Abstract
Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.
Highlights
The field of molecular evolution investigates how genes and genomes evolve over time
Among groups developing simple toy models of evolution, models incorporating some biophysical realism have been quite popular in recent years
Statistical models of sequence evolution incorporating biophysical realism are being developed by some groups but are not being routinely applied in sequence-analysis applications
Summary
The field of molecular evolution investigates how genes and genomes evolve over time It has its origin in the late 1960s, when the first DNA and protein sequences were becoming available. A side effect of the strong emphasis on developing sophisticated methods for sequence analysis has been that the underlying biophysical objects represented by the sequences, DNA molecules, RNA molecules, and proteins, have taken a back-seat in much computational molecular-evolution work. My overall message, that it is time to bring the molecules back into molecular evolution, applies to other genetic sequences, such as intergenic regions, RNA genes, or the various forms of short RNAs. I will consider three broad areas, corresponding to three distinct research goals: (i) reconstructing and interpreting past evolutionary events; (ii) identifying fundamental principles of molecular evolution; and (iii) predicting probable evolutionary trajectories
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