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Saving seeds: optimal ex situ collections for genetic preservation

Sean Hoban IUFRO meeting. Saving seeds: optimal ex situ collections for genetic preservation. Photos by S Hoban. 21 st century challenges to forests: Severe, and growing. Ex situ collections.

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Saving seeds: optimal ex situ collections for genetic preservation

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  1. Sean Hoban IUFRO meeting Saving seeds: optimal ex situ collections for genetic preservation Photos by S Hoban

  2. 21st century challenges to forests: Severe, and growing

  3. Ex situ collections

  4. Multiple Purposes: breeding, reforestation/ restoration, preserve endangered flora, basic study of plant ecology Challenge: gather a sample of genetic diversity from a plant species’ native distribution

  5. What, where, how to sample • How many • populations • maternal plants • seeds • What spatial distribution • among populations • within populations

  6. The sampling problem Efficiency: Limited money, resources, personnel, space, and time (especially for living collections) Effectiveness: Loss of genes/ species is permanent

  7. The sampling problem How to make an efficient collection- minimum sample size Probability-based Approaches • Brown & Marshall 1975, 1991, 1995 • 50 samples, every population

  8. The sampling problem How to make an efficient collection- minimum sample size Probability-based Approaches • Brown & Marshall 1975, 1991, 1995 • 50 samples, every population 60% of major collecting organizations use this protocol

  9. The sampling problem • Simplifying assumptions: • No genetic structure • No spatial patterns • Always random mating

  10. The sampling problem Calls for trait-based protocols • CPC 1991 • Guerrant2004, 2014 • Hoban et al 2015 Thus far, only qualitative Photo by S Hoban Hoban, Fraga, Richards, Strand & Schlarbaum. 2015. Biological Conservation. “Developing quantitative seed sampling protocols using simulations”

  11. The sampling problem How to quantitativelyguide collections, based on knowledge of geographic distribution, rarity type, ecology, reproductive biology?

  12. The sampling problem How to quantitativelyguide collections, based on knowledge of geographic distribution, rarity type, ecology, reproductive biology? How we assess invasive species How we estimate extinction risk

  13. How to sample different species

  14. A sampling solution Simulations allow to estimate how each protocol would perform in a given situation, a priori.

  15. How to sample different species Biological characteristics • Dispersal kernels: short and long • Selfing: high (0.8) and zero • Stages: annual (2 stage), perennial (3 stage) All combinations- 8 species

  16. How to sample different species Number of seeds per maternal trees Number of maternal trees

  17. How to sample different species Contours are proportion of genes Red contour is 95% of genetic variation Conservation target Number of seeds per maternal trees Number of maternal trees

  18. How to sample different species Increased selfing, decreased dispersal Number of seeds per maternal trees Number of maternal trees

  19. How to sample different species Self-incompatible and high dispersal species requires ~300 seeds Highly selfing species and low dispersal requires ~1600 seeds more than five times as many seeds Hoban & Strand. 2015. Biological Conservation. “Ex situ conservation seed sampling can be improved …”

  20. How to sample different species Dysoxylum malabaricum Tree/ shrub India Quercus lobata Tree California Heliconia acuminata Herbaceous S America Open-access data Dryad Spatial and genetic

  21. Number of seeds per maternal plant Number of maternal plants

  22. Same sampling protocol captures extremely different amounts of diversity Number of seeds per maternal plant Number of maternal plants

  23. How to sample in space

  24. Population on landscape Grey dots- individuals Red dots- samples Ideal sampling Random Grid

  25. Population on landscape Grey dots- individuals Red dots- samples Ideal sampling Random Grid Realistic sampling Transect Corner

  26. 36 maternal plants Proportion of genetic variation captured grid random transect corner

  27. Post oak Gambel oak

  28. How to sample across range Comparing to the currently prevalent guideline

  29. How to sample across range Comparing to the currently prevalent guideline

  30. How to sample across range Comparing to the currently prevalent guideline

  31. Naomi Fraga Rancho Santa Ana BG Chris Richards, USDA Allan Strand, C of Charleston Scott Schlarbaum, Tennessee Hoban & Schlarbaum. 2014. Biological Conservation. “Optimal sampling of seeds from plant populations for ex situ conservation …” Hoban, Fraga, Richards, Strand & Schlarbaum. 2015. Biological Conservation. “Developing quantitative seed sampling protocols using simulations” Hoban & Strand. 2015. Biological Conservation. “Ex situ conservation seed sampling can be improved …” Hoban & Way. 2016 (in review). Samara. “Improving the sampling of seeds for conservation…” Photo by S Hoban

  32. Caveats to note: • Mostly considering rare species • Overall genome-level diversity • Assuming all seeds viable, no duplication- lower bound sample size

  33. How are we doing? • Analysis of >5000 collections • From North America from 1970s to present • Millennium Seed Bank Partnership • For the past ten years the target has been 50 Hoban & Way. 2016 (in review). Samara. “Improving the sampling of seeds for conservation…”

  34. Number of maternal plants sampled Suggested guideline of 50 plants

  35. Number of maternal plants sampled Suggested guideline of 50 plants

  36. Number of maternal plants sampled Suggested guideline of 50 plants

  37. Number of plants sampled in each collection (all plant forms) Number of plants sampled in each collection (only trees) Number of collections Number of plants sampled Number of plants sampled

  38. Trees are harder to access Produce a lot more seed Makes sense for the collector Collectors do get more seed per plant

  39. Trees are harder to access Produce a lot more seed Makes sense for the collector Collectors do get more seed per plant

  40. Spatial context among and within populations • Reproductive biology • Diminishing returns of more seeds per plant Realism matters

  41. A given sampling protocol will capture different amounts of diversity for different species… Much of our current sampling is suboptimal

  42. What next?

  43. What next? • Other traits • Dominance, habit, density, successional stage… • any characteristic influencing spatial genetics • Recent history • population contraction, expansion (postglacial)

  44. What next? Plan collection for specific taxa Including those with some existing collection

  45. Fraxinus excelsior in the UK • 11% of area cover of deciduous trees • 14% of standing volume • 126 million trees

  46. Parameters of this model result in genetic differentiation that is observed in a real genetic study (FST etc.)

  47. First goal is estimate how much has been captured in the 57 accessions and few hundred thousand seed collected so far

  48. Greater emphasis here Or here Or here

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