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New and old ways of looking at shape: morphometric analysis of leaves
- 1. New and old ways of looking at shape: morphometric analysis of leaves Dan Chitwood Donald Danforth Plant Science Center September 3, 2016
- 2. Chitwood & Sinha, 2016 Leaf shape varies by evolution, genetics, development and by present climates & ancient climates
- 3. Leaf shape varies by evolution, genetics, development and by present climates & ancient climates Chitwood & Sinha, 2016
- 4. Paleomap, scotese.com Leaf shape varies by evolution, genetics, development and by present climates & ancient climates Chitwood & Sinha, 2016
- 5. There are many ways to measure shape: Pseudo-landmarks Chitwood & Sinha, 2016
- 6. There are many ways to measure shape: Elliptical Fourier Descriptors Chitwood & Sinha, 2016
- 7. There are many ways to measure shape: Homologous landmarks Chitwood & Sinha, 2016
- 8. There are many ways to measure shape: All methods are comprehensive, but they’re not equivalent Landmarks Elliptical Fourier Descriptors Chitwood & Sinha, 2016
- 9. Grapevine Examples of leaf morphometrics Passiflora Persistent homology
- 10. Homologous landmarks: On every grape leaf
- 11. Homologous landmarks: On every grape leaf
- 12. Homologous landmarks: On every grape leaf
- 13. Homologous landmarks: On every grape leaf
- 14. Homologous landmarks: On every grape leaf
- 15. Homologous landmarks: On every grape leaf
- 17. Shoot base Shoot tip Leaf number Developmental stage Unequal expansion Different leaf types Homologous landmarks: Species differences manifest in a developmental context
- 18. Shoot base Shoot tip Leaf number Developmental stage Unequal expansion Different leaf types Homologous landmarks: Species differences manifest in a developmental context
- 19. Shoot base Shoot tip Leaf number Developmental stage Unequal expansion Different leaf types Homologous landmarks: Species differences manifest in a developmental context
- 20. Evolutionary vs. developmental paths in the leaf morphospace Species effects
- 21. Evolutionary vs. developmental paths in the leaf morphospace Developmental effects
- 22. Species can be predicted independently from development
- 23. Development can be predicted independently from species
- 24. Vein landmarks more sensitive to development
- 25. Vein landmarks more sensitive to development
- 26. Discriminating leaves from different years: Same vines, same developmental stages
- 27. Discriminating leaves from different years: Same vines, same developmental stages
- 28. Climate interannual variability: 2014/15 was colder & drier than 2012/13
- 29. Climate interannual variability: 2014/15 was colder & drier than 2012/13
- 30. Climate interannual variability: Plasticity and evolutionary changes in leaf shape go in the same direction?
- 31. Measuring future climates: To California, wine grapes, and rootstocks!
- 32. Grapevine Examples of leaf morphometrics Passiflora Persistent homology
- 34. Landmarks vs. Elliptical Fourier Descriptors
- 35. Landmarks vs. Elliptical Fourier Descriptors
- 36. Landmarks vs. Elliptical Fourier Descriptors: Similar morphospaces
- 37. Landmarks vs. Elliptical Fourier Descriptors: Similar morphospaces
- 38. Landmarks vs. Elliptical Fourier Descriptors: Similar morphospaces
- 39. Landmarks vs. Elliptical Fourier Descriptors
- 41. Landmarks vs. Elliptical Fourier Descriptors: Correlational matrix
- 46. Grapevine Examples of leaf morphometrics Passiflora Persistent homology
- 47. These slides made by: Mao Li Donald Danforth Plant Science Center Chitwood Lab & Topp Lab Persistent homology: a tool to universally measure plant morphologies across organs and scales
- 48. r • Persistence: track the evolution of features across scales • 0-homology: connected components • 1-homology: loops (holes) Verri et al. Biological Cybernetics, 1993 Carlsson, Bulletin AMS, 2009 Edelsbrunner et al., AMS, 2010 Persistent Homology, WHY? WHAT?
- 49. Sublevel Set Filtration: Blue Red Superlevel Set Filtration: Red Blue A Persistent Homology Primer How to get a nest sequence of shapes
- 50. r Persistent Homology, HOW? Persistence Barcode #connectedcomponents r Now, apply!
- 51. tomato introgression lines Eshed et al. , Genetic, 1999 Chitwood et al., The Plant Cell 2013 (domesticated, cv. M82) (wild) IL4_3 • Significant difference is caused by the gene in the small region • The difference is usually subtle
- 53. 16 annulus (rings) density estimator A tool: Local and smooth side view Blind to size, position, and orientation
- 54. • A robust metric between barcodes: bottleneck distance plane height (level value) connectedcomponent
- 55. CV1 • Our approach integrates very different morphological characteristics into a single descriptor. Leaf Shape QTL Statistical techniques: Multidimensional scaling (MDS, reduce dimension) Canonical variate analysis (CVA, feature that most distinguish groups)
- 58. Coarse approximation Elliptical Fourier Transform http://haitham.ece.illinois.edu First harmonics 5 harmonics 10 harmonics 20 harmonics
- 59. Euler characteristics = # connected component - # loops level
- 66. Persistent homology detects concerted changes in shoot and root architecture Leaf Shape Root Architecture Serrations
- 67. Persistent homology detects concerted changes in shoot and root architecture median values plots
- 68. Persistent Homology • robust to noise • invariant with respect to orientation • capable of application across diverse scales • compatible with diverse functions to quantify disparate plant morphologies, architectures, and textures
- 69. Acknowledgments FSU Mio Lab Donald Danforth Plant Science Center Topp Lab Donald Danforth Plant Science Center Chitwood Lab