presentation3 - representa & divmapas tools
DESCRIPTION
CAPFITOGEN english presentations for workshopsTRANSCRIPT
Mauricio Parra QuijanoFAO consultant International Treaty on Plant Genetic Resources for Nutrition and Agriculture CAPFITOGEN Program Coordinator
Tools
Representa
Evaluates the ecogeographical representativeness of germplasm collections
Genetic representation
A B C
accggtccc accggtcgc accggtctc
A B C
A A A
A B C
AAA
A
B
B B
B
C BA
Ecogeographic representation
A BBBBBBB CCC
A B C Unique
A BB CC Even
A BBBB CC Proportional
Representativeness based on ELC maps
y
x
Coordinates of passport dataELC map of Cuba (from ELC mapas tool)
Sites with species´ occurrences
1 2 3 4 5 6 7 8 9 10
ELC categoriesN
en
trie
s
100
200
300
Genebank set
1 2 3 4 5 6 7 8 9 10
ELC categories
N e
ntr
ies
100
200
300
External sources set1 2 3 4 5 6 7 8 9 10
ELC categories
% c
ells
25
50
75
Overall distributionCategories of the map
Χ2 test
upperupper midlower midlower
Quartiles
Validation through germplasm evaluation/characterization
-Apparents
-Non-apparents
Adaptive traits:
DIVmapas
Provides maps of phenotypic, genotypic and/or eco-geographical diversity
Measuring the diversity of the collections
Characterization
Morphological
Biochemical / Molecular /ADN
Agronomical / Physiological / PhytopathologicalEntomological
Eco-geographical
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1454
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05
10
15
Cluster analysis
hclust (*, "average")
He
ight
How we have visualized the genetic diversity
-0.2 0.0 0.2 0.4
-0.3
-0.2
-0.1
0.0
0.1
0.2
0.3
PCO for genotypic characterization
PCO 1
PC
O 2
d = 2
1
2
3 4 5 6
7 8 9 10 11 12
13 14
25 26
33 34 35 36 37 38 39 40
41 42 43 44 45 46 47
48 49 50 51 52
54 55 56 57
58 59 60 61 62 63 64
65 66 67
69
74
75
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79 80
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86 87 88
89 90 91
92 93 94 95 96 97 98 99
100 101 102 103 104 105 106
107 108
109
113 120
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122
123 124
125 126 127
128 129 130
131
132 133 134 135
136
137
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139
140 141 142 143
144
145
148 149 150
151 152
153 154
157 158
159
160 161 162 163
164
165 166
167 168
169
170 171
172
173 174
175
176
177
178
179 180
181 182 183 184
185
186 187 188 189 190
192 193
X
alt
slope
bio_15
bio_12
bio_18
bio_17
bio_1
bio_9
t_sand
t_caco3
t_cec_clay
t_silt
t_ph_h2o
t_ece
Eigenvalues
How we have visualized the genetic diversity
DIVmapas
A different way to visualize the diversity Collecting sites with a minimum level of geo-referencing quality
DIVmapas
Overlapping a grid (N x N km cells)
DIVmapas
Selection of cells that include collecting sites (centroids are points in yellow )
DIVmapas
Detection of neighbouring cells which centroids (green points) falls at X km (radius ) around of the presence cell centroid (yellow points)
DIVmapas
Generation of areas of influence from each centroid
Detection of accessions collected within each area of influence
DIVmapas
OTU 89 233 152
89 0
233 10 0
152 15 14 0
OTU VAR1 VAR2 VAR3 VAR4 VAR5
89 233 0.56 13 600 0
233 198 1.43 13 700 0
152 201 0.88 10 600 1
Distance algorithm
Averaged distance = (10+15+14)/3
= 13
Local multivariate analysis
DIVmapas
Same process for all cells that include collecting sites
DIVmapas
Same process for neighbouring cells
DIVmapas
0 0 0 0 1 3 2
1 1 0 1 1 2 1
1 1 0 1 1 0 0
0 0 0 0 0 0 0
Result 1:Number of analyzed accessions by cell
DIVmapas
0 13 8
0 0 0 0 2 0
0 0 0 0
Result 2:Averaged distances assigned to each cell
DIVmapas
Bias in sampling? Correction via "bootstrapping"
1
2......n
Median = 2
Applied DIVmapas
Ecuadorian collection ofArachis hipogaea L.
Applied DIVmapas
Number of collecting sites per cell
Applied DIVmapas
Averagedeuclidean distance