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

Quantifying Phenotypic Variation in Tomato Introgression Lines through Local Persistent Homology

New and old ways of looking at shape: morphometric analysis of leavesDan ChitwoodDonald Danforth Plant Science CenterSeptember 3, 2016

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


There are many ways to measure shape:Homologous landmarks


There are many ways to measure shape:All methods are comprehensive,but theyre not equivalent

LandmarksElliptical Fourier DescriptorsChitwood & Sinha, 2016

GrapevineExamples of leaf morphometrics

Passiflora

Persistent homology

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 effects

Evolutionary vs. developmental pathsin the leaf morphospace

Developmental effects

Species can be predictedindependently from development

Development can be predictedindependently 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!


Passiflora

Persistent homology

Landmarks vs. Elliptical Fourier Descriptors


Landmarks vs. Elliptical Fourier Descriptors:Similar morphospaces




Landmarks vs. Elliptical Fourier Descriptors:Correlational matrix

Heteroblasty in PassifloraMetamorphosis

Heteroblastyin PassifloraMetamorphosis

Heteroblastyin PassifloraMetamorphosis

Heteroblasty in PassifloraMetamorphosis


Passiflora

Persistent homology

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

r

Persistence: track the evolution of features across scales 0-homology: connected components 1-homology: loops (holes)Verri et al. Biological Cybernetics, 1993Carlsson, Bulletin AMS, 2009Edelsbrunner et al., AMS, 2010

Persistent Homology, WHY? WHAT?

Sublevel Set Filtration:

Blue RedSuperlevel Set Filtration:

Red BlueA Persistent Homology Primer How to get a nest sequence of shapes

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

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 approximation

Elliptical Fourier Transformhttp://haitham.ece.illinois.edu

First harmonics5 harmonics10 harmonics20 harmonics

Euler characteristics = # connected component - # loopslevel

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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

Acknowledgments

FSUMio LabDonald Danforth Plant Science CenterTopp LabDonald Danforth Plant Science CenterChitwood Lab