Uses of GBIF in scientific research

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

List of publications

  • 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.

  • 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

  • Nxumalo MM, Lalla R R (2016)

    Hydrocleys nymphoides (Humb. & Bonpl. ex Willd.) Buchenau: first record of naturalisation in South Africa

    BioInvasions Records 5.

    Hydrocleys nymphoides (water poppy), an aquatic plant native to South America, has been recorded as invasive on several continents (Europe, Australia and Asia). Here we report on the first known natura lized population in South Africa, in a dam in the KwaZulu-Natal (K ZN) Midlands region, near the town of Howick. This popu lation, first detected and identified in 2009, had by the end of the 2013 summer seas on occupied 1.8ha (30% of the dam). Surveys of 34 surrounding water bodies during the period between 2012 and 2013 did not result in detection of any new populations. The only other population (0.1 ha) was recorded growin g in cultivation at the Durban Botanic Gardens. This note re ports on the history of H. nymphoides in South Africa, details its current and potential distribution, looks at the risk it poses, and outlines plans for nation-wid e eradication.

    Keywords: South, invasive alien aquatic plant, water poppy

  • Tolley K, Alexander G, Branch W, Bowles P, Maritz B (2016)

    Conservation status and threats for African reptiles

    Biological Conservation.

    The assimilation of information on taxonomy, distribution, basic ecology and conservation status of Africa's reptiles lags far behind that for most other continents. Many regions of mainland Africa are rarely surveyed, resulting in severe knowledge gaps that currently limit effective conservation of African reptiles. Here, we provide a précis on the knowledge gaps and conservation status of mainland African reptiles, and quantify the main threats based on IUCN Red List of Threatened Species assessments using publicly available distribution data. Our results show that these data are insufficient to confidently identify areas of high biodiversity, with large gaps in knowledge in the Horn of Africa, central Africa and West Africa. There is a strong overall taxonomic bias in extinction risk with 45% of families more threatened than expected by chance. Furthermore, Amphisbaenidae, Chameleonidae, Gerrhosauridae, Testudinidae, Viperidae all have a high percentage of their constituent species at risk. Overall, land transformation for agriculture, particularly subsistence farming, constitutes the primary threat to African reptiles, and our derived Threat Index based on socio-economic traits of African countries show that risk is high in Burundi, Ethiopia, Liberia, Malawi, Rwanda and Sierra Leone. These findings highlight important challenges facing the conservation of African reptiles, and we suggest that conservation priorities in mainland Africa be focussed on areas where the potential for overall loss of biodiversity is high, particularly in regions where knowledge is inadequate.

    Keywords: Biodiversity, Conservation, Global Reptile Assessment, Habitat loss, Species richness

  • Visser V, Wilson J, Fish L, Brown C, Cook G, Richardson D (2016)

    Much more give than take: South Africa as a major donor but infrequent recipient of invasive non-native grasses

    Global Ecology and Biogeography.

    Aim Some regions donate more invaders from particular taxonomic and functional groups than they receive. We demonstrate a particularly striking donor–recipient asymmetry in invasion ecology in grasses. Specifically, we explore whether low numbers of invasive grasses in South Africa can be explained by sampling biases, introduction dynamics, species traits or invasibility of ecosystems. Location South Africa, Australia, Chile, Europe and the USA. Methods We tested for a donor–recipient asymmetry using lists of native and non-native grasses in five regions across the globe. Then, using distribution, trait and environmental data, we tested whether regions differed in: (1) herbarium sampling effort; (2) introduction dynamics of non-native grasses (primary uses, area of origin and minimum residence time of non-native grasses); (3) traits of native and non-native grasses (leaf size, height, life history, growth form, C3:C4 ratio and taxonomic placement); and (4) fire frequency. Results South Africa has fewer invasive grasses, and fewer widespread invasive grasses, than other regions; while grasses native to South Africa are much more likely to be invasive elsewhere than other grasses. This asymmetry cannot be explained by sampling biases, historical trade links or minimum residence time. Rather it is likely to be due to a combination of: (1) the massive scale of the introduction of South African grasses around the world; (2) specific traits that make South African grasses successful competitors; and (3) the high fire frequency of many South African ecosystems to which many native grasses are adapted, but introduced grasses are not. Main conclusion South Africa has a high diversity of grasses that possess specific traits to cope with fire, grazing and disturbance. This makes them more competitive. Moreover, the high diversity of certain grass lineages in South Africa acts as a reservoir of potential invaders and possibly helps limit invasions in South Africa by promoting fire.

    Keywords: Africa, South Africa, biological invasions, fire, grass invasions, grazing, introduction dynamics, invasive species, plant traits

  • Weyl P, Martin G (2016)

    Have grass carp driven declines in macrophyte occurrence and diversity in the Vaal River, South Africa?

    African Journal of Aquatic Science 1-5.

    The Vaal River, South Africa, historically had a rich diversity of native submerged macrophytes with at least 13 species from 5 families recorded. Over the past 10 years there has been a noticeable reduction in the occurrence and diversity of submerged macrophytes in the river. It is possible that this is linked to the recent increase in the populations of invasive alien grass carp Ctenopharyngodon idella Cuvier & Valenciennes (Cyprinidae) in the river, where populations have been a concern since 2005. Grass carp invasions worldwide have been shown to have severe impacts on macrophyte biodiversity and ecosystem functioning. This fish is an aggressive feeder on submerged macrophytes, as well as being an ecosystem engineer that can change water and sediment chemistry.

    Keywords: Ctenopharyngodon idella, aquatic ecosystem, biodiversity, fresh water, impact, invasion

  • Assis J, Zupan M, Nicastro K, Zardi G, McQuaid C, Serrão E (2015)

    Oceanographic Conditions Limit the Spread of a Marine Invader along Southern African Shores.

    PloS one 10(6) e0128124.

    Invasive species can affect the function and structure of natural ecological communities, hence understanding and predicting their potential for spreading is a major ecological challenge. Once established in a new region, the spread of invasive species is largely controlled by their dispersal capacity, local environmental conditions and species interactions. The mussel Mytilus galloprovincialis is native to the Mediterranean and is the most successful marine invader in southern Africa. Its distribution there has expanded rapidly and extensively since the 1970s, however, over the last decade its spread has ceased. In this study, we coupled broad scale field surveys, Ecological Niche Modelling (ENM) and Lagrangian Particle Simulations (LPS) to assess the current invaded distribution of M. galloprovincialis in southern Africa and to evaluate what prevents further spread of this species. Results showed that all environmentally suitable habitats in southern Africa have been occupied by the species. This includes rocky shores between Rocky Point in Namibia and East London in South Africa (approx. 2800 km) and these limits coincide with the steep transitions between cool-temperate and subtropical-warmer climates, on both west and southeast African coasts. On the west coast, simulations of drifting larvae almost entirely followed the northward and offshore direction of the Benguela current, creating a clear dispersal barrier by advecting larvae away from the coast. On the southeast coast, nearshore currents give larvae the potential to move eastwards, against the prevalent Agulhas current and beyond the present distributional limit, however environmental conditions prevent the establishment of the species. The transition between the cooler and warmer water regimes is therefore the main factor limiting the northern spread on the southeast coast; however, biotic interactions with native fauna may also play an important role.

    Keywords: Ctenopharyngodon idella, aquatic ecosystem, biodiversity, fresh water, impact, invasion

  • Brummitt N, Bachman S, Griffiths-Lee J, Lutz M, Moat J, Farjon A et al. (2015)

    Green Plants in the Red: A Baseline Global Assessment for the IUCN Sampled Red List Index for Plants.

    PloS one 10(8) e0135152.

    Plants provide fundamental support systems for life on Earth and are the basis for all terrestrial ecosystems; a decline in plant diversity will be detrimental to all other groups of organisms including humans. Decline in plant diversity has been hard to quantify, due to the huge numbers of known and yet to be discovered species and the lack of an adequate baseline assessment of extinction risk against which to track changes. The biodiversity of many remote parts of the world remains poorly known, and the rate of new assessments of extinction risk for individual plant species approximates the rate at which new plant species are described. Thus the question 'How threatened are plants?' is still very difficult to answer accurately. While completing assessments for each species of plant remains a distant prospect, by assessing a randomly selected sample of species the Sampled Red List Index for Plants gives, for the first time, an accurate view of how threatened plants are across the world. It represents the first key phase of ongoing efforts to monitor the status of the world's plants. More than 20% of plant species assessed are threatened with extinction, and the habitat with the most threatened species is overwhelmingly tropical rain forest, where the greatest threat to plants is anthropogenic habitat conversion, for arable and livestock agriculture, and harvesting of natural resources. Gymnosperms (e.g. conifers and cycads) are the most threatened group, while a third of plant species included in this study have yet to receive an assessment or are so poorly known that we cannot yet ascertain whether they are threatened or not. This study provides a baseline assessment from which trends in the status of plant biodiversity can be measured and periodically reassessed.

    Keywords: Ctenopharyngodon idella, aquatic ecosystem, biodiversity, fresh water, impact, invasion

  • Cheek M (2015)

    First official record of a naturalised population of Mimosa albida Humb. & Bonpl. ex Willd. var. albida in Africa

    BioInvasions Records 4.

    Mimosa albida var. albida is a woody shrub indigenous to Central and South America that is well adapted to disturbed habitats. This paper is the first formal report of this species outside of cultivation in Africa. A total of 61 plants were recorded along a 1.5km arc of the Mkhomazi River in KwaZulu-Natal, South Africa. Effort s are underway to eradicate the population.

    Keywords: South Africa, ornament al plants, riparian weeds

  • Gallien L, Saladin B, Boucher F, Richardson D, Zimmermann N (2015)

    Does the legacy of historical biogeography shape current invasiveness in pines?

    The New phytologist.

    Why are some introduced species more successful at establishing and spreading than others? Until now, characteristics of extant species have been intensively investigated to answer this question. We propose to gain new insights on species invasiveness by exploring the long-term biogeographic and evolutionary history of lineages. We exemplify our approach using one of the best-studied invasive plant genera, Pinus. We notably estimated the historical biogeography of pines and the rates of trait evolution in pines. These estimates were analysed with regard to species invasiveness status. The results revealed that currently invasive species belong to lineages that were particularly successful at colonizing new regions in the past. We also showed that highly mobile lineages had faster rates of niche evolution, but that these rates are poor proxies for species adaptive potential in invaded regions (estimated by niche shift among native and invaded regions). In summary, working at the interface of ecology, historical biogeography and evolutionary history offers stimulating perspectives to improve our understanding of the drivers of invasion success.

    Keywords: Pinus, biological invasions, evolutionary history, invasiveness, migration, model averaging, niche shift, tree invasions