Comparative genomics of adaptive evolution

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Comparative genomics of adaptive evolution

• Toby Bradshaw
• University of Washington toby_at_u.washington.edu

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Microevolutionary genomics

• Understand, at the molecular level, adaptive
  evolution in natural populations

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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

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What are the goals of microevolutionary genomics?

• Identify adaptive phenotypes in natural
  populations

Timberline 3050m
Mather 1400m
Stanford 30m
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What are the goals of microevolutionary genomics?

• Find and characterize alleles that produce
  adaptive phenotypes
• Comparative genomics/candidate genes
• QTL mapping/cloning
• Mutagenesis
• Transgenesis

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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

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What are the goals of microevolutionary genomics?

• Discover the genes that produce evolutionary
  novelties and lead to adaptive radiations

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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?

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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

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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 DARWINS GHOST SMITE US DEAD IF WE CLAIM TO
  BE STUDYING THE ADAPTOME

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