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

  • Faulkner K, Robertson M, Rouget M, Wilson J (2017)

    Prioritising surveillance for alien organisms transported as stowaways on ships travelling to South Africa

    PLOS ONE 12(4) e0173340.

    The global shipping network facilitates the transportation and introduction of marine and terrestrial organisms to regions where they are not native, and some of these organisms become invasive. South Africa was used as a case study to evaluate the potential for shipping to contribute to the introduction and establishment of marine and terrestrial alien species (i.e. establishment debt) and to assess how this varies across shipping routes and seasons. As a proxy for the number of species introduced (i.e. ‘colonisation pressure’) shipping movement data were used to determine, for each season, the number of ships that visited South African ports from foreign ports and the number of days travelled between ports. Seasonal marine and terrestrial environmental similarity between South African and foreign ports was then used to estimate the likelihood that introduced species would establish. These data were used to determine the seasonal relative contribution of shipping routes to South Africa’s marine and terrestrial establishment debt. Additionally, distribution data were used to identify marine and terrestrial species that are known to be invasive elsewhere and which might be introduced to each South African port through shipping routes that have a high relative contribution to establishment debt. Shipping routes from Asian ports, especially Singapore, have a particularly high relative contribution to South Africa’s establishment debt, while among South African ports, Durban has the highest risk of being invaded. There was seasonal variation in the shipping routes that have a high relative contribution to the establishment debt of the South African ports. The presented method provides a simple way to prioritise surveillance effort and our results indicate that, for South Africa, port-specific prevention strategies should be developed, a large portion of the available resources should be allocated to Durban, and seasonal variations and their consequences for prevention strategies should be explored further.


  • Grossenbacher D, Brandvain Y, Auld J, Burd M, Cheptou P, Conner J et al. (2017)

    Self-compatibility is over-represented on islands

    New Phytologist.

    Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families.

    Keywords: Baker's law, biogeography, ecological filtering, island, mainland, self‐incompatibility


  • 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


  • Maquart P, Noort S (2017)

    Description of a new species of Capederces (Coleoptera: Cerambycidae: Cerambycinae) from South Africa

    Zootaxa 4244(4) 583.

    A new species of longhorned beetle in the tribe Tillomorphini, Capederces madibai sp. nov., is described from the “Albany district” in south-eastern South Africa. Adult specimens are illustrated and compared with the only other known species from this previously mono-specific genus: C. hauseri Adlbauer, 2001. An illustration of the female of C. hauseri is provided for the first time.

    Keywords: Biodiversity, Coleoptera, Ethiopian region, Taxonomy, Tillomorphini


  • Visser V, Wilson J, Canavan K, Canavan S, Fish L, Le Maitre D et al. (2017)

    Grasses as invasive plants in South Africa revisited: Patterns, pathways and management

    Bothalia 47(2).

    Background: In many countries around the world, the most damaging invasive plant species are grasses. However, the status of grass invasions in South Africa has not been documented recently. Objectives: To update Sue Milton’s 2004 review of grasses as invasive alien plants in South Africa, provide the first detailed species level inventory of alien grasses in South Africa and assess the invasion dynamics and management of the group. Method: We compiled the most comprehensive inventory of alien grasses in South Africa to date using recorded occurrences of alien grasses in the country from various literature and database sources. Using historical literature, we reviewed past efforts to introduce alien grasses into South Africa. We sourced information on the origins, uses, distributions and minimum residence times to investigate pathways and patterns of spatial extent. We identified alien grasses in South Africa that are having environmental and economic impacts and determined whether management options have been identified, and legislation created, for these species. Results: There are at least 256 alien grass species in the country, 37 of which have become invasive. Alien grass species richness increased most dramatically from the late 1800s to about 1940. Alien grass species that are not naturalised or invasive have much shorter residence times than those that have naturalised or become invasive. Most grasses were probably introduced for forage purposes, and a large number of alien grass species were trialled at pasture research stations. A large number of alien grass species in South Africa are of Eurasian origin, although more recent introductions include species from elsewhere in Africa and from Australasia. Alien grasses are most prevalent in the south-west of the country, and the Fynbos Biome has the most alien grasses and the most widespread species. We identified 11 species that have recorded environmental and economic impacts in the country. Few alien grasses have prescribed or researched management techniques. Moreover, current legislation neither adequately covers invasive species nor reflects the impacts and geographical extent of these species. Conclusion: South Africa has few invasive grass species, but there is much uncertainty regarding the identity, numbers of species, distributions, abundances and impacts of alien grasses. Although introductions of alien grasses have declined in recent decades, South Africa has a potentially large invasion debt. This highlights the need for continued monitoring and much greater investment in alien grass management, research and legislation.

    Keywords: Alien, Grass, Invasive species, Poaceae


  • Yessoufou K, Daru B, Tafirei R, Elansary H, Rampedi I (2017)

    Integrating biogeography, threat and evolutionary data to explore extinction crisis in the taxonomic group of cycads

    Ecology and Evolution.

    Will the ongoing extinction crisis cause a severe loss of evolutionary information accumulated over millions of years on the tree of life? This question has been largely explored, particularly for vertebrates and angiosperms. However, no equivalent effort has been devoted to gymnosperms. Here, we address this question focusing on cycads, the gymnosperm group exhibiting the highest proportion of threatened species in the plant kingdom. We assembled the first complete phylogeny of cycads and assessed how species loss under three scenarios would impact the cycad tree of life. These scenarios are as follows: (1) All top 50% of evolutionarily distinct (ED) species are lost; (2) all threatened species are lost; and (3) only all threatened species in each IUCN category are lost. Finally, we analyzed the biogeographical pattern of cycad diversity hotspots and tested for gaps in the current global conservation network. First, we showed that threatened species are not significantly clustered on the cycad tree of life. Second, we showed that the loss of all vulnerable or endangered species does not depart significantly from random loss. In contrast, the loss of all top 50% ED, all threatened or all critically endangered species, would result in a greater loss of PD (Phylogenetic Diversity) than expected. To inform conservation decisions, we defined five hotpots of diversity, and depending on the diversity metric used, these hotspots are located in Southern Africa, Australia, Indo-Pacific, and Mexico and all are found within protected areas. We conclude that the phylogenetic diversity accumulated over millions of years in the cycad tree of life would not survive the current extinction crisis. As such, prioritizing efforts based on ED and concentrating efforts on critically endangered species particularly in southern Africa, Australia, Indo-Pacific, and Mexico are required to safeguarding the evolutionary diversity in the cycad tree of life.

    Keywords: Alien, Grass, Invasive species, Poaceae


  • 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