Background: Gene duplication has been suggested to be an important process in the generation of evolutionary novelty. Neofunctionalization, as an adaptive process where one copy mutates into a function that was not present in the pre-duplication gene, is one mechanism that can lead to the retention of both copies. More recently, subfunctionalization, as a neutral process where the two copies partition the ancestral function, has been proposed as an alternative mechanism driving duplicate gene retention in organisms with small effective population sizes. The relative importance of these two processes is unclear. Results: A set of lattice model genes that fold and bind to two peptide ligands with overlapping binding pockets, but not a third ligand present in the cell was designed. Each gene was duplicated in a model haploid species with a small constant population size and no recombination. One set of models allowed subfunctionalization of binding events following duplication, while another set did not allow subfunctionalization. Modeling under such conditions suggests that subfunctionalization plays an important role, but as a transition state to neofunctionalization rather than as a terminal fate of duplicated genes. There is no apparent selective pressure to maintain redundancy. Conclusion: Subfunctionalization results in an increase in the preservation of duplicated gene copies, including those that are neofunctionalized, but never represents a substantial fraction of duplicate gene copies at any evolutionary time point and ultimately leads to neofunctionalization of those preserved copies. This conclusion also may reflect changes in gene function after duplication with time in real genomes.

The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state‐of‐the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high‐throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.

Gene duplication is postulated to have played a major role in the evolution of biological novelty. Here, gene duplication is examined across levels of biological organization in an attempt to create a unified picture of the mechanistic process by which gene duplication can have played a role in generating biodiversity. Neofunctionalization and subfunctionalization have been proposed as important processes driving the retention of duplicate genes. These models have foundations in population genetic theory, which is now being refined by explicit consideration of the structural constraints placed upon genes encoding proteins through physical chemistry. Further, such models can be examined in the context of comparative genomics, where an integration of gene‐level evolution and species‐level evolution allows an assessment of the frequency of duplication and the fate of duplicate genes. This process, of course, is dependent upon the biochemical role that duplicated genes play in biological systems, which is in turn dependent upon the mechanism of duplication: whole genome duplication involving a co‐duplication of interacting partners vs. single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined. J. Exp. Zool. (Mol. Dev. Evol.) 306B, 2006.

Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >>1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (Magnoliophytes) without saturation of 4- fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta- sheets, but were less negative and more variant on the surface and away from the hydrophobic core. Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes.