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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
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
How to quantify shape?An example, using violins
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
How to measure shape:
Shape = { xn, yn }
How to measure shape:Coordinates, landmarks, pseudo-landmarks
How to measure shape:Chain code
How to measure shape:Chain code
How to measure shape:Chain code
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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0
How to measure shape:Chain code
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0 0
How to measure shape:Chain code
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0 0 0
How to measure shape:Chain code
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0 0 0 7
How to measure shape:Chain code
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0 0 0 7 0
How to measure shape:Chain code
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0 0 0 7 0 6
How to measure shape:Chain code
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0 0 0 7 0 6 0
How to measure shape:Chain code
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0 0 0 7 0 6 0 6
How to measure shape:Chain code
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0 0 0 7 0 6 0 6 6
How to measure shape:Chain code
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0 0 0 7 0 6 0 6 6 6
How to measure shape:Chain code
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0 0 0 7 0 6 0 6 6 66
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6 6
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6 6 4
How to measure shape:Chain code
0
12
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56
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6
How to measure shape:Chain code
0
12
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56
7
0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6
How to measure shape:Chain code
0
12
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56
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6
How to measure shape:Chain code
0
12
3
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56
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6
How to measure shape:Chain code
0
12
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 6
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0
How to measure shape:Chain code
0
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6
How to measure shape:Chain code
0
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3
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6
How to measure shape:Chain code
0
12
3
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0 0 0 7 0 6 0 6 6 66 6 6 6 4 6 6 6 6 60 0 6 6 6
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
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
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
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
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 6
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
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
How to measure shape:Chain code
0
12
3
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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
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
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
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
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
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
How to measure shape:Chain code
0
12
3
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56
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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
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 4
How to measure shape:Chain code
0
12
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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
How to measure shape:Chain code
0
12
3
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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
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
How to measure shape:Chain code
0
12
3
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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
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
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
How to measure shape:Chain code
0
12
3
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56
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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
How to measure shape:Chain code
0
12
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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
How to measure shape:Chain code
0
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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
How to measure shape:Chain code
0
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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 2
How to measure shape:Chain code
0
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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
How to measure shape:Chain code
0
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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
How to measure shape:Chain code
0
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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
How to measure shape:Chain code
0
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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
How to measure shape:Chain code
0
12
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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
How to measure shape:Chain code
0
12
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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
How to measure shape:Chain code
0
12
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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 0 0
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 0 0 2
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 0 0 2 2
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 0 0 2 2 2
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 0 0 2 2 22
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 0 0 2 2 22 2
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 0 0 2 2 22 2 3
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 0 0 2 2 22 2 3 2
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 0 0 2 2 22 2 3 2 2
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
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
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 0 0 2 2 22 2 3 2 2 2 2 2
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 0 0 2 2 22 2 3 2 2 2 2 2 2
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
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
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
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
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
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
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Graphic: Christine Daniloff
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Graphic: Christine Daniloff Graphic: Cardiff University
Graphic: Workshop Mizzotti
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)
How to measure shape:Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)
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 ={ }
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:
The morphological evolution of violins:
The morphological evolution of violins:The effects of time, space, & people on violin shape
The morphological evolution of violins:The effects of time, space, & people on violin shape
The morphological evolution of violins:Linear Discriminant 1 is especially correlated with time
The morphological evolution of violins:Why does shape correlate with time? Violin makers?
The morphological evolution of violins:Why does shape correlate with time? Violin makers?
The morphological evolution of violins:Innovators and copiers of shape
Unique
Copiers/copied
The morphological evolution of violins:Does violin shape have a “genetic” basis?
House Gagliano:Giuseppe (Joseph)
Gennaro (Januarius)NicolóFerdinando
**
*
*
*
House Testore:Carlo Giuseppe
Carlo Antonio
*
House Degani:Giulio
Eugenio
**
House Guarneri:Giuseppe (del Gesú)
Giuseppe (filius Andrea)
Pietro (of Venice)
Pietro (of Mantua)
Andrea
*
**
*
*
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
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
Species effects
Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
Stephen Hales, Vegetable staticks, 1727
Developmental stage:Allometric expansion
Chitwood and Sinha, 2015
Leaf number:The heteroblastic series
Species, developmental stage,& leaf number effects
Species, developmental stage,& leaf number effects
Species, developmental stage,& leaf number effects
Shootbase
Shoottip
Species, developmental stage,& leaf number effects
L1 L2
L1
L3 L4 L5 L6 L7 L8 L9 L10
LeafNumberL1 -> L10
Shootbase
Shoottip
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
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
Species, developmental stage,& leaf number effects
Shootbase
Shoottip
Leaf number
Developmental stage
Evolutionary vs. developmental pathsin the Vitis leaf morphospace
Evolutionary vs. developmental pathsin the Vitis leaf morphospace
Evolutionary vs. developmental pathsin the Vitis leaf morphospace
Species identity can be predictedindependently from development
Species identity can be predictedindependently from development
Developmental stage can be predictedindependently from species identity
Leaf number can be predictedindependently from species identity
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
Predicted leaf number correlateswith first appearance of tendrils
Predicted leaf number correlateswith first appearance of tendrils
Developmental stage and leaf number areInversely related, but distinct
The morphospace ofwild & domesticated Vitis
The morphospace ofwild & domesticated Vitis
Changes in developmental timingin domesticated grape
Changes in developmental timingin domesticated grape
Changes in developmental timingin domesticated grape
Changes in developmental timingin domesticated grape
Changes in developmental timingin domesticated grape
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
Chitwood and Topp, Curr. Opin. Plant. Biol., 2015
St. Louis UniversityLaura KleinAllison Miller
USDA Geneva, NYJason LondoBeth TakacsBruce Reisch
Thanks!
Margaret FrankViktoriya Coneva
Donald DanforthPlant Science Center
