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

  • García-Roselló, E., Guisande, C., Manjarrés-Hernández, A., González-Dacosta, J., Heine, J., Pelayo-Villamil, P., González-Vilas, L., Vari, R., Vaamonde, A., Granado-Lorencio, C., Lobo, J., 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

  • Mendoza, ., Ospina, O., Cárdenas-Henao, H., García-R, J., 2015.

    A likelihood inference of historical biogeography in the world's most diverse terrestrial vertebrate genus: Diversification of direct-developing frogs (Craugastoridae: Pristimantis) across the Neotropics.

    Molecular phylogenetics and evolution 85 50-58.

    The geology of the northern Andean region has driven the evolutionary history of Neotropical fauna through the creation of barriers and connections that have resulted in speciation and dispersal events, respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic placement of 12 species from the montane Andes of Colombia in a broader geographical context with a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40 million years and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic history of the genus using ancestral range reconstruction by biogeographic regions and elevational ranges. We recognized the middle elevational band (between 1000 and 3000 m) in the Northwestern Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species. Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion of lowland species.

    Keywords: Ancestral range reconstruction, Andes, Biogeography, Diversification, Terrarana

  • Onstein, R., Carter, R., Xing, Y., Richardson, J., Linder, H., 2015.

    Do Mediterranean-type ecosystems have a common history? - insights from the Buckthorn family (Rhamnaceae).

    Evolution; international journal of organic evolution.

    Mediterranean-type ecosystems (MTEs) are remarkable in their species-richness and endemism, but the processes which have led to this diversity remain enigmatic. Here, we hypothesize that continent-dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile and Western Australia. To test this hypothesis, we built a phylogenenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations and use Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent-dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four out of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter-rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions. This article is protected by copyright. All rights reserved.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation

  • Parsa, S., Hazzi, N., Chen, Q., Lu, F., Herrera Campo, B., Yaninek, J., Vásquez-Ordóñez, A., 2015.

    Potential geographic distribution of two invasive cassava green mites.

    Experimental & applied acarology 65(2) 195-204.

    The cassava green mites Mononychellus tanajoa and M. mcgregori are highly invasive species that rank among the most serious pests of cassava globally. To guide the development of appropriate risk mitigation measures preventing their introduction and spread, this article estimates their potential geographic distribution using the maximum entropy approach to distribution modeling. We compiled 1,232 occurrence records for M. tanajoa and 99 for M. mcgregori, and relied on the WorldClim climate database as a source of environmental predictors. To mitigate the potential impact of uneven sampling efforts, we applied a distance correction filter resulting in 429 occurrence records for M. tanajoa and 55 for M. mcgregori. To test for environmental biases in our occurrence data, we developed models trained and tested with records from different continents, before developing the definitive models using the full record sets. The geographically-structured models revealed good cross-validation for M. tanajoa but not for M. mcgregori, likely reflecting a subtropical bias in M. mcgregori's invasive range in Asia. The definitive models exhibited very good performance and predicted different potential distribution patterns for the two species. Relative to M. tanajoa, M. mcgregori seems better adapted to survive in locations lacking a pronounced dry season, for example across equatorial climates. Our results should help decision-makers assess the site-specific risk of cassava green mite establishment, and develop proportional risk mitigation measures to prevent their introduction and spread. These results should be particularly timely to help address the recent detection of M. mcgregori in Southeast Asia.

    Keywords: Cassava green mite, Manihot esculenta, Mononychellus mcgregori, Mononychellus tanajoa, Pest risk map, Species distribution modeling

  • van Kleunen, M., Dawson, W., Essl, F., Pergl, J., Winter, M., Weber, E., Kreft, H., Weigelt, P., Kartesz, J., Nishino, M., Antonova, L., Barcelona, J., Cabezas, F., Cárdenas, D., Cárdenas-Toro, J., Castaño, N., Chacón, E., Chatelain, C., Ebel, A., Figueiredo, E., Fuentes, N., Groom, Q., Henderson, L., Kupriyanov, A., Masciadri, S., Meerman, J., Morozova, O., Moser, D., Nickrent, D., Patzelt, A., Pelser, P., Baptiste, M., Poopath, M., Schulze, M., Seebens, H., Shu, W., Thomas, J., Velayos, M., Wieringa, J., Pyšek, P., 2015.

    Global exchange and accumulation of non-native plants

    Nature advance on.

    Keywords: Cassava green mite, Manihot esculenta, Mononychellus mcgregori, Mononychellus tanajoa, Pest risk map, Species distribution modeling

  • Cadima, X., van Zonneveld, M., Scheldeman, X., Castañeda, N., Patiño, F., Beltran, M., Van Damme, P., 2014.

    Endemic wild potato (Solanum spp.) biodiversity status in Bolivia: Reasons for conservation concerns

    Journal for Nature Conservation 22(2) 113-131.

    Crop wild relatives possess important traits, therefore ex situ and in situ conservation efforts are essential to maintain sufficient options for crop improvement. Bolivia is a centre of wild relative diversity for several crops, among them potato, which is an important staple worldwide and the principal food crop in this country. Despite their relevance for plant breeding, limited knowledge exists about their in situ conservation status. We used Geographic Information Systems (GIS) and distribution modelling with the software Maxent to better understand geographic patterns of endemic wild potato diversity in Bolivia. In combination with threat layers, we assessed the conservation status of all endemic species, 21 in total. We prioritised areas for in situ conservation by using complementary reserve selection and excluded 25% of the most-threatened collection sites because costs to implement conservation measures at those locations may be too high compared to other areas. Some 70% (15 of 21 species) has a preliminary vulnerable status or worse according to IUCN red list distribution criteria. Our results show that four of these species would require special conservation attention because they were only observed in <15 locations and are highly threatened by human accessibility, fires and livestock pressure. Although highest species richness occurs in south-central Bolivia, in the departments Santa Cruz and Chuquisaca, the first priority area for in situ conservation according to our reserve selection exercise is central Bolivia, Cochabamba; this area is less threatened than the potato wild relatives’ hotspot in south-central Bolivia. Only seven of the 21 species were observed in protected areas. To improve coverage of potato wild relatives’ distribution by protected areas, we recommend starting inventories in parks and reserves with high modelled diversity. Finally, to improve ex situ conservation, we targeted areas for germplasm collection of species with <5 accessions conserved in genebanks.

    Keywords: Crop wild relatives, Ex situ conservation, IUCN red listing, In situ conservation, Potato breeding material, Reserve selection, Species distribution modelling, Threat assessment

  • Flantua, S., Hooghiemstra, H., Boxel, J., Cabrera, M., González, Z., González-Arango, C., 2014.

    Connectivity dynamics since the Last Glacial Maximum in the northern Andes; a pollen-driven framework to assess potential migration

    98 - 123.

    We provide an innovative pollen-driven connectivity framework of the dynamic altitudinal distribution of North Andean biomes since the Last Glacial Maximum (LGM). Altitudinally changing biome distributions reconstructed from a pollen record from Lake La Cocha (2780 m) are assessed in terms of their changing surface and connectivity within the study area. The upper forest line (UFL) ecotone lodged during much of the time around 2000 m (LGM), 2400 m (ca. 14–8 ka), 2800 m (ca. 8–3 ka), and 3550–3600 m (modern time). This resulted in a four-fold increase of the area covered by mountain forest (Andean and sub-Andean), a decrease of 96% of páramo, and a disappearance of permanent snow. Upslope migration of the UFL of 20 vertical m yr–1 and more, as inferred from the pollen record, was spatially assessed: reduced surface area, dispersal limitation, reduced connectivity, and extirpation of the subpáramo biome during a few centuries is shown. The study area includes abundant higher mid-range altitudes (2600–3400 m), with a steep reduction of available surface area and increased dispersal distance in the high and low altitudes. In this range, each 100-m altitudinal rise of the UFL results in 20%–60% reduction of the surface area available for páramo and connectivity. The critical elevations where large biome surfaces start to disconnect depend on the elevation of lowest thresholds in the landscape and the elevation of summits. The 2500–3600 m elevation range is most dynamic in terms of geography and ecological species sorting; the 1000–1500 m interval is relatively stable and is permanently covered by Andean forest, making this interval less sensitive for monitoring climate change. When forests migrate to higher elevations, distribution nuclei of species are compressed, resulting temporarily in a higher species diversity. The species dissimilarity coefficient reflects rate of (ecological) change more adequately than the rate of palynological turnover, because the latter is much influenced by the lengths of the time steps between the pollen samples. Spatial analysis of site-specific dynamics provides exciting new insights into past vegetation dynamics, with potential for better understanding species-area distributions, distribution patterns of biodiversity, and conservation of mountain ecosystems.

    Keywords: Andean biome dynamics, GIS, Last Glacial Maximum, elevational distribution patterns, landscape connectivity, palynological turnover rate, upper forest line

  • Galluzzi, G., López Noriega, I., 2014.

    Conservation and Use of Genetic Resources of Underutilized Crops in the Americas—A Continental Analysis

    Sustainability 6(2) 980-1017.

    Latin America is home to dramatically diverse agroecological regions which harbor a high concentration of underutilized plant species, whose genetic resources hold the potential to address challenges such as sustainable agricultural development, food security and sovereignty, and climate change. This paper examines the status of an expert-informed list of underutilized crops in Latin America and analyses how the most common features of underuse apply to these. The analysis pays special attention to if and how existing international policy and legal frameworks on biodiversity and plant genetic resources effectively support or not the conservation and sustainable use of underutilized crops. Results show that not all minor crops are affected by the same degree of neglect, and that the aspects under which any crop is underutilized vary greatly, calling for specific analyses and interventions. We also show that current international policy and legal instruments have so far provided limited stimulus and funding for the conservation and sustainable use of the genetic resources of these crops. Finally, the paper proposes an analytical framework for identifying and evaluating a crop’s underutilization, in order to define the most appropriate type and levels of intervention (international, national, local) for improving its status.

    Keywords: Latin America, NUS, conservation and sustainable use, genetic resources, international policies, underutilized crops

  • Lozano-Jaramillo, M., Rico-Guevara, A., Cadena, C., 2014.

    Genetic differentiation, niche divergence, and the origin and maintenance of the disjunct distribution in the Blossomcrown Anthocephala floriceps (Trochilidae).

    PloS one 9(9) e108345.

    Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7-2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.

    Keywords: Colombia, biogeography, ecological niches, geographic distribution, geography, historical geography, mitochondria, paleoclimato