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

  • 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.

  • 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

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

  • 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

  • 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

  • Demos T, Kerbis Peterhans J, Agwanda B, Hickerson M (2014)

    Uncovering cryptic diversity and refugial persistence among small mammal lineages across the Eastern Afromontane biodiversity hotspot.

    Molecular Phylogenetics and Evolution 71 41-54.

    The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness accompanied by significant conservation threat, a pattern typical across biodiversity hotspots. Using multi-locus molecular data under a coalescent species tree framework we identify major cryptic biogeographic patterns within and between two endemic montane small mammal species complexes, Hylomyscus mice and Sylvisorex shrews, co-distributed across the Albertine Rift and Kenya Highlands of the Eastern Afromontane Biodiversity Hotspot (EABH). Hypotheses put forward to account for the high diversity of the region include retention of older palaeo-endemic lineages across major regions in climatically stable refugia, as well as the accumulation of lineages associated with more recent differentiation between allopatric populations separated by unsuitable habitat during periods of Pleistocene aridification. Sympatric pairs of sister lineages were found to have significantly older divergence times than allopatric pairs. Genetic analyses and historical distribution modeling suggest that regional meta-populations have persisted since the Pliocene to mid-Pleistocene across a climatic gradient from the Albertine Rift in the west to the Kenya Highlands in the east for both focal taxa. Differing patterns of regional sub-division and demographic expansion were detected and are consistent with differing life histories as well as shared responses to regional variation in stability of suitable habitat. There is also strong support in both mice and shrew species for Late Miocene divergence with subsequent range expansion into sympatry in previously unidentified cryptic species pairs. These results highlight the broad temporal scale at which climatic and geological changes may have facilitated rare dispersal events between montane habitats as well as the long-term persistence of populations in both the Albertine Rift and the Kenyan Highlands that together contributed to the high species diversity and endemism in the EABH.

    Keywords: Albertine Rift, Biogeography, Coalescent, Forest refugia, Hylomyscus, Kenya

  • Habel J, Mulwa R, Gassert F, Rödder D, Ulrich W, Borghesio L et al. (2014)

    Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird

    Heredity 113(3) 205-14.

    The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size.

    Keywords: Albertine Rift, Biogeography, Coalescent, Forest refugia, Hylomyscus, Kenya

  • Kindt R, Lillesø J, van Breugel P, Bingham M, Demissew S, Dudley C et al. (2014)

    Correspondence in forest species composition between the Vegetation Map of Africa and higher resolution maps for seven African countries

    Applied Vegetation Science 17(1) 162-171.

    Abstract Question How well does the forest classification system of the 1:5,000,000 vegetation map of Africa developed by Frank White correspond with classification systems and more extensive information on species assemblages of higher resolution maps developed for Ethiopia, Kenya, Malawi, Rwanda, Tanzania, Uganda and Zambia? Methods We reviewed various national and sub-national vegetation maps for their potential in increasing the resolution of the African map. Associated documentation was consulted to compile species assemblages, and to identify indicator species, for national forest vegetation types. Indicator species were identified for each regional forest type by selecting those species that, among all the species listed for the same phytochorion (regional centre of endemism), were listed only for that forest type. For each of the national forest types, we counted the number of indicator species of the anticipated regional type. Floristic relationships (expressed by four different ecological distance measures) among national forest types were investigated based on distance-based redundancy analysis, permutational multivariate analysis of variance (PERMANOVA) using distance matrices and hierarchical clustering. Results For most of the national forests, the analysis of indicator species and floristic relationships confirmed the regional classification system for the majority of national forest types, including the allocation to different phytochoria. Permutation tests confirmed allocation of national forest types to regional typologies, although the number of possible permutations limited inferences for the Zambezian and Lake Victoria phytochoria. Two forest types from Ethiopia and Kenya did not correspond to regional forest types. Conclusions Our analysis provides support that as the classification systems are compatible, the resolution and information content of the vegetation map of Africa can be directly improved by adding information from national maps, probably leading to improved liability of its application domains. We found statistical evidence for a distinct Afromontane phytochorion. We suggest expanding the regional forest classification system with ‘Afromontane moist transitional forest’. Among the various application domains of the higher resolution maps, these maps allow for an enhanced phytochoristic analysis of eastern Africa.

    Keywords: Ethiopia, Frank White, Kenya, Kulczynski distance, Malawi, Rwanda, Tanzania, Uganda, Zambia, beta-sim distance, indicator species, phytochorion