Research Description

We study the mechanisms and dynamics by which genes and the proteins they code for evolved their diverse functions. We employ a synthesis of evolutionary and phylogenetic techniques with functional molecular biology and biochemistry. Our current model system is a gene family of great biological and biomedical importance.

We are interested in two kinds of fundamental issues: 1) first, the nature of evolutionary processes, such as how complexity evolves, whether adaptation proceeds by many small steps or a few large ones, whether interactions among mutations limits the pathways and outcomes that evolution can explore, and whether the outcomes of evolution are deterministic or contingent upon low-probability chance events; and 2) the genetic, biochemical, and biophysical mechanisms by which proteins evolve new functions. All of these questions depend upon the map that relates changes in gene sequence to changes in gene function and, ultimately, in phenotype. These issues remain unresolved because evolutionary biologists have, until recently, ignored the connection between genotype and phenotype by treating genes as mere strings of letters. We have helped to develop and articulate the Functional Synthesis in molecular biology and evolution -- a combination of evolutionary approaches for reconstructing history with the experimental strategies of molecular biology and biochemistry to rigorously test hypotheses about the mechanisms of evolution. This approach is uniquely powerful for elucidating both the proximal and ultimate causes of protein function.

We have played an important role in developing a new strategy for studying protein evolution called ancestral gene resurrection. We use computational phylogenetic methods to infer ancestral sequences, followed by gene synthesis to synthesize them and experimental techniques to characterize them. We use cell biological, biochemical, and biophysical methods, as well as (by collaboration) X-ray crystallography and molecular dynamics approaches, to elucidate the functions, structures, and biophysical properties of ancestral proteins. With ancient proteins in hand, we can also introduce the mutations that occurred during crucial evolutionary periods to test hypotheses about the the specific effects caused by each historical genetic change.

How did hormones and their diverse functions in humans and other animals evolve? We study the evolution of vertebrate steroid hormones -- such as estrogen, testosterone, and the stress hormone cortisol -- and the receptor proteins that mediate these hormones' effects on the body's cells. Our goal is to reveal the specific molecular events by which hormones, receptors, and their DNA targets evolved their specific partnerships during the last 600 million years or so. We are characterizing receptor biodiversity across the animal kingdom, testing hypotheses about the functions of ancient proteins, and determining the specific mutations and changes in protein structure by which new receptor functions evolved hundreds of millions of years ago.

We are also evaluating and developing new phylogenetic methods for analyzing gene family evolution. We are particularly interested in understanding how uncertainty and heterogeneity in the evolutionary process affects the accuracy of current techniques for reconstructing phylogenies and inferring ancestral sequences. We also develop new methods that perform better when sequences evolve with a high degree of complexity.

Selected Publications

• Bridgham JT, Eick G, Larroux C, Deshpande K, Harms MJ, Gauthier MEA, Ortlund EA, Degnan BM, Thornton JW (2010). Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biol 8(10): e1000497.
• Harms MJ, Thornton JW (2010). Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology 20:360-366.
• Hanson-Smith V, Thornton JW (2010). Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution, 27(9): 1988-1999.
• Bridgham JT, Ortlund EA, Thornton JW (2009). An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519.
• Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007). Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548.
• Dean AM, Thornton JW (2007). Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics 8:675-688.
• Bridgham JB, Carroll SM. Thornton JW (2006). Evolution of hormone-receptor complexity by Molecular Exploitation. Science 312:87-101, 2006.
• Kolaczkowski B, Thornton JW (2004). Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
• Thornton JW (2004). Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews Genetics 5:366-375.
• Thornton JW, Need E, Crews D (2003). Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301:1714-1717, 2003.