Deagrarianisation (cropland, field abandonment) is a widespread global phenomenon with high potential for carbon sequestration and for reversing biodiversity extinction debt thus promoting environmental sustainability and conservation. To date, much work on this topic has focused on plant succession and associated plant diversity, but few studies have considered faunal communities, particularly in Africa. Here we used passive acoustic monitoring to record insectivorous bat communities within forest fragments and former fields under communal land tenure in the Transkei region (Eastern Cape) of South Africa. Insectivorous bat diversity of fields, abandoned in the 1960s to 1980s, resembling late stages of succession, were compared to fragments of Transkei Coastal Scarp forest embedded within the landscape. We found that former fields hosted 14 species from 11 genera, comprising greater species richness, activity, Shannon-Weiner diversity, and functional diversity, irrespective of age, as compared to the forest fragments. Furthermore, the former fields exhibited comparable species richness to, and higher functional diversity than, three large neighbouring intact Transkei Scarp forests. Interestingly, the time since cultivation had ceased (35—64 years ago) had no measurable effect on species and functional diversity. Former fields are dominated by the invasive alien shrub Lantana camara and the indigenous pioneer tree Vachellia karoo, but nonetheless in terms of insectivorous bats, these landscapes have a conservation value as they are diverse both in terms of species and function. Mutual mechanisms to enhance both biodiversity conservation and the utility of the land to local communities should be further considered.

We investigated the effect of anthropogenically-driven habitat modifications on insectivorous bat activity and diversity along a stretch of the Eerste River, Stellenbosch, South Africa, by determining insect abundance, water quality and vegetation and river characteristics at four sites of varying anthropogenic impact. Passive acoustic monitoring was used to determine species composition and activity of bats at each of the sites. A total of 14,457 bat passes was recorded, with the same six species being found at each of the sites: four clutter edge foragers (Myotis tricolor, Eptesicus hottentotus, Miniopterus natalensis and Laephotis capensis) and a single clutter forager (Rhinolophus clivosus) and open-air forager (Tadarida aegyptiaca). Bat activity was greater at the lower two most eutrophied sites, and greatest at the residential (urban) site. Laephotis capensis, an urban-adapted species, was by far the most active, probably on account of both insensitivity to light pollution, and roost-site availability. The highest and most pristine site (Eiland) and the lowest and most polluted site (Spier) displayed the greatest diversity, despite highly elevated levels of chloride and nitrate at the latter site. So anthropogenic effects on water quality appear not to have negatively affected bat diversity along this stretch of the Eerste River. As these effects are likely to increase, this study serves as a baseline for future monitoring of bats along its course.

Two subspecies of the Yellow-throated Woodland Warbler Phylloscopus ruficapilla (family Phylloscopidae) have been recognised in South Africa based on the extent and intensity of yellow colouration. Our previous multi-locus population genetic survey across much of the Eastern Cape and southern KwaZulu-Natal provinces, conducted from 2017 to 2023, revealed a single homogenous regional population. That finding, derived from 93 individuals sampled from nine sites-six northeast of the Great Kei River (n = 72) and three to the southwest (n = 21)-did not support a subspecies boundary near the Great Kei River. Here, using 188 publicly archived photographic records for this species in South Africa, we show that the phenotypes of both subspecies are present on either side of this divide. The observed genetic homogeneity and lack of clear phenotypic vicariance suggest that P. ruficapilla is more dispersive than currently appreciated, and that the plumage-based subspecies may not represent significant population-level differences.

Individual patterns of scent marking can aid our understanding of the function of animal latrines. African wild dogs are pack-living social carnivores that regularly visit latrines, called shared marking sites, used by multiple neighbouring packs. Here we analysed scent marking by individual African wild dogs video captured at continuously monitored marking sites. Scent marking differed by sex and dominance status depending on social context (interpack versus intrapack exchanges). Dominants marked more frequently than subdominants, and patterns, particularly the order of overmarking, differed between the sexes. Dominant females were more likely than dominant males to overmark when the previous scent mark had been left by an individual from a different pack. Dominant males were more likely to leave the final, or top mark, regardless of social context or origin. Results are consistent with a resource defence advertisement function for wild dog latrines. However, sex-specific scent marking suggests the resource defended may differ between dominant females, which are more attentive to interpack scent marks, and dominant males, which are focused on overmarking a mate. The pattern of dominant male scent marking indicates that unambiguous advertisement of a bonded reproductive pair may be a critical component of communicating with neighbours about pack residence and territoriality.

Apex predators ideally require vast intact spaces that support sufficient prey abundances to sustain them. In a developing world, however, it is becoming extremely difficult to maintain large enough areas to facilitate apex predators outside of protected regions. Free-roaming leopards (Panthera pardus) are the last remaining apex predator in the Greater Cape Floristic Region, South Africa, and face a multitude of threats attributable to competition for space and resources with humans. Using camera-trap data, we investigated the influence of anthropogenic land modification on leopards and the availability of their natural prey species in two contrasting communities—primarily protected (Cederberg) and agriculturally transformed (Piketberg). Potential prey species composition and diversity were determined, to indicate prey availability in each region. Factors influencing spatial utilisation by leopards and their main prey species were also assessed. Estimated potential prey species richness (Cederberg = 27, Piketberg = 26) and diversity indices (Cederberg—H′ = 2.64, Ds = 0.90; Piketberg—H′ = 2.46, Ds = 0.89), supported by both the Jaccard’s Index (J = 0.73) and Sørensen’s Coefficient (CC = 0.85), suggested high levels of similarity across the two regions. Main leopard prey species were present in both regions, but their relative abundances differed. Grey rhebok, klipspringer, and rock hyrax were more abundant in the Cederberg, while Cape grysbok, Cape porcupine, chacma baboon, and common duiker were more abundant in Piketberg. Leopards persisted across the agriculturally transformed landscape despite these differences. Occupancy modelling revealed that the spatial dynamics of leopards differed between the two regions, except for both populations preferring areas further away from human habitation. Overall, anthropogenic factors played a greater role in affecting spatial utilisation by leopards and their main prey species in the transformed region, whereas environmental factors had a stronger influence in the protected region. We argue that greater utilisation of alternative main prey species to those preferred in the protected region, including livestock, likely facilitates the persistence of leopards in the transformed region, and believe that this has further implications for human-wildlife conflict. Our study provides a baseline understanding of the potential direct and indirect impacts of agricultural landscape transformation on the behaviour of leopards and shows that heavily modified lands have the potential to facilitate mammalian diversity, including apex predators. We iterate that conservation measures for apex predators should be prioritised where they are present on working lands, and encourage the collaborative development of customised, cost-effective, multi-species conflict management approaches that facilitate coexistence.

Summary The Amathole forest complex is the breeding stronghold of the endemic and vulnerable Cape Parrot Poicephalus robustus , and is also one of only two forest complexes in South Africa formally harvested for timber. The aim of this study was to determine if formal harvesting of indigenous trees, primarily the two yellowwood species Afrocarpus falcatus and Podocarpus latifolius, in 9 of 16 Amathole forests has had any effect on the presence of Cape Parrots and three primary nest-excavating species, as well as on parrot breeding. The study used logging data from the past 25 years (1997–2021) as well as data collected by acoustic recording units over two breeding seasons from 2019 to 2021. Cape Parrots were present in 15 of 16 forests, but breeding calls were identified in only seven forests: five in logged and two in unlogged forests. Fourteen of the forests harboured all three primary excavators: Knysna Woodpecker Campethera notata , Olive Woodpecker Dendropicos griseocephalus , and Red-fronted Tinkerbird Pogoniulus pusillus. The last two species were absent from the adjacent Mount Thomas and Kologha forests, respectively, in which parrots were present, but no breeding calls were recorded. Logging of yellowwoods was not found to affect parrot breeding. However, due to the overlap between preferred parrot breeding sites and preferred trees for harvesting, we recommend that harvesting in the five harvested forest blocks where parrot breeding occurs be limited to tree falls, with no standing dead, dying, or damaged trees harvested, to ensure that potential nesting trees are not harvested.

Cryptic species present a challenge for conservation, as species diversity may remain undetected. In zoological research, DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) has become a useful heuristic tool for aiding species resolution and informing species discovery. Despite concerted efforts to genetically barcode bats and birds, comprehensive assessments have yet to be undertaken across the Afrotropics. We retrieved available DNA barcodes of native breeding Afrotropical bat and bird species. Using Bayesian phylogenetic modelling, we assessed DNA barcode performance at species identification, and sought to detect notable intraspecific clade partitioning hinting at cryptic speciation. Available DNA barcodes represent only 42.3% and 23.6% of the relevant bat and bird species diversity, respectively, with only 18.7% of bat species and 7.2% of bird species having geographically spread records. DNA barcodes afforded greater taxonomic resolution of Afrotropical bird species than of bats (96.8% vs. 84.0%), with bats having a higher proportion of species non-monophyly (25.5% vs. 4.8%). Well-supported (≥ 95% posterior probability) clade partitioning was inferable from twenty-one bat species and fifteen bird species, and a further single under-sampled bat species and fifteen such bird species showed deep (> 2.0%) intraspecific divergences. These phylogenetic signatures allude to cryptic speciation within these volant taxa, and serve to prompt more comprehensive assessments of Afrotropical fauna. These findings also indirectly affirm the importance of paleoclimatic refugia to endemic vertebrate diversity. The current taxonomic status of birds is better supported by this molecular evidence than that of bats.

April 2021 he took up office at the age of 38the youngest person

Aim Pleistocene climate shifts were influential in shaping biodiversity patterns for forest-dependent species. Within southern Africa, palaeoclimatic shifts possibly homogenised subtropical Afromontane forest biodiversity, yet these forests continue to harbour unique diversity. For the three songbird species with different natural histories, we investigated the refugial role of subtropical Afromontane and scarp forests and explored specifically how palaeoclimatic events impacted genetic connectivity among forest patches. Location Maputaland-Pondoland-Albany Biodiversity Hotspot, south-eastern South Africa. Taxon Batis capensis, Phylloscopus ruficapilla and Pogonocichla stellata. Methods Mitochondrial control region sequences and microsatellite data were used to assess genetic diversity and population structure among 406 birds. Demographic change was inferred using Bayesian skyline plots (BSPs), and approximate Bayesian computations (ABCs) were used to identify gene flow trends among putative refugia. Environmental niche models (ENMs) were used to infer past occurrence probabilities. Results Species BSPs supported regional presence predating the Last Glacial Maximum (21 kya) and indicated post-glacial population expansions. ABC modelling revealed that present-day gene flow trends emerged largely during the current interglacial (<12 kya), suggesting that thermal maxima promote regional forest expansion. The north-eastern source of gene flow in all the three species suggested a post-glacial influx from refugia further north, while southern scarp forests sustained secondary source populations for B. capensis and P. ruficapilla. High gene flow signatures from south-western forests in B. capensis and especially P. stellata alluded to hidden source populations in the under-surveyed southern Afrotemperate forests-the southernmost Afromontane forest bloc. ENMs corroborated both scarp and southern Afrotemperate forests as glacial refugia and demonstrated persistent regional population presence over the past 120 kya. Main Conclusions The population genetics and palaeodistribution of the three bird species indicate their regional persistence throughout the late Pleistocene, suggesting that Afromontane and scarp forests of south-eastern South Africa served as refugia for subtropical African avian forest biota.

Summary The Amathole mistbelt forests in the Eastern Cape, South Africa harbour the largest remnant population of the nationally endangered endemic Cape Parrot Poicephalus robustus, a secondary-cavity nester whose persistence is limited by suitable nest sites. These are also the only forests within Cape Parrot range in which selective timber harvesting remains permitted, but the impact of harvesting on the availability of parrot nest sites has not been investigated. This study aimed to determine the degree to which current harvest selection criteria stand to impact nest site availability. Results showed that Cape Parrots have specific nest tree requirements; and that there is overlap in the species and condition of trees selected for nesting, and harvesting. The two yellowwood species found in the region, Afrocarpus falcatus and Podocarpus latifolius, represented the majority of both harvested trees (78%), and Cape Parrot nest trees (79%). Moreover, both Cape Parrot and harvest selection criteria require large (≥50 cm diameter at breast height; ≥12 m high), old, dead, dying, or crown-damaged yellowwoods, such that 32% of trees considered potential nest trees were also candidates for harvesting. Current selection criteria need to be revised to ensure that timber use is compatible with biodiversity conservation in the Amathole forests. We suggest that all harvesting of dead standing yellowwoods be discontinued; and that the harvesting of live trees with crown damage, which are frequently used by parrots for nesting, be limited by a species-specific maximum harvestable diameter.

Abstract South African small mammals are under-represented in DNA barcoding efforts, particularly from the eastern forested regions of the country. This study reports DNA barcoding of Rhabdomys taxa from previously unsampled parts of the Eastern Cape and KwaZulu-Natal provinces of South Africa. The complete mitochondrial DNA cytochrome oxidase I (COI) gene was sequenced for 101 Rhabdomys sp. individuals from 16 localities from all three main forest groups (coastal, mistbelt, and scarp forests). Molecular data were supplemented with external morphological measurements, including those deemed potential taxonomically diagnostic characters. Findings indicate the area to be inhabited solely by Rhabdomys dilectus chakae. Haplotypes distributed across the three forest groups were separated by shallow sequence divergences ranging from 0.001–0.015 (Kimura 2-parameter model) and displayed very little population genetic structure (FST= 0.071787). Morphological data revealed some regional metric differences in external morphology, but all the head-and-body to tail (HB: tail) ratios match that of R. d. chakae, and consequently, molecular and morphological data are congruent. These data confirm a range extension of R. d. chakae, supporting the utility of COI barcodes in the identification of small mammalian species.

Scent marks deposited as semiochemical signals are a primary mode of communication for a broad range of mammal species. Such scent signals are often deposited at specific, frequently visited marking sites called latrines. Despite descriptions of widespread latrine use by numerous mammal species, detailed understanding of site visit rates and latrine function is lacking. Here we report for the first time a quantitative assessment of scent-marking behaviours that represent interpack olfactory communication by African wild dogs, Lycaon pictus, at latrines visited by multiple resident neighbouring packs, hereafter called a 'shared marking site' (SMS). We show that multiple packs visited specific SMSs frequently and regularly throughout the year, with a notable decrease in visits during the 3-month denning season coinciding with a contraction in range size. In addition to resident neighbouring packs, dispersing in-dividuals visited and scent-marked at SMSs, suggesting that latrines function at least in part as sites communicating information about residence and possibly reproductive status. Further detailed investi-gation of the relevance of latrine use to territorial behaviour, ranging, habitat use and dispersal in this species is required, particularly as it may have direct applied conservation implications for this wide-ranging but territorial endangered species.(c) 2022 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Abstract Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest‐dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest‐dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost‐distances along least‐cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest‐thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors— where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land‐cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest‐dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.

Aim Forest fragmentation is a major driver of biodiversity loss causing declines in species richness and functional diversity of biotic communities. Bats are essential components of ecosystems and are useful bio-indicators of habitat disturbance, yet the response and vulnerability of bats to fragmentation have been poorly studied in Africa. We aim to assess the effects of forest biogeographical history and fragmentation on functional diversity of bats and their functional traits. Location Eastern Cape and southern KwaZulu-Natal, South Africa. Taxon Insectivorous bats. Methods We surveyed forest-utilizing bats to derive four functional diversity indices. Generalized linear models were used to assess the response of diversity indices to biogeographical history and fragmentation, represented by forest type and five landscape fragmentation metrics. RLQ and fourth-corner analysis were used to investigate the interaction of traits with fragmentation metrics and forest type. Results Pondoland Scarp forests displayed high functional richness, while Eastern Cape Dune forests exhibited high functional divergence yet low functional richness and dispersion. Two fragmentation metrics affected functional diversity dynamically: edge density had a positive effect on functional evenness; and dispersion was negatively affected by river length through forests. Results showed stronger interactions of functional traits with forest type than fragmentation metrics, with filtering effects on body size and wing morphology. Main conclusions The large-scale processes related to biogeographical history, and associated forest structure, are important determinants of functional richness, divergence and dispersion of insectivorous bat communities. Scarp forests showed the highest species and functional richness as they experienced less extreme climatic extinction filtering than Mistbelt forests during the Last Glacial Maximum, whereas the low diversity of Eastern Cape Dune forests results from their younger evolutionary history and homogenous vegetation structure. Little is known of the sensitivity of bats to habitat fragmentation in Africa: here, we show larger-sized insectivorous species; and species exhibiting low wing loading may be more vulnerable to fragmentation.

The Eastern Cape Province harbours 46% of South Africa’s remaining indigenous forest cover, and is one of the country’s poorest and least developed provinces. Forest resources thus represent a vital component of rural livelihoods in this region. Consequently, forest management policies aim to balance the needs of resource users with the ecological integrity of forest ecosystems. In a recent study, forest bird ranges were shown to have declined in the Eastern Cape over the past 20 years, despite increases in forest cover over the same time period, indicating that habitat degradation may be driving forest bird losses. Given that harvesting of forest products represents the primary human disturbance in forests in the Eastern Cape today, insight is needed regarding the link between resource use and habitat modification. We report on effects of harvesting of three key forest products – poles, timber and medicinal bark – on habitat structure at the ground, understorey and canopy layers in indigenous forests in the province. Harvest activities had considerable impacts on habitat structure, depending on the nature and extent of harvesting. Bark and timber harvesting resulted in canopy gaps, whereas pole harvesting reduced tree density, resulting in understorey gaps. Overall, harvest activities increased the frequency of canopy disturbance, and density of understorey layer foliage. Unsustainable bark harvesting practices increased the mortality rate of canopy trees, thereby increasing dead wood availability. By providing insight into human-mediated habitat modification in forests of the Eastern Cape, this study contributes to the development of ecologically informed sustainable resource management policies. Significance: Unregulated harvesting of forest products in state-managed indigenous forests of the Eastern Cape results in habitat modification. The nature and extent of habitat modification is dependent on the type and intensity of resource use, indicating that resource use may be sustainably managed. Timber and medicinal bark harvesting activities result in canopy disturbances, thereby altering natural canopy gap dynamics, with concomitant impacts on understorey habitat structure. Changes in forest habitat structure associated with high levels of resource use are likely to have ramifying effects on forest biodiversity.

Forests in South Africa are under threat from a variety of anthropogenic land use changes; however, the impacts of these changes on wildlife populations are poorly understood. To address this issue, a pan-European trait-based risk assessment framework was modified for use in South Africa. This framework allows the identification of habitats and species most at risk, as well as the most important threats to species' persistence. The original model was expanded through the addition of any positive effects of land use change on species, to create a net risk model. Range changes were predicted by risk scores in montane forests, where the major risks were found to be invasion by alien trees and bark collection for traditional medicine. Risk scores within lowland species were higher, indicating potential population declines not accounted for by the SABAP range change data, as well as greater risk in the near future due to land use changes. Five hole-nesting species of birds, out of only ten holenesting species included in the study, consistently emerged as having the highest risk scores overall, and across forest types: the black-bellied starling, Narina trogon, trumpeter hornbill, crowned hornbill and green barbet. Consistent with this, using the net method, nesting risk was found to be higher than foraging risk for species across all forest types and within each type, suggesting that land use changes in South Africa are rendering forestdependent hole-nesting species particularly vulnerable.

The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.