Uses of GBIF in scientific research

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

List of publications

  • Bush M, McMichael C (2016)

    Holocene Variability of an Amazonian Hyperdominant

    Journal of Ecology.

    Little is known regarding the long-term stability or instability of Amazonian plant communities. We assessed whether the most abundant species, hyperdominants, may have risen to prominence at the Pleistocene-Holocene transition, following subsequent changes in moisture regimes, or as a result of human activity later in the Holocene. The fossil pollen history of the commonest western Amazonian tree, Iriartea deltoidea (hereafter Iriartea), is investigated using fossil pollen data from 13 lakes. Iriartea is a monospecific genus with diagnostic pollen. It is also considered a ‘useful’ plant, and its abundance could have been enriched by human action. Iriartea pollen was found to have increased in abundance in the last 3000 years, but did not show a consistent relationship with human activity. The suggestion that the hyperdominants in modern Amazonian forests are a legacy of pre-Columbian people is unsupported. The abundance of Iriartea pollen is related to increasing precipitation, not human activity over the last 3000 years. This member of the hyperdominant category of Amazonian trees has only recently acquired this status. Synthesis: Our findings our consistent with the observation that communities in complex systems are ephemeral. The populations of even the most abundant species can change over a few tens of generations. The relative abundance of tree species, even in relatively stable systems such as those of Amazonian floodplains, changes on ecological not evolutionary timescales.

    Keywords: Anthropocene, Climate change, Forest enrichment, Fossil charcoal, Fossil pollen, Human disturbance, Hyperdominant tree, Iriartea deltoidea, Palaeoecology, Plant–climate interactions


  • Bush M, Correa-Metrio A, McMichael C, Sully S, Shadik C, Valencia B et al. (2016)

    A 6900-year history of landscape modification by humans in lowland Amazonia

    Quaternary Science Reviews 141 52-64.

    A sedimentary record from the Peruvian Amazon provided evidence of climate and vegetation change for the last 6900 years. Piston cores collected from the center of Lake Sauce, a 20 m deep lake at 600 m elevation, were 19.7 m in length. The fossil pollen record showed a continuously forested catchment within the period of the record, although substantial changes in forest composition were apparent. Fossil charcoal, found throughout the record, was probably associated with humans setting fires. Two fires, at c. 6700 cal BP and 4270 cal BP, appear to have been stand-replacing events possibly associated with megadroughts. The fire event at 4270 cal BP followed a drought that caused lowered lake levels for several centuries. The successional trajectories of forest recovery following these large fires were prolonged by smaller fire events. Fossil pollen of Zea mays (cultivated maize) provided evidence of agricultural activity at the site since c. 6320 cal BP. About 5150 years ago, the lake deepened and started to deposit laminated sediments. Maize agriculture reached a peak of intensity between c. 3380 and 700 cal BP. Fossil diatom data provided a proxy for lake nutrient status and productivity, both of which peaked during the period of maize cultivation. A marked change in land use was evident after c. 700 cal BP when maize agriculture was apparently abandoned at this site. Iriartea, a hyperdominant of riparian settings in western Amazonia, increased in abundance within the last 1100 years, but declined markedly at c. 1070 cal BP and again between c. 80 and −10 cal BP.

    Keywords: Agriculture, Forest enrichment, Fossil charcoal, Fossil diatoms, Fossil pollen, Human disturbance, Iriartea, Maize, Mauritia, Pre-Columbian


  • Deblauwe V, Droissart V, Bose R, Sonké B, Blach-Overgaard A, Svenning J et al. (2016)

    Remotely sensed temperature and precipitation data improve species distribution modelling in the tropics

    Global Ecology and Biogeography.

    Aim Species distribution modelling typically relies completely or partially on climatic variables as predictors, overlooking the fact that these are themselves predictions with associated uncertainties. This is particularly critical when such predictors are interpolated between sparse station data, such as in the tropics. The goal of this study is to provide a new set of satellite-based climatic predictor data and to evaluate its potential to improve modelled species–climate associations and transferability to novel geographical regions. Location Rain forests areas of Central Africa, the Western Ghats of India and South America. Methods We compared models calibrated on the widely used WorldClim station-interpolated climatic data with models where either temperature or precipitation data from WorldClim were replaced by data from CRU, MODIS, TRMM and CHIRPS. Each predictor set was used to model 451 plant species distributions. To test for chance associations, we devised a null model with which to compare the accuracy metric obtained for every species. Results Fewer than half of the studied rain forest species distributions matched the climatic pattern better than did random distributions. The inclusion of MODIS temperature and CHIRPS precipitation estimates derived from remote sensing each allowed for a better than random fit for respectively 40% and 22% more species than models calibrated on WorldClim. Furthermore, their inclusion was positively related to a better transferability of models to novel regions. Main conclusions We provide a newly assembled dataset of ecologically meaningful variables derived from MODIS and CHIRPS for download, and provide a basis for choosing among the plethora of available climate datasets. We emphasize the need to consider the method used in the production of climate data when working on a region with sparse meteorological station data. In this context, remote sensing data should be the preferred choice, particularly when model transferability to novel climates or inferences on causality are invoked.

    Keywords: Association test, CHIRPS, GLM, MODIS, MaxEnt, TRMM, WorldClim, ecological niche model, habitat suitability, null model


  • Herkt K, Barnikel G, Skidmore A, Fahr J (2016)

    A high-resolution model of bat diversity and endemism for continental Africa

    Ecological Modelling 320 9-28.

    Bats are the second-most species-rich mammal group numbering more than 1270 species globally. Our knowledge of their geographic distributions and diversity patterns however is very limited – possibly the poorest among mammals – mainly due to their nocturnal and volant life history, and challenging fieldwork conditions in the tropics where most bat species occur. This knowledge gap obscures the geographic extent of ecosystem services provided by bats (i.e. pollination, seed dispersal and insect control), translates into inefficient conservation policies, and restricts macroecological analyses to coarse spatial resolutions. In contrast to the currently prevailing method of estimating species distributions using expert-drawn range maps, correlative species distribution models (SDMs) can provide estimates at very fine spatial grains and largely account for widespread sample bias as well as the prevalent Wallacean shortfall in species occurrence data. Very few such studies have hitherto been published that cover a large and complete taxonomic group with fine resolution at continental extent. Using an unparalleled amount of occurrence data, the MaxEnt algorithm and tailored solutions to specific modelling challenges, we created SDMs for nearly all 250 African bat species to explore emerging diversity patterns at a resolution of 1km2. Predicted species richness generally increases towards the equator conforming to expectations. Within the tropical area of elevated richness, several pronounced richness peaks and lows stand out, hinting at a complex interplay of determining factors. Richness gradients are often steep, decreasing strongly away from streams, and especially so in savanna biomes. Species richness also seems positively associated with rugged terrain, in particular at lower elevations. Centres of endemism are found primarily at low latitudes near major elevational ranges. Overlap with hotspots of species richness is rather low, and confined to five or six topodiverse, relatively low lying areas between western Guinea and the East African coast. Several poorly sampled regions are identified that may represent rewarding future survey targets. Our results demonstrate the value of stacking SDMs to infer plausible continent-wide diversity gradients at a spatial resolution fine enough to directly inform conservation policies and to open up new avenues in macroecological research.

    Keywords: Africa, Chiroptera, Range size rarity, Spatial resolution, Species distribution modelling (SDM), Species richness


  • Janssens S, Vandelook F, De Langhe E, Verstraete B, Smets E, Vandenhouwe I et al. (2016)

    Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia.

    The New phytologist.

    Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.

    Keywords: Africa, Chiroptera, Range size rarity, Spatial resolution, Species distribution modelling (SDM), Species richness


  • Langejans G, Dusseldorp G, Thackeray J (2016)

    Pleistocene molluscs from Klasies River (South Africa): Reconstructing the local coastal environment

    Quaternary International.

    We explore if taxonomic analysis of archaeological mollusc assemblages can be used to reconstruct Late Pleistocene (MIS 5–3) coastal environments at Klasies River in South Africa. To obtain a balanced reconstruction, we analyse the large molluscs separately from the so-called incidentals, the small mollusc species. Based on modern mollusc habitat preferences and tolerances we identify four different eco-profiles to help characterise sea surface temperatures and the character of the shore: temperature profile; geographical distribution; substrate; wave interaction. We hypothesise that changes in the Klasies River mollusc community/eco-profiles can be linked to global glacial and interglacial events and we define several testable assumptions. We found that in response to global warming and cooling events, the Klasies River mollusc communities change slightly, yet significantly. Other sources of marine environmental data confirm that average sea surface temperatures gradually decreased, but probably remained within the modern southern east coast range of variation. It appears that coastal sea surface temperatures of the warm Agulhas current were not particularly depressed during the occupation sequence. The character of the coastal topography does change more apparently during the occupation sequence of the sites and with it the mollusc assemblages: from an interglacial rocky shore in the Klasies and two Mossel Bay phases to a more glacial sandy environment during the Howiesons Poort and the MSA III. In conclusion, the temperature tolerance levels of many Klasies River mollusc species are too broad to reflect small changes in sea surface temperatures. However, in conjunction with other eco-profiles and environmental proxies, such as substrate requirements and oxygen isotopes, the temperature approximations are useful, particularly when evaluating large scale sea surface temperature fluctuations. For the characterisation of the shore and substrate we found the eco-profile approach very useful.

    Keywords: Climatic and environmental change, Klasies River, Late Pleistocene, Middle Stone Age, Molluscs, South Africa


  • Ornelas J, González C, Hernández-Baños B, García-Moreno J (2016)

    Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

    Ecology and Evolution.

    The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue-throated populations (Sierra Madre del Sur); two groups of amethyst-throated populations (Trans-Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue- and amethyst-throated populations does not correspond to the 2-MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest-interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.

    Keywords: Feather iridescence, Lampornis amethystinus, Mesoamerican highlands, glacial cycles


  • 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


  • Pârâu L, Strubbe D, Mori E, Menchetti M, Ancillotto L, Kleunen A et al. (2016)

    Rose-ringed Parakeet Populations and Numbers in Europe: A Complete Overview

    The Open Ornithology Journal 9(1) 1-13.

    Purpose: Alien species are considered one of the major causes contributing to the current loss of biodiversity. Over the past few decades, a large and increasing number of alien species have become invasive in many parts of the world. Their impacts range from competition for resources with native species to damage of urban infrastructure. In Europe, over a thousand alien species are now established, of which 74 are birds. Among 12 established alien parrot species in Europe, Introduction: The Rose-ringed Parakeet (RRP) Psittacula krameri (Scopoli, 1769) is the most abundant and widespread. Since the 1960's, RRPs have established more than 100 wild populations in several European countries. For Western Europe, long-term demographic data indicate the species has grown considerably in number, although some populations have failed to persist. Data: Is scarce and dispersed for countries in Central, Eastern and Northern Europe. Therefore, here we present detailed demographic data of RRP for 90 populations in 10 European countries. Furthermore, we present information on the status of the species in another 27 European countries, for which previously no data were published. Conclusion: Our synthesis reveals a positive demographic trend across the continent, although locally, some populations appear to have reached carrying capacity.

    Keywords: Demography, Europe, Invasive alien species, Parrots, Population, Psittaciformes


  • Sanín M, Kissling W, Bacon C, Borchsenius F, Galeano G, Svenning J et al. (2016)

    The Neogene rise of the tropical Andes facilitated diversification of wax palms ( Ceroxylon : Arecaceae) through geographical colonization and climatic niche separation

    Botanical Journal of the Linnean Society.

    he tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands out in the palm family (Arecaceae) due to its adaptation to cold, mountainous environments. Here, we reconstruct the biogeography and climatic preference of this lineage to test the hypothesis that Andean uplift allowed diversification by providing suitable habitats along climatic and elevational gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among clades along elevational temperature gradients. We conclude that the Neogene Andean uplift has facilitated the diversification of this iconic plant group via opportunities for geographical migration and separation within its climatic niche

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion