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Assessing the impacts of non-native species is essential for preventing, monitoring and eradicating introduced species. In South Africa, impact assessment has been adopted for species introduced through various pathways, including the legal and illegal wildlife trade. We conducted a comprehensive literature search to collate information on the impacts associated with 76 non-native reptiles sold as pets in South Africa, using the Generic Impact Scoring System (GISS), Environmental Impact Classification for Alien Taxa (EICAT), and Socio-Economic Impact Classification for Alien Taxa (SEICAT). Using GISS, we found that 12 species were associated with environmental impacts (E_GISS), and 10 had socio-economic impacts (SE_GISS). For EICAT and SEICAT, 12 species had environmental and seven had socio-economic impacts, respectively. Despite extensive research efforts, most (82 %) of the evaluated species had no documented impacts, implying that these species are unlikely to have significant impacts. Environmental impact scores differed between GISS and EICAT, indicating that both schemes should be used when assessing environmental impacts. In contrast, while the socio-economic impact scores of GISS and SEICAT were comparable, both schemes provide a comprehensive assessment by capturing different aspects. Popular pet species such as the Iguana iguana, Python bivittatus, and Trachemys scripta elegans, already introduced in the country, scored the highest impacts in all schemes, prompting strict monitoring and policy development regarding their trade. Using multiple impact schemes, we show that despite extensive research efforts, 82 % of reptile species sold as pets in South Africa have no documented impacts. Concerningly, species with documented impacts showed high environmental but minor socio-economic impacts.

Urbanisation and water developments in South Africa have created numerous challenges in managing water resources. Consequently, the native fish species Oreochromis mossambicus, prominent to freshwater ecosystems in South Africa now faces the threat of extinction amidst introductions of alien Oreochromis species. The species has recently been classified as Vulnerable on the IUCN Red List. Despite the economic importance of O. mossambicus within the South African region, little is known about the genetic and population dynamics of the species. In this study, we aimed to establish baseline genetic and population data, and determine the impact of water management practices on population structure. This data is crucial for the conservation and monitoring of this species across South Africa. The study revealed relatively low genetic diversity within sample localities but significant differentiation among populations. The analyses identified 16 geographically correlated genetic clusters, indicating substantial differentiation across catchments. Anthropogenic activities, changes in catchment use, and water management strategies significantly influenced the genetic population structure in the studied regions. Given the distinct genetic patterns, conservation-oriented management should prioritise maintaining existing genetic diversity to ensure the long-term survival of this vulnerable species.

Abstract Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

Abstract Apex predators typically affect the distribution of key soil and vegetation nutrients through the heterogeneous deposition of prey carcasses and excreta, leading to a nutrient concentration in a hotspot. The exact role of central-place foragers, such as tropical raptors, in nutrient deposition and cycling, is not yet known. We investigated whether harpy eagles (Harpia harpyja) in Amazonian Forests—a typically low soil fertility ecosystem—affect soil nutrient profiles and the phytochemistry around their nest-trees through cumulative deposition of prey carcasses and excreta. Nest-trees occurred at densities of 1.5–5.0/100 km2, and each nest received ~ 102.3 kg of undressed carcasses each year. Effects of nests were surprisingly negative over local soil nutrient profiles, with soils underneath nest-trees showing reductions in nutrients compared with controls. Conversely, canopy tree leaves around nests showed significant 99%, 154% and 50% increases in nitrogen, phosphorus and potassium, respectively. Harpy eagles have experienced a 41% decline in their range, and many raptor species are becoming locally extirpated. These are general examples of disruption in biogeochemical cycles and nutrient heterogeneity caused by population declines in a central-place apex predator. This form of carrion deposition is by no means an exception since several large raptors have similar habits.

Abstract Resource selection functions (RSFs) are among the most commonly used statistical tools in both basic and applied animal ecology. They are typically parameterized using animal tracking data, and advances in animal tracking technology have led to increasing levels of autocorrelation between locations in such data sets. Because RSFs assume that data are independent and identically distributed, such autocorrelation can cause misleadingly narrow confidence intervals and biased parameter estimates. Data thinning, generalized estimating equations and step selection functions (SSFs) have been suggested as techniques for mitigating the statistical problems posed by autocorrelation, but these approaches have notable limitations that include statistical inefficiency, unclear or arbitrary targets for adequate levels of statistical independence, constraints in input data and (in the case of SSFs) scale‐dependent inference. To remedy these problems, we introduce a method for likelihood weighting of animal locations to mitigate the negative consequences of autocorrelation on RSFs. In this study, we demonstrate that this method weights each observed location in an animal's movement track according to its level of non‐independence, expanding confidence intervals and reducing bias that can arise when there are missing data in the movement track. Ecologists and conservation biologists can use this method to improve the quality of inferences derived from RSFs. We also provide a complete, annotated analytical workflow to help new users apply our method to their own animal tracking data using the ctmm R package.

Abstract Forest transformation has major impacts on biodiversity and ecosystem functioning. Identifying the influence of forest habitat structure and composition on avian functional communities is important for conserving and managing forest systems. This study investigated the effect of forest structure and composition characteristics on bird species community structure, habitat use and functional diversity in 14 Mistbelt Forest patches of the Midlands of KwaZulu‐Natal in South Africa. We surveyed bird communities using point counts. We quantified bird functional diversity for each forest patch using three diversity indices: functional richness, functional evenness and functional divergence. We further assessed species‐specific responses by focussing on three avian forest specialists, orange ground‐thrush Geokichla gurneyi, forest canary Crithagra scotops and Cape parrot Poicephalus robustus. We found that bird community and forest‐specialist species responses to forest structure and tree species diversity differed. Also, forest structural complexity, canopy cover and tree species richness were the main forest characteristics better at explaining microhabitat influence on bird functional diversity. Forest patches with relatively high structural complexity and tree species richness had higher functional richness. Different structural characteristics influenced habitat use by the three forest specialists. Tree species diversity influenced C. scotops and G. gurneyi positively, while P. robustus responded negatively to forest patches with high tree species richness. Our study showed that site‐scale forest structure and composition characteristics are important for bird species richness and functional richness. Forest patches with high tree species diversity and structural complexity should be maintained to conserve forest specialists, bird species richness and functional richness.

Ground-nesting bird species are typically threatened when their natural habitats are removed or altered through urbanisation. Despite this, some species, like the Spotted Thick-knee (Burhinus capensis), persist in urban mosaic landscapes. Our study was undertaken to collect novel information on Spotted Thick-knee persistence in an urban mosaic landscape by investigating facets of its nesting ecology in Pietermaritzburg, South Africa. We collected Spotted Thick-knee nesting and nest site data between July 2019 and December 2020. We conducted direct observations at 33 nest sites, and additional remote monitoring with camera traps at eight nest sites. Spotted Thick-knee breeding pairs showed select habitat and nest-site preferences (greater use of shrub-like species for nest-site placement, more grass cover, shorter grass, and flatter slopes at nest sites) compared with random sites. Successful nesting outcomes were significantly greater than failed nesting outcomes. Incubation activity was significantly longer during the day, and incubation activity had a significant adverse relationship with disturbance in human-modified habitats. Land use and human activity influenced nest-site selection and survival of nests. Spotted Thick-knee used residential gardens and recreational areas as nest sites in the urban mosaic, although nests were more successful in residential gardens. They used shrub-like vegetation as nest-cover structures, possibly because of added protection from extreme weather or less visual detection. Risks associated with nesting in human-modified habitats included increased threats from domestic animals and incubation activity costs because of disturbance around nest sites. There are relatively few studies on ground-nesting birds in urban areas, so further research is needed to determine how our results compare with other species.

Invasive alien plant species have been identified as a major threat to biodiversity and the relationship with native avian dispersers may increase their invasion potential. The impact of invasive plant species needs to be quantified using comparable assessment tools across different habitats and species to allocate limited resources to high-priority species. Here, we used the Generic Impact Scoring System (GISS) to assess the impacts of 16 fleshy-fruited alien invasive plant species in South Africa generally dispersed by native avian species. The results showed that fleshy-fruited invasive species have both environmental and socio-economic impacts. The cumulated impact scores for lantana (Lantana camara) and the tree of heaven (Ailanthus altissima) were the highest, with scores of 42 and 32, respectively. Some species, such as white mulberry (Morus alba), camphor tree (Cinnamomum camphora), American bramble (Rubus cuneifolius) and Brazilian pepper tree (Schinus terebinthifolius), had low overall impact scores of 8, 18, 14 and 16, respectively, but scored the maximum impact of 5 for certain mechanisms. Environmental impacts of fleshy-fruited invasive plant species had a high impact magnitude through effects on the ecosystem and vegetation. Socio-economic impacts were mainly through effects on forest production, agriculture and human health. Species with large crop sizes, small seeds and fruit sizes had higher environmental and socio-economic impact magnitude. The information generated in this study is important for guiding resource allocation and preventing the uncontrolled introduction of invasive species in South Africa. The impact of the fleshy-fruited invasive species transcended sectors and, therefore, effective management of invasive species will require the collaboration of multiple and inter-sectoral stakeholders in South Africa.

Diurnal basking (“sunning”) is common in many ectotherms and is generally thought to be a behavioural mechanism for thermoregulation. Recent studies have reported the occurrence of nocturnal basking in a few distantly-related species of freshwater turtles, but the true extent of this behaviour is unknown, and it may be underreported due to sampling biases (e.g., not surveying for turtles at night). Therefore, we initiated a global, collaborative effort to systematically document and quantify basking activity (diurnal and nocturnal) across a wide range of freshwater turtle species and locations. We conducted camera trap or manual surveys in North America, the Caribbean, Europe, Asia, Africa, the Seychelles, and Australia. We collected 873,111 trail camera photographs (25,273 hrs of search effort) and obtained data on 29 freshwater turtle species from seven families. Nocturnal basking was documented in 13 species, representing six families (Chelidae, Emydidae, Geoemydidae, Kinosternidae, Pelomedusidae, and Trionychidae), including representatives in Central America, Trinidad and Tobago, Africa, the Seychelles, Asia, and Australia. Nocturnal basking was restricted to tropical and sub-tropical locations, suggesting that environmental temperature plays a role in this behaviour. However, the primary factors driving nocturnal basking are yet to be determined and may vary geographically and by species. The frequency and duration of nocturnal basking varied among species and seasons, but nocturnal basking events were often substantially longer than diurnal events. This is the first study to document a widespread occurrence of nocturnal basking, and our results suggest that nocturnal basking may be a common, although overlooked, aspect of many species’ ecology.

Camera traps have been used increasingly as a research tool to monitor wildlife globally, and have become more advanced, thereby improving their performance and lowering costs. Their use has allowed researchers to study a range of species, including rare and elusive species, particularly in remote areas, in a non-invasive, reliable and cost-effective way. In this review, we sought to document the camera trapping research on terrestrial wildlife conducted in Africa, identifying countries and habitat types of focus, and how these camera trap research trends in Africa could be improved in the future. Through a systematic literature search, we found 408 peer-reviewed publications using camera traps to study terrestrial wildlife in Africa, with the first being in 2005 and up to 2021. Although camera trap studies were conducted in 38 African countries, most were in South Africa (28.9 %). Most studies assessed the occupancy of species (41.4 %). The studies covered a range of taxa, with mammals being the most popular. The majority of research focussed on large carnivores (24.8 %), with a particular focus on leopards (Panthera pardus) (60 studies). Most studies (43.9 %) focused on a single species, with forests (174 studies, 42.6 %) and savannah/bushveld (145 studies, 35.5 %) being the habitat type of focus. There was also a strong preference for camera trap studies to be conducted in protected areas (68.9 %). The camera trap methods used varied considerably between studies, which included: the number of camera trap stations, survey length, trap effort, camera trap make and model, camera trap flash type, interval delay, camera multishot, height of camera trap placement, camera trap layout method and whether the camera trap was baited. These variations are expected because of the difference in research goals posed by each study. However, studies with similar objectives and/or focus still display a clear lack of standardisation (studies do not conform to a specific standard), which could negatively impact the results obtained, as inappropriate camera trap protocols could affect the detectability of certain species. Future camera trap studies will hopefully extend to countries and taxa that have received little attention, with further research informing appropriate conservation strategies that could reduce the threats to biodiversity.

Abstract Apex predators are threatened globally, and their local extinctions are often driven by failures in sustaining prey acquisition under contexts of severe prey scarcity. The harpy eagle Harpia harpyja is Earth’s largest eagle and the apex aerial predator of Amazonian forests, but no previous study has examined the impact of forest loss on their feeding ecology. We monitored 16 active harpy eagle nests embedded within landscapes that had experienced 0 to 85% of forest loss, and identified 306 captured prey items. Harpy eagles could not switch to open-habitat prey in deforested habitats, and retained a diet based on canopy vertebrates even in deforested landscapes. Feeding rates decreased with forest loss, with three fledged individuals dying of starvation in landscapes that succumbed to 50–70% deforestation. Because landscapes deforested by > 70% supported no nests, and eaglets could not be provisioned to independence within landscapes > 50% forest loss, we established a 50% forest cover threshold for the reproductive viability of harpy eagle pairs. Our scaling-up estimate indicates that 35% of the entire 428,800-km2 Amazonian ‘Arc of Deforestation’ study region cannot support breeding harpy eagle populations. Our results suggest that restoring harpy eagle population viability within highly fragmented forest landscapes critically depends on decisive forest conservation action.

Changes to natural environments as a consequence of human population growth are a major threat to biodiversity. Natural habitat modifications, changes in vegetation structure and habitat characteristics have resulted in decreased species richness and functional diversity in wildlife populations. Species’ distributions, abundance and persistence are generally reliant on habitat suitability, landscape configuration and ability to disperse and colonise habitats. We aimed to determine the influence of vegetation structure, patch size and isolation distance on avian communities in Southern Mistbelt Forests in the provinces of KwaZulu-Natal and Eastern Cape, South Africa, across a variety of forest patches during the breeding and non-breeding seasons. We conducted fixed-radius point-count surveys to determine avian species richness and functional diversity, and quantified the vegetation foliage profile in 54 distinct forest patches across three study areas. Multivariate analyses showed significant differences in vegetation structure among forest patches and subsequent variation in avian species richness and functional diversity across the study areas during the non-breeding season. Avian beta diversity was significantly driven by the reduction in forest patch size and habitat structural complexity. Reduction in forest size and complexity reduced avian species richness and functional diversity. Increasing isolation distance negatively influenced avian diversity. We recommend further improving the regulatory standards concerning sustainable utilisation of forest resources that subsequently change forest characteristics to promote a healthy and diverse habitat structure and safeguard avian communities.

The pet trade is one of the most important pathways by which small mammals are introduced to non-native areas. To prevent the introduction and invasion of non-native pets, an impact assessment protocol is useful in understanding which pets might have potential negative impacts should they escape or be released from captivity. In this study, we used the Generic Impact Scoring System (GISS) to assess the potential effects associated with 24 non-native small mammal species sold in the South African pet trade. European rabbits Oryctolagus cuniculus, house mice Mus musculus, Norwegian rats Rattus norvegicus and eastern grey squirrels Sciurus carolinensis had the highest potential impacts for both socio-economic and environmental categories. We found no statistically significant difference between the overall environmental and socio-economic impact scores. Impacts on agricultural and animal production (livestock) were the main mechanisms in the socio-economic category, while the impacts on animals (predation), competition and hybridisation prevailed for environmental impacts. The non-native mammal pet species with high impacts should be strictly regulated to prevent the potential impacts and establishment of feral populations in South Africa.

Understanding population trends is important when managing wildlife in protected areas. The common hippopotamus, Hippopotamus amphibius (hereafter hippo), is an iconic African species that, in South Africa, is mainly restricted to protected areas. Ndumo Game Reserve (NGR), South Africa, was established as a sanctuary for hippos in 1924. However, NGR and its hippo population are under increased anthropogenic threat, outlining the importance of long-term and current data on hippo population dynamics. We collated census data from 1951 to 2021 to identify trends in hippo population numbers. We also conducted monthly unmanned aerial vehicle (UAV) censuses from August 2016- July 2017 to identify changes in the distribution of hippos in the most important water bodies in NGR. Historical census data were collected using a variety of methods, and observed trends revealed a decrease in the hippo population in the past 40 years. Monthly census data from 2016 to 2017 revealed that wading locations in NGR hold differing values as wading sites, with 85–95% of the population using the uSuthu and Phongolo Rivers and associated floodplains. Areas in NGR experiencing the greatest anthropogenic land invasions are also the areas that represent the best hippo habitat in NGR. We, therefore, recommend that the conservation management authority, sections of the South African government like the Department of Land Affairs and local communities work together to reinstate the boundary of NGR to protect hippo and other wildlife in this important protected area.

Larger carnivores often trigger human-wildlife conflicts that arise from perceived threats to humans and domestic animals’ safety, which generate the need for management and removal strategies. These issues become especially challenging when humans and wildlife coexist close to one another, for example, in urban landscapes. African Crowned Eagles (Stephanoaetus coronatus) are powerful forest raptors that breed within the metropolitan green-space system of Durban and Pietermaritzburg, South Africa. Negative human-wildlife interactions can occur because eagles occasionally predate on pets, such as cats (Felis catus) and small dogs (Canis lupus familiaris), and provisioning domestic stock to nest sites has previously been quantified. Here, wildlife management becomes critical, usually aimed at reducing or eliminating causes of economic or social harm, but have to be balanced against conservation goals regarding threatened species. In this study, we (i) identified causes of harm or loss of Crowned Eagles because of injuries (n = 53 incidents; 31 mortalities); and (ii) describe interactions with negative perceptions to human livelihoods, particularly concerning predation on pets and livestock. Anthropogenic causes of mortality were more likely to be reported than remote natural deaths, which provides important opportunities for mitigation measures. Most avoidable are electrocution on utility poles, persecution via gunshot wounds and poisoning (targeted or secondary), while collisions with anthropogenic structures, such as glass panes, vehicles and fence wires, are more challenging to mitigate. Out of 44 verified Crowned Eagle vs. pets and livestock conflicts, we documented 19 dog attacks (2012–2020), with detrimental impacts on social perception and acceptance of urban eagles. Pet and livestock conflicts were primarily associated with juveniles and immature eagles (83%). Of these, 19% occurred during September alone, which marks the end of the post-fledging dependency period; 70% occurred outside the breeding season. We provide management recommendations regarding various categories of Crowned Eagle human-wildlife interactions. For example, activities such as rehabilitation and falconry can coordinate to achieve a high standard of public support and conservation outcomes for Crowned Eagles. Finally, we discuss using different management intervention strategies, including rehabilitation, falconry, re-wildling processes, and lethal control of specific “problem” individuals toward achieving the goal of sustainable, healthy Crowned Eagle populations that coexist with humans in urban landscapes.

Freshwater resources are under stress because of anthropogenic activities and the demand for water increasing on a global scale, including hydropower. There are presently plans to expand the use of hydropower within eastern and southern Africa. A key river system identified as a potential source of energy is the Pungwe River, with the proposed Pavua Dam located within the middle reaches of the system in Mozambique. However, impoundments have been recorded to negatively influence ichthyofauna communities via alterations to water quality and discharge. Furthermore, information on the structure of the ichthyofauna community, community spatial shifts and fine-scale habitat preferences for the region are lacking. Accordingly, the research sought to address this issue, to provide baseline data as well as inform on management of the system. Ichthyofauna were collected utilising an array of passive and active techniques and species data modelled to fit spatial factors to ascertain spatial shifts. To ascertain fine-scale habitat preferences, fourth-corner modelling was undertaken to link mouth position and body shape traits to substrate composition and cover features. Spatial heterogeneity in environmental characteristics caused by the intrusion of the African Rift Valley had driven significant spatial shifts in the ichthyofauna community, with distinct groups of species occurring within the sample sites. The findings of the study indicated that the ichthyofauna community within the Muazi River were significantly different to the Pungwe River and the community will be lost from the region because of the dam footprint. Furthermore, habitat preferences were influenced by mouth position and body shape. Consequently, alteration to environmental characteristics and habitat features is likely to negatively influence the ichthyofauna community.

Urbanisation is rapidly transforming natural habitats with the potential to benefit synanthropic species, especially mesocarnivore species. Knowledge of the spatio-temporal ecology of mongoose species in an urban matrix is limited. Consequently, we examined the home range and habitat use of water mongoose (Atilax paludinosus, n = 14) in an urban matrix landscape. Mongooses were collared and radio-tracked using Global Positioning System (GPS)-Ultra high frequency (UHF) transmitters between July 2018 and October 2019 in the Upper Highway area’s urban matrix, eThekwini Municipality, Durban, KwaZulu-Natal, South Africa. Habitat selection for water mongoose indicated that the species avoided built-up urban areas favouring fragments of forest and bushland habitat types close to natural water sources within the urban mosaic. The adaptability and generalist nature of water mongoose has facilitated their persistence in the urban mosaic. Variability in the home range size and habitat use of individuals of the water mongooses highlights their ability to adapt to anthropogenically modified landscape, yet they were highly dependent on natural refugia in this urban matrix.

Increase in anthropogenic pressures on freshwater ecosystems, globally and locally in South Africa, has made it difficult to meet environmental flow requirements and maintain these systems. The Letaba-Olifants catchment is one such example, where the upstream water demands place pressure on the river downstream as it flows through the Kruger National Park. We used the activity rates of Hydrocynus vittatus as a line of evidence to assess (1) the effects of telemeter tagging on their activity rates in three potential post-tagging recovery periods and (2) their vulnerability to predation and the causality related to the environmental stressors placed on the river catchment in the Olifants River Gorge, Kruger National Park, South Africa. We determined H. vittatus activity rates as locomotive movement using radio telemetry methods linked remotely to an online data management system. We telemeter tagged nine individuals from 08 May to 28 June 2018. However, only seven fish were successfully tracked for the duration of our study, and two individuals moved out of range of the remote network shortly after release and could not be located. The tagged H. vittatus individuals were found to have reduced activity at least within the first 7 days after tagging compared with the time after that. The results showed that three individuals were preyed on by predators after the tagging procedure recovery period. This coincided with abnormal low flow conditions, where the Letaba River ran dry. African fish eagles Haliaeestus vocifer were the only confirmed predator, whilst predation by other species was also evident. Conservation implications: Monitoring of H. vittatus using telemetry is a viable tool to use when assessing environmental stressors in remote locations. The abnormally low water levels in the Olifants and Letaba Rivers (cessation of flow in the Letaba River) during our study may have compromised the predator avoidance strategies of tagged H. vittatus and may further be affecting the viability of the H. vittatus populations in Kruger National Park. The synergistic effects of natural and anthropogenic stressors impact negatively H. vittatus populations and potentially other aquatic biotas.

The rivers of KwaZulu-Natal, South Africa, are being impacted by various anthropogenic activities that threaten their sustainability. Our study demonstrated how Bayesian networks could be used to conduct an environmental risk assessment of macroinvertebrate biodiversity and their associated ecosystem to assess the overall effects of these anthropogenic stressors in the rivers. We examined the exposure pathways through various habitats in the study area using a conceptual model that linked the sources of stressors through cause-effect pathways. A Bayesian network was constructed to represent the observed complex interactions and overall risk from water quality, flow and habitat stressors. The model outputs and sensitivity analysis showed ecosystem threat and river health (represented by macroinvertebrate assessment index – MIRAI) could have high ecological risks on macroinvertebrate biodiversity and the ecosystem, respectively. The results of our study demonstrated that Bayesian networks can be used to calculate risk for multiple stressors and that they are a powerful tool for informing future strategies for achieving best management practices and policymaking. Apart from the current scenario, which was developed from field data, we also simulated three other scenarios to predict potential risks to our selected endpoints. We further simulated the low and high risks to the endpoints to demonstrate that the Bayesian network can be an effective adaptive management tool for decision making.

The use of reference conditions is essential to the monitoring and management of aquatic ecosystems. We examined existing and potential reference sites through historical data, maps, and field data collected from river sites in KwaZulu-Natal (KZN), South Africa. In our study, we applied nine criteria that best reflect the characteristics of South African rivers on 24 a priori selected reference sites. These nine criteria comprised of catchment conditions (flow modification and natural landscape) and site-specific attributes (water quality, human disturbance, river channel, water abstraction, riparian vegetation, riparian zone modification, and instream habitat quality). The a priori selected reference sites were subjected to validation using multivariate methods, such as analysis of similarities (ANOSIM), similarity percentages (SIMPER), and non-parametric multidimensional scaling (MDS) based on the macroinvertebrate fauna by applying a SASS5 threshold considered to be an indicator of undisturbed sites in South African rivers. We identified differences in the macroinvertebrate assemblages of the reference conditions for each river group based on their ecoregions, geomorphology and seasonal variations. Ecoregions and river geomorphology were better in the grouping of sites with similar reference conditions than the seasons. Our findings indicated that all of the selected sites could be considered as valid reference sites; however, caution should be taken in applying this method to lowland rivers because of their noticeable seasonal variability and habitat instability which tend to alter their reference states. We recommend that a type-specific reference condition be developed for lowland rivers. Also, statistical validation of reference conditions should be a continuous process in river biomonitoring.

Background Climate plays a key role in the life histories of tropical vertebrates. However, tropical forests are only weakly seasonal compared with temperate and boreal regions. For species with limited ability to control core body temperature, even mild climatic variation can determine major behavioural outcomes, such as foraging and predator avoidance. In tropical forests, sloths are the arboreal vertebrate attaining the greatest biomass density, but their capacity to regulate body temperature is limited, relying on behavioural adaptations to thermoregulate. Sloths are largely or strictly nocturnal, and depend on crypsis to avoid predation. The harpy eagle (Harpia harpyja) is a sloth-specialist and exerts strong top-down control over its prey species. Yet the role of environmental variables on the regulation of predator–prey interactions between sloths and harpy eagles are unknown. The harpy eagle is considered Near Threatened. This motivated a comprehensive effort to reintroduce this species into parts of Mesoamerica. This effort incidentally enabled us to understand the prey profile of harpy eagles over multiple seasons. Methods Our study was conducted between 2003 and 2009 at Soberanía National Park, Panamá. Telemetered harpy eagles were seen hunting and feeding on individual prey species. For each predation event, field assistants systematically recorded the species killed. We analysed the effects of climatic conditions and vegetation phenology on the prey species profile of harpy eagles using generalised linear mixed models. Results Here we show that sloth predation by harpy eagles was negatively affected by nocturnal ambient light (i.e. bright moonshine) and positively affected by seasonally cool temperatures. We suggest that the first ensured low detectability conditions for sloths foraging at night and the second posed a thermally unsuitable climate that forced sloths to forage under riskier daylight. We showed that even moderate seasonal variation in temperature can influence the relationship between a keystone tropical forest predator and a dominant prey item. Therefore, predator–prey ecology in the tropics can be modulated by subtle changes in environmental conditions. The seasonal effects shown here suggest important demographic consequences for sloths, which are under top-down regulation from harpy eagle predation, perhaps limiting their geographic distribution at higher latitudes.

The loss and fragmentation of natural habitats is a major threat to biodiversity globally. In fragmented landscapes, species are not only affected by patch-level attributes but also by the influence of the whole mosaic of landscape elements surrounding habitat patches. Therefore, it is important to understand the simultaneous effects of local and landscape-level attributes on biodiversity. In this study, we determined the influence of landscape context on species richness of forest mammals in an urban-forest mosaic of the EThekwini Municipality Area, Durban, South Africa. We determined presence/absence of mammals in 28 patches using remote-triggered camera traps over two sampling periods. We applied generalised linear modelling within an information-theoretic framework to quantify the effects of within-patch, isolation, matrix, and landscape level attributes on species richness. The results showed the importance of landscape context for occurrence patterns of mammals in fragmented landscapes. In particular, they showed that patch size, shape complexity, habitat amount in the immediate environment, habitat proximity and road density were the most important factors influencing mammalian richness patterns. Overall, the results stressed the importance of habitat area (patch size, habitat amount in the immediate environment, and habitat proximity) and its spatial configuration to faunal preservation and suggest that management efforts in this landscape should be aimed at protecting fragments from further loss and disturbance and matrix improvement to increase landscape connectivity. Keywords: Fragmentation, Forest, Habitat, Isolation, Mammal, Species richness, Urban mosaic

The pet trade is one of the main pathways of introduction of several mammals worldwide. In South Africa, non-native mammalian species are traded as pets, and so far, only four of these species are considered invasive. We used a list of 24 companion mammalian species compiled from a previous study. We selected a subset of 14 species for species distribution modeling (SDM) based on their trade popularity, invasion history and potential economic and socio-economic impacts. We aimed to estimate their potential distribution using their distribution records. Our SDM indicated that climate in South Africa was suitable for most traded species. However, commonly and easily available species had the broadest areas of suitable climates, such as house mice (Mus musculus) and Norwegian rats (Rattus norvegicus). In addition, the model with a human footprint suggested a high risk of invasion for Norwegian rats but less for house mice distribution. This assessment suggests the need of strict trade regulations and management strategies for pet mammals with broader suitability, which are already invasive, and most available for sale. In addition, our results provide a baseline approach that can be used to identify mammalian pet species with a potential risk of invasion so that urgent preventive measures can be implemented.

Anthropogenic forest disturbance poses a significant threat to the persistence of wildlife. Generally, disturbance of forest environments alters vegetation structure, affecting specialised niche-dependent avian species. We investigated the influence of a comprehensive suite of vegetation structures on the taxonomic and functional diversity of avian forest species in five protected forest areas in the urban mosaic of eThekwini Municipality, Durban, South Africa during the austral breeding season of 2016. We conducted 135 fixed-radius point-count surveys between the vegetation classes of Indigenous Forest (IF) and Coastal Thicket/Dense Bush (TDB; a secondary wooded-habitat that represents regenerating Indigenous Forest), and recorded microhabitat structure covariates at each survey site. We conducted RLQ analyses to examine the association between avian functional traits and microhabitat structures present at each survey site. There was no significant difference in vegetation structure nor species richness between IF and TDB. Species with specialised ecological niches (e.g. large-bodied frugivores; small-bodied insectivores, cavity-nesters) were present in both IF and TDB, indicating that TDB in Durban represents an advanced stage of forest regeneration. We highlight the importance of both IF and TDB for providing critical habitat for both avian generalised and specialised functional traits in the forest patches in the urban mosaic. Crucially, we show that forested areas under conservation management in urbanised areas successfully provide species with a wide variety of functional traits critical to ecosystem functioning and human health. Keywords: Avian forest specialists, Avian functional traits, Ecosystem services, Forest structural complexity, Regenerating forest, RLQ analysis

Background: Habitat loss and fragmentation continue to threaten the survival of many species. One such species is the Blue Swallow Hirundo atrocaerulea, a critically endangered grassland specialist bird species endemic to sub-Saharan Africa. Objectives: Past research has shown a serious decline in range and abundance of this species, predominantly because of habitat transformation and fragmentation. Method: The influence of land cover on Blue Swallow habitat and foraging home range, in both natural and transformed habitats, was investigated by radio tracking adult birds. Results: Results showed that tracked birds spent over 80% of their forage time over grasslands and wetland habitats, and preferentially used these ecotones as forage zones. This is likely owing to an increase in insect mass and abundance in these habitats and ecotones. There was reduced selection and avoidance of transformed habitats such as agricultural land, and this is a concern as transformed land comprised 71% of the home range with only 29% of grassland and wetland mosaic remaining for the Blue Swallows to breed and forage in, highlighting the importance of ecotones as a key habitat requirement. The results indicate that management plans for the conservation of Blue Swallows must consider protecting and conserving natural habitats and maintaining mosaic of grassland and wetland components to maximise ecotones within conserved areas. Conclusion: To this end, the stewardship programme spearheaded by local conservation agencies, which aims to formally conserve privately owned patches of untransformed grassland and other natural habitats, may have a strong impact on the long-term persistence of Blue Swallow populations.

Habitat features can have a profound effect on the nesting success of birds. Savannas are often managed with predators and large herbivores as priority species, with little thought to the many bird species that management decisions could affect. Using a data set spanning seven breeding seasons, we examined how nesting success of Southern Ground-hornbills (SGHs) Bucorvus leadbeateri in the Kruger National Park varied as a result of various environmental and habitat factors within a radius of 3 km surrounding the nest site. Identifying which factors affect nesting success will allow for targeted management efforts to ensure the long-term survival of SGHs both within and outside of protected areas. Habitat structure and diversity of the vegetation surrounding the nest were the most influential factors on SGH nesting success. SGHs require open grassy areas for foraging and areas with large trees for nesting. Savanna habitat drivers such as elephants and fire should be managed to ensure that sufficient large trees are able to establish in the landscape and to control for bush encroachment. This is especially important in areas earmarked for SGH reintroductions. Nest sites of SGHs should be monitored to mitigate any structural changes in the habitat surrounding the nests. Nests should be modified or artificial nest sites provided, where nests have been damaged or lost, to ensure the continued presence of these birds in African savannas. Conservation implications: Habitat structure and diversity surrounding Southern Groundhornbill nests has a significant impact on their nesting success. This highlights the importance of monitoring vegetation change in savanna habitats where they occur. Management of savanna areas should take factors that influence bush encroachment, such as fire and elephants, into account to ensure the long-term persistence of these birds.

Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.

Eastern mistbelt forests are naturally fragmented forests with grassland which occur from the Eastern Cape to KwaZulu-Natal, South Africa. These were heavily logged by colonial settlers and continue to be harvested despite being protected. Consequently we documented a checklist of the plants of the forests and grasslands in the Weza district (3029DA WEZA), southern KwaZulu-Natal, including Ngeli Forest and nearby indigenous forest patches to highlight their biodiversity status and need for conservation. We also reviewed their status in the Red Data List. Of the 1554 records included in this summary of plant species for the Weza district, there were 6 lichens (0.4%), 46 bryophytes (3.0%), 58 pteridophytes (3.7%), 6 gymnosperms (0.4%) and the remaining 1424 species angiosperms (92.5%). Of the angiosperms, 27.3% were monocotyledons and 72.7% were dicotyledons. The most species-rich family was Asteraceae (239 species) followed by Fabaceae (115 species), Liliaceae (used for purposes of comparison against older studies – 89 species), Orchidaceae (89 species), Iridaceae (59 species), Poaceae (58 species), Asclepidaceae (again used for purposes of comparison against older studies – 57 species), Scrophulariaceae (42 species), Euphorbiaceae (32 species), Lamiaceae (32 species) and Rubiaceae (27 species). These 10 families each comprised more than 2% of the species in the list. Together they contributed 55% of the angiosperm species and 34.1% of the angiosperm genera. The biodiversity and conservation value of the study area are conserved pockets of eastern mistbelt forest, Drakensberg foothill moist grassland and mistbelt grassland. More than 4% of the species are under some degree of threat, as was evidenced by the number of species regarded as endangered (5), vulnerable (18), near threatened (10), critically rare (1), rare (20) or declining (11) amongst the 1554 species covered in the list. Conservation implications: In terms of taxa under some degree of threat, number of endemic and near endemic species the biodiversity and conservation value of the Ngele (3029DA WEZA) area is reinforced. This necessitates that the area is appropriately protected from invasive alien species, and uncontrolled and illegal use by the neighbouring communities.

The study of movement patterns and home range is fundamental in understanding the spatial requirements of animals and is important in generating information for the conservation and management of threatened species. Ndumo Game Reserve, in north-eastern KwaZulu-Natal, bordering Mozambique, has the third largest Nile crocodile (Crocodylus niloticus) population in South Africa. Movement patterns of 50 Nile crocodiles with a total length of between 202 cm and 472 cm were followed over a period of 18 months, using mark-resight, radio and satellite telemetry. The duration of radio transmitter attachment (131 ± 11.4 days) was significantly and negatively related to total length and reproductive status. Satellite transmitters failed after an average of 15 ± 12.5 days. Home range was calculated for individuals with 10 or more radio locations, spanning a period of at least 6 months. There was a significant relationship between home range size and total length, with sub-adults (1.5 m – 2.5 m) occupying smaller, more localised home ranges than adults (> 2.5 m). The largest home ranges were for adults (> 2.5 m). Home ranges overlapped extensively, suggesting that territoriality, if present, does not result in spatially discrete home ranges of Nile crocodiles in Ndumo Game Reserve during the dry season. Larger crocodiles moved farther and more frequently than smaller crocodiles. The reserve acts as a winter refuge and spring breeding site for an estimated 846 crocodiles, which also inhabit the Rio Maputo during the summer months. Nile crocodile movement out of the reserve and into the Rio Maputo starts in November and crocodiles return to the reserve as water levels in the floodplain recede in May. Conservation implications: Movement patterns of Nile crocodiles show the important role the reserve plays in the conservation of Nile crocodile populations within the greater Ndumo Game Reserve–Rio Maputo area.

Despite the extent of subsistence farmland in Africa, little is known about endangered species that persist within them. The Cape Vulture (Gyps coprotheres) is regionally endangered in southern Africa and at least 20% of the population breeds in the subsistence farmland area previously known as the Transkei in the Eastern Cape province of South Africa. To understand their movement ecology, adult Cape Vultures (n = 9) were captured and fitted with global positioning system/global system for mobile transmitters. Minimum convex polygons (MCPs),and 99% and 50% kernel density estimates (KDEs) were calculated for the breeding and non breeding seasons of the Cape Vulture. Land use maps were constructed for each 99% KDE and vulture locations were overlaid. During the non-breeding season, ranges were slightly larger(mean [± SE] MCP = 16 887 km2 ± 366 km2) than the breeding season (MCP = 14 707 km2 ± 2155 km2). Breeding and non-breeding season MCPs overlapped by a total of 92%. Kernel density estimates showed seasonal variability. During the breeding season, Cape Vultures used subsistence farmland, natural woodland and protected areas more than expected. In the non-breeding season, vultures used natural woodland and subsistence farmland more than expected, and protected areas less than expected. In both seasons, human-altered landscapes were used less, except for subsistence farmland. Conservation implications: These results highlight the importance of subsistence farm land to the survival of the Cape Vulture. Efforts should be made to minimise potential threats to vultures in the core areas outlined, through outreach programmes and mitigation measures.The conservation buffer of 40 km around Cape Vulture breeding colonies should be increased to 50 km.

The gap between scientific knowledge and implementation in the fields of biodiversity conservation, environmental management, and climate change adaptation has resulted in many calls from practitioners and academics to provide practical solutions responding effectively to the risks and opportunities of global environmental change, e.g., Future Earth. We present a framework to guide the implementation of science-action partnerships based on a real-world case study of a partnership between a local municipality and an academic institution to bridge the science-action gap in the eThekwini Municipal Area, South Africa. This partnership aims to inform the implementation of sustainable land-use planning, biodiversity conservation, environmental management, and climate change adaptation practice and contributes to the development of human capacity in these areas of expertise. Using a transdisciplinary approach, implementation-driven research is being conducted to develop several decision-making products to better inform land-use planning and management. Lessons learned through this partnership are synthesized and presented as a framework of enabling actions operating at different levels, from the individual to the interorganizational. Enabling actions include putting in place enabling organizational preconditions, assembling a functional well-structured team, and actively building interpersonal and individual collaborative capacity. Lessons learned in the case study emphasize the importance of building collaborative capacity and social capital, and paying attention to the process of transdisciplinary research to achieve more tangible science, management, and policy objectives in science-action partnerships. By documenting and reflecting on the process, this case study provides conceptual and practical guidance on bridging the science-action gap through partnerships.