presentation 5 representa di_vmapas
TRANSCRIPT
Mauricio Parra QuijanoFAO consultant International Treaty on Plant Genetic Resources for Nutrition and Agriculture CAPFITOGEN Program Coordinator
http://www.capfitogen.net
ToolsRepresenta & DIV mapas
INTRODUCTION TO
Representa
Evaluates the ecogeographical representativeness of germplasm collections
Genetic representation
A B C
accggtccc accggtcgc accggtctc
A B C
A A A
A B CAAA
A
B
BBB
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 10ELC categories
N e
ntrie
s
100
200
300
Genebank set
1 2 3 4 5 6 7 8 9 10ELC categories
N e
ntrie
s
100
200
300External 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 / Phytopathological Entomological
Eco-geographical
1246
711
883
1247
012
471
1247
212
473
1248
312
484 11
461
1247
812
479
1148
111
868
2302
1186
911
401
1140
511
406
1140
711
408
1183
511
832
1183
311
484
1182
711
828
1154
211
539
1154
012
468
1189
112
465
1149
311
494
1150
811
506
1150
711
496
1149
211
490
1149
1 1148
911
501
1156
311
504
1150
211
503
1154
311
546
1154
712
474
1183
811
534
1153
211
533
1152
911
527
1152
811
535
1156
411
764
1152
411
523
1152
211
521
1152
011
519
1151
711
518
1185
411
841
1184
212
477
1247
512
476
1246
911
473
1147
211
471
1146
911
470
1147
711
474
1147
511
467
1146
8 1151
611
514
1151
512
461
1184
812
480
1154
912
466
1246
212
463
1187
911
875
1187
211
874
1245
512
456
1148
012
448
1146
011
458
1145
912
453
1245
412
458
1245
912
452
1145
511
453
1145
211
451
1144
811
450 1
1454
1145
611
457
1246
411
466
1146
511
462
1146
4 1245
711
857
1185
311
852
1185
011
851
1244
912
450
1245
112
440
1141
211
410
1141
111
413
1141
412
436
1243
7 1141
612
441
1243
812
439
1141
711
419
1143
111
430
1142
811
427
1142
611
425
1142
411
423
1142
111
422
1243
511
432
1143
311
551
1143
811
439 1155
011
437
1143
611
434
1143
512
442
1244
311
556
1156
011
557
1155
812
447
1244
412
445
1144
711
445
1144
611
440
1144
111
444
1144
211
443
1148
811
482
1228
312
284
1148
511
487
05
1015
Cluster analysis
hclust (*, "average")
Hei
ght
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
76 77 78
79 80
81 82 83 84 85
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
121
122
123 124
125 126 127
128 129 130
131
132 133 134 135
136
137
138
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"
12......n
Median = 2
Applied DIVmapas
Ecuadorian collection ofArachis hipogaea L.
Applied DIVmapas
Number of collecting sites per cell
Applied DIVmapas
Averagedeuclidean distance