Uses of GBIF in scientific research

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

List of publications

  • 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

  • González-Maya, J., Castañeda, F., González, R., Pacheco, J., Ceballos, G., 2014.

    Distribution, Range Extension, And Conservation Of The Endemic Black-Headed Bushmaster (Lachesis Melanocephala) In Costa Rica And Panama

    Herpetological Conservation and Biology 9(2) 369-377.

    The Black-headed Bushmaster, Lachesis melanocephala (Viperidae: Crotalinae), is an endemic pit viper from south-eastern Costa Rica. Despite its importance with regard to medicine and conservation, the ecology and distribution of this species are still poorly known, mainly because it was only recently recognized as a full species and records are scarce across its range. Known only from the Pacific slopes of the Talamanca mountain range, L. melanocephala is considered uncommon, restricted to undisturbed habitats, and likely threatened with extinction. Here we summarize its distribution, in terms of the Extent of Occurrence (EOO) and Species Distribution Model (SDM), and present a new locality record for the Las Tablas Protected Zone, at an elevation of 1,873 m, in a mixed premontane and montane oak forest habitat with steep slopes. The new record is located 14 km from the Panama border, so it is very likely that the species is also found in that country. Our results indicate that L. melanocephala has a very small geographic range, between 3,432 and 10,507 km2, depending on the method of assessment. It is found mostly in undisturbed habitats, including tropical, premontane and montane humid, very humid, and pluvial forests. Due to its restricted geographic range and habitat specificity, the severe and continued loss of lowland and mid-elevation forests throughout its range pose serious threats to the persistence of the Black-headed Bushmaster. Key

    Keywords: Crotalinae, Las Tablas, Talamanca, endemism, niche, snake

  • van Zonneveld, M., Castañeda, N., Scheldeman, X., van Etten, J., Van Damme, P., 2014.

    Application of consensus theory to formalize expert evaluations of plant species distribution models

    Applied Vegetation Science 17(3) 528-542.

    Aim: Application of environmental envelope modelling (EEM) for conservation planning requires careful validation. Opinions of experts who have worked with species of interest in the field can be a valuable and independent information source to validate EEM because of their first-hand experience with species occurrence and absence. However, their use in model validation is limited because of the subjectivity of their feedback. In this study, we present a method on the basis of cultural consensus theory to formalize expert model evaluations. Methods We developed, for five tree species, distribution models with nine different variable combinations and Maxent EEM software. Species specialists validated the generated distribution maps through an online Google Earth interface with the scores from Invalid to Excellent. Experts were also asked about the commission and omission errors of the distribution models they evaluated. We weighted expert scores according to consensus theory. These values were used to obtain a final average expert score for each of the produced distribution models. The consensus-weighted expert scores were compared with un-weighted scores and correlated to four conventional model performance parameters after cross-validation with test data: Area Under Curve (AUC), maximum Kappa, commission error and omission error. Results The median consensus-weighted expert score of all species–variable combinations was close to Fair. In general, experts that reached more consensus with peers were more positive about the EEM outcomes, compared to those that had more opposite judgements. Both consensus-weighted and un-weighted scores were significantly correlated to corresponding AUC, maximum Kappa and commission error values, but not to omission errors. More than half of the experts indicated that the distribution model they considered best included areas where the species is known to be absent. One third also indicated areas of species presence that were omitted by the model. Conclusions Our results indicate that experts are fairly positive about EEM outcomes. This is encouraging, but EEM application for conservation actions remains limited according to them. Methods to formalize expert knowledge allow a wider use of this information in model validation and improvement, and they complement conventional validation methods of presence-only modelling. Online GIS and survey applications facilitate the consultation of experts.

    Keywords: cultural consensus theory, envelope modelling, expert opinion, google earth, in situ conservation, mapforgen, model validatation, online survey, species distribution modelling

  • Feeley, K., Hurtado, J., Saatchi, S., Silman, M., Clark, D., 2013.

    Compositional shifts in Costa Rican forests due to climate-driven species migrations

    Global Change Biology 19(11) 3472-80.

    Species are predicted to shift their distributions upslope or poleward in response to global warming. This prediction is supported by a growing number of studies documenting species migrations in temperate systems but remains poorly tested for tropical species, and especially for tropical plant species. We analyzed changes in tree species composition in a network of 10 annually censused 1-ha plots spanning an altitudinal gradient of 70-2800 m elevation in Costa Rica. Specifically, we combined plot data with herbarium records (accessed through GBIF) to test if the plots' community temperature scores (CTS, average thermal mean of constituent species weighted by basal area) have increased over the past decade as is predicted by climate-driven species migrations. In addition, we quantified the contributions of stem growth, recruitment, and mortality to the observed patterns. Supporting our a priori hypothesis of upward species migrations, we found that there have been consistent directional shifts in the composition of the plots, such that the relative abundance of lowland species, and hence CTS, increased in 90% of plots. The rate of the observed compositional shifts corresponds to a mean thermal migration rate (TMR) of 0.0065 °C yr(-1) (95% CI = 0.0005-0.0132 °C yr(-1) ). While the overall TMR is slower than predicted based on concurrent regional warming of 0.0167 °C yr(-1) , migrations were on pace with warming in 4 of the 10 plots. The observed shifts in composition were driven primarily by mortality events (i.e., the disproportionate death of highland vs. lowland species), suggesting that individuals of many tropical tree species will not be able to tolerate future warming and thus their persistence in the face of climate change will depend on successful migrations. Unfortunately, in Costa Rica and elsewhere, land area inevitably decreases at higher elevations; hence, even species that are able to migrate successfully will face heightened risks of extinction.

    Keywords: cultural consensus theory, envelope modelling, expert opinion, google earth, in situ conservation, mapforgen, model validatation, online survey, species distribution modelling

  • Villalobos, F., 2013.

    Tree squirrels: A key to understand the historic biogeography of Mesoamerica?

    Mammalian Biology 78(4) 258-266.

    A multi-taxon historical biogeography approach (Brooks Parsimony Analysis) was used to estimate rela- tionships among the Mesoamerican lowland and highland areas and the particular biogeographic history of Mesoamerican squirrels (Sciurus, Microsciurus and Syntheosciurus species). A total of 15 lowland areas and 12 highland areas plus 41 clades comprising 240 species (45,135 records) were employed to obtain Taxon-Area Cladograms and Area Cladograms. A single most parsimonious General Area Cladogram indi- cated a strong vicariant relationship between Southern Mexico and the remainder of Mesoamerica, and identified several vicariant nodes (Modern Chiapanencan Volcanic Arc, Honduras’ Great Central Depres- sion, and Nicaraguan Depression) as well as historically independent highland areas. A secondary BPA in relation with Sciurus species showed several instances of post speciation dispersal or range expansion, lack of response to vicariant events, and, possibly, lineage duplication. The results obtained suggest that Mesoamerican biotas have been subjected to several major vicariant events, but the reticulated nature of some of its areas also indicates that dispersal (post-speciation dispersal and range expansion) had been important in the diversification of the Mesoamerican biota. This trend was also observed in the particular biogeographic history of Mesoamerican tree squirrels.

    Keywords: Sciurus, Vicariance, brooks parsimony analysis, dispersal, speciation

  • Rojas, C., Herrera, N., Stephenson, S., 2012.

    An update on the myxomycete biota (Amoebozoa: Myxogastria) of Colombia

    Check List 8(4) 617-619.

    Twelve new records of myxomycetes are reported for Colombia. These additions increase the number of myxomycetes known from this country to 108 species. Since the Colombian territory is part of a biodiversity-rich region in the heart of the Neotropics, the present effort may be considered as a minor contribution. However, due to scarcity of myxomycete research in this country and the importance of inventories involving microorganisms for such purposes as restoration ecology and ecosystem functioning projects, the data presented herein represent a necessary contribution to an understudied aspect of tropical ecology

    Keywords: Sciurus, Vicariance, brooks parsimony analysis, dispersal, speciation