ESTABLISHING STRATIGRAPHIC PRINCIPLES OF MICROBIAL GENOME EVOLUTIONARNY HISTORY

Cross-cutting relationships between different geological features are a basic and essential geological principle used in relative dating of strata. Intrusive material is always younger than host material, with the specific observed relationship providing key information about complex geological processes interacting across geological timescales. These processes are directly analogous to those observed within genome evolution, which also contain complex histories of inheritance of genetic material along lineages. Specifically, in the case of horizontal gene transfer, genetic material not inherited by normal speciation and vertical descent processes is acquired from another lineage, and becomes part of the recipient lineage genome. This represents an intrusion event, with the transferred genetic information being more recently present in the genomic context than other vertically inherited information. Additionally, any speciation events following the transfer event must be younger than the speciation event leading to the transfer donor lineage. These events are abundant within microbial lineages, and present a rich, unique opportunity for establishing relative orderings of divergence times between groups at all geological timescales. Additionally, the time of intrusion itself becomes an additional event that can be dated, permitting, in some cases, the relative ordering of physiological character acquisitions within a lineage, information that is not preserved by any other means. Finally, directly analogous to traditional biostratigraphy methods, lineages with absolute date constraints can propagate these constraints across the Tree of Life, via gene transfers to and from other lineages that may not have left any physical record. The key challenge to establishing a discipline of genome stratigraphy is developing the phylogenetic tools to unravel the very complex history of gene families across multiple lineages, and extracting a reliable, robust evolutionary signal for dating, i.e., a set of benchmark “index” transfers. I outline several principles that can guide rigorous, consistent, and biologically sound methodological approaches to extending stratigraphic principles to genome evolution across billions of years of planetary history.