Uses of GBIF in scientific research

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

List of publications

  • Hirsch H, Gallien L, Impson F, Kleinjan C, Richardson D, Le Roux J (2017)

    Unresolved native range taxonomy complicates inferences in invasion ecology: Acacia dealbata Link as an example

    Biological Invasions 1-8.

    Elaborate and expensive endeavours are underway worldwide to understand and manage biological invasions. However, the success of such efforts can be jeopardised due to taxonomic uncertainty. We highlight how unresolved native range taxonomy can complicate inferences in invasion ecology using the invasive tree Acacia dealbata in South Africa as an example. Acacia dealbata is thought to comprise two subspecies based on morphological characteristics and environmental requirements within its native range in Australia: ssp. dealbata and spp. subalpina. Biological control is the most promising option for managing invasive A. dealbata populations in South Africa, but it remains unknown which genetic/taxonomic entities are present in the country. Resolving this question is crucial for selecting appropriate biological control agents and for identifying areas with the highest invasion risk. We used species distribution models (SDMs) and phylogeographic approaches to address this issue. The ability of subspecies-specific and overall species SDMs to predict occurrences in South Africa was also explored. Furthermore, as non-overlapping bioclimatic niches between the two taxonomic entities may translate into evolutionary distinctiveness, we also tested genetic distances between the entities using DNA sequencing data and network analysis. Both approaches were unable to differentiate the two putative subspecies of A. dealbata. However, the SDM approach revealed a potential niche shift in the non-native range, and DNA sequencing results suggested repeated introductions of different native provenances into South Africa. Our findings provide important information for ongoing biological control attempts and highlight the importance of resolving taxonomic uncertainties in invasion ecology.

    Keywords: DNA sequencing, Fabaceae, Species distribution models, Subspecies, Tree invasions

  • Kennedy M, Lang P, Grimaldo J, Martins S, Bruce A, Moore I et al. (2017)

    Niche-breadth of freshwater macrophytes occurring in tropical southern African rivers predicts species global latitudinal range

    Aquatic Botany 136 21-30.

    The study tested the hypothesis that measurement, using multivariate Principal Components Analysis (PCA), of the niche-breadth of river macrophyte species in southern tropical Africa, may predict their larger-scale biogeographical range. Two measures of niche-breadth were calculated for 44 riverine macrophyte species, from 20 families commonly occurring in Zambia, using an approach based on PCA ordination with 16 bio-physico-chemical input variables. These included altitude, stream order, stream flow, pH, conductivity and soluble reactive phosphate concentration (SRP). In the absence of additional chemical water quality data for Zambian rivers, invertebrate-based measures of general water quality were also used. These were benthic macroinvertebrate Average Score per Taxon (ASPT), and individual abundance of nine macroinvertebrate families with differing water quality tolerance, indicated by their Sensitivity Weightings within the Zambian Invertebrate Scoring System (ZISS). Macrophyte large-scale latitudinal range was derived from world geopositional records held by online databases, and additional records held by the authors. The two niche-breadth metrics divided the species into narrow-niche and intermediate/broad-niche categories, showing significant variation (from one or both of correlation and ANOVA test outcomes) in altitude, stream flow, conductivity, SRP, pH and ASPT, but not stream order. Macrophyte alpha-diversity (as a measure of number of individual niches co-existing per habitat) showed no significant relationship with individual species niche-breadth. Narrow-niche species included a higher proportion of Afrotropical endemics than did species with broader niche size. There were significant predictive relationships between macrophyte niche-breadth and latitudinal range of the target species at global and Afrotropical scales, but not for the Neotropics.

    Keywords: Africa, Aquatic plants, Benthic macroinvertebrates, Freshwater ecology, Latitudinal distribution, Niche analysis, Rivers

  • Canavan S, Richardson D, Visser V, Roux J, Vorontsova M, Wilson J (2016)

    The global distribution of bamboos: assessing correlates of introduction and invasion.

    AoB PLANTS plw078.

    There is a long history of species being moved around the world by humans. These introduced species can provide substantial benefits, but they can also have undesirable consequences. We explore the importance of human activities on the processes of species dissemination and potential invasions using the grass subfamily Bambusoideae ("bamboos"), a group that contains taxa that are widely utilised and that are often perceived as weedy. We (1) compiled an inventory of bamboo species and their current distributions; (2) determined which species have been introduced and become invasive outside their native ranges; and (3) explored correlates of introduction and invasion. Distribution data were collated from Kew's GrassBase, the Global Biodiversity Information Facility and other online herbarium information sources. Our list comprised 1662 species in 121 genera, of which 232 (14%) have been introduced beyond their native ranges. Twelve species were found to be invasive. A non-random selection of bamboos have been introduced and become invasive. Asiatic species in particular have been widely introduced. There was a clear over-representation of introduced species in the genera Bambusa and Phyllostachys which also contain most of the listed invasive species. The introduction of species also correlated with certain traits: taxa with larger culm dimensions were significantly more likely to have been moved to new areas; and those with many cultivars had a higher rate of dissemination and invasion. It is difficult to determine whether the patterns of introduction and invasion are due simply to differences in propagule pressure, or whether humans have deliberately selected inherently invasive taxa. In general, we suggest that human usage is a stronger driver of introductions and invasions in bamboos than in other taxa that have been well studied. It is likely that as bamboos are used more widely, the number and impact of invasions will increase unless environmental risks are carefully managed.

    Keywords: Bamboo, Bambusoideae, biological invasions, cultivars, introduced species, invasive species

  • Carlson C, Dougherty E, Getz W, Attar N, Dick G, Kitchen S et al. (2016)

    An Ecological Assessment of the Pandemic Threat of Zika Virus

    PLOS Neglected Tropical Diseases 10(8) e0004968.

    The current outbreak of Zika virus poses a severe threat to human health. While the range of the virus has been cataloged growing slowly over the last 50 years, the recent explosive expansion in the Americas indicates that the full potential distribution of Zika remains uncertain. Moreover, many studies rely on its similarity to dengue fever, a phylogenetically closely related disease of unknown ecological comparability. Here we compile a comprehensive spatially-explicit occurrence dataset from Zika viral surveillance and serological surveys based in its native range, and construct ecological niche models to test basic hypotheses about its spread and potential establishment. The hypothesis that the outbreak of cases in Mexico and North America are anomalous and outside the native ecological niche of the disease, and may be linked to either genetic shifts between strains, or El Nino or similar climatic events, remains plausible at this time. Comparison of the Zika niche against the known distribution of dengue fever suggests that Zika is more constrained by the seasonality of precipitation and diurnal temperature fluctuations, likely confining autochthonous non-sexual transmission to the tropics without significant evolutionary change. Projecting the range of the diseases in conjunction with three major vector species (Aedes africanus, Ae. aegypti, and Ae. albopictus) that transmit the pathogens, under climate change, suggests that Zika has potential for northward expansion; but, based on current knowledge, our models indicate Zika is unlikely to fill the full range its vectors occupy, and public fear of a vector-borne Zika epidemic in the mainland United States is potentially informed by biased or limited scientific knowledge. With recent sexual transmission of the virus globally, we caution that our results only apply to the vector-borne transmission route of the pathogen, and while the threat of a mosquito-carried Zika pandemic may be overstated in the media, other transmission modes of the virus may emerge and facilitate naturalization worldwide.

    Keywords: Bamboo, Bambusoideae, biological invasions, cultivars, introduced species, invasive species

  • Charles-Dominique T, Davies T, Hempson G, Bezeng B, Daru B, Kabongo R et al. (2016)

    Spiny plants, mammal browsers, and the origin of African savannas.

    Proceedings of the National Academy of Sciences of the United States of America 113(38) E5572-9.

    Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils.

    Keywords: Africa, Bovidae, coevolution, mammalian herbivory, savanna

  • Cheek M, Semple J (2016)

    First official record of naturalised populations of Solidago altissima L. var. pluricephala M.C. Johnst. (Asteraceae: Astereae) in Africa

    South African Journal of Botany 105 333-336.

    Solidago altissima var. pluricephala is recorded for the first time as naturalised in Africa, with two populations detected in South Africa. One 0.5ha population has been found near Harding and another of 403 shoots near Hilton, both in KwaZulu-Natal. A projected species distribution model for South Africa indicates that the grassland biome is the most at risk from invasion by this species. These plants are most likely garden escapees although we are uncertain how widely they are cultivated in South Africa.

    Keywords: Distribution model, Golden rods, Grasslands, Invasive species, Ornamental plants

  • Cindi DD & Jaca TP (2016)

    First record of Opuntia pubescens H.L.Wendland ex Pfeiffer, 1835 naturalised in South Africa

    BioInvasions Records 5(4) 213-219.

    Opuntioid cacti have caused some of the most damaging plant inva sions globally. While many of these invaders were introduced fo r ornamental and some agriculture use, there are an increasing number of r ecords of invasive ornamental sp ecies. Here we report the first de tailed invasion by Opuntia pubescens and investigate the potential for eradicating the species fr om South Africa. We found the species only at one location (Pretoria National Botanical Gardens) where the population was approximately 5023 plants over th e undeveloped area of 3.66 ha. The plant was not found during surveys of neighbouring natural areas. We be lieve it was introduced to staff gardens as an ornamental plan t, but we have not found it on sale in nurseries nor mentioned in histori cal literature. However, as the species was initially confused w ith O. aurantiaca , surveys were conducted in the neighbouri ng hills and Gauteng province for all known O. aurantiaca infested farms. Initial efforts on surveying the Limpopo, KwaZulu-Natal and East ern Cape provinces with the assistance of Department of Agriculture, Forestry and Fisheries Land Use and Soil Management Resource Auditors have been initiate d, but more work still needs to be done. Therefore, while prel iminary control efforts in the garden looking promising; it is not clear whether nation-wide eradication is feasible. The Australian We ed Risk Assessment was used to collate informati on and determine the invasive potential of O. pubescens in South Africa. This method has been used worldwide and within the programme to determine risk potential of invasive species in the country. To determine the potential d istribution of O. pubescens we developed a species distribution model using MaxEnt 3.3.3e based on native and non-native range. This study highlights the need to discourage the use of Opuntioid cacti as ornamental sp ecies due to their invasiveness, even if they are not yet known t o be invasive.

    Keywords: Opuntia pubescens, alien succulent, cacti, eradication, feasibility

  • Congrains C, Carvalho A, Miranda E, Cumming G, Henry D, Manu S et al. (2016)

    Genetic and paleomodelling evidence of the population expansion of the cattle egret Bubulcus ibis in Africa during the climatic oscillations of the Late Pleistocene

    Journal of Avian Biology.

    Increasing aridity during glacial periods produced the retraction of forests and the expansion of arid and semi-arid environments in Africa, with consequences for birds. Cattle egret (Bubulcus ibis) is a dispersive species that prefers semiarid environments and requires proximity to bodies of water. We expected that climatic oscillations led to the expansion of the range of the cattle egret during arid periods, such as the Last Maximum Glacial (LGM) and contraction of distribution during the Last Interglacial (LIG) period, resulting in contact of populations previously isolated. We investigated this hypothesis by evaluating the genetic structure and population history of 15 cattle egret breeding colonies located in West and South Africa using the mitochondrial DNA (mtDNA) control region, mtDNA ATPase 8 and 6, and an intron of nuclear gene transforming growth factor beta-2. Occurrence data and bioclimatic information were used to generate ecological niche models of three periods (present, LGM and LIG). We used the genetic and paleomodelling data to assess the responses of the cattle egret from Africa to the climatic oscillations during the late Pleistocene. Genetic data revealed low levels of genetic differentiation, signs of isolation-by-distance, as well as recent increases in effective population size that started during the LGM. The observed low genetic structure may be explained by recent colonization events due to the demographic expansion following the last glacial period and by dispersal capacity of this species. The paleomodels corroborated the expansion during the LGM, and a more restricted potential distribution during the LIG. Our findinds supports the hypothesis that the species range of the cattle egret expanded during arid periods and contracted during wet periods.

    Keywords: Opuntia pubescens, alien succulent, cacti, eradication, feasibility

  • Cramer M, Verboom G (2016)

    Measures of biologically relevant environmental heterogeneity improve prediction of regional plant species richness

    Journal of Biogeography.

    Aim Relatively few models of species richness explicitly consider aspects of environmental heterogeneity, other than topographic heterogeneity. We hypothesized that environmental heterogeneity is an important determinant of species richness, especially in ancient climatically stable environments. Location South Africa, which accommodates a range of biomes that differ strongly in species richness. Methods We included measures of climatic, edaphic and biotic variables and their spatial heterogeneities in boosted regression tree models of vascular plant species richness. Species richness was assessed using herbarium records per quarter degree square (QDS). To avoid autocorrelation and problems of variable collection rates we iteratively randomly subsampled 20% of the available QDS. We also verified estimates of species richness using an independent data source. Results The models predicted 68% of QDS species richness and 95% of biome richness. Spatial variability in diurnal temperature range was the strongest predictor of species richness, and inclusion of edaphic and biotic terms as well as spatial heterogeneities increased the explanatory power of the model considerably. Heterogeneity variables featured strongly (8 of 13) as predictors of species richness, but several resource variables (e.g. precipitation, seasonality and evapotranspiration) were also important. The spatial heterogeneities of some variables (e.g. water availability, fire) were related to their mean values, possibly explaining why some global models that have not explicitly included heterogeneity (other than topographic) perform well. Main conclusions Environmental heterogeneities are important predictors of species richness, yielding accurate predictions even in the absence of any consideration of diversification rates or environmental stability. Greater heterogeneity of some resource variables when limiting, contributed to modelled species richness, adding to understanding of why species richness of some resource-poor Mediterranean-ecosystems is high. We suggest that species richness in ancient, climatically stable Mediterranean-ecosystems is contingent on resource and environmental heterogeneity that has enabled both the diversification and maintenance of regional species richness.

    Keywords: Africa, biodiversity, biome, ecosystems, extinction, niche, productivity, resource, speciation

  • Geerts S, Mashele B, Visser V, Wilson J (2016)

    Lack of human-assisted dispersal means Pueraria montana var. lobata (kudzu vine) could still be eradicated from South Africa

    Biological Invasions 1-8.

    The legume, Pueraria montana var. lobata (kudzu vine) is one of the worst plant invaders globally. Here we present the first study of P. montana in South Africa. We found only seven P. montana populations covering an estimated condensed area of 74 hectares during the height of the growing season. Based on a species distribution model, it appears that large parts of the globe are suitable, including parts of the eastern escarpment of South Africa (where most populations occur). South African populations of P. montana appear to have a similar ecology to populations in the USA: high growth rates, low seed germination, no natural long-distance dispersal, little herbivory and vigorous post-fire resprouting. In contrast to the USA, most South African populations do flower and flowers are capable of producing seed in the absence of pollinators. However, P. montana appears to have never been widely planted in South Africa, and the incursion was for many years restricted to a single introduction site. The comparison between the invasions of P. montana in the USA and South Africa highlights the often overriding importance of human-assisted dispersal and cultivation in creating widespread invasions, and should serve as a warning to people who have proposed to utilize the species in Africa.

    Keywords: Africa, Alien invasive weed, Climate models, FabaceaeLegume, Pollination