gene amoA suggest that pH is an important driver of
 niche specialization in these organisms. Although the ecological
 distribution and ecophysiology of extant Thaumarchaeota have been studied
 extensively, the evolutionary rise of these prokaryotes to ecological
 dominance in many habitats remains poorly understood. To characterize
 processes leading to their diversification, we investigated coevolutionary
 relationships between amoA, a conserved marker gene for Thaumarchaeota,
 and soil characteristics, by using deep sequencing and comprehensive
 environmental data in Bayesian comparative phylogenetics. These analyses
 reveal a large and rapid increase in diversification rates during early
 thaumarchaeotal evolution; this finding was verified by independent
 analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota
 diversification regime was strikingly coupled to pH adaptation but less
 clearly correlated with several other tested environmental factors.
 Interestingly, the early radiation event coincided with a period of pH
 adaptation that enabled the terrestrial Thaumarchaeota ancestor to
 initially move from neutral to more acidic and alkaline conditions. In
 contrast to classic evolutionary models, whereby niches become rapidly
 filled after adaptive radiation, global diversification rates have
 remained stably high in Thaumarchaeota during the past 400–700 million
 years, suggesting an ongoing high rate of niche formation or switching for
 these microbes. Our study highlights the enduring importance of
 environmental adaptation during thaumarchaeotal evolution and, to our
 knowledge, is the first to link evolutionary diversification to
 environmental adaptation in a prokaryotic phylum.
description: 370_sequence amoA
 treeBayesian amoA
 phylogenetic tree derived from 454 sequencingAmoA_370.nwkNucleotide alignment for the 370-sequence amoA treeNucleotide alignment (codon positions 1 and 2) for the 370-sequence amoA treeAmoA_370_CP1+Cp2.fas508-sequence 16S rRNA treeBayesian 508-sequence phylogenetic 16S rRNA tree derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset.Global_16S.nwk613_sequence amoA treeBayesian 613-sequence phylogenetic amoA tree derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset.Global_amoA.nwkNucleotide alignment for the 508-sequence 16S rRNA treeNucleotide alignment for the 508-sequence 16S rRNA tree, derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset.16SrRNA_508.fasNucleotide alignment for the 613-sequence amoA treeNucleotide alignment for the 613-sequence amoA tree (codon positions 1 and 2), derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset.AmoA_613_CP1+2.fas