1. Comparative genomics of adaptive evolution
Toby Bradshaw
University of Washington

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

3. 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

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

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

6. 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

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

8. 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?

9. 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

10. 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

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