In this study, multiple genes from whole genome sequences of prokaryotes were used to construct highly resolved phylogenetic trees. The geochemical record of the early Earth was then used to assign relative age constraints on the origination of multiple clades. From these age constraints, the presence or absence of known extant lineages (and their metabolisms) was deduced for the Archean and Paleoproterozoic eras. From this, it could be concluded that methanogenesis using carbon dioxide was likely present on the Archean Earth, although the divergence of the Methanosarcinales (which can use organic material) did not occur until after oxygenation of the atmosphere (about 2.3 Ga). Sulfate reduction was initially present in thermophilic bacterial lineages, and then expanded to mesophilic bacterial lineages (perhaps around 2.4 Ga), followed by acquisition of the genes for sulfate reduction by the thermophilic Archeoglobales (at or after 2.3 Ga). Nitrate reduction has been independently acquired multiple times in the archeal domain, well after 2.3 Ga. This suggests that nitrate reduction is not an ancient process, becoming more widespread in the biosphere following oxygenation. Analysis of carbon metabolism suggests that the metabolism of complex organics may be more ancestral than autotrophy. It is not clear what the source of organic material may have been, however abiotic sources are a likely candidate and need further investigation.

Age constraints on the archeal and bacterial trees suggest that microbial life may have been restricted to geothermal environments until nearly the end of the Archean era. This may offer an explanation for the sudden increase in the carbon isotopic composition of organic carbon around 2.7 Ga, why stromatolites are not common in the geologic record until the end of the Archean, and why the distinctive microfossils of the Cyanobacteria are not seen until after the sudden rise of oxygen. This hypothesis also agrees with estimates of high ocean temperatures in the Archean era.

While these age constraints paint a picture that is consistent with many observations in the geologic and geochemical records of the early Earth, they are not consistent with the findings of cyanobacterial and eukaryotic lipids 2.7 Ga. Further work is needed to clarify this disagreement.