African Birds Research Articles

Predicting the distribution of the Vulnerable Yellow-breasted Pipit (Anthus chloris) using Species Distribution Modelling

ABSTRACTThe Yellow-breasted Pipit (Anthus chloris) is endemic to the eastern escarpment of South Africa, marginally entering eastern Lesotho. This species is classified as globally Vulnerable due to a perceived decreasing population size and loss of habitat. We employed Species Distribution Modelling to investigate the predicted range of this species to determine whether additional purportedly suitable habitat exists where this species may be found, and to assess the degree to which habitat loss has affected this species. We used a database of 250 independently obtained and verified sightings to predict the summer breeding distribution of this species and compare our verified sightings and predicted range to the sightings currently in the Second Southern African Bird Atlas Project (SABAP2) database and the latest regional conservation assessment. Our models closely approximate the current distribution of the Yellow-breasted Pipit, and suggest that most of the purportedly suitable habitat is occupied, at least at the macro scale. Our models further suggest that the Eastern Cape Province does not hold much suitable habitat for this species, and that the purported range contraction in this region may have been overestimated.

Birdwatchers evoke longer escape distances than pedestrians in some African birds

ABSTRACTBirdwatching attracts many bird enthusiasts to developing economies, and is generally considered an innocuous activity with few impacts on birds. Birdwatchers generally attempt to remain as inconspicuous as possible when approaching birds, and their movement is different to that of other users of natural areas. However, how birds respond to birdwatchers, compared with humans conducting other activities, has rarely been tested. We randomly conducted pedestrian (i.e. consistent walking) and ‘birdwatcher’ (i.e. stops each 5 paces to view a bird through binoculars) approaches to 20 East African bird species and measured their escape responses. Four species (α = 0.05; 7 if α = 0.10) exhibited significantly and substantially (1.7–2.2 times) longer flight-initiation distances (FIDs) to birdwatcher approaches. No differences in escape mode (flying versus on foot) were evident. While birdwatching appears no more disturbing per episode than walking for most species, some species evidently judge birdwatchers as more threatening. This information has important implications for management strategies focused on minimizing birdwatching impacts in natural areas.

The second Southern African Bird Atlas Project: Causes and consequences of geographical sampling bias.

Using the Southern African Bird Atlas Project (SABAP2) as a case study, we examine the possible determinants of spatial bias in volunteer sampling effort and how well such biased data represent environmental gradients across the area covered by the atlas. For each province in South Africa, we used generalized linear mixed models to determine the combination of variables that explain spatial variation in sampling effort (number of visits per 5′ × 5′ grid cell, or “pentad”). The explanatory variables were distance to major road and exceptional birding locations or “sampling hubs,” percentage cover of protected, urban, and cultivated area, and the climate variables mean annual precipitation, winter temperatures, and summer temperatures. Further, we used the climate variables and plant biomes to define subsets of pentads representing environmental zones across South Africa, Lesotho, and Swaziland. For each environmental zone, we quantified sampling intensity, and we assessed sampling completeness with species accumulation curves fitted to the asymptotic Lomolino model. Sampling effort was highest close to sampling hubs, major roads, urban areas, and protected areas. Cultivated area and the climate variables were less important. Further, environmental zones were not evenly represented by current data and the zones varied in the amount of sampling required representing the species that are present. SABAP2 volunteers' preferences in birding locations cause spatial bias in the dataset that should be taken into account when analyzing these data. Large parts of South Africa remain underrepresented, which may restrict the kind of ecological questions that may be addressed. However, sampling bias may be improved by directing volunteers toward undersampled regions while taking into account volunteer preferences.

Invasive potential of the pied crow (Corvus albus) in eastern Brazil: best to eradicate before it spreads

Biological invasion is one of the main drivers of biodiversity loss and ecosystem damage. Invasive species are difficult to eradicate and prevention is considered the best approach. The pied crow (Corvus albus) was recently recorded in eastern Brazil (South America). This African bird species is being considered as a “native invader” in South Africa, and has the potential of causing serious ecological impacts. Therefore, it is important to identify the potential suitable areas and entry points of this species in Brazil. This sort of information allows for a better assessment of where surveillance is needed and if eradication procedures are required. We used ecological niche models to assess the potential distribution of the pied crow in Brazil. Models predicted high suitability for the Southeast, Central and Northeast regions of Brazil, mainly in the Atlantic Forest region. Pied crow occurrence was associated with human infrastructure. Binary models failed to include published records for C. albus in Brazil. However, suitable areas are found 46km away from known occurrence records. We argue that ports are non-intentional points of entry and that surveillance measures should be put into place to prevent novel propagules from arriving and establishing in Brazil.

Waterbird flight initiation distances at Barberspan Bird Sanctuary, South Africa

With tourism in South Africa expanding, the number of avitourists increases. The increase in infrastructure and human activities in protected areas, if not managed properly, can be harmful to birds. Flight initiation distances (FID) can be used as a method to monitor habituation to disturbances. This study was performed at the Barberspan Bird Sanctuary, North West province, South Africa, to determine the levels of habituation among waterbirds and make appropriate recommendations regarding the management of the reserve. Our results indicated a 0.29 m increase in FID per gram reported mean biomass. Compared with conspecific or congeneric birds from Australia, Europe and North America, South African birds have relatively larger FIDs to human disturbance, which may indicate lower habituation. We also calculated buffer zones based on the maximum FID of the waterbirds for three mass groups. These buffer zones were then matched with the spatial distribution of the birds along the shoreline. We recommend that the mean FID for the blacksmith lapwing, Vanellus armatus (62 m), can be used as approach distance outside the breeding season in areas where the birds are sparsely distributed and 104 m during the breeding season in breeding areas. A large buffer of 200 m is suggested for areas with threatened, sensitive and skittish species. However, it is still preferable for avitourists to use the bird hides along the shores.Conservation implications: This study provides information for conservation management at Barberspan, based on typical birder activity. Smaller birds would need smaller buffer zones, while larger birds need much greater distances from observers to minimise disturbance. Similar studies can be applied elsewhere.

Is there genetic connectivity among the critically endangered White‐winged Flufftail (Sarothrura ayresi) populations from South Africa and Ethiopia?

AbstractThe White‐winged Flufftail (Sarothrura ayresi) is known to occur in the highland marshes of Ethiopia, as well as almost 4000 km in South Africa. The White‐winged Flufftail is listed globally as Critically Endangered. In South Africa the population is estimated to be <50 birds. These birds are severely threatened by habitat destruction. Thus far, no genetic studies have been conducted on S. ayresi to confirm genetic connectivity between the South African and Ethiopian populations. In this study, analysis of mitochondrial and nuclear markers was conducted for White‐winged Flufftail samples from South African and Ethiopian birds, as well as Red‐chested Flufftail (Sarothrura rufa) for species comparison. Analyses of the DNA regions identified three variations between the two populations, supporting the hypothesis that these two populations are not different species or subspecies but are rather one migrating population with different seasonal occupied ranges. However, these results do not exclude the possibility of additional breeding and nonbreeding sites. Low genetic diversity in the populations of White‐winged Flufftails was observed, which needs to be further elucidated with fast evolving co‐dominant markers such as microsatellites, as this low diversity may ultimately contribute to the extinction of the species.

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure.

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST, integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population’s indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.

Declining ranges of southern African breeding cuckoos do not reflect host species’ range changes

ABSTRACTGlobal declines in cuckoo numbers have been variously attributed to reduced prey availability; changes in their hosts’ ranges; or climate-induced changes. We used data from two Southern African Bird Atlas Projects to determine whether migrant cuckoo species breeding in South Africa, Lesotho and Swaziland have experienced range shifts during the past 25 years; and whether such changes corresponded to shifts in host species distribution. Changes in presence/absence data indicated that of the nine cuckoo species found breeding in this region, six showed reductions in range (African Cuckoo, African Emerald Cuckoo, Diederik Cuckoo, Great Spotted Cuckoo, Jacobin Cuckoo and Red-chested Cuckoo); two are expanding (Black Cuckoo and Levaillant’s Cuckoo) and one remains stable (Klaas’s Cuckoo). Occupancy modelling of these data indicated that the host ranges of only four of the nine species (Great Spotted Cuckoo, Klaas’s Cuckoo, Levaillant’s Cuckoo and Red-chested Cuckoo) predicted cuckoo distribution in the first instance. Of these, only in Levaillant’s Cuckoo is range expansion related to changes in the range of its sole known host species in the region, the Arrow-marked Babbler. These results imply that factors other than changes in the ranges of their hosts appear to be driving the range reductions observed in six southern African cuckoo species.

Estimating conservation metrics from atlas data: the case of southern African endemic birds

SummaryThe robust assessment of conservation status increasingly requires population metrics for species that may be little-researched, with no prospect of immediate improvement, but for which citizen science atlas data may exist. We explore the potential for bird atlas data to generate population metrics of use in red data assessment, using the endemic and near-endemic birds of southern Africa. This region, defined here as South Africa, Lesotho and Swaziland, is home to a large number of endemic bird species and an active atlas project. The Southern African Bird Atlas Projects (SABAP) 1 and 2 are large-scale citizen science data sets, consisting of hundreds of thousands of bird checklists and > 10 million bird occurrence records on a grid across the subcontinent. These data contain detailed information on species’ distributions and population change. For conservationists, metrics that guide decisions on the conservation status of a species for red listing can be obtained from SABAP, including range size, range change, population change, and range connectivity (fragmentation). We present a range of conservation metrics for these bird species, focusing on population change metrics together with an associated statistical confidence metric. Population change metrics correlate with change metrics calculated from dynamic occupancy modelling for a set of 191 common species. We identify four species with neither international nor local threatened status, yet for which bird atlas data suggest alarming declines, and two species with threatened status for which our metrics suggest could be reconsidered. A standardised approach to deciding the conservation status of a species is useful so that charismatic or flagship species do not receive disproportionate attention, although ultimately conservation status of any species must always be a consultative process.

Comparison of a mixed modes solar dryer to a direct mode solar dryer for African indigenous vegetable and chili processing

A mixed modes solar dryer was modified from a Horticultural Innovation Laboratory design and its performance compared to a direct mode solar dryer to process horticultural crops. The mixed modes and the direct mode solar dryers dried vegetables at different rates with the mixed modes being faster for all products (p ≤ .001). Leaves and flowers of the spider plant (Cleome gynandra) had the shortest drying time (270 ± 6 min) while the fruit of the African bird's eye chili (Capsicum frutescens) took the longest time (3,866 ± 31 min). Moisture content of the dried vegetables met the industry standard for dehydrated fruits and vegetables (≤8.4%) and of chilies which had a moisture content of (9.5 ± 0.15%). This low cost mixed modes dryer is suitable for small-scale vegetable processors and farmers as it does not require grid electricity to operate. Practical applications Fruits and vegetable production is a key economic activity in Kenya. To preserve such produce, farmers practice open sun drying which not only takes longer to dry produce than solar dryers but is also prone to contamination from flies and dust. Prolonged drying times result in products with inconsistent colors and lower nutritional value. Yet, there are simple low cost mixed modes dryers that can be used to dry fruits and vegetables faster than open-air solar drying. The study aimed at providing local farmers with a modified mixed modes solar dryer to quickly dry fresh produce with a minimal loss of nutrients and color retention in the final product. Globally, such a dryer can be used as one of the simplest innovations toward reduction of postharvest food losses of fruits and vegetables.

Atlas data indicate forest dependent bird species declines in South Africa

SummaryForest ecosystems in South Africa are at risk from a variety of anthropogenic threats impacting the faunal species dependent on them. These impacts often differ depending on species-specific characteristics. Range data on forest dependent bird species from the South African Bird Atlas Project (SABAP1 and SABAP2) were analysed to determine links between deforestation, species characteristics and range declines. Half of the species studied were found to have declining ranges. Range change data for these species were correlated with data on changes in land cover from 1990 to 2014. To determine which land cover changes affect extinction, occupancy was modelled for 30 sites across South Africa which experienced a loss of more than 10 species. Most species lost were birds of prey or insectivores. Indigenous forest decreased in 17% (n = 5) sites, while plantations/woodlots decreased in 60% (n = 18) sites. Occupancy modelling showed extinction to be mitigated by plantations in 6/28 species, and forest expansion mitigated extinction in 7/28 species. Responses to deforestation did not appear to be related to particular species characteristics. Half of South Africa’s forest-dependent bird species have declining ranges, with the loss of these species most prominent in the Eastern Cape province. Four responses to changes in forest and plantation cover are discussed: direct effects, with forest loss causing species loss; matrix effects, where plantation loss resulted in species loss; degradation of indigenous forest; and the advent of new forest arising from woody thickening caused by carbon fertilisation, which may not result in optimal habitat for forest-dependent birds.

How well do bird atlas reporting rates reflect bird densities? Correlates of detection from the Fynbos biome, South Africa, with applications for population estimation

Relationships between true population densities and reporting indices from atlas data are important for the calculation of population sizes, though these relationships are remarkably little-known and likely confounded by issues of detection. We examine issues of detection for a single-observer point-count survey across the Fynbos biome in South Africa. We created an index of relative abundance comparable to atlas reporting rate and calculated detection coefficients for each species. We explore various models that explain relative abundance as a function of detection covariates, e.g. mass, colour, group size, vocal behaviour and density. Density was consistently included across models and the best predictor when used alone in a validation exercise. We then calculated mean reporting rates for the citizen science South African Bird Atlas Project2 (SABAP2). A model of species’ reporting rates as determined by density for this set of birds suggested the correlation between atlas reporting rates and density estimates was weak, with species capable of using modified habitats exhibiting higher reporting rates than expected from the density estimates. There was a positive correlation between bird density and reporting rates corrected for by species mass. We used this relationship to calculate densities for the Fynbos bird species and compare results to published data.

Early warning systems for biodiversity in southern Africa – How much can citizen science mitigate imperfect data?

It is a hard reality that virtually all countries, no matter how well resourced, take conservation and land use decisions based on highly patchy and imperfect data - if indeed any data at all. Despite a mushrooming of scientific evidence and journals in the past decade, and open-access provision of many expensive global datasets, developing countries in particular often have to make do with inaccurate and coarse-scale global data, in the absence of targeted, local data to solve immediate conservation problems. To what extent can citizen science data compensate for the patchiness of conventional government-gathered scientific data in order to support planning, policy and management? We demonstrate how southern Africa's citizen science-based “early warning system for biodiversity” is used to support land-use planning and conservation decisions, including Red List, strategic and project-based environmental impact assessments and national protected area expansion and implementation strategies. This system integrates volunteer-based species atlases such as the Protea Atlas Project and Southern African Bird Atlas Project (SABAP), species population monitoring such as the Custodians of Rare and Endangered Wildflowers (CREW) project, and site-based rapid assessment and monitoring such as MyBirdPatch and BioBlitz. Countries in southern Africa are on a sharp continuum of research capacity, funding, political engagement and own datasets. Yet there is the capacity for adaptive management systems based in significant part on civil society volunteerism. Crucially, these must be underpinned by statistically sound, simple, repeatable scientific protocols, which are still rare in Africa.

Show me a sign of sweetness to come

Behavioral Ecology Communication between humans and domesticated animals is common. Regular communication between humans and wild animals, however, is rare. African honey-guide birds are known to regularly lead human honey-hunters to bee colonies, and the humans, on opening up the nest, leave enough

Reciprocal signaling in honeyguide-human mutualism.

Greater honeyguides (Indicator indicator) lead human honey-hunters to wild bees' nests, in a rare example of a mutualistic foraging partnership between humans and free-living wild animals. We show experimentally that a specialized vocal sound made by Mozambican honey-hunters seeking bees' nests elicits elevated cooperative behavior from honeyguides. The production of this sound increased the probability of being guided by a honeyguide from about 33 to 66% and the overall probability of thus finding a bees' nest from 17 to 54%, as compared with other animal or human sounds of similar amplitude. These results provide experimental evidence that a wild animal in a natural setting responds adaptively to a human signal of cooperation.

Deforestation does not affect the prevalence of a common trypanosome in African birds

In spite of numerous reports of avian Trypanosoma spp. in birds throughout the world, patterns of the distribution and prevalence of these blood parasites remains insufficiently understood. It is clear that spatial heterogeneity influences parameters of parasite distributions in natural populations, but data regarding avian trypanosomes are scarce. Using microscopy and molecular diagnostic methods, we analysed the variation of prevalence of avian Trypanosoma parasites in two widespread African bird species, the yellow-whiskered greenbul Andropadus latirostris and the olive sunbird Cyanomitra olivacea. In all, 353 birds were captured in pristine forests and agroforest sites in Cameroon and Ghana. Overall, the prevalence of avian trypanosomes was 51.3%. Five morphospecies were reported (Trypanosoma everetti, T. anguiformis, T. avium, T. naviformis, T. ontarioensis). Trypanosoma everetti predominated, representing 98% of all Trypanosoma spp. reports, and it was present in both avian hosts. The prevalence of T. everetti was significantly less in the yellow-whiskered greenbul (19%) than olive sunbird (83%), and the same pattern of prevalence was reported in these avian hosts at different study sites. We found no interaction between sites and the prevalence of T. everetti. For both avian hosts, the prevalence did not differ significantly between pristine forests and agroforests. This indicates the same pattern of transmission at sites with different levels of deforestation and suggests that spatial heterogeneity related to deforestation does not affect the prevalence of avian Trypanosoma infections. It is likely that host-related factors, but not environmental conditions favour or reduce these parasite infections in forests of sub-Saharan Africa. Microscopic and PCR-based diagnostics showed the same sensitivity in diagnostics of T. everetti. We discuss the implications of these findings for the epidemiology of avian trypanosomiasis in natural populations.

Escape Distance in Ground-Nesting Birds Differs with Individual Level of Camouflage.

Camouflage is one of the most widespread antipredator strategies in the animal kingdom, yet no animal can match its background perfectly in a complex environment. Therefore, selection should favor individuals that use information on how effective their camouflage is in their immediate habitat when responding to an approaching threat. In a field study of African ground-nesting birds (plovers, coursers, and nightjars), we tested the hypothesis that individuals adaptively modulate their escape behavior in relation to their degree of background matching. We used digital imaging and models of predator vision to quantify differences in color, luminance, and pattern between eggs and their background, as well as the plumage of incubating adult nightjars. We found that plovers and coursers showed greater escape distances when their eggs were a poorer pattern match to the background. Nightjars sit on their eggs until a potential threat is nearby, and, correspondingly, they showed greater escape distances when the pattern and color match of the incubating adult's plumage-rather than its eggs-was a poorer match to the background. Finally, escape distances were shorter in the middle of the day, suggesting that escape behavior is mediated by both camouflage and thermoregulation.

The heron that laid the golden egg: metals and metalloids in ibis, darter, cormorant, heron, and egret eggs from the Vaal River catchment, South Africa.

Metal pollution issues are afforded the highest priority in developing countries. Only one previous study has addressed metals in African bird eggs. We determined the concentration of metals and metalloids in bird eggs from four sites in the Vaal River catchment (VRC) of South Africa to provide data on the current situation. We analysed 16 pools of 77 heron, ibis, darter, egret, and cormorant eggs for 18 metals and metalloids using ICP-MS. We found high concentrations of gold (Au), uranium (U), thallium (Tl), and platinum (Pt) in Grey Heron eggs from Baberspan. Great white egrets from Bloemhof Dam had high concentrations of mercury (Hg). Multivariate analyses revealed strong associations between Au and U, and between palladium (Pd) and Pt. The toxic reference value (TRV) for Hg was exceeded in seven pools. Selenium exceeded its TRV in one pool; in the same pool, copper (Cu) reached its TRV. Compared with other studies, VRC bird eggs had high concentrations of contaminants. Based on these high concentrations, human health might be at risk as Grey Herons and humans share similar food and are therefore exposed to the same contaminants.

A new amplicon based approach of whole mitogenome sequencing for phylogenetic and phylogeographic analysis: An example of East African white-eyes (Aves, Zosteropidae)

Classical Sanger sequencing is still frequently used to generate sequence data for phylogenetic and phylogeographic inference. In this contribution we present a novel approach to genotype whole mitogenomic haplotypes using Illumina MiSeq reads from indexed amplicons. Our new approach reduces preparation time by multiplexing loci within a single or few PCR reactions and by plate format library construction. The use of paired-end reads allows covering amplicons of about 0.5kb and thus no nebulisation and assembly are necessary. We tested the power and effectiveness of this technique by analysing the mitogenomic diversity of East African white-eye bird species (Zosteropidae), a taxonomically highly diverse and complex species flock found in various ecosystems spread across major parts of Africa. We compare the newly generated mitogenomic data set with published data of three mitochondrial genes for a similar set of populations and taxa. The comparison demonstrates that our new procedure represents a cost effective use of NGS for medium throughput phylogenetic analyses. Using this method, we were able to increase the amount of phylogenetic information significantly, while reducing the costs and effort in the laboratory. The mitogenomic data show a higher resolution than previous studies providing higher support and new insights in the relationships of Zosterops species. Our data suggest to split Z. poliogaster into four distinct species, three of which had previously been proposed: Z. silvanus, Z. mbulensis, Z. kikyuensis and Z. kulalensis. Our approach allows the genotyping of whole mitogenomes for a large number of individuals and thus allows more reliable reconstruction of phylogenetic and phylogeographic relationships – also for non-model organisms.

Choice of baseline climate data impacts projected species' responses to climate change.

Climate data created from historic climate observations are integral to most assessments of potential climate change impacts, and frequently comprise the baseline period used to infer species-climate relationships. They are often also central to downscaling coarse resolution climate simulations from General Circulation Models (GCMs) to project future climate scenarios at ecologically relevant spatial scales. Uncertainty in these baseline data can be large, particularly where weather observations are sparse and climate dynamics are complex (e.g. over mountainous or coastal regions). Yet, importantly, this uncertainty is almost universally overlooked when assessing potential responses of species to climate change. Here, we assessed the importance of historic baseline climate uncertainty for projections of species' responses to future climate change. We built species distribution models (SDMs) for 895 African bird species of conservation concern, using six different climate baselines. We projected these models to two future periods (2040-2069, 2070-2099), using downscaled climate projections, and calculated species turnover and changes in species-specific climate suitability. We found that the choice of baseline climate data constituted an important source of uncertainty in projections of both species turnover and species-specific climate suitability, often comparable with, or more important than, uncertainty arising from the choice of GCM. Importantly, the relative contribution of these factors to projection uncertainty varied spatially. Moreover, when projecting SDMs to sites of biodiversity importance (Important Bird and Biodiversity Areas), these uncertainties altered site-level impacts, which could affect conservation prioritization. Our results highlight that projections of species' responses to climate change are sensitive to uncertainty in the baseline climatology. We recommend that this should be considered routinely in such analyses.