Reconstructing Ancient Phenotypes

When accessing the deep past, we have two main datasets to draw upon in reconstructing major transitions in the biosphere: the rock record (i.e., fossils, biosignatures and geologic indicators of environment) and extant biotic diversity (i.e., genetic sequences, proteins and organismal variability). Under this theme, we explore paleogenetic methodologies that allows us to reconstruct and then resurrect ancient protein sequences and utilize these modern  tools for interpreting ancient biosignatures recorded in the rocks, and for shedding light on significant past events in evolution.

Molecular Evolution of Rubisco proteins

In order to understand how the ancestral behavior of proteins and their host systems change through time, we are reconstructing key proteins that are involved in phenotypically distinct metabolic pathways that are of interest to biologists and geologists. Through our collaborations with paleobiologists and phylogeneticists, we aim to answer the question of whether the phenotypes we observe relate to larger scale changes in the global biogeochemical system. I am currently accepting graduate students interested in studying evolution of Rubisco proteins in Cyanobacteria.


Our paper looking for the Great Oxidation Event in Rubisco evolution:

Please note that all of the Rubisco sequences for all of the tree variants and ancestors are available here:

Ancient Thiobiosphere (collaborative research, funded by NSF)

Currently recruiting a postdoc (or equivalent research experience) with background in molecular evolution for a new collaborative project exploring the biochemical, genetic, metabolic and isotopic constraints on an ancient thiobiosphere. No astrobiology/origins of life/geobiology background is necessary. This project is funded by NSF and the position is available August 2018. Contact me for details.

Phylogenetic reconstruction and in vivo resurrection of the Precambrian nitrogen fixation pathway

The evolutionary history of biological nitrogen fixation remains poorly constrained. Stable nitrogen isotope ratios in Archean and Proterozoic sedimentary rocks record the contributions of biological processes to nitrogen cycling, but this record can only be interpreted by constraining the history and biochemical characteristics of the enzymes and pathways that were present throughout this time. We created phylogenies of Nitrogen fixation components and currently recruiting graduate students interested in understanding the biochemical evolution of nitrogen fixation pathway through the study of ancient nitrogenase proteins.

More on what we do.