This research will integrate biological and planetary change across geological timescales by developing a more accurate and precise time-calibrated Tree of Life (ToL), i.e., a Chronogram of Life (CoL) based on novel methods for dating microbial evolution. The geological record has long been our sole source of information about planetary history. In contrast, the deep time record preserved within genomes has only been recently discovered, and remains poorly characterized. When unlocked through phylogenetic analysis, molecular clocks, and robust calibration, this genomic record will provide unique insights into geochemical, atmospheric, and climate processes across Earth's history. The timing of many events linking the co-evolution of life and the planet remain uncertain. This is especially true for very early events in Earth's history, where the fossil and geochemical record is often sparse, ambiguous, or entirely absent. In fact, across much of the Archaean (and possibly Hadean) Eons, the only remaining record may be the one preserved within genomes. To reveal this record, the research has three major aims: (1) identifying ancient time calibrations in genome evolution across the ToL by using HGT (Horizontal Gene Transfer) events via genome stratigraphy; (2) linking the fossil record to microbial history via sequencing co-evolving microbiomes of ancient animal lineages; and (3) developing new bioinformatics approaches to integrate these constraints, generating an accurate and reliable chronology of early life evolution and planetary history, directly testing several hypotheses related to the deep biogeochemical history of the Earth.
The deep, intertwined relationship between the evolution of life and the planet is of fundamental importance. While many previous investigations have proposed scenarios linking events in early microbial evolution to the preserved biogeochemical record, in order to actually test these different co-evolutionary hypotheses, independent methods are required to time-calibrate microbial evolution itself. To this end, the key intellectual contribution of this work is using horizontal gene transfer (HGT) as a powerful new tool for determining the timing of events on the early Earth. Flows of genes across the ToL constrain the relative divergence times of distantly related lineages. This interpretation of HGT permits genomic stratigraphy, wherein time calibrations available for some groups within the ToL (i.e., via biomarker and/or fossil records) can be propagated to other groups. This approach is analogous to biostratigraphy, which uses the presence or absence of different fossils to date strata of sedimentary rocks. Similarly, dates from fossil calibrations can be propagated across the ToL through co-speciation events, as are often observed between microbial symbionts and their animal hosts. Expanding this technique to previously unsampled microbiomes of the most ancient arthropod lineages will greatly extend the temporal reach of this method. Together, these novel stratigraphic uses for genomic information will translate the ToL into an accurate CoL. This work will permit direct evaluation of major questions in the evolution of Earth's early biosphere, geosphere and atmosphere, including the emergence of oxygenic and anoxygenic photosynthesis, methane production via methanogenesis, and the establishment of microbial nitrogen, carbon, sulfur, and oxygen cycles
