Comparative genomics of convergent evolution

Abstract

We define convergent evolution as the repeated and independent emergence of a given adaptive trait in two or more lineages whose last common ancestor did not possess the respective character. The genomic basis of convergent evolution is not well understood but constitutes a decisive element in understanding its origins, prevalence, and adaptive value throughout the three domains of life. Recent studies indicate that convergent evolution is actually occurring on the molecular sequence level and, indeed, genome-wide at multiple loci in many instances. So far, a number of different mechanisms for genome evolution have been identified that drive an increase in biological novelty and complexity. Information and (biological) systems theory are beginning to reframe the phenomenon of convergent evolution in terms of top-down causation and resulting functional equivalence classes. Comparative genomic studies of convergent evolution will benefit from such a theoretical perspective, since convergence appears to be a fundamental property of complex adaptive systems, especially in biology and technology. Here we explore the convergent emergence of complex traits across different levels of organizational bio-complexity within a phylogenetically inspired context that is being supported by the ever-increasing wealth of available genome data. The discipline of comparative genomics is maturing into a decisive factor in the systems biology revolution of the twenty-first century by providing a computational paradigm for exploring the evolutionary sequence space across multiple levels and scales of bio-complexity.