Capacity for recovery in Bornean orangutan populations when limiting offtake and retaining forest

The analysis would not have been possible without the Specialist and High-Performance Computing systems provided by Information Services at the University of Kent.Peer reviewe

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

Orangutan movement and population dynamics across human-modified landscapes: implications of policy and management

Context: Agricultural expansion is a leading cause of deforestation and habitat fragmentation globally. Policies that support biodiversity and facilitate species movement across farmland are therefore central to sustainability efforts and wildlife conservation in these human-modified landscapes. Objectives: We investigated the conservation impact of several potential management scenarios on animal populations and movement in a human-modified tropical landscape, focusing on the critically endangered Bornean orangutan, Pongo pygmeus. Methods: We used an individual-based modelling platform to simulate population dynamics and movements across four possible landscape management scenarios for a highly modified oil palm-dominated landscape in Sabah, Malaysian Borneo. Results: Scenarios that maximised the retention of natural forest remnants in agricultural areas through sustainability certification standards supported stable orangutan populations. These populations were up to 45% larger than those supported under development-focused scenarios, where forest retention was not prioritised. The forest remnants served as corridors or stepping-stones, increasing annual emigration rates across the landscape, and reducing orangutan mortality by up to 11%. Sensitivity analyses demonstrated that this outcome was highly contingent on minimising mortality during dispersal. Conclusions: Management that promotes maximising natural forest cover through certification, such as that promoted by the Roundtable on Sustainable Palm Oil, can maintain viable orangutan populations over the lifespan of an oil palm plantation and facilitate movement among otherwise isolated populations. However, minimising hunting and negative human-orangutan interactions, while promoting peaceful co-existence between apes and people, will be imperative to insure positive conservation outcomes

Importance of small forest fragments in agricultural landscapes for maintaining orangutan metapopulations

Historically, orangutans (Pongo spp.) lived in large contiguous areas of intact rainforest. Today, they are also found in highly modified and fragmented landscapes dominated by oil palm or industrial timber plantations; a situation that calls for new conservation approaches. Here we report signs of orangutan presence in more than 120 small forest fragments of <500 ha in size and isolated in extensive oil palm plantations across Borneo. We confirmed the long-term presence of adult resident females with dependent young in 42% of the fragments assessed by ground survey (n = 50), and the regular sightings of males traveling across the landscape. We argue that orangutans using and living in small isolated forest patches play an essential part in the metapopulation by maintaining gene flow among larger sub-populations distributed across multiple-use landscapes. In some cases, translocations may be necessary when the animals are in imminent danger of being killed and have no other refuge. However, the impacts of removing animals from spatially dispersed metapopulations could inadvertently decrease critical metapopulation functionality necessary for long-term viability. It is clear that orangutans need natural forest to survive. However, our findings show that forest fragments within agricultural landscapes can also complement conservation areas if they are well-distributed, properly connected and managed, and if orangutan killing is prevented. Efforts to better understand the dynamics and the functionality of an orangutan metapopulation in forest-farmland landscape mosaics characteristic of the Anthropocene are urgently needed to design more efficient conservation strategies for the species across its range

Impacts of logging, hunting, and conservation on vocalizing biodiversity in Gabon

Tropical forests support two-thirds of the world's biodiversity, contribute to global climate regulation, and support the culture and livelihoods of forest-dependent people. Much of extant tropical forest is subject to selective logging and hunting - extractive activities that potentially alter ecosystem function and species diversity. However, the collective impact of these threats, especially in the context of protected vs unprotected areas, is not fully understood. Here we assess how vocalizing biodiversity responds to logging and hunting, across the diel cycle, seasonally, and between protected and unprotected landscapes in Gabon. We compared soundscape saturation across 109 sites in national parks, Forest Stewardship Council (FSC) certified, and non-certified logging concessions. We estimated hunting pressure by quantifying gunshots and relative accessibility per site. Overall, we found that the soundscapes of FSC-certified concessions resembled national parks (selectively logged 20+ years ago) more so than non-certified concessions. We also found that never logged sites, part of a proposed community conserved area, had different soundscapes than all other categories, including national parks. Unlogged sites had higher saturation than logging concessions at dusk and dawn. Soundscapes and hunting pressure were highly variable across different concessions. We found that higher gunshot rates and recent logging were associated with lower soundscape saturation overall. Based on our findings, we recommend that (i) the very few never logged forests that remain (and are not yet protected) should be urgently withdrawn from selective logging, and (ii) FSC or other certification schemes should be promoted in Gabon, with an emphasis on sustainable hunting

Benign effects of logging on aerial insectivorous bats in Southeast Asia revealed by remote sensing technologies

Logging is the most widespread disturbance in tropical forests, altering ecological communities and functions. However, many species can persist in logged forests, particularly where disturbance is low. Despite a growing understanding of how logging effects wildlife, there remains little information for Southeast Asia’s bats – in part due to major challenges in monitoring. We integrated remote sensing data from passive acoustic bat detectors with LiDAR-derived measures of forest structure from a human-modified landscape in Sabah, Borneo. Our appraisal of logging effects benefitted from a semi-automated classifier of bat calls that vastly speeds up the analysis of acoustic recording data. We recorded 105,576 bat passes from 21 phonic groups across a habitat disturbance gradient, comprising old-growth forest, repeatedly logged forest, and tree plantations. We show that logging pressure (as depicted by changes to habitat quality e.g. canopy height or shape) had negligible impact on the acoustic activity of bats. However, bat activity was higher in areas with a greater extent of high-biomass forest, as well as areas with greater topographical ruggedness. Logged forest supported higher levels of activity for several common bat phonic groups compared to old-growth forest. Across the landscape, plantations supported the lowest levels of bat activity, representing a three-fold decrease compared to old growth forest, and several species were not recorded in this habitat We found different call groups demonstrated different responses to forest disturbance. Sheath-tailed bats (Emballonura spp.) were active across all habitat types and were the most resilient to logging. Edge/open foragers were more prevalent in highly forested and topographically-rugged areas. Horseshoe and Running title: The effects of logging on bats in Southeast Asia 3 leaf-nosed bats (flutter clutter foragers) demonstrated idiosyncratic responses to logging but were consistently absent from plantations. Synthesis and applications. Logged forests can provide an important refuge for many common bat species in Southeast Asia, but do not capture the full breadth of forest-specialist species. Nevertheless, logged forests provide substantially better habitat for bats than tree plantations. While aerial insectivorous bats sampled via acoustic methods are poor indicators of forest disturbance overall, several species that respond predictably to logging could be targeted for biodiversity monitoring using acoustic and capture-based method

Riparian reserves promote insectivorous bat activity in oil palm dominated landscapes

The expansion of oil palm agriculture has contributed to biodiversity loss in Southeast Asia and elsewhere in the tropics. Riparian reserves (areas of native forest along waterways) have the potential to maintain forest biodiversity and associated ecological processes within these agricultural landscapes. Using acoustic sampling, we investigated the value of riparian reserves for insectivorous bats in oil palm plantations in Sabah, Malaysian Borneo. We compared general bat activity, foraging activity, and species occupancy between riparian areas in forest and riparian reserves in oil palm plantations. Overall bat activity varied little between riparian reserves in oil palm and riparian forest. Rather, activity was greatest in areas with a high forest canopy, irrespective of how much forest was available within or outside the riparian reserve. Bat foraging activity, as well as the occupancy of two species, was greatest in the forest sites, and while bats were detected in the oil palm riparian reserves, both foraging and occupancy were more associated with topographic ruggedness than forest amount or height. Our results indicate that habitat structure within riparian reserves may be more important than reserve size for supporting insectivorous bat diversity within oil palm landscapes. These findings provide important insights into the extent of the ecological benefits provided by conservation set-asides in forest-agricultural landscapes in the tropics

Effectiveness of 20 years of conservation investments in protecting orangutans

Conservation strategies are rarely systematically evaluated, which reduces transparency, hinders the cost-effective deployment of resources, and hides what works best in different contexts. Using data on the iconic and critically endangered orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments. We show that around USD 1 billion was invested between 2000 and 2019 into orangutan conservation by governments, non-governmental organizations, companies and communities. Broken down by allocation to different conservation strategies, we find that habitat protection, patrolling and public outreach had the greatest return-on-investment for maintaining orangutan populations. Given variability in threats, land-use opportunity costs, and baseline remunerations in different regions, there were differential benefits-per-dollar invested across conservation activities and regions. We show that, while challenging from a data and analysis perspective, it is possible to fully understand the relationships between conservation investments and outcomes, and the external factors that influence these outcomes. Such analyses can provide improved guidance towards more effective biodiversity conservation. Insights into the spatiotemporal interplays between the costs and benefits driving effectiveness can inform decisions about the most suitable orangutan conservation strategies for halting population declines. While our study focuses on the three extant orangutan species of Sumatra and Borneo, our findings have broad application for evidence-based conservation science and practice worldwide

Whole-genome sequencing reveals host factors underlying critical COVID-19

Altres ajuts: Department of Health and Social Care (DHSC); Illumina; LifeArc; Medical Research Council (MRC); UKRI; Sepsis Research (the Fiona Elizabeth Agnew Trust); the Intensive Care Society, Wellcome Trust Senior Research Fellowship (223164/Z/21/Z); BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070, BBS/E/D/30002275); UKRI grants (MC_PC_20004, MC_PC_19025, MC_PC_1905, MRNO2995X/1); UK Research and Innovation (MC_PC_20029); the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z); the Edinburgh Clinical Academic Track (ECAT) programme; the National Institute for Health Research, the Wellcome Trust; the MRC; Cancer Research UK; the DHSC; NHS England; the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health (CTSA award number UL1TR001878); the Perelman School of Medicine at the University of Pennsylvania; National Institute on Aging (NIA U01AG009740); the National Institute on Aging (RC2 AG036495, RC4 AG039029); the Common Fund of the Office of the Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS.Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care or hospitalization after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease