Biodiversity of fresh and brackish waters fish species in Africa is both highly diverse and of great regional importance to livelihoods and economies. Many areas in Africa are still not well surveyed such that available information on fish species is insufficient for environmental and development planning. Lack of basic information on species distribution and threatened status has long been a key obstacle facing freshwater ecosystem managers in Africa. Therefore, IRD has put in place FAUNAFRI an online GIS to collate, store, manage, and make widely available information about the distributions of fresh and brackish waters fish species in Africa. The application is accessible at the address http://www.ird.fr/poissons-afrique/faunafri/

1. FAUNAFRIFAUNAFRI
act to save the freshwater biodiversity beyond our borders
Conception and development
Rainer Zaiss
IRD Secteur Cartographie
32, Avenue Henry Varagnat
9343 Bondy
Scientific responsibility
Didier Paugy
Antenne IRD
MNHN – DMPA
75231 Paris cedex 05
Claroteidae ChrysichthysAlestidae Hydrocynus Aplocheilidae Aphyosemion Amphilidae Amphilus Tetraodontidae Tetraodon
act to save the freshwater biodiversity beyond our borders
Use of SVG to map
the geographical distribution of
fish species in Africa

2. Institut de recherche
pour le développement
French public science and technology
research institute
IRD conducts scientific programs contributing to
the development of the countries of the South
with an emphasis on the relationship between
man and the environment
• 2 200 employees
• 30 centers around the world
• A budget of 220 million euros
• 66 research and service units
key figures

3. Claroteidae Chrysichthys
 Build up a centralized geographical
information system to compile,
conserve and share biodiversity data of
fresh and brackish waters fish species in
Africa.
 Develop a Graphical User Interface (GUI)
to map, compare and analyze the
distribution of families, genera and
species from the continental level down
to the sample site.
FAUNAFRIFAUNAFRI
Museum of Natural History in Paris
act to save the freshwater biodiversity beyond our bordersact to save the freshwater biodiversity beyond our borders
Fish collection

4.  High species richness (around 3500 species)
 High numbers of endemic species
 Africa’s freshwater systems are being degraded at an alarming rate
 IUCN Red List 2006 (61 species critically endangered , 116 endangered, 152
vulnerable)
 Many of Africa's fresh waters are yet to be explored
 Much taxonomic work remains to be completed
 According to IUCN, lack of basic information on species
distribution and threatened status is a key obstacle facing
freshwater ecosystem managers in Africa.
Some facts about the distribution of fresh
and brackish waters fish species in Africa

5. Baseline map
Sources of information
Source Type Thematic
GNS Point Place names
VMAP0 Poly/Line Hydrographie
DCW Poly Wetlands
VMAP0 Line Coastline
SRTM Raster Topography
VMAP0 Line International border
MODIS Raster Landcover
RasterImage
RasterClassification
Landcover
RasterElevation
RasterHillshade
Topography
LineInternational boundary
PolyWetlands
LineRivers
Hydrography
Estuaries
Lakes
Main rivers
PolyIchthyological regions
PolyDrainage bassins
Poly
Poly
Poly
TypeThematic
“Geoprocessing”
GIS FAUNAFRI

6. The biodiversity data
Data providers
Tetraodontidae Tetraodon
Claroteidae Chrysichthys
Latidae Lates
Citharinidae Citharinus
Aplocheilidae Aphyosemion
0 25 000 50 000
(MRAC) Musée Royal de l'Afrique Centrale, Belgium
(Others) IRD and Scientific Literature
(BMNH) Natural History Museum, U.K.
(SAIAB) South African Institute for Aquatic Biodiversity, South Africa
(MNHN) Muséum National d'Histoire naturelle, France
(USNM) National Museum of Natural History, Washington D.C., U.S.A.
(AMNH) American Museum of Natural History, New York, U.S.A.
(NMZB) Natural History Museum of Zimbabwe
(KMMA) Koninklijk Museum voor Midden-Afrika, Belgium
(ZMH) Zoologisches Museum der Humboldt Universität, Germany
Other museum collections
number of samples

7. 0
5 000
10 000
15 000
20 000
25 000
<19001900-19101910-19201920-19301930-19401940-19501950-19601960-19701970-19801980-19901990-20002000-2010
period
numberofsamples
Alestidae Brycinus
The biodiversity data
number of samples by 10 year period
Claroteidae Chrysichthys
Alestidae Hydrocynus
Amphilidae Amphilus
Tetraodontidae Tetraodon

8. Country
Ichthyologic region
Drainage basin
Ruzizi 1
Georeferencing
Biodiversity data Amphilidae Amphilus
Burundi N
Tanganyika 1
Lake Tanganyika 1
GIS FAUNAFRI
River
Lake
Estuary
Wetland
Grande Rusizi N
1
1
1
Hydrography
Geography
Sample site

9. Mapping application
map the geographical distribution of a species
Aggregation of biodiversity data
Sample site Drainage basin Ichthyological region
Geography
Legend
1. Genera : Citharinops

10. Aggregation of biodiversity data
Mapping application
map the geographical distribution of a species
400 km 300 km 200 km 50 km
Squaring
Legend
1. Genera : Citharinops

11. 1
Mapping application
compare the geographical distribution of different species
2. Genera : Citharidium+1. Genera : Citharinops
Overlay + 25% transparency Typology=
1. Genera : Citharinops
2. Genera : Citharidium
1 + 2
2 2
1
=
2
1
3
1 + 2 + 3
3
4
1 + 2 + 3 + 4
42
1
3

12. Filter feColorMatrix + opacity
Mapping application
compare the geographical distribution of different species
25 % 50 % 0 %
Opacity
Red: 1,0,0,0,0,
Green: 0,1,0,0,0,
Blue: 0,0,1,0,0,
Alpha: 0,0,0,4,0

13. Mapping application
dynamic and comprehensible legends

14. Mapping application
geography as entry point
Species information
Click Information panel
Information Window

15. Mapping application
geography as entry point
Information WindowGeography windowSource Window

16. 0 1,500 km 0 540 km
Level 3
0 324 km
Level 5
0 194 km
Level 6
0 117 km
Level 7
0 70 km
Level 8
0 42 km
Level 9
Mapping application
level of detail and symbology depending on map scale
Level 1
0 15 km
Level 11

17. Mapping application
toolkits / APIs to put in place the application
 Evaluation of different SVG and flash based web mapping toolkits
 They did not really offer out of the box the necessary functionalities to develop
the application…
 Framework from Carto:Net
 Flexible SVG full web mapping API
SVG GUI elementsTemplate navigation and

18. Alestidae Hydrocynus
first version of FAUNAFRI
http://www.ird.fr/poissons-afrique/faunafri/
 First loading of the page takes too long
 We have to change slightly the architecture of the application
 Work on database issues and data quality
End of 2007
2008
 SVG, Flash or Open layers ?
2009
 Target Microsoft IE + Adobe SVG plug-in
 Microsoft announced to implement SVG natively into IE9
2010
 Final version with carto:net API and SVG ?

19. Architecture first version
Vector data Raster data
 Graphical User Interface (GUI) SVG Scalable Vector Graphics
XML /
JSON
Ajax png

20. <g id="HY“/>
Client server data loading
AJAX request
http://...sendGeom.php?layer=HY& xul=4000& yul =4000 & xlr=6000 & ylr=2000 & timestamp=12000
XML fragment
<g id="HY_geom" attrib:timestamp=“12000” >
<path d="M 4000 ...></g>
Zoom
Javascript
1. Timestamp: 1200
2. Area of interest (xul: 4000, yul: 4000, xlr: 6000, ylr: 2000)
if map window timestamp = xml timestamp
<g id="HY_geom" attrib:timestamp=“12000” >
<path d="M 4000 ...></g>
Source: Williams, J., Neumann, A (2006): Dynamic Loading of Vector Geodata for SVG Mapping Applications Using Postgis, PHP and
getURL()/XMLHttpRequest(). http://www.carto.net/papers/svg/postgis_geturl_xmlhttprequest/.
Timestamp:
12000

21. Timestamp:
12000
Timestamp:
13000
<g id="HY_geom" attrib:timestamp=“12000” >
<path d="M 4000 ...></g>
<g id="HY_geom" attrib:timestamp=“13000” >
<path d="M 3000 ...></g>
Delete child group
<g id="HY“/>
Client server data loading
Source: Williams, J., Neumann, A (2006): Dynamic Loading of Vector Geodata for SVG Mapping Applications Using Postgis, PHP and
getURL()/XMLHttpRequest(). http://www.carto.net/papers/svg/postgis_geturl_xmlhttprequest/.
if map window timestamp = xml timestamp
AJAX request
http://...sendGeom.php?layer=HY& xul=3000& yul =3000 & xlr=5000 & ylr=1000 & timestamp=13000
XML fragment
<g id="HY_geom" attrib:timestamp=“13000” >
<path d="M 3000 ...></g>
Zoom
Javascript
1. Timestamp: 13000
2. Area of interest (xul: 3000, yul: 3000, xlr: 5000, ylr: 1000)
+ Add new geometry

22. <g id="HY_geom" attrib:timestamp=“14000” >
<path d="M 4000 ...></g>
Timestamp:
13000
Client server data loading
AJAX request
http://...sendGeom.php?layer=HY& xul=4000& yul =4000 & xlr=6000 & ylr=2000 & timestamp=14000
XML fragment
<g id="HY_geom" attrib:timestamp=“14000” >
<path d="M 4000 ...></g>
Zoom
Javascript
1. Timestamp: 1400
2. Area of interest (xul: 4000, yul: 4000, xlr: 6000, ylr: 2000)
if map window timestamp = xml timestamp
Source: Williams, J., Neumann, A (2006): Dynamic Loading of Vector Geodata for SVG Mapping Applications Using Postgis, PHP and
getURL()/XMLHttpRequest(). http://www.carto.net/papers/svg/postgis_geturl_xmlhttprequest/.
Timestamp:
14000
Delete child group + Add new geometry
<g id="HY_geom" attrib:timestamp=“13000” >
<path d="M 3000 ...></g>
<g id="HY“/>

23.  Timestamp
 No server or client side caching
 Reloading of data for previous visited areas
 Extraction of the exact coordinates of the area of interest
 No predictive fetch
 Loading of the total data even for slightly different areas
Client server data loading
disadvantages of the carto:net method

24. <path id=“HYC3” d="M 1500 .../>
Client server data loading
AJAX requests for missing tiles
1. http://...sendGeom.php?layer=HY& index=C3
…
4. http://...sendGeom.php?layer=HY& index=D4
XML fragments of missing tiles
1. <path id=“HYC3” d="M 1500 .../>
2. <path id=“HYC4” d="M 3500 .../>
3. <path id=“HYD3” d="M 1500 .../>
4. <path id=“HYD4” d="M 3500 .../>
<g id="HY“/>
<path id=“HYC4” d="M 3500 .../>
<path id=“HYD3” d="M 1500 .../>
<path id=“HYD4” d="M 3500 .../>
Append childs
A0 A1 A2 A3 A4 A5
B0 B1 B2 B3 A4 A5
C0 C1 C2 C3 C4 C5
D0 D1 D2 D3 D4 D5
E0 E1 E2 E3 E4 E5
F0 F1 F2 F3 F4 F5
Zoom
Javascript
Loop to identify tiles hat are necessary to cover the area of interest : C3, C4, D3, D4
Tiles already loaded: -

25. Append childs
<path id=“HYC3” d="M 1500 .../>
Client server data loading
Append childs
<g id="HY“/>
<path id=“HYC4” d="M 3500 .../>
<path id=“HYD3” d="M 1500 .../>
<path id=“HYD4” d="M 3500 .../>
<path id=“HYE3” d="M 1500 .../>
<path id=“HYE4” d="M 1500 .../>
AJAX requests for missing tiles
1. http://...sendGeom.php?layer=HY& index=E3
2. http://...sendGeom.php?layer=HY& index=E4
XML fragments of missing tiles
1. <path id=“HYE3” d="M 1500 .../>
2. <path id=“HYE4” d="M 3500 .../>
A0 A1 A2 A3 A4 A5
B0 B1 B2 B3 A4 A5
C0 C1 C2 C3 C4 C5
D0 D1 D2 D3 D4 D5
E0 E1 E2 E3 E4 E5
F0 F1 F2 F3 F4 F5
Zoom
Javascript
Loop to identify tiles hat are necessary to cover the area of interest : D3, D4, E3, E4
Tiles already loaded: C3, C4, D3, D4

26.  Client and server based caching is possible
 Predictive fetch
 No reloading of data for previous visited areas
Client server data loading
advantages of the tile based method

27. Claroteidae Chrysichthys Amphilidae Amphilus Tetraodontidae Tetraodon Latidae Lates
Thank you / Questions
Museum of Natural History in Paris Fish collection
The project FAUNAFRI has received funds from IRD.
We would like in particular to acknowledge the major contributions to the project provided by
N. Rahmani, L. Ruhier, J.J. Troubat and M. Vienne.