A biogeographical appraisal of the threatened South East Africa Montane Archipelago ecoregion

Recent biological surveys of ancient inselbergs in southern Malawi and northern Mozambique have led to the discovery and description of many species new to science, and overlapping centres of endemism across multiple taxa. Combining these endemic taxa with data on geology and climate, we propose the 'South East Africa Montane Archipelago' (SEAMA) as a distinct ecoregion of global biological importance. The ecoregion encompasses 30 granitic inselbergs reaching > 1000 m above sea level, hosting the largest (Mt Mabu) and smallest (Mt Lico) mid-elevation rainforests in southern Africa, as well as biologically unique montane grasslands. Endemic taxa include 127 plants, 45 vertebrates (amphibians, reptiles, birds, mammals) and 45 invertebrate species (butterflies, freshwater crabs), and two endemic genera of plants and reptiles. Existing dated phylogenies of endemic animal lineages suggests this endemism arose from divergence events coinciding with repeated isolation of these mountains from the pan-African forests, together with the mountains' great age and relative climatic stability. Since 2000, the SEAMA has lost 18% of its primary humid forest cover (up to 43% in some sites)-one of the highest deforestation rates in Africa. Urgently rectifying this situation, while addressing the resource needs of local communities, is a global priority for biodiversity conservation.

Depth variation in benthic community response to repeated marine heatwaves on remote Central Indian Ocean reefs

Coral reefs are increasingly impacted by climate-induced warming events. However, there is limited empirical evidence on the variation in the response of shallow coral reef communities to thermal stress across depths. Here, we assess depth-dependent changes in coral reef benthic communities following successive marine heatwaves from 2015 to 2017 across a 5-25 m depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our analyses show an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge and reef pavement following successive marine heatwaves on the remote reef system. Our findings indicate that the changes in benthic communities in response to elevated seawater temperatures varied across depths. We found greater changes in benthic group cover at shallow depths (5-15 m) compared with deeper zones (15-25 m). The loss of hard coral cover was better predicted by initial thermal stress, while the loss of soft coral was associated with repeated thermal stress following successive warming events. Our study shows that benthic communities extending to 25 m depth were impacted by successive marine heatwaves, supporting concerns about the resilience of shallow coral reef communities to increasingly severe climate-driven warming events.

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927. Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the 'odd man out' pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER, here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.

Health service needs and perspectives of a rainforest conserving community in Papua New Guinea's Ramu lowlands: a combined clinical and rapid anthropological assessment with parallel treatment of urgent cases

OBJECTIVES

Determine community needs and perspectives as part of planning health service incorporation into Wanang Conservation Area, in support of locally driven sustainable development.

DESIGN

Clinical and rapid anthropological assessment (individual primary care assessments, key informant (KI) interviews, focus groups (FGs), ethnography) with treatment of urgent cases.

SETTING

Wanang (pop. c189), a rainforest community in Madang province, Papua New Guinea.

PARTICIPANTS

129 villagers provided medical histories (54 females (f), 75 males (m); median 19 years, range 1 month to 73 years), 113 had clinical assessments (51f, 62m; median 18 years, range 1 month to 73 years). 26 ≥18 years participated in sex-stratified and age-stratified FGs (f<40 years; m<40 years; f>40 years; m>40 years). Five KIs were interviewed (1f, 4m). Daily ethnographic fieldnotes were recorded.

RESULTS

Of 113 examined, 11 were 'well' (a clinical impression based on declarations of no current illness, medical histories, conversation, no observed disease signs), 62 (30f, 32m) were treated urgently, 31 referred (15f, 16m), indicating considerable unmet need. FGs top-4 ranked health issues concorded with KI views, medical histories and clinical examinations. For example, ethnoclassifications of three ((A) 'malaria', (B) 'sotwin', (C) 'grile') translated to the five biomedical conditions diagnosed most ((A) malaria, 9 villagers; (B) upper respiratory infection, 25; lower respiratory infection, 10; tuberculosis, 9; (C) tinea imbricata, 15) and were highly represented in declared medical histories ((A) 75 participants, (B) 23, (C) 35). However, 29.2% of diagnoses (49/168) were limited to one or two people. Treatment approaches included plant medicines, stored pharmaceuticals, occasionally rituals. Travel to hospital/pharmacy was sometimes undertaken for severe/refractory disease. Service barriers included: no health patrols/accessible aid post, remote hospital, unfamiliarity with institutions and medicine costs. Service introduction priorities were: aid post, vaccinations, transport, perinatal/birth care and family planning.

CONCLUSIONS

This study enabled service planning and demonstrated a need sufficient to acquire funding to establish primary care. In doing so, it aided Wanang's community to develop sustainably, without sacrificing their forest home.

Mid-frequency song and low-frequency calls of sei whales in the Falkland Islands

Although sei whales (Balaenoptera borealis) are distributed throughout the globe, their behaviour and vocal repertoire are poorly described. We used passive acoustic monitoring to describe the vocal behaviour of sei whales in the Falkland Islands, between December 2018 and April 2019. We isolated more than 2000 low-frequency calls for manual classification, of which 510 calls with high signal-to-noise ratio were quantitatively measured. Five categories of stereotyped call types in the 15-230 Hz range were described, some with multiple subcategories. These included some similar to previously described calls (e.g. downsweeps), but others that were novel in acoustic structure and frequency band. In the mid-frequency range, we documented a highly stereotyped, hierarchically structured and rhythmically repetitive song display. Songs were arranged in phrases with a structure composed of repetitive sub-phrases, and a diverse variety of sounds in the 1-5 kHz range. Singing commenced in late February, despite the presence of whales and calls since early December, and continued through April. These acoustic properties and behavioural characteristics indicate that this is likely a male breeding display similar to songs and singing of other balaenopterids. This is the first detailed description of a song display for sei whales, highlighting the importance of the Falkland Islands.

Automated audiovisual behavior recognition in wild primates

Large video datasets of wild animal behavior are crucial to produce longitudinal research and accelerate conservation efforts; however, large-scale behavior analyses continue to be severely constrained by time and resources. We present a deep convolutional neural network approach and fully automated pipeline to detect and track two audiovisually distinctive actions in wild chimpanzees: buttress drumming and nut cracking. Using camera trap and direct video recordings, we train action recognition models using audio and visual signatures of both behaviors, attaining high average precision (buttress drumming: 0.87 and nut cracking: 0.85), and demonstrate the potential for behavioral analysis using the automatically parsed video. Our approach produces the first automated audiovisual action recognition of wild primate behavior, setting a milestone for exploiting large datasets in ethology and conservation.

Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.

Climatic and local stressor interactions threaten tropical forests and coral reefs

Tropical forests and coral reefs host a disproportionately large share of global biodiversity and provide ecosystem functions and services used by millions of people. Yet, ongoing climate change is leading to an increase in frequency and magnitude of extreme climatic events in the tropics, which, in combination with other local human disturbances, is leading to unprecedented negative ecological consequences for tropical forests and coral reefs. Here, we provide an overview of how and where climate extremes are affecting the most biodiverse ecosystems on Earth and summarize how interactions between global, regional and local stressors are affecting tropical forest and coral reef systems through impacts on biodiversity and ecosystem resilience. We also discuss some key challenges and opportunities to promote mitigation and adaptation to a changing climate at local and global scales. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Quantitative assessment of plant-arthropod interactions in forest canopies: A plot-based approach

Research on canopy arthropods has progressed from species inventories to the study of their interactions and networks, enhancing our understanding of how hyper-diverse communities are maintained. Previous studies often focused on sampling individual tree species, individual trees or their parts. We argue that such selective sampling is not ideal when analyzing interaction network structure, and may lead to erroneous conclusions. We developed practical and reproducible sampling guidelines for the plot-based analysis of arthropod interaction networks in forest canopies. Our sampling protocol focused on insect herbivores (leaf-chewing insect larvae, miners and gallers) and non-flying invertebrate predators (spiders and ants). We quantitatively sampled the focal arthropods from felled trees, or from trees accessed by canopy cranes or cherry pickers in 53 0.1 ha forest plots in five biogeographic regions, comprising 6,280 trees in total. All three methods required a similar sampling effort and provided good foliage accessibility. Furthermore, we compared interaction networks derived from plot-based data to interaction networks derived from simulated non-plot-based data focusing either on common tree species or a representative selection of tree families. All types of non-plot-based data showed highly biased network structure towards higher connectance, higher web asymmetry, and higher nestedness temperature when compared with plot-based data. Furthermore, some types of non-plot-based data showed biased diversity of the associated herbivore species and specificity of their interactions. Plot-based sampling thus appears to be the most rigorous approach for reconstructing realistic, quantitative plant-arthropod interaction networks that are comparable across sites and regions. Studies of plant interactions have greatly benefited from a plot-based approach and we argue that studies of arthropod interactions would benefit in the same way. We conclude that plot-based studies on canopy arthropods would yield important insights into the processes of interaction network assembly and dynamics, which could be maximised via a coordinated network of plot-based study sites.

Spatio-temporal ecology of sympatric felids on Borneo. Evidence for resource partitioning?

Niche differentiation, the partitioning of resources along one or more axes of a species' niche hyper-volume, is widely recognised as an important mechanism for sympatric species to reduce interspecific competition and predation risk, and thus facilitate co-existence. Resource partitioning may be facilitated by behavioural differentiation along three main niche dimensions: habitat, food and time. In this study, we investigate the extent to which these mechanisms can explain the coexistence of an assemblage of five sympatric felids in Borneo. Using multi-scale logistic regression, we show that Bornean felids exhibit differences in both their broad and fine-scale habitat use. We calculate temporal activity patterns and overlap between these species, and present evidence for temporal separation within this felid guild. Lastly, we conducted an all-subsets logistic regression to predict the occurrence of each felid species as a function of the co-occurrence of a large number of other species and showed that Bornean felids co-occurred with a range of other species, some of which could be candidate prey. Our study reveals apparent resource partitioning within the Bornean felid assemblage, operating along all three niche dimension axes. These results provide new insights into the ecology of these species and the broader community in which they live and also provide important information for conservation planning for this guild of predators.

Kupeantha (Coffeeae, Rubiaceae), a new genus from Cameroon and Equatorial Guinea

Two new coffee relatives (tribe Coffeeae, Rubiaceae), discovered during botanical expeditions to Cameroon, are examined for generic placement, and the placement of three previously known species (Argocoffeopsis fosimondi, A. spathulata and Calycosiphonia pentamera) is reinvestigated using plastid sequence (accD-psa1, rpl16, trnL-F) and morphological data. Seed biochemistry of the new species and pollen micromorphology (only one of the two species) are also studied. Based on the plastid sequence data, the new taxa are nested in a well-supported monophyletic group that includes Argocoffeopsis and Calycosiphonia. Within this clade, three well-supported subclades are recovered that are morphologically easy to diagnose: (1) Calycosiphonia (excluding C. pentamera), (2) Argocoffeopsis (excluding A. fosimondi and A. spathulata), and (3) a clade including the above excluded species, in addition to the new species. Based on the results, Kupeantha, a new genus of five species, is described, including two new Critically Endangered taxa from the Highlands of Cameroon: Kupeantha ebo and K. kupensis. Phytochemical analysis of Kupeantha seeds reveals compounds assigned as hydroxycinnamic acid derivatives, amino acids and ent-kaurane diterpenoids; caffeine was not detected. Kupeantha is the first new genus described in tribe Coffeeae in 40 years.

Orangutans venture out of the rainforest and into the Anthropocene

Conservation benefits from understanding how adaptability and threat interact to determine a taxon's vulnerability. Recognizing how interactions with humans have shaped taxa such as the critically endangered orangutan (Pongo spp.) offers insights into this relationship. Orangutans are viewed as icons of wild nature, and most efforts to prevent their extinction have focused on protecting minimally disturbed habitat, with limited success. We synthesize fossil, archeological, genetic, and behavioral evidence to demonstrate that at least 70,000 years of human influence have shaped orangutan distribution, abundance, and ecology and will likely continue to do so in the future. Our findings indicate that orangutans are vulnerable to hunting but appear flexible in response to some other human activities. This highlights the need for a multifaceted, landscape-level approach to orangutan conservation that leverages sound policy and cooperation among government, private sector, and community stakeholders to prevent hunting, mitigate human-orangutan conflict, and preserve and reconnect remaining natural forests. Broad cooperation can be encouraged through incentives and strategies that focus on the common interests and concerns of different stakeholders. Orangutans provide an illustrative example of how acknowledging the long and pervasive influence of humans can improve strategies to preserve biodiversity in the Anthropocene.

Bat detective-Deep learning tools for bat acoustic signal detection

Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity, especially for echolocating bat species. To better assess bat population trends there is a critical need for accurate, reliable, and open source tools that allow the detection and classification of bat calls in large collections of audio recordings. The majority of existing tools are commercial or have focused on the species classification task, neglecting the important problem of first localizing echolocation calls in audio which is particularly problematic in noisy recordings. We developed a convolutional neural network based open-source pipeline for detecting ultrasonic, full-spectrum, search-phase calls produced by echolocating bats. Our deep learning algorithms were trained on full-spectrum ultrasonic audio collected along road-transects across Europe and labelled by citizen scientists from www.batdetective.org. When compared to other existing algorithms and commercial systems, we show significantly higher detection performance of search-phase echolocation calls with our test sets. As an example application, we ran our detection pipeline on bat monitoring data collected over five years from Jersey (UK), and compared results to a widely-used commercial system. Our detection pipeline can be used for the automatic detection and monitoring of bat populations, and further facilitates their use as indicator species on a large scale. Our proposed pipeline makes only a small number of bat specific design decisions, and with appropriate training data it could be applied to detecting other species in audio. A crucial novelty of our work is showing that with careful, non-trivial, design and implementation considerations, state-of-the-art deep learning methods can be used for accurate and efficient monitoring in audio.

Measuring local depletion of terrestrial game vertebrates by central-place hunters in rural Amazonia

The degree to which terrestrial vertebrate populations are depleted in tropical forests occupied by human communities has been the subject of an intense polarising debate that has important conservation implications. Conservation ecologists and practitioners are divided over the extent to which community-based subsistence offtake is compatible with ecologically functional populations of tropical forest game species. To quantify depletion envelopes of forest vertebrates around human communities, we deployed a total of 383 camera trap stations and 78 quantitative interviews to survey the peri-community areas controlled by 60 semi-subsistence communities over a combined area of over 3.2 million hectares in the Médio Juruá and Uatumã regions of Central-Western Brazilian Amazonia. Our results largely conform with prior evidence that hunting large-bodied vertebrates reduces wildlife populations near settlements, such that they are only found at a distance to settlements where they are hunted less frequently. Camera trap data suggest that a select few harvest-sensitive species, including lowland tapir, are either repelled or depleted by human communities. Nocturnal and cathemeral species were detected relatively more frequently in disturbed areas close to communities, but individual species did not necessarily shift their activity patterns. Group biomass of all species was depressed in the wider neighbourhood of urban areas rather than communities. Interview data suggest that species traits, especially group size and body mass, mediate these relationships. Large-bodied, large-group-living species are detected farther from communities as reported by experienced informants. Long-established communities in our study regions have not "emptied" the surrounding forest. Low human population density and low hunting offtake due to abundant sources of alternative aquatic protein, suggest that these communities represent a best-case scenario for sustainable hunting of wildlife for food, thereby providing a conservative assessment of game depletion. Given this 'best-case' camera trap and interview-based evidence for hunting depletion, regions with higher human population densities, external trade in wildlife and limited access to alternative protein will likely exhibit more severe depletion.