Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Kenya.
For all researches, please visit our "Peer-reviewed publications" page.

List of publications

  • De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)

    Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

    Biodiversity Data Journal 5 e10989.

    The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data


  • Biber-Freudenberger L, Ziemacki J, Tonnang H, Borgemeister C (2016)

    Future Risks of Pest Species under Changing Climatic Conditions.

    PloS one 11(4) e0153237.

    Most agricultural pests are poikilothermic species expected to respond to climate change. Currently, they are a tremendous burden because of the high losses they inflict on crops and livestock. Smallholder farmers in developing countries of Africa are likely to suffer more under these changes than farmers in the developed world because more severe climatic changes are projected in these areas. African countries further have a lower ability to cope with impacts of climate change through the lack of suitable adapted management strategies and financial constraints. In this study we are predicting current and future habitat suitability under changing climatic conditions for Tuta absoluta, Ceratitis cosyra, and Bactrocera invadens, three important insect pests that are common across some parts of Africa and responsible for immense agricultural losses. We use presence records from different sources and bioclimatic variables to predict their habitat suitability using the maximum entropy modelling approach. We find that habitat suitability for B. invadens, C. cosyra and T. absoluta is partially increasing across the continent, especially in those areas already overlapping with or close to most suitable sites under current climate conditions. Assuming a habitat suitability at three different threshold levels we assessed where each species is likely to be present under future climatic conditions and if this is likely to have an impact on productive agricultural areas. Our results can be used by African policy makers, extensionists and farmers for agricultural adaptation measures to cope with the impacts of climate change.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data


  • Drees C, Husemann M, Homburg K, Brandt P, Dieker P, Habel J et al. (2016)

    Molecular analyses and species distribution models indicate cryptic northern mountain refugia for a forest-dwelling ground beetle

    Journal of Biogeography.

    Aim Identification of potential glacial refugia and post-glacial colonization processes of a flightless, cold-adapted ground beetle Location Central and eastern Europe. Methods We analysed the genetic structure of 33 Carabus sylvestris populations sampled across its entire distribution range using nuclear and mitochondrial markers. We further compiled occurrence records to develop species distribution models to predict distribution ranges for the last glacial period and the present based on the species’ current climatic niche. Results Distinct genetic lineages were detected for a number of mountain ranges and were congruent for both molecular marker systems. Most genetic splits were the results of vicariance, whereas dispersal was rare. Our models suggest that the species’ distribution range was larger and more interconnected in the past. Main conclusions Our data support multiple glacial refugia for C. sylvestris, some of which were located north of the Alps. Some lower mountain ranges were likely recolonized post-glacially.

    Keywords: 2014-SGR-1491, DEB-1353301, EF-1065753, EF-1065826, EF-1065864, National Science Foundation grants . Grant Numbers


  • Liu H, Zhang S, Wan T, Kamau P, Wang Z, Grall A et al. (2016)

    Exploring the pteridophyte flora of the Eastern Afromontane biodiversity hotspot

    Journal of Systematics and Evolution 54(6) 691-705.

    In this review, we explore our current understanding of the fern and lycophyte diversity occurring in the Eastern Afromontane Biodiversity Hotspot (EABH). The review explores the species diversity of this region in the context of the Afromadagascan pteridophyte diversity based on an exhaustive species list assembled in the synopsis of Afromadagascan pteridophytes published by Roux in 2009. The list was updated by incorporating recent progress in our understanding of the taxonomy and phylogeny of these plants. Evidence for a distinct pteridophyte flora occurring in the East African mountain region was discovered using ordination and clustering analyses. This EABH floras shares links to other Afromadagascan pteridophyte floras such as the one in the tropical lowland forests of central and western Africa. These floras share the dominance of species that preferably occur in humid climates whereas other African pteridophyte floras tend to contain a higher proportion of xeric adapted ferns. The phylogenetic composition of the EABH pteridophyte flora was assessed by comparing global versus local proportion of orders, families, and genera. This analysis revealed distinct patterns that are partly caused by the radiation of Blotiella and Triplophyllum besides selective colonization of species pre-adapted to Afromadagascan climates. In situ speciation in the East African tropical mountains may have contributed to the global diversity of widespread genera such as Asplenium and Pteris. In summary, this is the first comprehensive attempt to assess the pteridophyte diversity of the East African mountains providing the framework for future studies on their conservation, ecology, and evolution.

    Keywords: Africa, Madagascar, biodiversity assessment, ferns, lycophytes, phylogenetic composition


  • Mikula O, Šumbera R, Aghová T, Mbau J, Katakweba A, Sabuni C et al. (2016)

    Evolutionary history and species diversity of African pouched mice (Rodentia: Nesomyidae: Saccostomus )

    Zoologica Scripta.

    We explore diversity of African pouched mice, genus Saccostomus (Rodentia, Nesomyidae), by sampling molecular and morphological variation across their continental-scale distribution in southern and eastern African savannahs and woodlands. Both mitochondrial (cytochrome b) and nuclear DNA (IRBP, RAG1) as well as skull morphology confirm the distinction between two recognized species, S. campestris and S. mearnsi, with disjunct distribution in the Zambezian and Somali–Maasai bioregions, respectively. Molecular dating suggests the divergence of these taxa occurred in the Early Pliocene, 3.9 Ma before present, whereas the deepest divergences within each of them are only as old as 2.0 Ma for S. mearnsi and 1.4 Ma for S. campestris. Based on cytochrome b phylogeny, we defined five clades (three within S. campestris, two in S. mearnsi) whose species status was considered in the light of nuclear DNA markers and morphology. We conclude that S. campestris group consists of two subspecies S. campestris campestris (Peters, 1846; comprising two cytochrome b clades) and S. campestris mashonae (de Winton, 1897) that are moderately differentiated, albeit distinct in IRBP and skull form. They likely hybridize to a limited extent along the Kafue–Zambezi Rivers. Saccostomus mearnsi group consists of two species, S. mearnsi (Heller, 1910) and S. umbriventer (Miller, 1910), that are markedly differentiated in both nuclear markers and skull form and may possibly co-occur in south-western Kenya and north-eastern Tanzania. Analysis of historical demography suggests both subspecies of S. campestris experienced population expansion dated to the Last Glacial. In the present range of S. campestris group, the distribution modelling suggests a moderate fragmentation of suitable habitats during the last glacial cycle, whereas in the range of S. mearnsi group it predicts substantial shifts of its occurrence in the same period.

    Keywords: Africa, Madagascar, biodiversity assessment, ferns, lycophytes, phylogenetic composition


  • Moyes C, Shearer F, Huang Z, Wiebe A, Gibson H, Nijman V et al. (2016)

    Predicting the geographical distributions of the macaque hosts and mosquito vectors of Plasmodium knowlesi malaria in forested and non-forested areas.

    Parasites & vectors 9(1) 242.

    BACKGROUND: Plasmodium knowlesi is a zoonotic pathogen, transmitted among macaques and to humans by anopheline mosquitoes. Information on P. knowlesi malaria is lacking in most regions so the first step to understand the geographical distribution of disease risk is to define the distributions of the reservoir and vector species. METHODS: We used macaque and mosquito species presence data, background data that captured sampling bias in the presence data, a boosted regression tree model and environmental datasets, including annual data for land classes, to predict the distributions of each vector and host species. We then compared the predicted distribution of each species with cover of each land class. RESULTS: Fine-scale distribution maps were generated for three macaque host species (Macaca fascicularis, M. nemestrina and M. leonina) and two mosquito vector complexes (the Dirus Complex and the Leucosphyrus Complex). The Leucosphyrus Complex was predicted to occur in areas with disturbed, but not intact, forest cover (> 60 % tree cover) whereas the Dirus Complex was predicted to occur in areas with 10-100 % tree cover as well as vegetation mosaics and cropland. Of the macaque species, M. nemestrina was mainly predicted to occur in forested areas whereas M. fascicularis was predicted to occur in vegetation mosaics, cropland, wetland and urban areas in addition to forested areas. CONCLUSIONS: The predicted M. fascicularis distribution encompassed a wide range of habitats where humans are found. This is of most significance in the northern part of its range where members of the Dirus Complex are the main P. knowlesi vectors because these mosquitoes were also predicted to occur in a wider range of habitats. Our results support the hypothesis that conversion of intact forest into disturbed forest (for example plantations or timber concessions), or the creation of vegetation mosaics, will increase the probability that members of the Leucosphyrus Complex occur at these locations, as well as bringing humans into these areas. An explicit analysis of disease risk itself using infection data is required to explore this further. The species distributions generated here can now be included in future analyses of P. knowlesi infection risk.

    Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine


  • Plath M, Moser C, Bailis R, Brandt P, Hirsch H, Klein A et al. (2016)

    A novel bioenergy feedstock in Latin America? Cultivation potential of Acrocomia aculeata under current and future climate conditions

    Biomass and Bioenergy 91 186-195.

    Plant oil is a key commodity in the global economy, particularly for food and bioenergy markets. However, current production practices often impair smallholder livelihoods, cause land use changes, and compete for food production. The neotropical palm Acrocomia aculeata is currently being promoted as a novel sustainable biomass feedstock, particularly for bioenergy, but only little is known about the palm’s ecological requirements. Based on a comprehensive literature and database search for recorded occurrences of A. aculeata in Latin America, we computed an ecological niche modeling to determine the palm’s potential distribution area based on climatic and soil variables. We subsequently considered current land cover and predicted future climate change scenarios to discuss the cultivation potential of A. aculeata within its possible distribution area. The results revealed a large potential to cultivate A. aculeata in Latin America under current abiotic environmental conditions. The two core distribution regions identified were (1) Central America including the Caribbean, northern Colombia and Venezuela, and (2) southern Brazil and eastern Paraguay. A considerable proportion of the medium to highly suitable growing areas were found to be currently used for agricultural production or covered by land types with high conservation and carbon sequestration value. Applying the model under the IPCC’s A2A ‘business as usual’ emission scenario suggested that by 2080 the vast majority of suitable growing areas severely decline in extent or disappear entirely. Our ecological niche modeling thus shows that despite the palm’s high cultivation potential, a sustainable deployment of A. aculeata requires a precautious, evidence-based approach.

    Keywords: Biofuel, Ecological niche modeling, Macaw palm, Macaúba, Sustainability


  • Moraga P, Cano J, Baggaley R, Gyapong J, Njenga S, Nikolay B et al. (2015)

    Modelling the distribution and transmission intensity of lymphatic filariasis in sub-Saharan Africa prior to scaling up interventions: integrated use of geostatistical and mathematical modelling

    Parasites & Vectors 8(1) 560.

    BACKGROUND:Lymphatic filariasis (LF) is one of the neglected tropical diseases targeted for global elimination. The ability to interrupt transmission is, partly, influenced by the underlying intensity of transmission and its geographical variation. This information can also help guide the design of targeted surveillance activities. The present study uses a combination of geostatistical and mathematical modelling to predict the prevalence and transmission intensity of LF prior to the implementation of large-scale control in sub-Saharan Africa.METHODS:A systematic search of the literature was undertaken to identify surveys on the prevalence of Wuchereria bancrofti microfilaraemia (mf), based on blood smears, and on the prevalence of antigenaemia, based on the use of an immuno-chromatographic card test (ICT). Using a suite of environmental and demographic data, spatiotemporal multivariate models were fitted separately for mf prevalence and ICT-based prevalence within a Bayesian framework and used to make predictions for non-sampled areas. Maps of the dominant vector species of LF were also developed. The maps of predicted prevalence and vector distribution were linked to mathematical models of the transmission dynamics of LF to infer the intensity of transmission, quantified by the basic reproductive number (R 0 ).RESULTS:The literature search identified 1267 surveys that provide suitable data on the prevalence of mf and 2817 surveys that report the prevalence of antigenaemia. Distinct spatial predictions arose from the models for mf prevalence and ICT-based prevalence, with a wider geographical distribution when using ICT-based data. The vector distribution maps demonstrated the spatial variation of LF vector species. Mathematical modelling showed that the reproduction number (R 0 ) estimates vary from 2.7 to 30, with large variations between and within regions.CONCLUSIONS:LF transmission is highly heterogeneous, and the developed maps can help guide intervention, monitoring and surveillance strategies as countries progress towards LF elimination.

    Keywords: Basic reproductive number, Bayesian geostatistical modelling, Lymphatic filariasis, Mathematical modelling, Sub-Saharan Africa, Wuchereria bancrofti


  • Ya B (2015)

    Distribution and Conservation Status of the Mount Kilimanjaro Guereza (Colobus guereza caudatus) Thomas, 1885

    Primate Conservation 29.

    The Mount Kilimanjaro guereza Colobus guereza caudatus is considered to be endemic to northeast Tanzania. This paper presents the first records for C. g. caudatus in Kenya, describes the distribution of this subspecies, and assesses its con - servation status. In September 2014, we found C. g. caudatus in southeast Kenya in Kitobo Forest Reserve (1.6 km²) and Loito - kitok Forest Reserve (4.2 km²). This subspecies has an altitudinal range of c. 660–3,050 m asl and an ‘Extent of Occurrence’ of c. 4,040 km². These findings are important as they: (1) add one subspecies of primate to Kenya’s primate list; (2) remove one endemic subspecies of primate from Tanzania’s primate list; (3) establish C. g. caudatus as the most threatened primate subspe - cies in Kenya; (4) change the priorities for actions necessary to maintain Kenya’s primate diversity; and (5) indicate that detailed biodiversity surveys within Kitobo Forest and Loitokitok Forest are likely to yield new data crucial to the conservation of biodi - versity in southeast Kenya

    Keywords: Colobus guereza caudatus, biogeography, colobus


  • Cadima X, van Zonneveld M, Scheldeman X, Castañeda N, Patiño F, Beltran M et al. (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