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Human Pregnancy

Evolutionists have long been fascinated with how traits as complex and yet so closely tied to evolutionary fitness as pregnancy-related ones could have evolved. Recent discoveries stemming from comparisons with our closest living relatives, the chimpanzees, as well as other extinct hominins are revealing unmistakable signatures of the dramatically fast evolution of many pregnancy-related traits in our genomes, skeletons, brains, behaviors, and cultures. Perhaps less obvious, but no less important, is the story of how modern human pregnancy, much like the modern human body, evolved out of deeper ancestral vertebrate forms. We are working on a wide variety of research questions surrounding human pregnancy aiming to generate a synthetic portrait of its evolution; in parallel, we are working on constructing GEneSTATION, an ambitious discovery-enabling encyclopedia and web portal for the interactive study of human pregnancy that will aiding in the identification of candidate genetic and environmental disruptors.

Representative publications:
Eidem et al. (2017) Placenta
Abbot & Rokas (2017) Curr. Biol.
Kim et al. (2016) Nucleic Acids Res.

Fungal Lifestyle

A defining characteristic of Fungi is that, in contrast to animals, they are typically embedded in their food and digest it externally in the presence of competitors (think of the blue lines of mold in blue cheese). Thus, different fungi specialize in “eating” different foods, hence their diverse primary metabolism. In collaboration with the Hittinger and Kurtzman labs at UW-Madison and the USDA, respectively, we are in the process of sequencing and analyzing the genomes of all known yeast species from the subphylum Saccharomycotina to study the evolution of their diverse metabolic and ecological functions. For more information, please check the Y1000+ Project website.

Representative publications:
Steenwyk & Rokas (2017) G3
Shen et al. (2016) G3
Hittinger et al. (2015) Curr. Opin. Genet. Dev.

Because digestion happens externally, fungi have also evolved potent food defense mechanisms (hence their diverse secondary metabolism). The cholesterol-reducing drug lovastatin, the antibiotic penicillin, and the potent carcinogen aflatoxin are just a tiny sample of the pharmacopoeia stored in and manufactured by fungal DNA. Our lab studies elucidate how this diversity is generated and maintained.

Representative publications:
Wu et al. (2017) PLoS One
Lind et al. (2015) PLoS Genet.
Wisecaver & Rokas (2015) Front. Microbiol.

Phylogenetics

Understanding the key contributing factors to phylogenetic inaccuracy is critical for the generation of robust phylogenies and evolutionary hypothesis testing. Among eukaryotes, the fungal kingdom represents the premier model system for comparative functional genomic investigations, with complete genome sequences already available from more than eighty species. Importantly, the sequenced fungal genomes can be clustered to groups of very closely related organisms, groups of species at moderate evolutionary distances, as well as groups of very distantly related organisms. This clustered distribution of available genomes is crucial for phylogenetics research, as it allows the investigation of the factors influencing phylogenetic reconstruction at a wide variety of evolutionary depths. Using these diverse sets of fungal genomic data we are currently investigating the parameters affecting  phylogenetic accuracy and develop assays for the detection of conflicts in molecular phylogenies, and the effect of homoplasy and selection on phylogenetic estimation.

Representative publications:
Shen et al. (2017) Nature Ecol. Evol.
Salichos et al. (2014) Mol. Biol. Evol.
Salichos & Rokas (2013) Nature


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