Southern African Bird Research Articles

Invasion of Psittacula krameri in Gauteng, South Africa: are other birds impacted?

Anthropogenic activities have resulted in the dispersal of many species beyond their natural range and there is ongoing concern over their impacts on native ecosystems. However, these interactions are hard to disentangle from the effect of human-driven habitat alterations. Psittacula krameri (Rose-ringed Parakeet) is a recent coloniser in the heavily modified province of Gauteng, South Africa. We analysed this species across the region to assess its colonising status and potential impact to-date. Using presence data from the Second Southern African Bird Atlas Project (SABAP2) for the parakeet as well as a selected subgroup of 49 other bird species (potential competitor and control species), occurrence patterns in the province for the period of July 2007–June 2017 were determined. Reporting rates for species in SABAP2 were used as a proxy for relative abundance. While the parakeet’s range and abundance increased significantly, only two species showed a significant reporting rate decline in areas of parakeet occurrence. These declines persisted across a wider area where parakeets were not found. Broader-scale Gauteng reporting rate trends, not replicated in the parakeet range, were noted for nine other species, suggesting that the changing avifaunal composition in the anthropogenically transformed Gauteng may instead be driven by habitat change. A large proportion of species can be considered as newcomers to this largely modified ecosystem, and the possibility of vacant niche filling is strong in this case. In the context of novel ecosystems such as urban areas, a terminology based on adaptability rather than nativity status is encouraged.

Chronic, sublethal effects of high temperatures will cause severe declines in southern African arid-zone birds during the 21st century

Birds inhabiting hot, arid regions are among the terrestrial organisms most vulnerable to climate change. The potential for increasingly frequent and intense heat waves to cause lethal dehydration and hyperthermia is well documented, but the consequences of sublethal fitness costs associated with chronic exposure to sustained hot weather remain unclear. Using data for species occurring in southern Africa's Kalahari Desert, we mapped exposure to acute lethal risks and chronic sublethal fitness costs under past, present, and future climates. For inactive birds in shaded microsites, the risks of lethal dehydration and hyperthermia will remain low during the 21st century. In contrast, exposure to conditions associated with chronic, sublethal costs related to progressive body mass loss, reduced nestling growth rates, or increased breeding failure will expand dramatically. For example, by the 2080s the region will experience 10-20 consecutive days per year on which Southern Pied Babblers (Turdoides bicolor) will lose ∼4% of body mass per day, conditions under which this species' persistence will be extremely unlikely. Similarly, exposure to air temperature maxima associated with delayed fledging, reduced fledgling size, and breeding failure will increase several-fold in Southern Yellow-billed Hornbills (Tockus leucomelas) and Southern Fiscals (Lanius collaris). Our analysis reveals that sublethal costs of chronic heat exposure are likely to drive large declines in avian diversity in the southern African arid zone by the end of the century.

Implications of geographical range changes and resultant sympatry for three Accipiter hawks on the Cape Peninsula, South Africa

Some invasive species are known to compete with and even displace indigenous species. Two Accipiter species historically indigenous to eastern South Africa have colonised the Cape Peninsula in the south-west of the country and have become sympatric with a third local Accipiter species. We investigated the changes in the occurrence reporting rates of all three species on the Cape Peninsula between 1982 and 2018 using data from the Atlas of the Birds of the Southwestern Cape and from the two data collection periods of the Southern African Bird Atlas Project (SABAP1 and 2). We found that the Black Sparrowhawk Accipiter melanoleucus has become more abundant and that the African Goshawk A. tachiro and the historically local Rufous-breasted Sparrowhawk A. rufiventris have declined since the invasion of the Cape Peninsula by Black Sparrowhawks, suggesting that the latter species has outcompeted and at least partially displaced the other two species. Although that may be the case, since the three species seem to have relatively stabilised population sizes after 2010 this could suggest progressive resource partitioning with a level of ecological isolation following the initial dominance interactions. Since the westward expansion of the ranges of the Black Sparrowhawk and the African Goshawk along the southern coastal region of South Africa were most likely facilitated by anthropogenic alteration of the landscape ultimately leading to the sympatry of the three species on the Cape Peninsula, we suggest that this is therefore a case of indirect human-caused alien invasion.

Bird Distribution Dynamics - African black oystercatcher in South Africa

This is another paper on bird distribution dynamics in Biodiversity Observations. The objective of this series of papers is to report on the ranges of bird species as revealed by the Second Southern African Bird Atlas Project (SABAP2, 2007 onwards) and to describe how their ranges have changed since the first bird atlas (SABAP1, mainly 1987 /- 1991), about two decades apart. The African Black Oystercatcher Haemetopus moquini is neither considered a Red-listed species globally nor regionally however, this endemic and iconic bird was expected to decline due to a variety of anthropogenic and natural influences hence, it received much attention from the scientific community. SABAP data supported the findings of some previous projects that looked at both oytsercacther distribution, dispersion and feeding ecology along South Africa's (SA) coastline as well as that of the alien Mediterranean Mussel Mytilus galloprovincialis. Possible reasons for a relatively recent and northern presence along the SA coastline could be due to southern populations experiencing food shortages during the breeding season that result in seasonal dispersion or carrying capacity on the mainland has been reached. Inside the /oystercatcher's breeding range, the alien mussel serves as an additional food source that probably explains the largest SABAP2 reporting rates along the southern regions of the coastline as this area coincides with the /mussel's distribution range.

Efficient Bayesian analysis of occupancy models with logit link functions.

Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coefficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We develop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub (https://github.com/AllanClark/Rcppocc).

Modelling bird atlas reporting rate as a function of density in the southern Karoo, South Africa

The relationship between true population density and abundance indices derived from atlas data can be used to estimate population size, a metric that is vital for assessing the conservation status of animal species. However, this relationship remains understudied. Meanwhile, there is growing concern for the avifauna of South Africa's arid southern Karoo region, which is threatened with an increasing frequency of heat waves as well as the expansion of infrastructure in association with uranium mining, renewable energy production and shale gas extraction. We calculated density (individuals km−2) for 49 bird species using data from a standardised distance-sampling survey conducted across 64 pentads (sampling areas of approximately 81 km2) in the southern Karoo region. Reporting rates from the Southern African Bird Atlas Project (SABAP) were explained by individual density for 32 of the 49 species using logistic regression models, and for 37 species using group (cluster) densities. Within this set of species, there was a positive correlation between mean reporting rate and log-transformed mean density in a linear model that included log-transformed mass as a covariate. For seven species with a high uncertainty associated with their density estimates (high relative standard error), we found that we could use our model to produce intuitively reasonable density estimates based on their SABAP2 reporting rates. This relationship suggests that where density estimate–reporting rate relationships for communities are known, they are useful for cross-checking density estimates. We illustrate the utility of this relationship by calculating population estimates for a set of species, and discuss the importance of SABAP2 for conservation purposes in the Karoo.

Common Starling Sturnus vulgaris expansion in South Africa

The Common Starling Sturnus vulgaris has progressively expanded its range in South Africa since its introduction into Cape Town in the late 19th century. In the past few decades it has extended this range into Gauteng province. Using data from the Southern African Bird Atlas Project 2, this paper examines the spread and relative abundance changes for the species across South Africa over the past 10 years, with a detailed look at the recently-colonised Gauteng. Across South Africa, the Common Starling's distribution has shifted, and grown. As it spreads north along the coastline and northwards inland, some of the former range has been lost. In Gauteng, the species has shown a range and abundance expansion over the same period. If the observed trends are to continue, this species is likely to eventually become a prominent species across the entire country, and further north into the sub-region. However, the potential impact that this species has on indigenous avifauna is unknown and, in the face of rapid anthropogenic change, remains to be investigated.

Zulu bird names: A progression over the decades (I)

For nearly 250 years, beginning with Linnaeus in 1758 and continuing through the nineteenth and twentieth centuries, birds have been given scientific and vernacular names created by deliberate, conscious, and methodological taxonomical naming processes. On the other hand, Zulu names for birds, for centuries only residing in oral tradition, have only found their way into print through being recorded in writing. In this process, oral knowledge is recast as written knowledge. This article looks at the first hundred years of such recording of Zulu names, beginning with the first settlers and explorers in what is now KwaZulu-Natal and continuing through to the publication of Samuelson’s dictionary in 1923. The article, and its planned follow-up article, looks at the contribution of various lexicographers, including Bishop Colenso, the Reverend AT Bryant, and CM Doke and BW Vilakazi, and then interfaces their dictionaries with various works on southern African birds, beginning with Layard’s 1867 Birds of South Africa, looking closely at Woodward and Woodward’s 1899 Natal Birds, and ending with the seventh edition of Roberts Birds of Southern Africa, published in 2005. The primary focus is on how the Zulu oral tradition of bird knowledge has increasingly been revealed to the Western world through the efforts of naturalists and lexicographers. The article concludes with a brief look at recent developments in Zulu bird names between 2013 and 2017.

Molecular phylogeny and novel host associations of avian chewing lice (Insecta: Phthiraptera) from South Africa

AbstractCompared with Europe and the Americas, the ectoparasites of African birds are poorly understood, despite the avian fauna being relatively well known. Notably, previous studies documenting the host associations and genetic diversity of parasitic chewing lice of southern African birds have been limited in geographic and taxonomic scope. Recent field expeditions exploring the avian diversity in South Africa facilitated an opportunity to obtain louse specimens from a taxonomically diverse host assemblage. This study is the first to investigate avian louse host associations and diversity across a large portion of South Africa encompassing several distinct habitat types, while incorporating molecular genetic data (from portions of the mitochondrial COI and nuclear EF‐1α genes) for ectoparasite phylogenetic analyses. From 1105 South African bird individuals and 170 species examined for lice, a total of 105 new louse–host associations were observed. Morphological and genetic examination of lice with these new host associations reveals a maximum of 66 louse species new to science. Results of this study support the observation that examining museum specimens is a useful way to investigate louse diversity and host associations.

Preserving and Optimising a World-Class African Ornithological Collection

The Durban Natural Science Museum houses a world-class collection of African bird study skins and other ornithological specimens including eggs, nests, skeletons, open wings and ethanol specimens. This presentation briefly outlines the value of these holdings. The bird study skins comprise the core of the collection and number nearly 40 000. This ranks the collection as one of the top three or four on the continent. These study skins are globally renowned for the quality of their preparation, far exceeding that of other African museums. The study skin collection houses an unparalleled assemblage of holotypes and paratypes of (mainly) southern African subspecies. A recent landmark book on geographical variation in southern African birds was largely based on examination of this collection. The collection also boasts the largest collection of study skins in existence from Mozambique. The collection includes one of the most significant Dodo Raphus cucullatus skeletons in the world, which has been subject to intense investigation in recent years, as well as a complete egg of a Madagascar Elephant bird (Aepyornithidae). Also discussed are ongoing best-practice measures to both preserve this collection and render it of optimal value to users, including a brief summary of the key outside stakeholders exploiting the collection for research and other purposes. An issue of particular note is the increasing demand for tissue samples (typically 'toe-pads') from the study skins for molecular investigations - raising problematic challenges relevant to destructive sampling. Particular attention is paid to describing a recent migration of the digital database to a global standard in the form of the ‘Specify’ collection database and management tool.

Michael Patrick Stuart Irwin (1925–2017)

Michael Patrick Stuart Irwin (1925–2017)

Quantifying the decline of the Martial EaglePolemaetus bellicosusin South Africa

SummaryHuman populations in Africa are growing at a faster rate than in any other region; this growth will exert increasing pressures on the continent’s wildlife resources and declines in wildlife are already being observed. Species occupying higher trophic levels may be amongst the most useful indicators of this pressure and raptorial birds have already proven to be particularly useful in highlighting problems with their environment. The Martial Eagle is an African endemic which is thought to be declining and was recently uplisted to globally Vulnerable, although data on population trends are almost entirely lacking. The Southern African Bird Atlas Project (SABAP) 1 and 2 are citizen science projects that represent a rare opportunity, within an African context, to quantify population changes over a 20-year period. We use data from these surveys to explore changes in reporting rates for this species in South Africa between SABAP 1 (1987–1992) and SABAP 2 (2007–2012) at the scale of quarter-degree grid cells. Previous research suggests that such comparisons accurately reflect changes in breeding numbers for this species. We found an overall decline in reporting rates of c.60%, with more cells showing loss or declines (75%) than those showing colonisation or increases (25%). No differences in reporting rate change were found between provinces, suggesting a relative uniform decline across the country. There were, however, differences between biomes with declines recorded in all biomes apart from Albany Thicket, Succulent Karoo and Fynbos (south-western biomes). Declines differed inside and outside protected areas, with larger declines outside (64%) than inside (42%) protected areas, although even within large protected areas significant declines were observed. These results support the uplisting of the species’ conservation status and suggest that even within protected areas the species is not immune to the drivers of decline.

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.

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.

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.

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.

Using independent nest survey data to validate changes in reporting rates of Martial Eagles between the Southern African Bird Atlas Project 1 and 2

Repeat monitoring is vital to measure biodiversity change. However, monitoring protocols may change, as survey techniques improve or different questions are asked. Such modifications may cause difficulties when examining changes in wildlife populations. The Southern African Bird Atlas Project (SABAP) 1 and 2 are repeat national bird surveys undertaken 20 years apart. These surveys therefore offer unrivalled potential to examine bird population changes in an African context. However, changes in protocols, both spatially and temporally, between the two surveys have raised concerns over using these data to infer population changes. In this study we use independ- ent nest survey data to test whether changes in reporting rates of Martial Eagles in the Kalahari Gemsbok National Park between the two SABAP surveys were reflected in real change in numbers of nesting pairs. From 11 quarter degree squares (QDS), covering c. 8 000 km2, both SABAP and nest surveys suggested a near identical 44% decline. Levels of agreement were weaker at the individual QDS scale, although in 67% of cases the direction of change was the same using both surveys. These results suggest that comparisons in the reporting rates between SABAP 1 and SABAP 2 accurately reflect changes in the breeding population size of this species.

Electric crows: powerlines, climate change and the emergence of a native invader

AbstractAimClimate change and other anthropogenic global change drivers act in complex, mutually exacerbating ways to alter the abundance and distribution of species. In South Africa, pied crows Corvus albus have increased in numbers and range in recent decades. Popular opinion links these changes to urbanisation and infrastructure development, but there has been no empirical test of this idea. We aimed to clarify the drivers of pied crow population changes in South Africa.LocationSouth Africa.MethodsWe used publicly available long‐term datasets, the Southern African Bird Atlas Project and University of Delaware Gridded Climate Database, and spatial data from government bodies, to assess relationships between pied crow population and range changes, land use, infrastructure, urbanisation and climate change.ResultsPied crow numbers have increased significantly in the past three decades, but rate of increase varied geographically, with crows declining in the northeast and increasing in the south‐west of South Africa. Pied crow population changes were strongly correlated with climate change. Crows have benefited most from climate warming in the shrubland biomes of south‐western South Africa. Pied crows are tree nesters, and within these shrublands, there is a strong positive relationship between the rate of population increase and the density of powerline infrastructure, which may facilitate pied crows’ increase by providing nesting sites.Main conclusionsPied crow numbers have increased in response to climate warming, with their spread facilitated by electrical infrastructure in south‐western South Africa, providing a clear example of compound influence of multiple global change drivers promoting a significant change in species range and reporting rate. Pied crows are generalist predators and there is popular concern about their ecological impact in areas where increases have occurred. We highlight the importance of understanding the ecosystem‐level implications of increased numbers of pied crows in South Africa's shrubland biomes.

Understanding the Motivations and Satisfactions of Volunteers to Improve the Effectiveness of Citizen Science Programs

Citizen science is a useful approach for conducting scientific research; however, an understanding of the motivations, satisfactions, and other aspects of volunteers’ psychology is essential for conservation scientists wishing to mobilize this resource. We tested psychometric instruments for assessing the motivations, satisfactions, and advocacy role of volunteers with the Second Southern African Bird Atlas Project (SABAP2). Data were collected through stakeholder and volunteer surveys, and focus groups with the program's management. Qualitative and quantitative data analysis included content analysis, statistical tests of internal consistency, and factor analysis. An inventory, the Environmental Volunteer Functions Inventory (EVFI), was tested for assessing volunteer motivations along with scales for assessing volunteer satisfaction and level of advocacy. These scales revealed that volunteers in SABAP2 are satisfied with the program and exhibit behaviors suggesting they act as advocates for the program. Insights and a platform for adaptive management are provided for managers of the social dimensions of citizen science and other conservation programs.