Modestr: A software tool for studying of colombian aquatic ecosystems
DOI:
https://doi.org/10.17533/udea.acbi.329178Keywords:
distribution models, GBIF, macroecology, ModestR, species distribution, species richnessAbstract
The aim of this manuscript is to show the usefulness of the software package ModestR in studies of distribution of Colombian marine and freshwater species. This software is free available at the Website: <http://www.ipez.es/ModestR>. To show and test the potential of ModestR, here an exemplar assessment is presented of a database using all valid species of freshwater fishes of the orders Characiformes and Siluriformes, and their geographical records available in the Global Biodiversity Information Facility (GBIF, 2012), and of the order Carcharhiniformes as representatives of marine species. ModestR includes, in its initial phase, two applications: DataManager and MapMaker. The application DataManager is designed for an integrated taxonomic information and maps of the distribution of any species group. The application MapMaker has been designed to generate species distribution maps in four different ways: 1) by importing a CSV file with the name of the species and their geographical coordinates, 2) importing the geographical records automatically from GBIF, 3) importing geographical coordinates generated by distribution models, and 4) making expert maps by selecting distribution areas, according to the types of habitats occupied by the species. The possibility of working with habitats is one of the most important contributions of ModestR and, in particular, that are mapped small lotic ecosystems (creeks, streams, etc.), large lotic ecosystems (rivers) and lentic ecosystems (ponds, lakes, reservoirs, swamps, etc.). Moreover, it is also possible to select marine and terrestrial ecosystems. Therefore, although the manuscript has been focused on species of aquatic ecosystems, ModestR also allows the same type of studies with terrestrial species.
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References
Anselin L, Syabri I, Kho Y. 2006. GeoDa: An introduction to spatial data analysis. Geographical analysis, 38 (1): 5-22.
Arévalo-Uribe D. 2012. Una mirada a la agricultura de Colombia desde su huella hídrica. Colombia: WWF Reporte. p. 48.
Bellemans M, Sagna A, Fischer W, Scialabba N. 1988. Guide des ressources halieutiques du Sénégal et de la Gambie (espéces marines et d’eaux saumâtres) [Internet]. Fiches FAO d’identification des espéces pour les besoins de la péche. Roma: FAO. p. 227. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao. org/docrep/010/t0047f/t0047f00.htm#Contents>.
Bianchi G, Carpenter KE, Roux JP, Molloy FJ, Boyer D, Boyer HJ. 1999. The living marine resources of Namibia [Internet]. FAO species identification field guide for fishery purposes. Roma: FAO. p. 265. Fecha de acceso: diciembre de 2012. Disponible en: .
Bonfil R, Abdallah M. 2004. Field identification guide to the sharks and rays of the Red Sea and Gulf of Aden [Internet]. FAO species identification guide for fishery purposes. Roma: FAO. p. 71. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao. org/docrep/010/a1502e/a1502e00.htm>.
Carpenter KE, Niem VH (eds.). 1998-2001. The living marine resources of the Western Central Pacific [Internet]. FAO species identification guide for fishery purposes. Roma: FAO. Vols. 1-6, paginación variable. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.org/docrep/009/y0870e/y0870e00.htm>.
Cervigón F, Cipriani R, Fischer W, Garibaldi L, Hendrickx M, Lemus AJ, Márquez R, Poutiers JM, Robaina G, Rodríguez B. 1992. Guía de campo de las especies comerciales marinas y de aguas salobres de la costa septentrional de Sur América [Internet]. Fichas FAO de identificación de especies para los fines de la pesca. Roma: FAO. p. 513. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.org/docrep/010/t0544s/t0544s00.htm>.
Colwell RK. 2006. RangeModel —Tools for exploring and assessing geometric constraints on species richness (the mid-domain effect) along transects [Internet]. Fecha de acceso: diciembre de 2012. Disponible en: <http://viceroy.eeb.uconn.edu/RangeModel/>.
Colwell RK. 2011. EstimateS: Statistical estimation of species richness and shared species from samples [Internet]. Fecha de acceso: diciembre de 2012. Disponible en: <http://viceroy.eeb.uconn.edu/estimates/>.
Colwell RK, Chao A, Gotelli NJ, Lin SY, Mao CX, Chazdon RL, Longino JT. 2012. Models and estimators linking individual-based and sample-based rarefaction, extrapolation, and comparison of assemblages. Journal of Plant Ecology, 5: 3-21.
Compagno LJV. 1984a. Sharks of the World. An annotated and illustrated catalogue of shark species known to date. Part 1: Hexanchiformes to Lamniformes [Internet]. FAO species catalogue. Roma: FAO. Vol. 4, Part 1. FAO Fish. Synop. 125 (4/1): 1-249. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.
org/documents/en/empty.jsp?cx=0181706201437011
%3Aqq82jsfba7w&cof=FORID%3A11&q=Compagno+LJV&x=9&y=9&search_radio=fao>.
Compagno LJV. 1984b. Sharks of the World. An annotated and illustrated catalogue of shark species known to date. Part 2: Carcharhiniformes [Internet]. FAO species catalogue. Roma: FAO. Vol. 4, Part 2. FAO Fish. Synop., 125 (4/2): 251-655. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.
org/documents/en/empty.jsp?cx=0181706201437011 04933%3Aqq82jsfba7w&cof=FORID%3A11&q=Co mpagno+LJV&x=9&y=9&search_radio=fao>.
Compagno LJV. 2003. Sharks of the order Carcharhiniformes. Massachusetts (EE. UU.): Blackburn Press. p. 572.
Compagno LJV, Dando M, Fowler S. 2005. A field guide to the sharks of the World. New Jersey (Princeton): Princeton University Press. p. 368.
Eschmeyer WN, Fricke R (eds.). 2012. Catalog of fishes electronic version [Internet]. Fecha de acceso: diciembre de 2012. California: California Academic of Sciences: Research. Fecha de acceso: diciembre de 2012. Disponible en: <http://research.calacademy.org/
research/ichthyology/catalog/fishcatmain.asp>.
Fischer W, Bianchi G, Scott WB (eds.). 1981. Eastern Central Atlantic; fishing area 34, 47 (in part) [Internet]. FAO species identification sheets for fishery purposes. Ottawa (Canada): Department of Fisheries and Oceans of Canada and FAO. Vols. 1-7, paginación variable. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.org/docrep/009/ag419e/ag419e00.htm>.
Fischer W, Bauchot ML, Schneider M. 1987. Méditerranée et mer Noire. Zone de péche 37. Fiches FAO d’identification des espèces pour les besoins de la péche. (Révision 1). Roma: FAO. Vol. 2: Vértébrés,
p. 761-1530.
Fischer W, Krupp F, Schneider W, Sommer C, Carpenter KE, Niem VH. 1995. Pacífico Centro Oriental. Guía FAO para la identificación de especies para los fines de la pesca. Roma: FAO. Vol. 1, p. 1-646; Vol. 2, p. 647-1200; Vol. 3, p. 1201-1813.
Froese, R, Pauly D. (eds). 2012. FishBase. World Wide Web electronic publication [version (12/2012)] [Internet]. Fecha de acceso: noviembre de 2012. Disponible en: <http://www.fishbase.org/search.php?lang=Spanish>.
Frost DR. 2011. Amphibian species of the World: an online reference. Version 5.5 (31 January, 2011). New York (EE. UU.): American Museum of Natural History. Fecha de acceso: diciembre de 2012. Disponible en: <http://research.amnh.org/vz/herpetology/amphibia/>.
GBIF. 2012. Global Biodiversity Information Facility [Internet]. Fecha de acceso: diciembre de 2012. GBIF disponible en: <http://data.gbif.org>. Búsqueda de taxones: Access data portal: <http://data.gbif.org/welcome.htm>.
Guisan A, Thuiller W. 2005. Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8 (9): 993-1009.
Guisande C, Manjarrés-Hernández A, Pelayo-Villamil P, Granado-Lorencio C, Riveiro I, Acuña A, Prieto- Piraquive E, Janeiro E, Matías JM, Patti C, Patti B, Mazzola S, Jiménez S, Duque V, Salmerón F. 2010. IPez: An expert system for the taxonomic identification
of fishes based on machine learning techniques. Fisheries Research, 102 (3): 240-247.
Hanspach J, Kühn I, Schweiger IO, Pompe S, Klotz S. 2011. Geographical patterns in prediction errors of species distribution models. Global Ecology and Biogeography, 20 (5): 779-788.
Hijmans RJ, Guarino L, Cruz M, Rojas E. 2001. Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS. Plant Genetic Resources Newsletter, 127: 15-19.
Hijmans RJ, Guarino L, Jarvis A, O’Brien R, Mathur P, Bussink C, Cruz M, Barrantes I, Rojas E. 2005. DIVA- GIS [Internet]. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.diva-gis.org/>.
Hirzel AH, Hausser J, Chessel D, Perrin N. 2002. Ecological-niche factor analysis: How to compute habitat-suitability maps without absence data? Ecology, 87 (7): 2027-2036.
IUCN. 2010. IUCN Red List of Threatened Species [Internet]. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.iucnredlist.org/>.
Lloris D, Rucabado J. 1998. Guide d’identificationdes ressources marines vivantes du Maroc [Internet]. Guide FAO d’identification des espéces pour les besoins de la pêche. Roma: FAO. p. 263. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.
org/documents/en/empty.jsp?cx=0181706201437011
%3Aqq82jsfba7w&cof=FORID%3A11&q=Rucabado+J&x=10&y=7&search_radio=fao >.
Maldonado-Ocampo JA, Vari RP, Usma JS. 2008. Checklist of the freshwater fishes of Colombia. Biota Colombiana, 9 (2): 143-237.
Moreno MI, Arzuza D. 2006. Reporte final. Aves acuáticas en Colombia [Internet]. Bogotá (Colombia): ProAves and Waterbird Conservation for the Americas. p. 68. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.google.com.co/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CDkQFjAC&url=http%3A%2F%2Fwww.birdlife.org%2Faction%2Fscience%2Fspec
ies%2Fwaterbirds%2Fwaterbirds_pdf%2Fwaterbirds_report_colombia_2006.pdf&ei=m6zkUN6NNpOK9AS6gYGQBw&usg=AFQjCNEnq5rezlSkfI7LuR-4Vii7_Vj1AA&bvm=bv.1355534169,d.eWU>.
Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190 (3-4): 231-259.
Poveda G, Mesa OJ, Vélez JI, Mantilla R, Ramírez JM, Hernández O, Borja AF, Urzola JA. HidroSIG: An interactive digital atlas of Colombia ́s hydro- climatology. Journal of Hydroinformatics, 9 (2): 145-156.
R Development Core Team. 2009. R: a language and environment for statistical computing [Internet]. Vienna, Austria: R Foundation for Statistical Computing. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.r-project.org./>.
Rangel TF, Alexandre J, Diniz-Filho F, Bini LM. 2010. SAM: a comprehensive application for spatial analysis in Macroecology. Ecography, 33 (1): 46-50.
Rosenberg MS, Anderson CD. 2011. PASSAGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2. Methods in Ecology and Evolution, 2 (3): 229-232.
Scachetti-Pereira R. 2003. DesktopGARP [Internet]. Kansas (EE. UU.): University of Kansas Center for Research, Inc. (KUCR) and the University of Kansas. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.nhm.ku.edu/desktopgarp/>.
Schneider W. 1990. Field guide to the commercial marine resources of the Gulf of Guinea [Internet]. FAO species identification sheets for fishery purposes. Roma: FAO. p. 268. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.org/docrep/009/t0438e/t0438e00.htm>.
Serena F. 2005. Field identification guide to the sharks and rays of the Mediterranean and Black Sea [Internet]. FAO species identification guide for fishery purposes. Roma: FAO. p. 97. Fecha de acceso: diciembre de 2012. Disponible en: <http://www.fao.org/docrep/009/y5945e/y5945e00.htm>.
Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F, de Clerck O. 2012. Bio-ORACLE: a global environmental dataset for marine species distribution modelling. Global Ecology and Biogeography, 21 (2): 272-281.
Whitehead PJP, Bauchot ML, Hureau JC, Nielsen J, Tortonese E (eds.). 1984-1986. Fishes of the North- eastern Atlantic and the Mediterranean. Paris: UNESCO. Vols. 1-3, p. 1-1473.
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