Data from: The molecular signal for the adaptation to cold temperature during early life on Earth

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.

多项证据支持细菌域与古菌域的祖先为地球早期适应高温环境的嗜热生物，相关证据包括大规模系统发育树中嗜热支系的基部位置、单酶或大型蛋白串联体的祖先序列重建结果。据此，简约性推理可推导出最后通用共同祖先（last universal common ancestor，LUCA）同样为嗜热生物。
诸多学者采用支系特异性非均一进化模型，该模型可更好地捕捉不同支系间的分子组成变异，借此精准重建了核糖体RNA的祖先G+C含量以及高度保守蛋白的祖先氨基酸组成。他们证实了细菌域与古菌域祖先的嗜热性，但同时得出结论：二者的最后共同祖先LUCA为具有适中最适生长温度的嗜温生物。
本研究旨在探究驱动祖先序列重建以支持该非简约性场景的未知系统发育信号本质。我们发现，分子序列的位点间速率变异可通过在进化缓慢区域记录最古老的温度适应事件、在进化快速区域记录后续适应事件，从而在不同时间尺度上提供信息。