The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

Bird tolerance to humans in open tropical ecosystems.

Animal tolerance towards humans can be a key factor facilitating wildlife-human coexistence, yet traits predicting its direction and magnitude across tropical animals are poorly known. Using 10,249 observations for 842 bird species inhabiting open tropical ecosystems in Africa, South America, and Australia, we find that avian tolerance towards humans was lower (i.e., escape distance was longer) in rural rather than urban populations and in populations exposed to lower human disturbance (measured as human footprint index). In addition, larger species and species with larger clutches and enhanced flight ability are less tolerant to human approaches and escape distances increase when birds were approached during the wet season compared to the dry season and from longer starting distances. Identification of key factors affecting animal tolerance towards humans across large spatial and taxonomic scales may help us to better understand and predict the patterns of species distributions in the Anthropocene.

A global review of the temporal and spatial patterns of DDT and dieldrin monitoring in raptors.

Concentrations of organochlorine pesticides have been extensively monitored in birds, particularly from higher trophic guilds such as raptors. While monitoring of raptors has been ongoing for decades, patterns from monitoring activities have never been summarised on a global scale. In this study, we undertake a review to better describe the monitoring of two widespread organochlorine pesticides monitored globally in raptors, DDT and dieldrin. We provide a historical retrospective on the monitoring effort of a global environmental issue. Sampling was heavily biased geographically to the global north, with more than 90 % of studies conducted in this socio-geographic region, most from Europe and North America. Although monitoring occurred from at least 114 species, most samples came from relatively few species, with three species (Eurasian Sparrowhawk Accipiter nisus, Bald Eagle Haliaeetus leucocephalus, and Peregrine Falcon Falco peregrinus) comprising 50 % of samples. The types of raptors sampled have changed over time, with avian and mammal specialists dominating samples until the 1970s, but more diverse dietary guilds monitored in later decades, and greater proportions of samples coming from generalist species. The three most sampled tissues (egg, liver, and plasma) comprised 84 % of all samples. Eggs were the earliest tissue examined and the only tissue sampled in all decades. The geographical bias in monitoring effort and relatively narrow species focus, suggests that patterns in these pesticides are unlikely to be fully representative of all global environments occupied by raptors. While DDT has been banned throughout most of the global north, it remains in use in the global south, yet monitoring effort in the south, does not match that of the north. While monitoring remains prevalent in the global north, contemporary monitoring is limited in the global south with less than 10 % of raptors sampled in Asia, Africa, and South America, over the last 3 decades.

Malar stripe size and prominence in peregrine falcons vary positively with solar radiation: support for the solar glare hypothesis.

Many falcons (Falco spp.) exhibit a distinct dark plumage patch below the eye, termed the malar stripe. This stripe is hypothesized to reduce the amount of solar glare reflected into the eyes while foraging, thereby increasing hunting efficiency in bright conditions. Here, we use a novel, global-scale correlative approach to test this 'solar glare hypothesis' in peregrine falcons (Falco peregrinus), the most widespread falcon species, using web-sourced photographs from across the species' global range. We found that the size and prominence of the malar stripe were positively associated with average annual solar radiation, but not with other environmental variables, such as temperature and rainfall. Our results provide the first published evidence for the hypothesis that this plumage feature functions to reduce the amount of solar glare reflected into the falcon's eyes, thereby improving the ability to pinpoint and target agile prey in bright conditions.

Functional Traits Drive Dispersal Interactions Between European Waterfowl and Seeds.

Endozoochory by waterfowl is important for a broad range of angiosperms, most of which lack a fleshy fruit. This dispersal function contributes to the formation and maintenance of plant communities and may allow range shifts for plant species under global change. However, our current understanding of what seed or plant traits are important for this dispersal mechanism, and how they relate to variation in waterbird traits, is extremely limited. We addressed this question using a unique dataset identifying the plant species whose seeds are ingested by 31 different waterfowl species in Europe. We used RLQ and fourth-corner analyses to explore relationships between (1) bird morphological and foraging strategy traits, and (2) plant traits related to seed morphology, environmental preferences, and growth form. We then used Generalized Additive Models to identify relationships between plant/seed traits and the number of waterfowl species that disperse them. Although many waterfowl feed intentionally on seeds, available seed trait data provided little explanation for patterns compared to plant traits such as Ellenberg indicators of habitat preference and life form. Geese were associated with terrestrial plants, ingesting seeds as they graze on land. Diving ducks were associated with strictly aquatic plants, ingesting seeds as they feed at greater depths. Dabbling ducks ingest seeds from plants with high light and temperature requirements, especially shoreline and ruderal species growing in or around the dynamic and shallow microhabitats favored by these birds. Overall, the number of waterfowl vector species (up to 13 per plant species) increases for plants with greater soil moisture requirements and salinity tolerance, reflecting the inclination of most waterfowl species to feed in coastal wetlands. Our findings underline the importance of waterfowl dispersal for plants that are not strictly aquatic, as well as for plants associated with high salinities. Furthermore, our results reveal a soil moisture gradient that drives seed-bird interactions, in line with differences between waterfowl groups in their microhabitat preferences along the land-water continuum. This study provides an important advance in our understanding of the interactions that define plant dispersal in wetlands and their surroundings, and of what plants might be affected by ongoing changes in the distributions of waterfowl species.

The allometry of movement predicts the connectivity of communities.

Connectivity has long played a central role in ecological and evolutionary theory and is increasingly emphasized for conserving biodiversity. Nonetheless, connectivity assessments often focus on individual species even though understanding and preserving connectivity for entire communities is urgently needed. Here we derive and test a framework that harnesses the well-known allometric scaling of animal movement to predict community-level connectivity across protected area networks. We used a field translocation experiment involving 39 species of southern African birds to quantify movement capacity, scaled this relationship to realized dispersal distances determined from ring-and-recovery banding data, and used allometric scaling equations to quantify community-level connectivity based on multilayer network theory. The translocation experiment explained observed dispersal distances from ring-recovery data and emphasized allometric scaling of dispersal based on morphology. Our community-level networks predicted that larger-bodied species had a relatively high potential for connectivity, while small-bodied species had lower connectivity. These community networks explained substantial variation in observed bird diversity across protected areas. Our results highlight that harnessing allometric scaling can be an effective way of determining large-scale community connectivity. We argue that this trait-based framework founded on allometric scaling provides a means to predict connectivity for entire communities, which can foster empirical tests of community theory and contribute to biodiversity conservation strategies aimed at mitigating the effects of environmental change.

The relationship between wealth and biodiversity: A test of the Luxury Effect on bird species richness in the developing world.

The Luxury Effect hypothesizes a positive relationship between wealth and biodiversity within urban areas. Understanding how urban development, both in terms of socio-economic status and the built environment, affects biodiversity can contribute to the sustainable development of cities, and may be especially important in the developing world where current growth in urban populations is most rapid. We tested the Luxury Effect by analysing bird species richness in relation to income levels, as well as human population density and urban cover, in landscapes along an urbanization gradient in South Africa. The Luxury Effect was supported in landscapes with lower urbanization levels in that species richness was positively correlated with income level where urban cover was relatively low. However, the effect was reversed in highly urbanized landscapes, where species richness was negatively associated with income level. Tree cover was also positively correlated with species richness, although it could not explain the Luxury Effect. Species richness was negatively related to urban cover, but there was no association with human population density. Our model suggests that maintaining green space in at least an equal proportion to the built environment is likely to provide a development strategy that will enhance urban biodiversity, and with it, the positive benefits that are manifest for urban dwellers. Our findings can form a key contribution to a wider strategy to expand urban settlements in a sustainable way to provide for the growing urban population in South Africa, including addressing imbalances in environmental justice across income levels and racial groups.

Micro-plastic ingestion by waterbirds from contaminated wetlands in South Africa.

Despite a large literature on the impacts of micro-plastic pollution in marine ecosystems, very little research has focused on these pollutants in freshwater ecosystems. Recently, however, a few studies have demonstrated that micro-plastic pollutants are ingested by freshwater taxa, including birds. To explore this potential environmental threat in African freshwater systems we quantified micro-plastic pollutants in the faeces and feather brushings of seven southern African duck species. We analysed 283 faecal samples and 408 feather brushings, and found that 5% of faecal samples and 10% of feather samples contained micro-plastic fibres. The presence and abundance of micro-fibres differed between sampling sites, with significantly higher amounts recorded for the site that received effluent from a sewage treatment facility. Additionally, micro-fibre presence differed across duck species, indicating that foraging behaviour affects plastic ingestion. Our study confirms that African freshwater ecosystems and the biodiversity they support are under threat from micro-plastic contamination.

A framework for testing assumptions about foraging scales, body mass, and niche separation using telemetry data.

Ecological theory predicts that if animals with very similar dietary requirements inhabit the same landscape, then they should avoid niche overlap by either exploiting food resources at different times or foraging at different spatial scales. Similarly, it is often assumed that animals that fall in different body mass modes and share the same body plan will use landscapes at different spatial scales. We developed a new methodological framework for understanding the scaling of foraging (i.e. the range and distribution of scales at which animals use their landscapes) by applying a combination of three well-established methods to satellite telemetry data to quantify foraging patch size distributions: (1) first-passage time analysis; (2) a movement-based kernel density estimator; and (3) statistical comparison of resulting histograms and tests for multimodality. We demonstrate our approach using two sympatric, ecologically similar species of African ducks with quite different body masses: Egyptian Geese (actually a shelduck), and Red-billed Teal. Contrary to theoretical predictions, the two species, which are sympatric throughout the year, foraged at almost identical spatial scales. Our results show how ecologists can use GPS tracking data to explicitly quantify and compare the scales of foraging by different organisms within an animal community. Our analysis demonstrates both a novel approach to foraging data analysis and the need for caution when making assumptions about the relationships among niche separation, diet, and foraging scale.

Susceptibility and Status of Avian Influenza in Ostriches.

The extensive nature of ostrich farming production systems bears the continual risk of point introductions of avian influenza virus (AIV) from wild birds, but immune status, management, population density, and other causes of stress in ostriches are the ultimate determinants of the severity of the disease in this species. From January 2012 to December 2014, more than 70 incidents of AIV in ostriches were reported in South Africa. These included H5N2 and H7N1 low pathogenicity avian influenza (LPAI) in 2012, H7N7 LPAI in 2013, and H5N2 LPAI in 2014. To resolve the molecular epidemiology in South Africa, the entire South African viral repository from ostriches and wild birds from 1991 to 2013 (n = 42) was resequenced by next-generation sequencing technology to obtain complete genomes for comparison. The phylogenetic results were supplemented with serological data for ostriches from 2012 to 2014, and AIV-detection data from surveillance of 17 762 wild birds sampled over the same period. Phylogenetic evidence pointed to wild birds, e.g., African sacred ibis (Threskiornis aethiopicus), in the dissemination of H7N1 LPAI to ostriches in the Eastern and Western Cape provinces during 2012, in separate incidents that could not be epidemiologically linked. In contrast, the H7N7 LPAI outbreaks in 2013 that were restricted to the Western Cape Province appear to have originated from a single-point introduction from wild birds. Two H5N2 viruses detected in ostriches in 2012 were determined to be LPAI strains that were new introductions, epidemiologically unrelated to the 2011 highly pathogenic avian influenza (HPAI) outbreaks. Seventeen of 27 (63%) ostrich viruses contained the polymerase basic 2 (PB2) E627K marker, and 2 of the ostrich isolates that lacked E627K contained the compensatory Q591K mutation, whereas a third virus had a D701N mutation. Ostriches maintain a low upper- to midtracheal temperature as part of their adaptive physiology for desert survival, which may explain the selection in ratites for E627K or its compensatory mutations-markers that facilitate AIV replication at lower temperatures. An AIV prevalence of 5.6% in wild birds was recorded between 2012 and 2014, considerably higher than AIV prevalence for the southern African region of 2.5%-3.6% reported in the period 2007-2009. Serological prevalence of AI in ostriches was 3.7%, 3.6%, and 6.1% for 2012, 2013, and 2014, respectively. An annual seasonal dip in incidence was evident around March/April (late summer/autumn), with peaks around July/August (mid to late winter). H5, H6, H7, and unidentified serotypes were present at varying levels over the 3-yr period.

In search of a treatment for HIV--current therapies and the role of non-nucleoside reverse transcriptase inhibitors (NNRTIs).

The human immunodeficiency virus (HIV) causes AIDS (acquired immune deficiency syndrome), a disease in which the immune system progressively deteriorates, making sufferers vulnerable to all manner of opportunistic infections. Currently, world-wide there are estimated to be 34 million people living with HIV, with the vast majority of these living in sub-Saharan Africa. Therefore, an important research focus is development of new drugs that can be used in the treatment of HIV/AIDS. This review gives an overview of the disease and addresses the drugs currently used for treatment, with specific emphasis on new developments within the class of allosteric non-nucleoside reverse transcriptase inhibitors (NNRTIs).