Informing tropical mammal conservation in human-modified landscapes using remote technologies and hierarchical modelling

The aggressive expansion of anthropogenic activities is placing increasing pressure on biodiversity, particularly in tropical regions. Here, conservation efforts are hindered by poor understanding of species ecology and the failure of policy instruments to account for multiple stressors of land-use change. While protected areas are central to conservation strategies, there is a general consensus that the future of tropical biodiversity will be determined by how well modified landscapes are managed. In this thesis I advance our understanding of biodiversity persistence in modified tropical landscapes to inform emerging incentive-based policy mechanisms and supply-chain initiatives. Capitalising on recent advances in remote-sensing and hierarchical occupancy modelling, I provide a spatial appraisal of biodiversity in a modified landscape in Sabah, Malaysian Borneo. Fieldwork was conducted at the Stability of Altered Forest Ecosystems (SAFE) project, a large-scale landscape modification experiment, comprising a degradation gradient of old growth forest, selectively logged forest, remnant forest patches and oil palm plantations. The assessment focused on camera-trapping of tropical mammals, as they are sensitive to anthropogenic stressors, occupy key trophic positions, and prioritised in conservation. In Chapter 2 I link mammal occupancy data to airborne multispectral remote-sensing information to show how the conservation value of modified landscapes is dictated by the intensity of the underlying land-use. Logged forests retained appreciable levels of mammal diversity, and oil palm areas were largely devoid of forest specialists and threatened taxa. Moreover, many mammal species disproportionately occupied forested areas that retained old growth structural characteristics. The most influential structural measures accounted for vertical and horizontal components in environmental space, which cannot currently be derived from conventional satellite data. Using a novel application of ecological threshold analysis, I demonstrate how multispectral data and multi-scale occupancy models can help identify conservation and restoration areas in degraded forests. In Chapter 3 I assess the potential for carbon-orientated policy mechanisms (High Carbon Stock, HCS, Approach and REDD+) to prioritise high carbon areas with corresponding biodiversity value in highly modified landscapes. The areas of highest carbon value prioritised via HCS supported comparable species diversity to old growth forest. However, the strength, nature and extent of the biodiversity co-benefit was dependent on how carbon was characterised, the spatial resolution of carbon data, and the species considered. In Chapter 4 I further scrutinised HCS protocols to evaluate how well they delineated high priority forest patches that safeguard species most vulnerable to land-use change (i.e. IUCN threatened species). The minimum core area required to define a high priority patch (100 ha) supported only 35% of the mammal community. In fact the core area criterion would need to increase to 3,199 ha in order to sustain intact mammal assemblages, and an order of magnitude higher if hunting pressure was considered. These findings underline the importance of integrating secondary disturbance impacts into spatial conservation planning. Provided landscape interventions are directed to where they will have the greatest impact, they can be financially sustaining and garner local support for conservation. To this end I provide recommendations to guide policy implementation in modified tropical landscapes to support holistic conservation strategies

Room to roam for African lions Panthera leo: a review of the key drivers of lion habitat use and implications for conservation

1. Globally, large terrestrial carnivores (Carnivora) have suffered precipitous declines in population and range. Today, they must persist in increasingly isolated natural habitat patches within a human-dominated matrix. Effective conservation aimed at supporting carnivores in such landscapes requires species-specific understanding of habitat requirements. 2. We present results from a review of the published literature to assess the current state of knowledge regarding habitat preferences of the African lion Panthera leo, with the aim of identifying common drivers of habitat use across contexts. 3. Using the Web of Science, we identified 154 usable articles and extracted information relating to study topic, location, habitats described, land-use type, and any documented habitat preferences. 4. Only 31 studies documented evidence of habitat use, and collectively, they suggested that preferences for specific habitat types were varied and context-specific. The importance of prey abundance and proximity to water was highlighted in multiple studies. Anthropogenic factors interfered with expected patterns of habitat use. There was evident bias in study locations: 83% of the habitat-use studies were based in only three countries, and 70% were focussed on protected or managed areas. 5. Our synthesis suggests that lions demonstrate behavioural plasticity in habitat use in response to anthropogenic pressures. To understand the limits of this plasticity and to manage Africa’s changing landscapes effectively for roaming lions, future research should be focussed on analysis of habitat use outside protected areas, taking into account gradients of distance to water, prey abundance, and anthropogenic risk

Habitat modification destabilizes spatial associations and persistence of Neotropical carnivores.

Spatial relationships between sympatric species underpin biotic interactions, structure ecological communities, and maintain ecosystem health. However, the resilience of interspecific spatial associations to human habitat modification remains largely unknown, particularly in tropical regions where anthropogenic impacts are often greatest. We applied multi-state multi-species occurrence models to camera trap data across nine tropical landscapes in Colombia to understand how prominent threats to forest ecosystems influence Neotropical carnivore occurrence and interspecific spatial associations, with implications for biotic interactions. We show that carnivore occurrence represents a delicate balance between local environmental conditions and interspecific interactions that can be compromised in areas of extensive habitat modification. The stability of carnivore spatial associations depends on forest cover to mediate antagonistic encounters with apex predators and structurally intact forests to facilitate coexistence between competing mesocarnivores. Notably, we demonstrate that jaguars play an irreplaceable role in spatially structuring mesocarnivore communities, providing novel evidence on their role as keystone species. With increasing global change, conserving both the extent and quality of tropical forests is imperative to support carnivores and preserve the spatial associations that underpin ecosystem stability and resilience. [Abstract copyright: Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

A new species in the tree genus Polyceratocarpus (Annonaceae) from the Udzungwa Mountains of Tanzania

Polyceratocarpus askhambryan-iringae, an endemic tree species of Annonaceae from the Udzungwa Mountains of Tanzania, is described and illustrated. The new species is identified as a member of the genus Polyceratocarpus by the combination of staminate and bisexual flowers, axillary inflorescences, subequal outer and inner petals, and multi-seeded monocarps with pitted seeds. From Polyceratocarpus scheffleri, with which it has previously been confused, it differs in the longer pedicels, smaller and thinner petals, shorter bracts, and by generally smaller, less curved monocarps that have a clear stipe and usually have fewer seeds. Because Polyceratocarpus askhambryan-iringae has a restricted extent of occurrence, area of occupancy, and ongoing degradation of its forest habitat, we recommend classification of it as Endangered (EN) on the IUCN Red List

Implications of zero-deforestation commitments: forest quality and hunting pressure limit mammal persistence in fragmented tropical landscapes

Zero-deforestation commitments seek to decouple agricultural production and forest loss to improve prospects for biodiversity. However, the effectiveness of methods designed to meet these commitments is poorly understood. In a highly-fragmented tropical landscape dominated by oil palm, we tested the capacity for the High Carbon Stock (HCS) Approach to prioritise forest remnants that sustain mammal diversity. Patches afforded High Priority by HCS protocols (100 ha core area) provided important refuges for IUCN-threatened species and megafauna. However, patch-scale HCS area recommendations conserved only 35% of the mammal community. At least 3,000 ha would be required to retain intact mammal assemblages, with nearly ten times this area needed if hunting pressure was high. While current HCS protocols will safeguard patches capable of sustaining biodiversity, highly-fragmented tropical landscapes typical of zero-deforestation pledges will require thinking beyond the patch, towards strategically configured forest remnants at the landscape-level and enforcing strict controls on hunting

Life in the Canopy: Using Camera-Traps to Inventory Arboreal Rainforest Mammals in Borneo

Arboreal mammals form a diverse group providing ecologically important functions such as predation, pollination and seed dispersal. However, their cryptic and elusive nature, and the heights at which they live, makes studying these species challenging. Consequently, our knowledge of rainforest mammals is heavily biased towards terrestrial species, limiting our understanding of overall community structure and the possible impacts of human-induced disturbance. We undertook the first in-depth appraisal of an arboreal mammal community in Southeast Asia, using camera-traps set in unlogged and logged tropical rainforest in Sabah, Borneo. Using paired canopy and terrestrial camera-traps at 50 locations (25 in unlogged forest, 25 in logged), we assessed the effectiveness of camera-trapping at characterising the arboreal versus terrestrial community, and tested the influence of strata and forest type on community structure and composition. The paired design detected 55 mammal species across 15,817 camera-trap nights, and additional canopy sampling in a subset of trees added a further two arboreal species to the inventory. In total, thirty species were detected exclusively by terrestrial camera-traps, eighteen exclusively by canopy camera-traps, and nine by units set at both heights, demonstrating significant differences between arboreal and terrestrial communities. This pattern was strongest in unlogged forest, reflecting greater structural diversity of this habitat, but held in logged forest as well. Species accumulation curves revealed that canopy camera-trapping significantly boosted species inventories compared to terrestrial-only sampling, and was particularly effective at detecting gliding mammals, rodents and primates. Canopy inventories took longer to reach an asymptote, suggesting that a greater sampling effort is required when deploying canopy camera-traps compared to those set on the ground. We demonstrate that arboreal mammals in Borneo’s rainforest form a diverse and distinct community, and can be sampled effectively using canopy camera-traps. However, the additional costs incurred by sampling in the canopy can be substantial. We provide recommendations to maximise sampling effectiveness, while bringing down costs, to help encourage further study into one of the last frontiers of tropical forest research

High carbon stock forests provide co-benefits for tropical biodiversity

1. Carbon-based policies provide powerful opportunities to unite tropical forest conservation with climate change mitigation. However, their effectiveness in delivering biodiversity co-benefits is dependent on high levels of biodiversity being found in high carbon areas. Previous studies have focussed solely on the co-benefits associated with Reducing Emissions from Deforestation and forest Degradation (REDD+) over large spatial scales, with few empirically testing carbon-biodiversity correlations at management unit scales appropriate to decision-makers. Yet, in development frontiers, where most biodiversity and carbon loss occurs, carbon-based policies are increasingly driven by commodity certification schemes, which are applied at the concession-level. 2. Working in a typical human-modified landscape in Southeast Asia, we examined the biodiversity value of land prioritised via application of REDD+ or the High Carbon Stock (HCS) Approach, the emerging land-use planning tool for oil palm certification. Carbon stocks were estimated via low- and high-resolution datasets derived from global or local level biomass. Mammalian species richness was predicted using hierarchical Bayesian multi-species occupancy models of camera-trap data from forest and oil palm habitats. 3. At the community level, HCS forest supported comparable mammal diversity to control sites in continuous forest, while lower carbon strata exhibited reduced species occupancy. 4. No association was found between species richness and carbon when the latter was estimated using coarse-resolution data. However, when using high-resolution, field validated biomass data, diversity demonstrated positive relationships with carbon for threatened and disturbance-sensitive species, suggesting sensitivity of co-benefits to carbon data sources and the species considered. 5. Policy implications. Our work confirms the potential for environmental certification and REDD+ to work in tandem with conservation to mitigate agricultural impacts on tropical forest carbon stocks and biodiversity, especially if this directs development to low carbon, low biodiversity areas

Maximizing the value of forest restoration for tropical mammals by detecting three-dimensional habitat associations

Tropical forest ecosystems are facing unprecedented levels of degradation, severely compromising habitat suitability for wildlife. Despite the fundamental role biodiversity plays in forest regeneration, identifying and prioritising degraded forests for restoration or conservation, based on their wildlife value, remains a significant challenge. Efforts to characterize habitat selection are also weakened by simple classifications of human-modified tropical forests as intact versus degraded, which ignore the influence that three-dimensional forest structure may have on species distributions. Here, we develop a framework to identify conservation and restoration opportunities across logged forests in Borneo. We couple high-resolution airborne Light Detection and Ranging (LiDAR) and camera trap data to characterize the response of a tropical mammal community to changes in three-dimensional forest structure across a degradation gradient. Mammals were most responsive to covariates that accounted explicitly for the vertical and horizontal characteristics of the forest, and actively selected structurally-complex environments comprising tall canopies, increased plant area index throughout the vertical column, and the availability of a greater diversity of niches. We show that mammals are sensitive to structural simplification through disturbance, emphasising the importance of maintaining and enhancing structurally-intact forests. By calculating occurrence thresholds of species in response to forest structural change, we identify areas of degraded forest that would provide maximum benefit for multiple high conservation value species if restored. The study demonstrates the advantages of using LiDAR to map forest structure, rather than relying on overly simplistic classifications of human-modified tropical forests, for prioritising regions for restoration

Changing seasonal, temporal and spatial crop-raiding trends over 15 years in a human-elephant conflict hotspot

Human-wildlife conflict is increasing due to rapid natural vegetation loss and fragmentation. We investigated seasonal, temporal and spatial trends of elephant crop-raiding in the Trans Mara, Kenya during 2014–2015 and compared our results with a previous study from 1999 to 2000. Our results show extensive changes in crop-raiding patterns. There was a 49% increase in incidents between 1999 -2000 and 2014–2015 but an 83% decline in the amount of damage per farm. Crop-raiding went from highly seasonal during 1999–2000 to year-round during 2014–2015, with crops being damaged at all growth stages. Additionally, we identified a new elephant group type involved in crop-raiding, comprising of mixed groups. Spatial patterns of crop-raiding also changed, with more incidents during 2014–2015 neighbouring the protected area, especially by bull groups. Crop-raiding intensity during 2014–15 increased with farmland area until a threshold of 0.4 km2 within a 1 km2 grid square, and farms within 1 km from the forest boundary, 2 km from village centres were most at risk of crop-raiding. In the last 20 years the Mara Ecosystem has been impacted by climate change, agricultural expansion and increased cattle grazing within protected areas. Elephants seem to have responded by crop-raiding closer to refuges, more frequently and throughout the year but cause less damage overall. While this means the direct economic impact has dropped, more farmers must spend more time protecting their fields, further reducing support for conservation in communities who currently receive few benefits from living with wildlife