Uses of GBIF in scientific research

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

List of publications

  • 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

  • Kraft K, Brown C, Nabhan G, Luedeling E, Luna Ruiz J, Coppens d'Eeckenbrugge G et al. (2014)

    Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico

    Proceedings of the National Academy of Sciences of the United States of America 1-6.

    The study of crop origins has traditionally involved identifying geographic areas of high morphological diversity, sampling populations of wild progenitor species, and the archaeological retrieval of macroremains. Recent investigations have added identification of plant microremains (phytoliths, pollen, and starch grains), biochemical and molecular genetic approaches, and dating through (14)C accelerator mass spectrometry. We investigate the origin of domesticated chili pepper, Capsicum annuum, by combining two approaches, species distribution modeling and paleobiolinguistics, with microsatellite genetic data and archaeobotanical data. The combination of these four lines of evidence yields consensus models indicating that domestication of C. annuum could have occurred in one or both of two areas of Mexico: northeastern Mexico and central-east Mexico. Genetic evidence shows more support for the more northern location, but jointly all four lines of evidence support central-east Mexico, where preceramic macroremains of chili pepper have been recovered in the Valley of Tehuacán. Located just to the east of this valley is the center of phylogenetic diversity of Proto-Otomanguean, a language spoken in mid-Holocene times and the oldest protolanguage for which a word for chili pepper reconstructs based on historical linguistics. For many crops, especially those that do not have a strong archaeobotanical record or phylogeographic pattern, it is difficult to precisely identify the time and place of their origin. Our results for chili pepper show that expressing all data in similar distance terms allows for combining contrasting lines of evidence and locating the region(s) where cultivation and domestication of a crop began.

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

  • Ogada D (2014)

    The power of poison: pesticide poisoning of Africa's wildlife

    Annals of the New York Academy of Sciences 1322 1-20.

    Poisons have long been used to kill wildlife throughout the world. An evolution has occurred from the use of plant- and animal-based toxins to synthetic pesticides to kill wildlife, a method that is silent, cheap, easy, and effective. The use of pesticides to poison wildlife began in southern Africa, and predator populations were widely targeted and eliminated. A steep increase has recently been observed in the intensity of wildlife poisonings, with corresponding population declines. However, the majority of poisonings go unreported. Under national laws, it is illegal to hunt wildlife using poisons in 83% of African countries. Pesticide regulations are inadequate, and enforcement of existing legislation is poor. Few countries have forensic field protocols, and most lack storage and testing facilities. Methods used to poison wildlife include baiting carcasses, soaking grains in pesticide solution, mixing pesticides to form salt licks, and tainting waterholes. Carbofuran is the most widely abused pesticide in Africa. Common reasons for poisoning are control of damage-causing animals, harvesting fish and bushmeat, harvesting animals for traditional medicine, poaching for wildlife products, and killing wildlife sentinels (e.g., vultures because their aerial circling alerts authorities to poachers' activities). Populations of scavengers, particularly vultures, have been decimated by poisoning. Recommendations include banning pesticides, improving pesticide regulations and controlling distribution, better enforcement and stiffer penalties for offenders, increasing international support and awareness, and developing regional pesticide centers.

    Keywords: 20th Century, Africa, Animals, Conservation of Natural Resources, History, Pesticides, Pesticides: poisoning, Poisons, Poisons: history, Poisons: toxicity, Wild, Wild: physiology

  • Vinceti B, Loo J, Gaisberger H, van Zonneveld M, Schueler S, Konrad H et al. (2013)

    Conservation Priorities for Prunus africana Defined with the Aid of Spatial Analysis of Genetic Data and Climatic Variables

    PLoS ONE 8(3) e59987.

    Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites) from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1) was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2) at optimizing representativeness of the genetic diversity found throughout the species’ range. Populations in East African countries (especially Kenya and Tanzania) were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.

    Keywords: 20th Century, Africa, Animals, Conservation of Natural Resources, History, Pesticides, Pesticides: poisoning, Poisons, Poisons: history, Poisons: toxicity, Wild, Wild: physiology

  • Jaramillo J, Muchugu E, Vega F, Davis A, Borgemeister C, Chabi-Olaye A (2011)

    Some Like It Hot: The Influence and Implications of Climate Change on Coffee Berry Borer (Hypothenemus hampei) and Coffee Production in East Africa

    PLoS ONE 6(9) e24528.

    The negative effects of climate change are already evident for many of the 25 million coffee farmers across the tropics and the 90 billion dollar (US) coffee industry. The coffee berry borer (Hypothenemus hampei), the most important pest of coffee worldwide, has already benefited from the temperature rise in East Africa: increased damage to coffee crops and expansion in its distribution range have been reported. In order to anticipate threats and prioritize management actions for H. hampei we present here, maps on future distributions of H. hampei in coffee producing areas of East Africa. Using the CLIMEX model we relate present-day insect distributions to current climate and then project the fitted climatic envelopes under future scenarios A2A and B2B (for HADCM3 model). In both scenarios, the situation with H. hampei is forecasted to worsen in the current Coffea arabica producing areas of Ethiopia, the Ugandan part of the Lake Victoria and Mt. Elgon regions, Mt. Kenya and the Kenyan side of Mt. Elgon, and most of Rwanda and Burundi. The calculated hypothetical number of generations per year of H. hampei is predicted to increase in all C. arabica-producing areas from five to ten. These outcomes will have serious implications for C. arabica production and livelihoods in East Africa. We suggest that the best way to adapt to a rise of temperatures in coffee plantations could be via the introduction of shade trees in sun grown plantations. The aims of this study are to fill knowledge gaps existing in the coffee industry, and to draft an outline for the development of an adaptation strategy package for climate change on coffee production.

    Keywords: 20th Century, Africa, Animals, Conservation of Natural Resources, History, Pesticides, Pesticides: poisoning, Poisons, Poisons: history, Poisons: toxicity, Wild, Wild: physiology