Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Colombia.
Extracted from the Mendeley GBIF Public Library.

List of publications

  • Alimi T, Fuller D, Qualls W, Herrera S, Arevalo-Herrera M, Quinones M et al. (2015)

    Predicting potential ranges of primary malaria vectors and malaria in northern South America based on projected changes in climate, land cover and human population.

    Parasites & vectors 8 431.

    BACKGROUND: Changes in land use and land cover (LULC) as well as climate are likely to affect the geographic distribution of malaria vectors and parasites in the coming decades. At present, malaria transmission is concentrated mainly in the Amazon basin where extensive agriculture, mining, and logging activities have resulted in changes to local and regional hydrology, massive loss of forest cover, and increased contact between malaria vectors and hosts. METHODS: Employing presence-only records, bioclimatic, topographic, hydrologic, LULC and human population data, we modeled the distribution of malaria and two of its dominant vectors, Anopheles darlingi, and Anopheles nuneztovari s.l. in northern South America using the species distribution modeling platform Maxent. RESULTS: Results from our land change modeling indicate that about 70,000 km(2) of forest land would be lost by 2050 and 78,000 km(2) by 2070 compared to 2010. The Maxent model predicted zones of relatively high habitat suitability for malaria and the vectors mainly within the Amazon and along coastlines. While areas with malaria are expected to decrease in line with current downward trends, both vectors are predicted to experience range expansions in the future. Elevation, annual precipitation and temperature were influential in all models both current and future. Human population mostly affected An. darlingi distribution while LULC changes influenced An. nuneztovari s.l. distribution. CONCLUSION: As the region tackles the challenge of malaria elimination, investigations such as this could be useful for planning and management purposes and aid in predicting and addressing potential impediments to elimination.

    Keywords: An. darlingi, An. nuneztovari s.l, Climate, Land-use changes, Malaria, Maxent, Population expansion, South America, Species distribution models, change

  • Antonelli A, Zizka A, Silvestro D, Scharn R, Cascales-Miñana B, Bacon C (2015)

    An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics.

    Frontiers in genetics 6 130.

    Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having "pumped out" more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity.

    Keywords: Angiosperms, Latitudinal diversity gradient, biogeography, diversification rates, evolution, phylogenetics, tropical biodiversity

  • Arbeláez-Cortés E, Garzón-Z. J, Sierra M, Forero F, Cardona-Camacho P, Bayer A et al. (2015)

    Fourteen new additions to the list of birds of Quindío department, Colombia

    Check List 11(6) 1786.

    Recent records of bird species in the Colombian Andes have shown that this region is not as well known as was previously believed. We compiled data from a major collection of Colombian birds and from our recent field observations to complement the bird species list of Quindío department. We report the addition of 14 species to Quindío’s checklist and data of museum vouchers for 12 species reported only from field observations. The majority of additions were from localities below 1,900 m above sea level, a zone that has been highly transformed by human activities. Our dataset, and other information, raised the number of bird species in Quindío to 560. This information must be considered in decisions about the land use in this region of the Colombian Andes.

    Keywords: Andes, Aves, South America, biodiversity, new records

  • Botero-delgadillo E, Bayly N, GÓmez C, PulgarÍn-r. P, PÁez C (2015)

    An assessment of the distribution, population size and conservation status of the Santa Marta Foliage-gleaner Automolus rufipectus: a Sierra Nevada de Santa Marta endemic

    Bird Conservation International 1-15.

    The Santa Marta Foliage-gleaner Automolus rufipectus is one of 19 endemic bird species found in the Sierra Nevada de Santa Marta (SNSM) in northern Colombia but until recently it was considered a sub-species of the Ruddy Foliage-gleaner Automolus rubiginosus. Consequently, published information on its distribution and ecology is lacking, and while it is classified as near-threatened, this designation was based on limited quantitative data. To improve our knowledge of the Santa Marta Foliage-gleaner’s geographical distribution, elevation range, population density, habitat use and conservation status, we analysed both historical and recent site locality records and carried out variable distance transects within forested habitats and shade coffee plantations. We modelled the environmental niche of the species and subsequently estimated its extent of occurrence and area of occupancy, as well as population size. Our results consistently showed that the distribution of the Santa Marta Foliage-gleaner is more restricted than previously considered, both geographically and by elevation (we redefine elevation range as 600–1,875 m). This suggests that the species is more at risk of habitat transformation and combined with our estimates of population size (< 10,000 individuals), it is likely that the species will be uplisted to a higher threat category. More positively, and contrary to published accounts, we found that approximately 40% of the species’ range lies within protected areas. Nevertheless, we recommend the implementation of strategies to maintain forest cover on the western flank of the SNSM and further research to better define the species’ habitat needs and population dynamics.

    Keywords: Andes, Aves, South America, biodiversity, new records

  • Botero-Delgadillo E, Bayly N, Escudero-Páez S, Moreno M (2015)

    Understanding the distribution of a threatened bird at multiple levels: A hierarchical analysis of the ecological niche of the Santa Marta Bush-Tyrant ( Myiotheretes pernix )

    The Condor 117(4) 629-643.

    ABSTRACT An understanding of the ecological factors determining bird species' distributions is essential for making informed conservation decisions. These data are especially important for range-restricted species, such as the Santa Marta Bush-Tyrant (Myiotheretes pernix), a threatened endemic of the Sierra Nevada de Santa Marta (SNSM) in Colombia. Here we adopt a novel hierarchical analysis to describe the bush-tyrant's ecological niche and infer the regional and local determinants of its limited distribution. We first describe habitat selection based on local habitat use and microhabitats used for foraging. We then use a geoprocessing modeling algorithm to combine habitat selection data with a climatic niche model. The resulting model produced an index of habitat suitability, which we converted into a predicted geographic distribution. Santa Marta Bush-Tyrants showed no clear habitat preferences, but favored forested and secondary growth habitats over open areas, at elevations between 2,100 and 3,300 m....

    Keywords: Colombia, Sierra Nevada de Santa Marta, distribution, foraging ecology, habitat use, microhabitat

  • Báez S, Malizia A, Carilla J, Blundo C, Aguilar M, Aguirre N et al. (2015)

    Large-scale patterns of turnover and Basal area change in Andean forests.

    PloS one 10(5) e0126594.

    General patterns of forest dynamics and productivity in the Andes Mountains are poorly characterized. Here we present the first large-scale study of Andean forest dynamics using a set of 63 permanent forest plots assembled over the past two decades. In the North-Central Andes tree turnover (mortality and recruitment) and tree growth declined with increasing elevation and decreasing temperature. In addition, basal area increased in Lower Montane Moist Forests but did not change in Higher Montane Humid Forests. However, at higher elevations the lack of net basal area change and excess of mortality over recruitment suggests negative environmental impacts. In North-Western Argentina, forest dynamics appear to be influenced by land use history in addition to environmental variation. Taken together, our results indicate that combinations of abiotic and biotic factors that vary across elevation gradients are important determinants of tree turnover and productivity in the Andes. More extensive and longer-term monitoring and analyses of forest dynamics in permanent plots will be necessary to understand how demographic processes and woody biomass are responding to changing environmental conditions along elevation gradients through this century.

    Keywords: Colombia, Sierra Nevada de Santa Marta, distribution, foraging ecology, habitat use, microhabitat

  • Castañeda-Álvarez N, de Haan S, Juárez H, Khoury C, Achicanoy H, Sosa C et al. (2015)

    Ex situ conservation priorities for the wild relatives of potato (solanum L. Section petota).

    PloS one 10(4) e0122599.

    Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.

    Keywords: Colombia, Sierra Nevada de Santa Marta, distribution, foraging ecology, habitat use, microhabitat

  • García-Roselló E, Guisande C, Manjarrés-Hernández A, González-Dacosta J, Heine J, Pelayo-Villamil P et al. (2015)

    Can we derive macroecological patterns from primary Global Biodiversity Information Facility data?

    Global Ecology and Biogeography n/a-n/a.

    Aim To determine whether the method used to build distributional maps from raw data influences the representation of two principal macroecological patterns: the latitudinal gradient in species richness and the latitudinal variation in range sizes (Rapoport's rule). Location World-wide. Methods All available distribution data from the Global Biodiversity Information Facility (GBIF) for those fish species that are members of orders of fishes with only marine representatives in each order were extracted and cleaned so as to compare four different procedures: point-to-grid (GBIF maps), range maps applying an α-shape [GBIF-extent of occurrence (EOO) maps], the MaxEnt method of species distribution modelling (GBIF-MaxEnt maps) and the MaxEnt method but restricted to the area delimited by the α-shape (GBIF-MaxEnt-restricted maps). Results The location of hotspots and the latitudinal gradient in species richness or range sizes are relatively similar in the four procedures. GBIF-EOO maps and most GBIF-MaxEnt-maps provide overestimations of species richness when compared with those present in a priori well-surveyed cells. GBIF-EOO maps seem to provide more reasonable world macroecological patterns. MaxEnt can erroneously predict the presence of species in environmentally similar cells of another hemisphere or in other regions that lie outside the range of the species. Limiting this overpredictive capacity, as in the case of GBIF-MaxEnt-restricted maps, seems to mimic the frequency of observations derived from a simple point-to-grid procedure, with the utility of this procedure consequently being limited. Main conclusions In studies of macroecological patterns at a global scale, the simple α-shape method seems to be a more parsimonious option for extrapolating species distributions from primary data than are distribution models performed indiscriminately and automatically with MaxEnt. GBIF data may be used in macroecological patterns if original data are cleaned, autocorrelation is corrected and species richness figures do not constitute obvious underestimations. Efforts therefore should focus on improving the number and quality of records that can serve as the source of primary data in macroecological studies.

    Keywords: Distribution models, GBIF, Rapoport' rule, macroecological patterns, marine fishes, point-to-grid, range maps

  • Gelviz-Gelvez S, Pavón N, Illoldi-Rangel P, Ballesteros-Barrera C (2015)

    Ecological niche modeling under climate change to select shrubs for ecological restoration in Central Mexico

    Ecological Engineering 74 302-309.

    Shrub species were selected for potential use in restoration projects in the semiarid shrublands of Central Mexico. Ecological characteristics of the species were considered, including tolerance to climate change. Inventories of shrubs were carried out in 17 semiarid shrubland fragments of xeric shrubland. The 46 species recorded were ordered using a principal component analysis, considering ecological characteristics such as frequency, land cover, sociability and interaction with mycorrhizal fungi. From these, the 10 species that presented the highest values of the desired characteristics were selected. The response of these species to climate change was evaluated using current potential distribution models and by applying climate change scenario A2, using MaxEnt. The species that presented suitable ecological qualities for restoration and maintained or increased their distribution under the climate change scenario were Acacia schaffneri, Ageratina espinosarum, Bursera fagaroides, Dalea bicolor, Eysenhardtia polystachya and Karwinskia humboldtiana. These species are therefore recommended for use in medium and long-term ecological restoration projects in the semi-arid region in Central Mexico.

    Keywords: Degradation, Ecological attributes for restoration, Niche-base distribution models, Semiarid environments

  • González Vilas L, Guisande C, Vari R, Pelayo-Villamil P, Manjarrés-Hernández A, García-Roselló E et al. (2015)

    Geospatial data of freshwater habitats for macroecological studies: an example with freshwater fishes

    International Journal of Geographical Information Science 1-16.

    Global data sets are essential in macroecological studies. File formats of the few available data sets of freshwater ecosystems, however, are either incompatible with most macroecological software packages, incomplete, or of coarse spatial resolutions. We integrated more than 460 million geographical coordinates for freshwater habitats in the FRWater data set, partitioned into seven different habitats (lentic, wetlands, reservoirs, small rivers, large rivers, small ditches, large ditches, small channels, large channels, small drains and large drains) in ModestR ( A comprehensive collection of geospatial rasters was assembled, one for each of the seven freshwater habitats, with the area in km2 occupied by each habitat presented in cells of 5 arc-minute resolution. The utility of FRWater was evaluated using hierarchical partitioning via the identification of the contribution of the seven different freshwater habitats to both species richness and rarity. To this end, we used a dat...

    Keywords: freshwater fishes, freshwater habitats, rarity, species richness