DOI: 10.5061/dryad.8976
title: Data from: Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in Archaea

description: Methods to infer the ancestral conditions of life are commonly based on
 geological and palaeontological analyses. Recently, several studies
 focused on the use of genomes to gain information about past ecological
 conditions. Several used the property that the G+C and amino-acid contents
 of bacterial and archaeal rDNA genes and proteins, respectively, are
 strongly influenced by the environmental temperature. The adaptation to
 optimal growth temperature (OGT) since the Last Universal Common Ancestor
 (LUCA) over the universal tree of life was examined and it was concluded
 that LUCA was likely to have been a mesophilic organism and that a
 parallel adaptation to high temperature occurred independently along the
 two lineages leading to the ancestors of Bacteria on one side and of
 Archaea+Eukarya on the other side. Here, we focus on Archaea to gain a
 precise view of the adaptation to OGT over time in this domain. It has
 been often proposed on the basis of indirect evidence that the last
 archaeal common ancestor was a hyperthermophilic organism. Moreover, many
 results showed the influence of environmental temperature on the
 evolutionary dynamics of archaeal genomes: thermophilic organisms
 generally display lower evolutionary rates than mesophiles. However, to
 our knowledge, no study tried to explain the differences of evolutionary
 rates for the entire archaeal domain and to investigate the evolution of
 substitution rates over time. A comprehensive archaeal phylogeny and a
 non‐homogeneous model of the molecular evolutionary process allowed us to
 estimate ancestral base and amino acid compositions and optimal growth
 temperatures at each internal node of the archaeal phylogenetic tree. The
 last archaeal common ancestor is predicted to have been hyperthermophilic
 and adaptations to cooler environments can be observed for extant
 mesophilic species. Furthermore, mesophilic species present both long
 branches and high variation of nucleotide and amino acid compositions
 since the last archaeal common ancestor. The increase of substitution
 rates observed in mesophilic lineages along all their branches can be
 interpreted as an ongoing adaptation to colder temperatures and to new
 metabolisms. We conclude that environmental temperature is a major factor
 that governs evolutionary rates in Archaea.
description: GroussinGouy_ProteinAlignmentThis data file contains the protein alignment used in the study of the evolutionary rates within Archaea. Note that before the concatenation of the gene families, the Gblocks program was used. The resulting alignments were concatenated as they were, so that everybody can reproduce our results. This explains why numerous gaps are present in the data. All experiments were also performed with an alignment personally and manually modified and this does not change anything to our conclusions. This second alignment is available on request. Information about the species and gene families are available on the Supplementary File associated to our MBE article.GroussinGouy_rRNAalignmentThis data file contains the rRNA alignment used in the study of the evolutionary rates within Archaea. Information about the species are available on the Supplementary File associated to our MBE article.