Comparative genomics of adaptive evolution Toby Bradshaw University of Washington toby@u.washington.edu

Microevolutionary genomics Understand, at the molecular level, adaptive evolution in natural populations

Why study microevolutionary genomics? Adaptation is the most stunning manifestation of evolution by natural selection Differential adaptation is the principal cause of reproductive isolation, and therefore the origin of species and biodiversity

What are the goals of microevolutionary genomics? Identify adaptive phenotypes in natural populations Timberline 3050m Mather 1400m Stanford 30m

What are the goals of microevolutionary genomics? Find and characterize alleles that produce adaptive phenotypes Comparative genomics/candidate genes QTL mapping/cloning Mutagenesis Transgenesis

What are the goals of microevolutionary genomics? Determine the distribution of adaptive alleles within and among species Direct complementation by transgenesis Comparative mapping DNA sequence analysis

What are the goals of microevolutionary genomics? Discover the genes that produce evolutionary novelties and lead to adaptive radiations

Questions that could be answered by microevolutionary genomics When different taxa adapt to the same environment, do they share genetic mechanisms of adaptation, or does each taxon follow a unique evolutionary trajectory contingent upon genes/alleles not found in the other taxa? Can adaptive genetic variation/differentiation be assessed directly by examining non-neutral loci, rather than using neutral loci as a (useless) surrogate? Is adaptation ‘portable’; i.e., will adaptive alleles from one species function correctly in other species, or does adaptation really require coadapted gene complexes? Does the genetic basis of adaptive radiation differ in kind, or only in degree, from ‘ordinary’ adaptation?

What is needed to move microevolutionary genomics forward? Comprehensive studies of adaptive phenotypes in natural populations Increase support for organismal biology Increase support for whole-plant physiological ecology Improve estimation of species- and population-level phylogeny Develop high-throughput measurement of cryptic phenotypes (e.g., transcript profiling, metabolic profiling) Recognize that ‘natural variation’ is not necessarily adaptive Foster interdisciplinary collaboration

What is needed to move microevolutionary genomics forward? Commit to key model systems, and support them fully with appropriate genomics infrastructure For a wider phylogenetic range of taxa, develop resources for comparative mapping; e.g., pedigrees, inbred lines, stock centers, ortholog-based markers, physical maps, whole-genome sequences Encourage the development of low-cost, high-throughput genotyping systems Transformation and mutagenesis/tagging are key enabling technologies for any model system Improve bioinformatics for comparative genomics MAY DARWIN’S GHOST SMITE US DEAD IF WE CLAIM TO BE STUDYING THE ADAPTOME

Where do we go from here? Choose evolutionary genomics systems based upon compelling ecology and phylogeny, not current convenience