Yuqing Peng

Evolutionary biology has long been interested in investigating how molecular sequences are affected by natural selection. Understanding the mechanisms of molecular sequence evolution might be possible by comparing the number of substitutions at synonymous (silent) and nonsynonymous (amino acid-altering) locations (ω=dN/dS) in protein-coding genes. However, recent population genetic models of protein evolution have shown that the criteria ω>1 to detect adaptive evolution in proteins may be too conservative. Instead, it appears advantageous to estimate selection coefficients at amino acid sites directly and use those selection estimates to study the evolutionary dynamics of proteins.

In this project, I will collect phylogenomic data for >300 mammal species and will the use the newest population genetic models from the dos Reis lab to estimate the strength of natural selection at amino acid sites. I will test several models of selection including constant (or purifying) selection, discrete selection shifts, and persistent positive selection in the mammalian phylogeny. Estimates of selection coefficients will then be mapped to protein structure using AlphaFold’s predicted protein structure for mammals, to gain insight between the nature of selection and the protein’s functional constraints. The mammalian phylogeny will be calibrated to geological time using molecular-clock methods and this reference phylogeny will be used to place protein evolution within its geological context.