turning a new leaf with persistent homology: old and new ways of analyzing leaf shape and the...
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Quantifying Phenotypic Variation in Tomato Introgression Lines through Local Persistent Homology
Turning a new leaf with persistent homology:old and new waysof analyzing leaf shape and the topology of plantsDan ChitwoodDonald Danforth Plant Science CenterNovember 4, 2016
Does leaf shape contain information?
If so, what do leaves tell us and how do we measure leaf shape?
A primer on leaf shape and past morphometric methods
Does leaf shape contain information?
If so, what do leaves tell us and how do we measure leaf shape?
A primer on leaf shape and past morphometric methods
Does leaf shape contain information?
If so, what do leaves tell us and how do we measure leaf shape?
A primer on leaf shape and past morphometric methods
Chitwood & Sinha, 2016Leaf shape varies byevolution, genetics, development andby present climates & ancient climates
Leaf shape varies byevolution, genetics, development andby present climates & ancient climatesChitwood & Sinha, 2016
Paleomap, scotese.com
Leaf shape varies byevolution, genetics, development andby present climates & ancient climatesChitwood & Sinha, 2016
There are many ways to measure shape:Pseudo-landmarks
Chitwood & Sinha, 2016
There are many ways to measure shape:Elliptical Fourier Descriptors
Chitwood & Sinha, 2016
There are many ways to measure shape:Homologous landmarks
Chitwood & Sinha, 2016
There are many ways to measure shape:All methods are comprehensive,but theyre not equivalent
LandmarksElliptical Fourier DescriptorsChitwood & Sinha, 2016
Grapevine: discriminatinggenetic, developmental, and environmental shapesExamples of old and new morphometric methods for plants
Persistent homology: a topology based morphometric methodLeaf morphospaces & a universal theory of plant morphology
Landmark-based Procrustes analysis:Superimposed homologous coordinates
Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
Translate
Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
TranslateScale
Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
TranslateScaleRotate
Homologous landmarks:On every grape leaf
Homologous landmarks:On every grape leaf
Homologous landmarks:On every grape leaf
Homologous landmarks:On every grape leaf
Homologous landmarks:On every grape leaf
Homologous landmarks:On every grape leaf
Homologous landmarks:Species differences
ShootbaseShoottipLeaf numberDevelopmental stageUnequal expansionDifferent leaf typesHomologous landmarks:Species differences manifest in adevelopmental context
ShootbaseShoottipLeaf numberDevelopmental stageUnequal expansionDifferent leaf types
Homologous landmarks:Species differences manifest in adevelopmental context
ShootbaseShoottipLeaf numberDevelopmental stageUnequal expansionDifferent leaf typesHomologous landmarks:Species differences manifest in adevelopmental context
Evolutionary vs. developmental pathsin the leaf morphospace
Species effectsChitwood et al., New Phytol, 2016
Evolutionary vs. developmental pathsin the leaf morphospace
Developmental effectsChitwood et al., New Phytol, 2016
Species can be predictedindependently from development
Chitwood et al., New Phytol, 2016
Development can be predictedindependently from species
Chitwood et al., New Phytol, 2016
Vein landmarks more sensitive to development
Chitwood et al., Plant Physiol, 2016
Vein landmarks more sensitive to development
Chitwood et al., Plant Physiol, 2016
Discriminating leaves from different years:Same vines, same developmental stagesChitwood et al., Plant Physiol, 2016
Discriminating leaves from different years:Same vines, same developmental stagesChitwood et al., Plant Physiol, 2016
Climate interannual variability:2014/15 was colder & drier than 2012/13
Chitwood et al., Plant Physiol, 2016
Climate interannual variability:2014/15 was colder & drier than 2012/13Chitwood et al., Plant Physiol, 2016
Climate interannual variability:Plasticity and evolutionary changes in leaf shape go in the same direction?
Chitwood et al., Plant Physiol, 2016
Measuring future climates:To California, wine grapes, and rootstocks!
The Vitis Underground:Adapting perennial crops for climate change:Graft transmissible effects of rootstocks on grapevine shoots
Allison Miller, Saint Louis UniversityJason Londo, USDA-ARS, Geneva, NYAnne Fennel, South Dakota State UniversityMisha Kwasinewski, MizzouLaszlo Kovacs, Missouri State UniversityPeter Cousins, E&J Gallo Winery
Grapevine: discriminatinggenetic, developmental, and environmental shapesExamples of old and new morphometric methods for plants
Persistent homology: a topology based morphometric methodLeaf morphospaces & a universal theory of plant morphology
These slides made by:Mao LiDonald Danforth Plant Science CenterChitwood Lab & Topp LabPersistent homology: a tool to universally measureplant morphologies across organs and scales
These slides made by:Mao LiDonald Danforth Plant Science CenterChitwood Lab & Topp Lab
Persistent homology: a tool to universally measureplant morphologies across organs and scales
These slides made by:Mao LiDonald Danforth Plant Science CenterChitwood Lab & Topp Lab
Persistent homology: a tool to universally measureplant morphologies across organs and scales
These slides made by:Mao LiDonald Danforth Plant Science CenterChitwood Lab & Topp Lab
Persistent homology: a tool to universally measureplant morphologies across organs and scales
Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?How many groups are there? 3? 10? 1?
rVerri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?
How many groups are there? 3? 10? 1?
r
Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?
How many groups are there? 3? 10? 1?
r
Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?
How many groups are there? 3? 10? 1?
Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?
How many groups are there? 3? 10? 1?It depends on scale!
Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010Persistent Homology, WHY? WHAT?
Another example
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Sublevel Set Filtration:
Blue RedA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
Superlevel Set Filtration:
Red BlueA Persistent Homology Primer How to get a nest sequence of shapes
rPersistent Homology, HOW?
Persistence Barcode
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rPersistent Homology, HOW?
Persistence Barcode
66
rPersistent Homology, HOW?
Persistence Barcode
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rPersistent Homology, HOW?
Persistence Barcode
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rPersistent Homology, HOW?
Persistence Barcode
69
rPersistent Homology, HOW?
Persistence Barcode
# connected componentsr
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rPersistent Homology, HOW?
Persistence Barcode
# connected componentsrNow, apply!
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tomato introgression linesEshed et al. , Genetic, 1999Chitwood et al., The Plant Cell 2013
(domesticated, cv. M82)(wild)
IL4_3Significant difference is caused by the gene in the small regionThe difference is usually subtle
MeasureLeaf Shape
16 annulus (rings)density estimatorA tool: Local and smoothside view
Blind to size, position, and orientation
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
A robust metric between barcodes: bottleneck distanceplane height(level value)
connected component
CV1 Our approach integrates very different morphological characteristics into a single descriptor.Leaf Shape QTLStatistical techniques: Multidimensional scaling (MDS, reduce dimension) Canonical variate analysis (CVA, feature that most distinguish groups)
ResultLeaf Shape QTL
Measure Serrations
Coarse approximationElliptical Fourier Transformhttp://haitham.ece.illinois.edu
First harmonics5 harmonics10 harmonics20 harmonics
Euler characteristics = # connected component - # loopslevel
90
Euler characteristics = # connected component - # loopslevel
91
Leaf Serrations QTL
level
ResultLeaf Serrations QTL
MeasureRoot Architecture
Root Architecture QTL
ResultRoot Architecture QTL
Persistent homology detects concerted changes in shoot and root architecture
Leaf Shape Root Architecture Serrations
Persistent homology detects concerted changes in shoot and root architecturemedian values plots
Persistent Homologyrobust 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
Grapevine: discriminatinggenetic, developmental, and environmental shapesExamples of old and new morphometric methods for plants
Persistent homology: a topology based morphometric methodLeaf morphospaces & a universal theory of plant morphology
2,3929,6194,76534,6372,88517,8598655,7333,30186684,8595,8142,422
176,017 leaves!Demarcating aleaf morphospace
2,3929,6194,76534,6372,88517,8598655,7333,30186684,8595,8142,422
176,017 leaves!Demarcating aleaf morphospace
Discriminating leaves:Across flowering plant families
Discriminating leaves:Across sites around the world
Transect and Leafsnap dataTransect dataDana Royer, Wesleyan UniversityDaniel Peppe, Baylor UniversityPeter Wilf, Penn StateHuff PM, Wilf P, Azumah EJ. 2003. Digital future for paleoclimate estimation from fossil leaves? Preliminary results. Palaios 18: 266-274.
Royer DL, Wilf P, Janesko DA, Kowalski EA, Dilcher DL. 2005. Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil record. American Journal of Botany 92: 1141-1151.
Peppe DJ, Royer DL, Cariglino B, Oliver SY, Newman S, Leight E, Enikolopov G, Fernandez-Burgos M, Herrera F, Adams JM, Correa E, Currano ED, Erickson JM, Hinojosa LF, Iglesias A, Jaramillo CA, Johnson KR, Jordan GJ, Kraft N, Lovelock EC, Lusk CH, Niinemets U, Penuelas J, Rapson G, Wing SL, Wright IJ. 2011. Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applications. New Phytologist, 190: 724-739. Leafsnap: A Computer Vision System for Automatic Plant Species Identification
Neeraj Kumar, Peter N. Belhumeur, Arijit Biswas, David W. Jacobs, W. John Kress, Ida C. Lopez, Joo V. B. Soares
Proceedings of the 12th European Conference on Computer Vision (ECCV), October 2012
The leaf morphospace groupAnalysisMao Li, Danforth Center
IsolationRebekah Mohn, Miami University
PotatoShelley Jansky, USDA, Wisconsin-MadisonDiego Fajardo, National Center to Genome Resources
PepperAllen van Deynze, UC DavisTheresa Hill, UC Davis
TomatoViktoriya Coneva, Danforth CenterMargaret Frank, Danforth CenterChris Topp, Danforth Center
GrapeAllison Miller, Saint Louis UniversityJason Londo, USDA/ARS, Geneva, NYLaura Klein, Saint Louis University
PassifloraWagner Otoni, Universidade Federal de VicosaArabidopsisRuthie Angelovici, University of Missouri, ColumbiaBatushansky Albert, University of Missouri, ColumbiaClement Bagaza, University of Missouri, ColumbiaEdmond Riffer, University of Missouri, ColumbiaBraden Zink, University of Missouri, Columbia
BrassicaJ. Chris Pires, University of Missouri, ColumbiaHong An, University of Missouri, ColumbiaSarah Gebken, University of Missouri, Columbia
CottonVasu Kuraparthy, North Carolina State University
ViburnumErika Edwards, Brown UniversityElizabeth Spriggs, Yale UniversityMichael Donoghue, Yale UniversitySam Schmerler, American Museum of Natural History
GrassesLynn Clark, Iowa StateTimothy Gallaher, Iowa StatePhillip Klahs, Iowa State
A universal theory of plant morphology:Persistent homology and plant topology
Chris Topp, Keith Duncan, Ni Jiang, Mao Li
A universal theory of plant morphology:Persistent homology and plant topologyChris Topp, Keith Duncan, Ni Jiang, Mao Li
Chris Topp, Keith Duncan, Ni Jiang, Mao LiA universal theory of plant morphology:Persistent homology and plant topology
Chris Topp, Keith Duncan, Ni Jiang, Mao LiA universal theory of plant morphology:Persistent homology and plant topology
Acknowledgments
FSUMio LabDonald Danforth Plant Science CenterTopp LabDonald Danforth Plant Science CenterChitwood Lab
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