Seminar given on 1/28/15 at the University of Illinois, Urbana-Champaign. Introduces morphometric concepts such as landmark-based analyses and Elliptical Fourier Descriptors using violin evolution as an example. Then, the genetic, ontogenetic, and heteroblastic context of wild Vitis spp. leaves is discussed, and how these factors distinctly comprise the shape of leaves. Evolution through heterochronic mechanisms is discussed.

1. Dan Chitwood
Donald Danforth
Plant Science Center
January 28, 2015
A spectrum of shapes:
Distinct genetic,
developmental, and
environmental effects
comprise leaf morphology

2. But first:
How to quantify shape?
An example, using violins

8. 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

11. How to measure shape:

12. Shape = { xn, yn }
How to measure shape:
Coordinates, landmarks, pseudo-landmarks

13. How to measure shape:
Chain code

14. How to measure shape:
Chain code

15. How to measure shape:
Chain code

16. How to measure shape:
Chain code
0
1
2
3
4
5
6
7

17. How to measure shape:
Chain code
0
1
2
3
4
5
6
7

18. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0

19. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0

20. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0

21. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7

22. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0

23. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6

24. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0

25. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6

26. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6

27. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6

28. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6

29. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6

30. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6

31. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6

32. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4

33. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6

34. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6

35. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6

36. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6

37. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6

38. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0

39. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0

40. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6

41. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6

42. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6

43. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7

44. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6

45. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6

46. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5

47. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6

48. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6

49. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4

50. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6

51. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4

52. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4

53. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6

54. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4

55. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4

56. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4

57. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4

58. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4

59. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4

60. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3

61. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4

62. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3

63. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3

64. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3

65. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2

66. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2

67. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2

68. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2

69. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0

70. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2

71. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2

72. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2

73. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0

74. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0

75. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2

76. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2

77. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2

78. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2

79. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2

80. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3

81. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2

82. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2

83. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2

84. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2

85. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2

86. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2

87. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0

88. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2

89. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2 0

90. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2 0 1

91. How to measure shape:
Chain code
0
1
2
3
4
5
6
7
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2 0 1 0

92. How to measure shape:
Chain code
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2 0 1 0
Shape =
{ }
Chain code is lossless:
perfect reconstruction
from compressed data

93. How to measure shape:
Chain code + Fourier = Elliptical Fourier Descriptors
Fourier Transform:
thefullwiki.org

94. How to measure shape:
Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)

95. How to measure shape:
Chain code + Fourier = Elliptical Fourier Descriptors
Kuhl and Giardina Computer Graphics & Image Processing (1982)Kuhl and Giardina Computer Graphics & Image Processing (1982)

96. How to measure shape:
Chain code + Fourier = Elliptical Fourier Descriptors
0 0 0 7 0 6 0 6 6 6
6 6 6 6 4 6 6 6 6 6
0 0 6 6 6 7 6 6 5 6
6 4 6 4 4 6 4 4 4 4
4 4 3 4 3 3 3 2 2 2
2 0 2 2 2 0 0 2 2 2
2 2 3 2 2 2 2 2 2 0
2 0 1 0
Shape =
{ }

97. How to measure shape:
Chain code + Fourier = Elliptical Fourier Descriptors
a1, a2, a3 … an
b1, b2, b3 … bn
c1, c2, c3 … cn
d1, d2, d3 … dn
Shape =
{ }
Harmonic coefficients:

98. How to measure shape:
Elliptical Fourier Descriptors approximate contours
-1.0 -0.5 0.0 0.5 1.0
-1.0
-0.5
0.0
0.5
1.0
z4941_1
# harmonics
2
4
8
16
32
64

99. How to measure shape:
Elliptical Fourier Descriptors approximate contours
Deviations along the outline
Points sampled along the outline
Deviation(in%ofthecentroidsize)
30 60 90 120
0.050.100.150.200.25 # harmonics
2
4
8
16
32
64

100. The morphological evolution of violins:

101. The morphological evolution of violins:
Predecessors and relatives of the violin

102. The morphological evolution of violins:
Predecessors and relatives of the violin

103. The morphological evolution of violins:
Morphospace of violin and relatives

104. The morphological evolution of violins:
Morphospace of violin and relatives

105. The morphological evolution of violins:
Discriminating violins from violas, cellos, basses

106. The morphological evolution of violins:
Discriminating violins from violas, cellos, basses

107. The morphological evolution of violins:
Discriminating violins from violas, cellos, basses

108. The morphological evolution of violins:
Discriminating violins from violas, cellos, basses

109. The morphological evolution of violins:
Shape attributes defining different violin family types

110. The morphological evolution of violins:
The effects of time, space, & people on violin shape

111. The morphological evolution of violins:
The effects of time, space, & people on violin shape

113. The morphological evolution of violins:
Linear Discriminant 1 is especially correlated with time

114. The morphological evolution of violins:
Why does shape correlate with time? Violin makers?

115. The morphological evolution of violins:
Why does shape correlate with time? Violin makers?

116. The morphological evolution of violins:
Innovators and copiers of shape
Unique
Copiers/
copied

117. The morphological evolution of violins:
Does violin shape have a “genetic” basis?

119. House Gagliano:
Giuseppe (Joseph)
Gennaro (Januarius)
Nicoló
Ferdinando
**
*
*

120. *
House Testore:
Carlo Giuseppe
Carlo Antonio
*

121. House Degani:
Giulio
Eugenio
**

122. House Guarneri:
Giuseppe (del Gesú)
Giuseppe (filius Andrea)
Pietro (of Venice)
Pietro (of Mantua)
Andrea
*
*
*
*
*

123. The morphological evolution of violins:
Does violin shape have a “genetic” basis?

124. The morphological evolution of violins:
Four distinct morphs comprise violin shape

126. A modern ampelography:
Chitwood et al. (2014) Plant Physiology

127. A modern ampelography:
A genetic basis for leaf shape and
venation patterning in grape
Chitwood et al. (2014) Plant Physiology

133. 1,221 V. vinifera accessions
2,385 individuals
9,486 leaves
~7-8 leaves per accession

134. Pierre Galet (1952), Précis d’Ampélographie Pratique
Ampelography (“vine” + “writing”):
Identification of grapevines by phenotypic features

135. Elliptical Fourier Descriptors
of Vitis vinifera leaves
Chitwood et al. (2014) Plant Physiology

136. Landmark-based Procrustes analysis:
Superimposed homologous coordinates

137. Landmark-based Procrustes analysis:
Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)
International Journal of Evol. Biol.

138. Landmark-based Procrustes analysis:
Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)
International Journal of Evol. Biol.
Translate

139. Landmark-based Procrustes analysis:
Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)
International Journal of Evol. Biol.
Translate
Scale

140. Landmark-based Procrustes analysis:
Superimposed homologous coordinates
Kerschbaumer and Sturmbauer (2011)
International Journal of Evol. Biol.
Translate
Scale
Rotate

141. Outer analysis
Chitwood et al. (2014) Plant Physiology

142. Outer analysis
Inner analysis

143. Landmark-based Procrustes analysis
of Vitis vinifera leaves
Chitwood et al. (2014) Plant Physiology

144. Landmark-based Procrustes analysis
of Vitis vinifera leaves
Chitwood et al. (2014) Plant Physiology

145. The effects of biogeography and population structure
on grape leaf morphology

146. Genome wide association study
on grape leaf morphology
Chitwood et al. (2014) Plant Physiology

147. There is more underlying phenotype
than just genetics . . .

148. Within the shape of every leaf
is a spectrum of distinct shape attributes
Sure, leaf shape varies between
genetically different species . . .
. . . but within a
developmental
context of
ontogeny and the
heteroblastic
series.

149. Leaves can vary genetically,
regardless of context between species
V. riparia V. labrusca
V. cinerea V. rupestris

150. Stephen Hales, Vegetable staticks, 1727
Leaves can vary ontogenetically,
as a developmental progression of plastochron stages

151. Stephen Hales, Vegetable staticks, 1727
Leaves can vary ontogenetically,
as a developmental progression of plastochron stages

152. Stephen Hales, Vegetable staticks, 1727
Leaves can vary ontogenetically,
as a developmental progression of plastochron stages

153. Leaves can vary ontogenetically,
as a developmental progression of plastochron stages
V. riparia V. labrusca
V. cinerea V. rupestris
Average shape
of leaves from
each plastochron
1
2
3
4
5
6
7
8
9
10

154. Leaves can vary heteroblastically,
changes in the shape of leaves from successive nodes
Cynthia Jones, Amer. J. Botany (1995)

155. Careful!
Ontogeny (plastochron) is distinct from
Heteroblasty (leaf number) and
each runs contrary to the other
Cynthia Jones, Amer. J. Botany (1995)

156. Careful!
Ontogeny (plastochron) is distinct from
Heteroblasty (leaf number) and
each runs contrary to the other
Cynthia Jones, Amer. J. Botany (1995)
Ontogeny
P1*P2P3P4P5P6P7P8P9P10P11P12P13P14P15P16
*not actual P1

157. Careful!
Ontogeny (plastochron) is distinct from
Heteroblasty (leaf number) and
each runs contrary to the other
Cynthia Jones, Amer. J. Botany (1995)
Ontogeny
P1*P2P3P4P5P6P7P8P9P10P11P12P13P14P15P16
Heteroblasty
L16L15L14L13L12L11L10L9L8L7L6L5L4L3L2L1
*not actual P1

158. Heteroblasty and ontogeny are partially confounded
in terminally harvested shoots

159. Heteroblasty and ontogeny are partially confounded
in terminally harvested shoots
P1*
L12
P2
L11
P3
L10
P4
L9
P5
L8
P6
L7
P7
L6
P8
L5
*not actual P1

160. V. riparia V. labrusca
V. cinerea V. rupestris
Average shape
of leaves from
each node
1
2
3
4
5
6
7
8
9
10
Leaves can vary heteroblastically,
changes in the shape of leaves from successive nodes

161. Genotype, ontogeny, & heteroblasty are distinct shapes:
Genotype
-2
0
2
4
-4 -2 0 2
PC1
PC2
genus_species
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Vitis_labrusca
Vitis_piasezkii
Vitis_riparia
Vitis_rupestris
Vitis_thunbergii
-4
-2
0
2
-5.0 -2.5 0.0 2.5
PC3
PC4
genus_species
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Vitis_labrusca
Vitis_piasezkii
Vitis_riparia
Vitis_rupestris
Vitis_thunbergii
-4
-2
0
2
-5.0 -2.5 0.0 2.5
PC3
PC4
genus_species
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Vitis_labrusca
Vitis_piasezkii
Vitis_riparia
Vitis_rupestris
Vitis_thunbergii
A. acouitifolia
A. brevipedunculata
V. labrusca
V. piasezkii
V. riparia
V. rupestris
V. thunbergii
Species
PC1 (32%)
PC2(18%)
PC3 (12%)
PC4(11%)

162. Genotype, ontogeny, & heteroblasty are distinct shapes:
Ontogeny
P1
P2
P3
P4
P5
P6
P7
P8
P9
P10
Plastochron
PC1 (32%)
PC2(18%)
PC3 (12%)
PC4(11%)
-2
0
2
4
-4 -2 0 2
PC1
PC2
factor(position)
1
2
3
4
5
6
7
8
9
10
-4
-2
0
2
4
-6 -4 -2 0 2
PC3
PC4
factor(position)
1
2
3
4
5
6
7
8
9
10
-2
0
2
4
PC2
factor(position)
1
2
3
4
5
6
7
8
9
10

163. Genotype, ontogeny, & heteroblasty are distinct shapes:
Heteroblasty
L1
L2
L3
L4
L5
L6
L7
L8
L9
L10
Leaf
PC1 (32%)
PC2(18%)
PC3 (12%)
PC4(11%)
-2
0
2
4
PC2
factor(position)
1
2
3
4
5
6
7
8
9
10
-2
0
2
4
-4 -2 0 2
PC1
PC2
factor(leaf)
1
2
3
4
5
6
7
8
9
10
-4
-2
0
2
-5.0 -2.5 0.0 2.5
PC3
PC4
factor(leaf)
1
2
3
4
5
6
7
8
9
10

164. Different shape attributes are differentially conserved:
Conserved leaf ontogeny across Vitis spp.
Plastochron
PC1
PC4(11%)
-1
0
1
2
2.5 5.0 7.5 10.0
position
PC1
genus_species
Vitis_acerifolia
Vitis_aestivalis
Vitis_amurensis
Vitis_cinerea
Vitis_coignetiae
Vitis_labrusca
Vitis_riparia
Vitis_rupestris
Vitis_vulpina
P5 P10
-1
0
1
2.5 5.0 7.5 10.0
position
PC2
genus_species
Vitis_acerifolia
Vitis_aestivalis
Vitis_amurensis
Vitis_cinerea
Vitis_coignetiae
Vitis_labrusca
Vitis_riparia
Vitis_rupestris
Vitis_vulpinaPC2
Plastochron
P5 P10
V.acerifolia
V.aestivalis
V.amurensis
V.cinerea
V.coignetiae
V.labrusca
V.riparia
V.rupestris
V.vulpina
Species
-1
0
1
2
2.5 5.0 7.5 10.0
position
PC1
genus_species
Vitis_acerifolia
Vitis_aestivalis
Vitis_amurensis
Vitis_cinerea
Vitis_coignetiae
Vitis_labrusca
Vitis_riparia
Vitis_rupestris
Vitis_vulpina
Conserved early
leaf development

165. Discriminating different species,
regardless of plastochron or leaf number
Vitis_palmata
Vitis_vulpina
Vitis_cinerea
Vitis_labrusca
Vitis_aestivalis
Vitis_x_champinii
Vitis_rupestris
Vitis_riparia
Vitis_acerifolia
Vitis_piasezkii
Vitis_coignetiae
Vitis_amurensis
Vitis_thunbergii
Vitis_x_doaniana
Vitis_x_novae-angliae
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Ampelopsis_cordata
Vitis_palmata
Vitis_vulpina
Vitis_cinerea
Vitis_labrusca
Vitis_aestivalis
Vitis_x_champinii
Vitis_rupestris
Vitis_riparia
Vitis_acerifolia
Vitis_piasezkii
Vitis_coignetiae
Vitis_amurensis
Vitis_thunbergii
Vitis_x_doaniana
Vitis_x_novae-angliae
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Ampelopsis_cordata
Var1

166. Discriminating different species,
regardless of plastochron or leaf number
Vitis_palmata
Vitis_vulpina
Vitis_cinerea
Vitis_labrusca
Vitis_aestivalis
Vitis_x_champinii
Vitis_rupestris
Vitis_riparia
Vitis_acerifolia
Vitis_piasezkii
Vitis_coignetiae
Vitis_amurensis
Vitis_thunbergii
Vitis_x_doaniana
Vitis_x_novae-angliae
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Ampelopsis_cordata
Vitis_palmata
Vitis_vulpina
Vitis_cinerea
Vitis_labrusca
Vitis_aestivalis
Vitis_x_champinii
Vitis_rupestris
Vitis_riparia
Vitis_acerifolia
Vitis_piasezkii
Vitis_coignetiae
Vitis_amurensis
Vitis_thunbergii
Vitis_x_doaniana
Vitis_x_novae-angliae
Ampelopsis_acouitifolia
Ampelopsis_brevipedunculata
Ampelopsis_cordata
Var1

167. Discriminating ontogeny and heteroblasty,
regardless of species
1
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
8
9
10
Var2
Var1
1
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
8
9
10
Var2
Var1
Ontogeny
Plastochrons
Heteroblasty
Leaf position

168. Detecting heterochronic evolution:
Fast and slow ontogeny and heteroblasty
1
2
3
4
5
6
7
8
9
10
1 2 3 4 5 6 7 8 9 10
factor(position)
apparent
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
Actual plastochron Actual leaf number
Apparentplastochron
Apparentleafnumber
1
2
3
4
5
6
7
8
9
10
apparent
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
V.cinerea
V.labrusca
V.rupestris
V.riparia
1
2
3
4
5
6
7
8
9
10
1 2 3 4 5 6 7 8 9 10
factor(leaf)
apparent
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
Ontogeny
Plastochrons
Heteroblasty
Leaf position

169. -3
-2
-1
0
1
2
1 2 3 4 5 6 7 8 9 10
factor(position)
relative_position
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
-4
-2
0
2
1 2 3 4 5 6 7 8 9 10
factor(leaf)
relative_leaf
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
Detecting heterochronic evolution:
Fast and slow ontogeny and heteroblasty
Actual plastochron Actual leaf number
Relativeplastochron
Relativeleafnumber
1
2
3
4
5
6
7
8
9
10
apparent
genus_species
Vitis_cinerea
Vitis_labrusca
Vitis_rupestris
Vitis_riparia
V.cinerea
V.labrusca
V.rupestris
V.riparia
Ontogeny
Plastochrons
Heteroblasty
Leaf position

170. Detecting heterochronic evolution:
Cluster-tendril patterning, a heteroblastic standard candle
Boss and Thomas, Nature 2002
Pinot
Meunier
L1 plants
(mutant)
Pinot
Meunier/
Noir
L2 plants
(WT)

171. Detecting heterochronic evolution:
Plants with precocious leaf shape have more tendrils
-4
-2
0
2
0.0 0.2 0.4 0.6
log(n_ratio + 1)
rel_avg
-4
-2
0
2
0.0 0.2 0.4 0.6
log(t_ratio + 1)
rel_avg
Averagerelativeleafnumber
Averagerelativeleafnumber
Proportion absent positions
first 10 nodes
Proportion tendril positions
first 10 nodes
rho = -0.03
p = 0.60
rho = 0.24
p = 8 x 10-5

172. Perspectives
Phenotype is a highly multivariate problem

173. Perspectives
Phenotype is a highly multivariate problem
Morphology has a complex, developmental
context

174. Perspectives
Phenotype is a highly multivariate problem
Morphology has a complex, developmental
context
Leaf shape is comprised of distinct shape
attributes: ontogeny, heteroblasty, evolution

175. Perspectives
Phenotype is a highly multivariate problem
Morphology has a complex, developmental
context
Leaf shape is comprised of distinct shape
attributes: ontogeny, heteroblasty, evolution
Leaf shape changes across evolution can
affect all leaves equally, or be heterochronic,
modulating ontogeny or heteroblasty

176. Perspectives
Phenotype is a highly multivariate problem
Morphology has a complex, developmental
context
Leaf shape is comprised of distinct shape
attributes: ontogeny, heteroblasty, evolution
Leaf shape changes across evolution can
affect all leaves equally, or be heterochronic,
modulating ontogeny or heteroblasty
Heteroblastic changes in leaf shape track
changes in organ patterning in Vitis spp.

177. St. Louis University
Laura Klein
Allison Miller
USDA Geneva, NY
Jason Londo
Beth Takacs
Bruce Reisch
Wild Vitis spp.

178. Thanks!
Margaret Frank
Viktoriya Coneva
Chitwood Lab
Donald Danforth
Plant Science Center

179. Thanks!
Margaret Frank
Viktoriya Coneva
Chitwood Lab
Donald Danforth
Plant Science Center
Ranjan et al. (2015) An intracellular transcriptomic atlas of
the giant coenocyte Caulerpa taxifolia. PLOS Genet. 11:
e1004900