discriminating shapes: on violins & the latent morphology of grape leaves
TRANSCRIPT
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Dan Chitwood
Donald DanforthPlant Science Center
Seminar at U.C. Davis
April 3, 2015
Discriminating shapes:
On violins and thelatent morphology of
grape leaves
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A morphometrics primer:
The evolution of violin shape
Leaves as composites of latentdevelopmental & evolutionary shapes
Revealing plant cryptotypes:
Defining meaningful phenotypes
among infinite traits
Outline
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How to quantify shape?An example, using violins
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Photos from auction:
>9,000 instruments
>400 violin makers
>400 years of history
Chitwood (2014) Imitation, genetic lineages, and time
influenced the morphological evolution of the violin. PLOS ONE
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How to measure shape:
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Shape = { xn, yn }
How to measure shape:Coordinates, landmarks, pseudo-landmarks
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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How to measure shape:Chain code
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![Page 72: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/72.jpg)
How to measure shape:Chain code
0
12
3
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56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2
![Page 73: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/73.jpg)
How to measure shape:Chain code
0
12
3
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56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2
![Page 74: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/74.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0
![Page 75: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/75.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0
![Page 76: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/76.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2
![Page 77: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/77.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2
![Page 78: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/78.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 2
![Page 79: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/79.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22
![Page 80: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/80.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2
![Page 81: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/81.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3
![Page 82: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/82.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2
![Page 83: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/83.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2
![Page 84: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/84.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2
![Page 85: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/85.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2
![Page 86: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/86.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2
![Page 87: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/87.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2
![Page 88: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/88.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 0
![Page 89: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/89.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02
![Page 90: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/90.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02 0
![Page 91: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/91.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02 0 1
![Page 92: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/92.jpg)
How to measure shape:Chain code
0
12
3
4
56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02 0 1 0
![Page 93: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/93.jpg)
How to measure shape:Chain code
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02 0 1 0
Shape ={ }
Chain code is lossless:
perfect reconstruction
from compressed data
![Page 94: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/94.jpg)
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Graphic: Christine Daniloff
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How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Graphic: Christine Daniloff Graphic: Cardiff University
Graphic: Workshop Mizzotti
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How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)
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How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)
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How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6 7 6 6 5 66 4 6 4 4 6 4 4 4 44 4 3 4 3 3 3 2 2 22 0 2 2 2 0 0 2 2 22 2 3 2 2 2 2 2 2 02 0 1 0
Shape ={ }
![Page 99: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/99.jpg)
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
a1, a2, a3 … anb1, b2, b3 … bnc1, c2, c3 … cnd1, d2, d3 … dn
Shape ={ }Harmonic coefficients:
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The morphological evolution of violins:
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The morphological evolution of violins:The effects of time, space, & people on violin shape
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The morphological evolution of violins:The effects of time, space, & people on violin shape
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The morphological evolution of violins:Linear Discriminant 1 is especially correlated with time
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The morphological evolution of violins:Why does shape correlate with time? Violin makers?
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The morphological evolution of violins:Why does shape correlate with time? Violin makers?
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The morphological evolution of violins:Innovators and copiers of shape
Unique
Copiers/copied
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The morphological evolution of violins:Does violin shape have a “genetic” basis?
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House Gagliano:Giuseppe (Joseph)
Gennaro (Januarius)NicolóFerdinando
**
*
*
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*
House Testore:Carlo Giuseppe
Carlo Antonio
*
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House Degani:Giulio
Eugenio
**
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House Guarneri:Giuseppe (del Gesú)
Giuseppe (filius Andrea)
Pietro (of Venice)
Pietro (of Mantua)
Andrea
*
**
*
*
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A morphometrics primer:
The evolution of violin shape
Leaves as composites of latentdevelopmental & evolutionary shapes
Revealing plant cryptotypes:
Defining meaningful phenotypes
among infinite traits
Outline
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Landmark-based Procrustes analysis:Superimposed homologous coordinates
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Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
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Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
Translate
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Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
Translate
Scale
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Landmark-based Procrustes analysis:Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)International Journal of Evol. Biol.
Translate
Scale
Rotate
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Species effects
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Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
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Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
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Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
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Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
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Chitwood and Sinha, 2015
Leaf number:The heteroblastic series
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Species, developmental stage,& leaf number effects
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Species, developmental stage,& leaf number effects
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Species, developmental stage,& leaf number effects
Shootbase
Shoottip
![Page 137: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/137.jpg)
Species, developmental stage,& leaf number effects
L1 L2
L1
L3 L4 L5 L6 L7 L8 L9 L10
LeafNumberL1 -> L10
Shootbase
Shoottip
![Page 138: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/138.jpg)
Species, developmental stage,& leaf number effects
S1S2S9S10 S3S4S5S6S7S8
L1 L2
L1
L3 L4 L5 L6 L7 L8 L9 L10
DevelopmentalStage
S1 -> S10
LeafNumberL1 -> L10
Shootbase
Shoottip
![Page 139: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/139.jpg)
Species, developmental stage,& leaf number effects
S1S2S9S10 S3S4S5S6S7S8
L1 L2
L1
L3 L4 L5 L6 L7 L8 L9 L10
DevelopmentalStage
S1 -> S10
LeafNumberL1 -> L10
Shootbase
Shoottip
![Page 140: Discriminating shapes: on violins & the latent morphology of grape leaves](https://reader034.vdocument.in/reader034/viewer/2022042716/55aac9491a28ab721b8b45df/html5/thumbnails/140.jpg)
Species, developmental stage,& leaf number effects
Shootbase
Shoottip
Leaf number
Developmental stage
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Evolutionary vs. developmental pathsin the Vitis leaf morphospace
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Evolutionary vs. developmental pathsin the Vitis leaf morphospace
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Evolutionary vs. developmental pathsin the Vitis leaf morphospace
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Species identity can be predictedindependently from development
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Species identity can be predictedindependently from development
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Developmental stage can be predictedindependently from species identity
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Leaf number can be predictedindependently from species identity
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Predicted leaf number correlateswith first appearance of tendrils
S1S2S9S10 S3S4S5S6S7S8
L1 L2
L1
L3 L4 L5 L6 L7 L8 L9 L10
DevelopmentalStage
S1 -> S10
LeafNumberL1 -> L10
Shootbase
Shoottip
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Predicted leaf number correlateswith first appearance of tendrils
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Predicted leaf number correlateswith first appearance of tendrils
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Developmental stage and leaf number areInversely related, but distinct
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The morphospace ofwild & domesticated Vitis
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The morphospace ofwild & domesticated Vitis
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Changes in developmental timingin domesticated grape
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Changes in developmental timingin domesticated grape
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Changes in developmental timingin domesticated grape
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Changes in developmental timingin domesticated grape
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Changes in developmental timingin domesticated grape
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A morphometrics primer:
The evolution of violin shape
Leaves as composites of latentdevelopmental & evolutionary shapes
Revealing plant cryptotypes:
Defining meaningful phenotypes
among infinite traits
Outline
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Chitwood and Topp, Curr. Opin. Plant. Biol., 2015
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St. Louis UniversityLaura KleinAllison Miller
USDA Geneva, NYJason LondoBeth TakacsBruce Reisch
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Thanks!
Margaret FrankViktoriya Coneva
Donald DanforthPlant Science Center