My family and other animals: mixed broods of great and blue tits in the Loch Lomond woodlands

No abstract available

Understanding communities in complex agroforestry systems: methodological advances and ecological implications

Agroforestry, the practice of growing crops beneath a canopy of shade trees, is common in tropical regions, and has the potential to provide habitat for wildlife whilst maintaining agricultural production. However, the increasing demand for commodity crops is driving intensification of agriculture in the tropics, which results in the conversion of agroforestry systems into monocultures. This conversion to monocultures drives declines in biodiversity in these habitats, which may in turn cause a drop-off in yields due to loss of ecosystem services. However, the effects of agricultural management on animal communities and the downstream effects on productivity are poorly understood, especially in the Afrotropics. This project aimed to study the influence of farm management on wildlife communities, and the potential implications for productivity, in African cocoa agroforestry. My research was based on data of bird and arthropod communities in 28 cocoa farms in southern Cameroon. The study farms varied in their shade cover (a proxy for management intensity), from 20% to 100% cover. In these farms we surveyed arthropods using visual surveys, sweep-netting and malaise traps, and birds using mist-netting and acoustic recorders. I investigated trends in bird and arthropod community composition using several statistical methods, including data integration, hierarchical modelling and community modelling. My results show that the shade cover of farms had a strong influence on animal community composition. Shady (low-intensity) cocoa farms supported higher densities of vulnerable rainforest bird species such as ant-followers and forest specialists. Shady farms also contained higher densities of potential pollinators and natural enemies, and lower densities of pest insects. I investigated the interplay between shade management and interspecific interactions, and found that both these factors were important in shaping communities in these complex agricultural habitats. Overall, my results indicate that low-intensity management of agroforestry may be beneficial for both biodiversity conservation and productivity, as it favours populations of vulnerable species and ecosystem services providers, whilst reducing pest burdens. These findings shed light on the risks associated to the current push towards intensification of agriculture in the tropics

The first assessment of Batrachochytrium dendrobatidis in amphibian populations in the Kanuku Mountains Protected Area of Guyana

- Batrachochytrium dendrobatidis (Bd) is a fungal pathogen threatening hundreds of amphibian species with extinction across the globe, especially in Latin America. Extensive investigations have revealed the presence of Bd in many South American countries, but there has been a lack of such research conducted in Guyana. We assessed the presence of Bd in the amphibian populations of the Kanuku Mountains Protected Area, in the south-west of the country. We swabbed two hundred and fifty anurans and processed the samples using standard Polymerase Chain Reaction analysis to identify cutaneous presence of Bd, making this the most comprehensive investigation into the existence of Bd in Guyana. All samples were negative for the presence of Bd DNA. Given the presence of Bd in countries neighbouring Guyana, and the severe declines it has caused in amphibian populations, we consider Guyana to be under severe threat. We advocate further surveillance in Guyana to fully determine the presence or absence of Bd, and we emphasise the importance of biosecurity and monitoring in mitigating a potential outbreak of this fungal pathogen

Moult of overwintering Wood Warblers <i>Phylloscopus sibilatrix</i> in an annual-cycle perspective

Wood Warblers, an Afro-Palearctic migrant species, are declining steadily in Europe likely due to mortality outside their breeding grounds. However, little is known about their overwintering, and records about the sensitive life-cycle stage of moult in Africa are practically absent. To fill this gap, we report on moult of Wood Warblers captured over two winters (January–February) in 2019–2020 in Cameroon. We caught 14 individuals, of which 12 were monitored for flight feather moult. All inspected individuals showed advanced stages of flight feather renewal. Despite low sample sizes, Underhill-Zucchini moult models aptly explained variation in primary and secondary moult (R2 = 0.61). Estimated moult onset date was 26 December, completion date was 25 February, and moult duration was 61 days. These findings fit well with experimental data on the annual cycle and the timing of recently published migration tracks of Wood Warblers. Jointly, the data suggest that moult timing is set by an internal programme, which enables Wood Warblers to organise their multi-stage migration such that they reach suitable moulting habitat in time, and can depart in time with a fresh plumage for the breeding grounds. In our study, moult occurred during the peak of the dry season, which in Cameroon nonetheless shows high relative humidity. During our mist-netting on 28 cocoa plantations of varying shade cover, Wood Warblers were caught on 6 farms whose canopies were comparatively open. These data suggest that the birds encounter in Cameroon relatively stable climatic conditions for moult, and do not measurably prefer closed-canopy forests. Our findings are important, because successful moult increases survival prospects and because moult needs to be safely embedded in a migratory life cycle. Hence, information on moult timing and location is essential for identifying year-round vulnerabilities of Wood Warblers.<br/

Fewer pests and more ecosystem service‐providing arthropods in shady African cocoa farms: Insights from a data integration study

Agricultural intensification is leading to conversion of cocoa agroforestry towards monocultures across the tropics. In the context of cocoa agriculture, arthropods provide a range of ecosystem services and dis‐services. Arthropod pests (e.g., mirids and mealybugs) can cause major damage to crops, whilst pollinators and natural enemies (e.g., predatory insects and parasitoids) have the potential to enhance agricultural yields. Understanding how intensification of cocoa farming affects different arthropod groups is therefore important in maximising the abundance of beneficial arthropod taxa and reducing pest burdens. However, little is known about the influences of agricultural intensification on tropical arthropod communities, especially in Africa, where ~70% of the world's cocoa is produced. Most research on arthropod communities considers data from different sampling methods separately, as proxies of abundance; whilst these proxies can be informative, estimating true abundance enables direct comparison between arthropod taxa, and therefore the study of community dynamics. Here, we develop a Bayesian hierarchical model that integrates data from three common arthropod survey techniques to estimate population size of arthropod orders and to investigate how arthropod community composition responds to farm shade cover (an indicator of management intensity). Our results show that eight of 11 arthropod taxa responded to farm shade cover; importantly, brown capsids (the primary pest of cocoa in Africa), Coleoptera pests and Hemiptera pests decreased with increasing farm shade cover, whilst Araneae (natural enemies) and Diptera (potential pollinators) were more abundant in shady farms. Synthesis and applications. To achieve lower pest burdens and higher abundances of potential pollinators and natural enemies, African cocoa farms should maintain a dense canopy of shade trees. The current shift towards high‐intensity cocoa farming in Africa could result in long‐term losses due to pest infestations and loss of arthropod‐mediated ecosystem services

Not all farms are created equal: Shady African cocoa farms promote a richer bat fauna

Bats provide important pest suppression services with economic value to cocoa farmers, yet the impact of cocoa farm management on bat diversity metrics is still poorly understood. This is especially important if we consider that Afrotropical cocoa farms supply 68 % of the world's chocolate market, with expected increases in production in the forthcoming decades. In this study, we investigated for the first time how bat abundance, richness and diversity varied between African cocoa farms with different levels of shade tree cover, shade tree communities and cocoa characteristics. We found that shade tree cover and shade tree height were the main drivers associated with an increase of Shannon diversity, and abundance and richness of insectivores. Frugivorous and nectarivorous bats were positively associated with the presence of planted shade trees, but richness varied with the size of shade trees. The insectivorous Hipposideros fuliginosus was only present in high shade farms, being captured 51 times only in this shade system, while the frugivorous Myonycteris angolensis was associated with low shade farms. Our findings show that indeed not all farms are created equal, with high shade farms with large, tall forest shade trees (i.e., containing key plant resources) having richer bat communities. Therefore, policymakers seeking to conserve wildlife within cocoa farming systems should adopt cocoa management systems like those mentioned above and promote a combination of forest and planted shade trees to be able support a rich community of insectivorous, frugivorous and nectarivorous bats and maintain their associated ecosystems services

The role of landscape context in shaping bat assemblages in African cacao plantations

Cacao production is mostly concentrated in Africa, with this continent exporting an impressive 68.4 % of the world's cacao. The increasing demand for cacao from the Global North has already led to massive deforestation in Ghana and Ivory Coast and cacao-driven deforestation is likely to continue changing landscapes in Sub-Saharan Africa. Bats are affected by these landscape changes due to their dependence on multiple resources spread at a large spatial scale. Although bats can save cacao farmers millions of euros through pest suppression, no study has investigated how landscape context affects bat communities in African cacao plantations. Here for the first time, we studied how abundance and richness of insectivorous, frugivorous and nectarivorous bats within cacao landscapes could be affected by cover type and the distance between these habitats and each cacao plantation. We sampled bats using mist-nets in 38 cacao plantations spread throughout southern Cameroon from 2017 to 2020. We found that guilds responded differently to the distance and amount of cover of each of the land cover types, with the scale of response being habitat-dependent. Overall, insectivorous bats were associated positively with high cover of natural habitats (e.g., tree cover, rangeland, and flooded vegetation), and negatively with nearby anthropogenic disturbance (e.g., logging and intensive agriculture). Frugivorous and nectarivorous bats were associated to the presence of natural habitats with water and of nearby anthropogenic habitats (e.g., human settlements, community forests and unpaved roads), probably due to the presence of more fruiting and flowering trees. Considering the associations found between the landscape metrics and bats, we propose three different conceptual designs to manage cacao landscapes: one for insectivores, one for frugivores/nectarivores and a third design that maximises the trade-offs between these three guilds. By safeguarding the diversity of these three guilds farmers can maintain pest suppression services within their plantations and guarantee healthy and long-lasting sustainable cacao landscapes through bats' pollination and seed dispersal

Bird communities in African cocoa agroforestry are diverse but lack specialised insectivores

Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities. Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities. Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores. Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms. Synthesis and applications. Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity

Bird communities in African cocoa agroforestry are diverse but lack specialised insectivores

Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities. Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities. Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores. Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms. Synthesis and applications. Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity

Ecological filtering shapes the impacts of agricultural deforestation on biodiversity

Funding: This project was funded by the National Natural Science Foundation of China (Grants 32122057 and 3198810 to FH) and the Ministry of Science and Technology of China (Grant 2022YFF0802300 to FH), and received further support from Tsinghua University Initiative Scientific Research Program (Grant 20223080017 to LY).The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability—proxied by drier and more seasonal climates under a greater disturbance regime—and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation.Peer reviewe