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New and old ways of
looking at shape:
morphometric analysis
of leaves
Dan Chitwood
Donald Danforth Plant Science Center
October 11, 2016
Chitwood & Sinha, 2016
Leaf shape varies by
evolution, genetics, development and
by present climates & ancient climates
Leaf shape varies by
evolution, genetics, development and
by present climates & ancient climates
Chitwood & Sinha, 2016
Paleomap, scotese.com
Leaf shape varies by
evolution, genetics, development and
by present climates & ancient climates
Chitwood & 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 they’re not equivalent
Landmarks Elliptical Fourier Descriptors
Chitwood & Sinha, 2016
Grapevine
Examples of leaf morphometrics
Passiflora
Persistent homology
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.
Translate
Scale
Landmark-based Procrustes analysis:
Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)
International Journal of Evol. Biol.
Translate
Scale
Rotate
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
Shoot
base
Shoot
tip
Leaf number
Developmental stage
Unequal expansion
Different leaf types
Homologous landmarks:
Species differences manifest in a
developmental context
Shoot
base
Shoot
tip
Leaf number
Developmental stage
Unequal expansion
Different leaf types
Homologous landmarks:
Species differences manifest in a
developmental context
Shoot
base
Shoot
tip
Leaf number
Developmental stage
Unequal expansion
Different leaf types
Homologous landmarks:
Species differences manifest in a
developmental context
Evolutionary vs. developmental paths
in the leaf morphospace
Species effects
Evolutionary vs. developmental paths
in the leaf morphospace
Developmental effects
Species can be predicted
independently from development
Development can be predicted
independently from species
Vein landmarks more sensitive to development
Vein landmarks more sensitive to development
Discriminating leaves from different years:
Same vines, same developmental stages
Discriminating leaves from different years:
Same vines, same developmental stages
Climate interannual variability:
2014/15 was colder & drier than 2012/13
Climate interannual variability:
2014/15 was colder & drier than 2012/13
Climate interannual variability:
Plasticity and evolutionary changes in leaf shape
go in the same direction?
Measuring future climates:
To California, wine grapes, and rootstocks!
Grapevine
Examples of leaf morphometrics
Passiflora
Persistent homology
Landmarks vs. Elliptical Fourier Descriptors
Landmarks vs. Elliptical Fourier Descriptors
Landmarks vs. Elliptical Fourier Descriptors:
Similar morphospaces
Landmarks vs. Elliptical Fourier Descriptors:
Similar morphospaces
Landmarks vs. Elliptical Fourier Descriptors:
Similar morphospaces
Landmarks vs. Elliptical Fourier Descriptors
Landmarks vs. Elliptical Fourier Descriptors:
Correlational matrix
Heteroblasty in Passiflora
Metamorphosis
Heteroblasty
in Passiflora
Metamorphosis
Heteroblasty
in Passiflora
Metamorphosis
Heteroblasty in Passiflora
Metamorphosis
Grapevine
Examples of leaf morphometrics
Passiflora
Persistent homology
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
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?
Sublevel Set Filtration:
Blue Red
Superlevel Set Filtration:
Red Blue
A Persistent Homology Primer
How to get a nest sequence of shapes
r
Persistent Homology, HOW?
Persistence Barcode
#connectedcomponents r
Now, apply!
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
16 annulus (rings) density estimator
A tool: Local and smooth side view
Blind to size, position, and orientation
• A robust metric between barcodes: bottleneck distance
plane height
(level value)
connectedcomponent
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)
Result
Leaf Shape QTL
Coarse approximation
Elliptical Fourier Transform
http://haitham.ece.illinois.edu
First harmonics 5 harmonics 10 harmonics 20 harmonics
Euler characteristics = # connected component - # loops
level
Leaf Serrations QTL
level
Result
Leaf Serrations QTL
Root Architecture QTL
Result
Root 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 architecture
median values plots
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
Acknowledgments
FSU
Mio Lab
Donald Danforth Plant Science Center
Topp Lab
Donald Danforth Plant
Science Center
Chitwood Lab

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New and old ways of looking at shape: morphometric analysis of leaves