The Department of Biology is excited to invite you to a seminar entitled "Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model" by Dr. Dannie Durand, Associate Professor in the Department of Biological Sciences at Carnegie Mellon University on Monday, November 3rd at 3pm in BL234. We kindly ask you to make every effort to attend.

Host: Dr. David Liberles

More information about the speaker here: https://www.cs.cmu.edu/~durand/Lab/

Abstract: Reconstruction of the ancestral protein coding repertoire can reveal the historical coincidence of genetic and phenotypic shifts, as well as the tempo and mode of the processes that shape the ancestral repertoire. However, ancestral inference can be highly sensitive to methodological choices.

 Here, we use a phylogenetic Birth-Death-Gain model to investigate the evolution of the protein domain repertoire in metazoa.   Domains are protein modules with a distinct structure and function representing the basic components of the protein repertoire.  Given a species tree and the domain families encoded in present-day genomes, we estimated the most likely rates of domain family origination, duplication and loss. Rates were allowed to vary across species tree branches and across domain families, decoupling the two.  We examined family rates, independent of branch-specific effects, and observed a strong and significant association between family rate and family function. Interestingly, families that perform functions associated with metazoan innovations tend to have the fastest rates. 

 Using the same model, we inferred the protein coding repertoire in ancestral genomes, as well as the expected family gains, expansions, contractions, and extinctions on each branch. Our reconstruction reveals an ongoing process of family replacement and resizing, consistent with extensive remodeling of the protein coding repertoire.   [...]