Paleobiology Seminar: "Dating Microbial Phylogeny Using Horizontal Gene Transfer and Meta-Alignments"


Tuesday, October 20, 2015, 12:30pm to 1:30pm


Haller Hall (Geology Museum 102)

Speaker: Greg Fournier (MIT)


Date calibrations for applying molecular clocks to phylogeny are typically provided by fossil or other geologically preserved evidence.  However, for the vast majority of the Tree of Life, no fossil record exists.  While the paleontological record of lipid biomarkers and microbial microfossils provides some information, these records are extremely sparse, and often ambiguous.  I propose that this limitation can be overcome in part by using horizontal gene transfers (HGTs) as stratigraphic events. HGTs between distant groups cross-link parts of the Tree of Life, ordering the divergence times of the donor and recipient lineages.  If either lineage has an associated fossil record, absolute date constraints propagate along this cross-link.  Through this approach, many parts of the microbial Tree of Life can be dated, providing critical information about the early evolution of life, and the co-evolution of microbial metabolisms, physiology, and ecology with planetary systems.  New approaches to multiple sequence alignment maximize the utility of this technique.  Alignments of horizontally transferred genes generally do not contain enough sites for reliable molecular clock analyses to be performed.  Concatenations of additional protein sequences (e.g., ribosomal proteins) are generally used to generate molecular clocks, but these do not capture the reticulate history that is necessary for propagating the date constraint.  We show that independent alignments of ribosomal proteins from donor and recipient lineages can be concatenated with one (or many) HGT alignments, without violating the key assumption that all sites within an alignment evolve along the same “true” evolutionary history.  This permits the construction of a “meta-alignment” that directly incorporates calibration dates from HGT events within phylogenies based on much larger sequence datasets, as well as including the temporal information within the reticulating branch itself.  Preliminary applications of this technique using the transfer of a gene encoding the SMC protein from methanogens to cyanobacteria provide a novel constraint on the absolute age of both groups, providing more precise estimates than previous investigations.  Additional analyses of other HGT events constrain the absolute and relative ages of Proteobacteria, Cyanobacteria, Chloroflexi, and Chlorobiales. 

The EHAP/Geobiology Seminar Series is jointly hosted by OEB and EPS