Caroline Storer<br />SAFS GSS 2010<br />Genetic and epigenetic variation in sockeye salmon<br />
“Variation is the spice of life”<br />Kruglyak & Nickerson. 2001.<br />Nature Genetics. <br />
Everybody’s talking about variation<br />“Variation is the spice of life”; it is required for evolution<br />Genetic varia...
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Epigenetic variation <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA se...
Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A  <br />Epigenetic mechanisms can alter gene expression a...
Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A  <br /><ul><li> Epigenetic marks are:
Heritable
 Naturally occurring
 Can be altered by the environment</li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
“Variation is the spice of life” …<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
“Variation is the spice of life” …<br />for sockeye salmon<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Phenotypic variation in sockeye salmon <br />Beach (top) and stream (bottom) spawning ecotypes<br />Bossdorf, Richards, & ...
Genetic variation in sockeye salmon <br />Ackerman et al. In review<br />Genetically similar spawning populations<br />Bos...
Genetic variation in sockeye salmon <br /><ul><li> Our ability to detect variation is dependent on the number of markers w...
Currently there are 42 SNP markers for sockeye salmon </li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Epigenetic variation in sockeye salmon <br />?<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation...
Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation...
Describing genetic variation <br />Methods:<br />Genotype populations across the range at SNP loci<br />Assess genetic var...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
SNP discovery<br />Methods:<br />Identify candidate SNPs<br />Validate candidate SNPs<br />Results:<br />73 new SNPs valid...
Describing genetic variation<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Pen...
Genetic variation<br />Bristol Bay <br />Russia<br />Alaska Peninsula<br />South-central Alaska<br />Principal Coordinate ...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />
Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />Populations:<br />South-ce...
Describing epigenetic variation <br />Optimize methods for detecting population specific methyaltion patterns in sockeye s...
Describing epigenetic variation <br />Population 1<br />Population 2<br />Me Patterns:<br />CH3<br />A C T C G<br />A CAC ...
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Genetic and Epigenetic Variation in Sockeye Salmon

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Presentation for the UW School of Aquatic and Fishery Sciences Grad Student Symposium 2010

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  • 42 markers
  • Existing markers have revealed structure thus far, but larger marker panels improve res across range
  • 43 in-house
  • West Kamchatka, RussiaBolshaya RiverOzernaya RiverBristol Bay, Alaska Lake Kulik Pick CreekAlaska Peninsula Bear LakeCinder River Southcentral Alaska Coghill LakeMain Bay British Columbia, Canada Alsek Upper Tatshenshini NassDamdochax Creek Washington  Issaquah Creek Baker Lake
  • Genetic and Epigenetic Variation in Sockeye Salmon

    1. 1. Caroline Storer<br />SAFS GSS 2010<br />Genetic and epigenetic variation in sockeye salmon<br />
    2. 2. “Variation is the spice of life”<br />Kruglyak & Nickerson. 2001.<br />Nature Genetics. <br />
    3. 3. Everybody’s talking about variation<br />“Variation is the spice of life”; it is required for evolution<br />Genetic variation enables a population to evolve in response to environmental change on a long time scale<br />Epigenetic variation enables a population to evolve in response to environmental change on a short time scale<br />Genetic and epigenetic mechanisms work in concert<br />
    4. 4. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    5. 5. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    6. 6. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    7. 7. Epigenetic variation <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    8. 8. Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence <br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    9. 9. Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A <br /><ul><li> Epigenetic marks are:
    10. 10. Heritable
    11. 11. Naturally occurring
    12. 12. Can be altered by the environment</li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    13. 13. “Variation is the spice of life” …<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    14. 14. “Variation is the spice of life” …<br />for sockeye salmon<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    15. 15. Phenotypic variation in sockeye salmon <br />Beach (top) and stream (bottom) spawning ecotypes<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    16. 16. Genetic variation in sockeye salmon <br />Ackerman et al. In review<br />Genetically similar spawning populations<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    17. 17. Genetic variation in sockeye salmon <br /><ul><li> Our ability to detect variation is dependent on the number of markers we have
    18. 18. Currently there are 42 SNP markers for sockeye salmon </li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    19. 19. Epigenetic variation in sockeye salmon <br />?<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
    20. 20. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br />Describe epigenetic variation across the species’range<br />
    21. 21. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br />Describe epigenetic variation across the species’ range<br />
    22. 22. Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation<br />
    23. 23. Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation<br />Population 1<br />Population 2<br />A C T C G<br />A CAC G<br />SNP locus<br />
    24. 24. Describing genetic variation <br />Methods:<br />Genotype populations across the range at SNP loci<br />Assess genetic variation<br />Problem:<br /> Only 42 nuclear SNPs available for sockeye salmon<br />Solution: <br /> Discover more SNPs<br />
    25. 25. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br /> SNP discovery<br />Describe epigenetic variation across the species’range<br />
    26. 26. SNP discovery<br />Methods:<br />Identify candidate SNPs<br />Validate candidate SNPs<br />Results:<br />73 new SNPs validated<br />115 SNPs total<br />
    27. 27. Describing genetic variation<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Peninsula<br />Genotyped 12 populations, 61- 93 fish per population, representing 6 regions <br />Washington<br />
    28. 28. Genetic variation<br />Bristol Bay <br />Russia<br />Alaska Peninsula<br />South-central Alaska<br />Principal Coordinate 1 (44.5%)<br />British Columbia<br />Washington<br />Principal Coordinate 2 (15.5%)<br />
    29. 29. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br /> SNP discovery<br />Describe epigenetic variation across the species’range<br />
    30. 30. Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />
    31. 31. Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />Populations:<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Peninsula<br />Washington<br />
    32. 32. Describing epigenetic variation <br />Optimize methods for detecting population specific methyaltion patterns in sockeye salmon<br />Me-AFLP<br />MeDIP-CHIP<br />
    33. 33. Describing epigenetic variation <br />Population 1<br />Population 2<br />Me Patterns:<br />CH3<br />A C T C G<br />A CAC G<br />Me locus<br />
    34. 34. Conclusions<br />Discovered and validated new SNPs<br />Range wide variation; following geographic patterns<br /> Established a threshold of variation for comparison with epigenetic variation<br />
    35. 35. Possible implications<br />Often, genetic variation alone has not been able to explain observed phenotypic diversity<br />Epigenetics may be part of that missing link<br />Current management strategies are based on measures of genetic variation <br />Epigenetics could be used as an additional, more sensitive measure of variation <br />
    36. 36. Acknowledgements<br /><ul><li>Alaska Department of Fish and Game
    37. 37. Alaska Sustainable Salmon Fund
    38. 38. Bristol Bay Regional Seafood Development Association
    39. 39. University of Washington School of Aquatic & Fishery Sciences
    40. 40. The Gordon and Betty Moore Foundation
    41. 41. Applied Biosystems Foster City, CA
    42. 42. The Seeb and Roberts Labs</li></li></ul><li>Thank you.<br />Questions?<br />

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