Estimating site occupancy for four threatened mammals in southeastern Laos

textThe tropical forests of Indochina harbor a suite of globally threatened tropical mammal species. These species are difficult to detect, and subsequently understudied. Noninvasive camera trapping was used to survey terrestrial mammals from a protected area in southeastern Lao PDR (Xe Sap National Protected Area). The presence-absence of four mammals (mainland serow Capricornis milneedwardsii, muntjac Muntiacus spp., macaque Macaca spp., and wild pig Sus scrofa) was modeled in an occupancy framework thereby accounting for detection probabilities. Our goals were to establish baseline occupancy data to assist with biological monitoring and to better understand the factors influencing the distribution of the target species. Naïve occupancy, or the proportion of sites at which the target species was detected, was 0.58 for muntjac, 0.55 for macaque, 0.38 for wild pig, and 0.30 for serow. True occupancy estimates (Ψ ± SE) from top-ranked models was 0.79 ± 0.21 for macaque, 0.74 ± 0.13 for muntjac, 0.51 ± 0.13 for wild pig, and 0.48 ± 0.18 for serow. The results underscore the importance of accounting for imperfect detection rates when studying rare or elusive species. I included two site covariates (forest type and distance to nearest village) in the occupancy models. Estimating occupancy as a function of site covariates improved model performance and provided insight into landscape-level factors that affect species occurrence. In the top-ranked models, serow occupancy was higher in hill evergreen forest (HEGF) than semi-evergreen forest (SEGF). Muntjac occupancy was higher in areas further from villages. Macaque occupancy was higher in areas closer to villages. Wild pig occupancy was higher in areas further from villages and in HEGF. I recommend using an occupancy framework to analyze occurrence data for difficult-to-study tropical mammal species. The results highlight the importance of Xe Sap NPA for large mammal conservation in the region.Ecology, Evolution and Behavio

imageseg: An R package for deep learning-based image segmentation

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2022 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological SocietyConvolutional neural networks (CNNs) and deep learning are powerful and robust tools for ecological applications and are particularly suited for image data. Image segmentation (the classification of all pixels in images) is one such application and can, for example, be used to assess forest structural metrics. While CNN-based image segmentation methods for such applications have been suggested, widespread adoption in ecological research has been slow, likely due to technical difficulties in implementation of CNNs and lack of toolboxes for ecologists. Here, we present R package imageseg which implements a CNN-based workflow for general purpose image segmentation using the U-Net and U-Net++ architectures in R. The workflow covers data (pre)processing, model training and predictions. We illustrate the utility of the package with image recognition models for two forest structural metrics: tree canopy density and understorey vegetation density. We trained the models using large and diverse training datasets from a variety of forest types and biomes, consisting of 2877 canopy images (both canopy cover and hemispherical canopy closure photographs) and 1285 understorey vegetation images. Overall segmentation accuracy of the models was high with a Dice score of 0.91 for the canopy model and 0.89 for the understorey vegetation model (assessed with 821 and 367 images respectively). The image segmentation models performed significantly better than commonly used thresholding methods and generalized well to data from study areas not included in training. This indicates robustness to variation in input images and good generalization strength across forest types and biomes. The package and its workflow allow simple yet powerful assessments of forest structural metrics using pretrained models. Furthermore, the package facilitates custom image segmentation with single or multiple classes and based on colour or grayscale images, for example, for applications in cell biology or for medical images. Our package is free, open source and available from CRAN. It will enable easier and faster implementation of deep learning-based image segmentation within R for ecological applications and beyond.publishedVersio

Pangolins in global camera trap data: Implications for ecological monitoring

Despite being heavily exploited, pangolins (Pholidota: Manidae) have been subject to limited research, resulting in a lack of reliable population estimates and standardised survey methods for the eight extant species. Camera trapping represents a unique opportunity for broad-scale collaborative species monitoring due to its largely non-discriminatory nature, which creates considerable volumes of data on a relatively wide range of species. This has the potential to shed light on the ecology of rare, cryptic and understudied taxa, with implications for conservation decision-making. We undertook a global analysis of available pangolin data from camera trapping studies across their range in Africa and Asia. Our aims were (1) to assess the utility of existing camera trapping efforts as a method for monitoring pangolin populations, and (2) to gain insights into the distribution and ecology of pangolins. We analysed data collated from 103 camera trap surveys undertaken across 22 countries that fell within the range of seven of the eight pangolin species, which yielded more than half a million trap nights and 888 pangolin encounters. We ran occupancy analyses on three species (Sunda pangolin Manis javanica, white-bellied pangolin Phataginus tricuspis and giant pangolin Smutsia gigantea). Detection probabilities varied with forest cover and levels of human influence for P. tricuspis, but were low (<0.05) for all species. Occupancy was associated with distance from rivers for M. javanica and S. gigantea, elevation for P. tricuspis and S. gigantea, forest cover for P. tricuspis and protected area status for M. javanica and P. tricuspis. We conclude that camera traps are suitable for the detection of pangolins and large-scale assessment of their distributions. However, the trapping effort required to monitor populations at any given study site using existing methods appears prohibitively high. This may change in the future should anticipated technological and methodological advances in camera trapping facilitate greater sampling efforts and/or higher probabilities of detection. In particular, targeted camera placement for pangolins is likely to make pangolin monitoring more feasible with moderate sampling efforts

Assessing defaunation in the central Annamites ecoregion of Vietnam and Laos

Southeast Asia is a global biodiversity hotspot, but anthropogenic threats are causing loss of larger vertebrate species (defaunation) across the region. Both habitat alteration and unsustainable hunting have contributed to defaunation in Southeast Asia. Defaunation is particularly severe in the Annamites ecoregion of Vietnam and Laos PDR, where widespread indiscriminate snaring for the illegal wildlife trade has decimated ground-dwelling mammal and bird species. Several Annamite endemics are now facing imminent extinction as a result of this snaring crisis. To develop more effective conservation strategies to protect biodiversity in Southeast Asia, it is necessary to better understand the defaunation process, and to have an accurate assessment of biodiversity in defaunated areas. The aim of this thesis was to improve our understanding of how defaunation impacts tropical faunal communities in Southeast Asia, with a specific focus on the Annamites ecoregion, thereby providing insights that can help inform conservation strategies to prevent further defaunation in tropical hotspots. Scientists have an incomplete understanding of how different defaunation drivers impact faunal communities at large spatial scales. To investigate this issue, we collected landscape-scale camera-trapping data from two study areas with fundamentally different threats: habitat degradation (Malaysian Borneo) and indiscriminate snaring (Annamites). We used a defaunation index and occupancy models to assess how defaunation differentially impacts ground-dwelling mammal and bird communities in these regions (chapter 2). We found that, while both defaunation drivers negatively impact faunal communities, the hunted sites had higher levels of functional extinction, lower species occupancies, and species distributions that were primarily influenced by anthropogenic- rather than habitat-based measures. We conclude that intensive, indiscriminate hunting may be a more severe short-term threat to terrestrial mammal and bird species than moderate levels of habitat degradation. To optimize the use of limited conservation resources, it is often necessary to understand the spatial patterns of defaunation. However, accurately assessing biodiversity in defaunated tropical forests brings a unique set of challenges. We combined camera-trapping and leech-derived data from landscape-scale surveys with advanced statistical modelling techniques and innovative explanatory covariates to assess defaunation patterns in a central Annamites forest complex that has been subjected to high levels of snaring pressure (chapter 3). Our findings show that, despite severe levels of defaunation, conservation-priority species still persist, albeit at extremely low occupancies. Threatened and endemic species were primarily found at higher elevations and in more remote areas. The results provide information that can be used to inform targeted enforcement efforts in this landscape. Understanding how defaunation impacts individual species is important to developing effective conservation strategies. Such information is especially important for species that are understudied but occur in areas known to be under extreme anthropogenic pressure. We used data from landscape-scale camera-trapping in the central Annamites to investigate the ecology and distribution of the Annamite striped rabbit Nesolagus timminsi (chapter 4). We found that Annamite striped rabbit occupancy was best explained by a proxy for past hunting pressure, which likely indicates that populations have been negatively impacted by industrial snaring. We also found that that local abundance estimates were low at one site, and that the species is likely absent from a second site where hunting pressure appears to have been more intense. Our findings provide information on priority areas to target snare-removal efforts, and the first conservation baseline for the species.Südostasien ist ein globaler Biodiversitäts-Hotspot. Anthropogene Bedrohungen führen jedoch derzeit zu einem starken Verlust größerer Wirbeltiere (Defaunation) in der gesamten Region. Sowohl Lebensraumveränderungen als auch eine nicht nachhaltige Bejagung haben zur Defaunation Südostasiens beigetragen. Im Truong-Son Gebirge in Vietnam und Laos ist die Lage besonders gravierend. Hier hat die weit verbreitete und wahllose Jagd mit Drahtschlingen für den illegalen Wildtierhandel die bodenbewohnende Säugetier- und Vogelarten stark dezimiert. Mehrere endemische Arten des Truong-Son Gebirges stehen bereits kurz vor der Ausrottung. Um wirksamere Strategien zum gezielten Schutz der biologischen Vielfalt in Südostasien zu entwickeln, ist es notwendig, den Prozess des Artenverlusts besser zu verstehen, sowie einen detaillierten Überblick über das derzeitige Artenvorkommen zu haben. Ziel dieser Arbeit war es, zu untersuchen wie sich die Defaunation auf die tropischen Artengemeinschaften Südostasiens – mit besonderem Augenmerk auf das zentrale Truong-Son Gebirge – auswirkt. Des Weiteren sollte diese Arbeit erste Informationen über das räumliche Vorkommen einiger stark bedrohter, endemischer Arten liefern, um somit gezieltere Schutzmaßnahmen zu unterstützen. Zurzeit besteht nur eine unvollständige Kenntnis davon, wie sich verschiedene Faktoren die zur Defaunation beitragen, auf Artengemeinschaften in größeren räumlichen Maßstäben auswirken. Um dies zu untersuchen sammelten wir großskalig Kamerafallendaten aus zwei Regionen in Südostasien, die durch grundlegend unterschiedliche Einflussfaktoren bedroht werden (Kapitel 2): Im Malaysischen Teil von Borneo ist die Artengemeinschaft primär durch die Degradadirung des Regenwaldes bedroht, wohingegen im Truong-Son Gebirge die Jagd mit Drahtschlingen die Hauptbedrohung darstellt. Mit modernen multi-species occupancy Modellen und einem Defaunation-Index konnten wir feststellen, dass sowohl Walddegradation, als auch Wilderei negative Auswirkungen auf die Artengemeinschaften haben. Jedoch zeigten unsere Ergebnisse auch, dass Arten in den illegal bejagten Gebieten nicht nur ein deutlich höheres Aussterberisiko hatten, sondern auch, dass die Verbreitung der noch vorkommenden Arten durch die intensive Jagd viel stärker zurückgegangen ist, als die Verbreitung ihrer Schwesterarten in den durch kommerzielle Forstwirtschaft degradierten Regenwäldern. Mit diesen Ergebnissen konnten wir sehr deutlich zeigen, dass die intensive, wahllose Wilderei im Vergleich zur Walddegradation momentan die schwerwiegendere Bedrohung für bodenlebende Säugetier- und Vogelarten darstellt. Aufgrund begrenzter finanzieller und personeller Ressourcen für den Artenschutz ist es notwendig Maßnahmen gegen Wilderei gezielt dort einzusetzen, wo noch letzte Populationen der stark bedrohten Arten vorkommen. Dafür ist es wichtig die räumlichen Muster der Defaunation zu verstehen, was jedoch in tropischen Regenwäldern eine Reihe von Herausforderungen mit sich bringt. Um Vorkommensnachweise auch von besonders seltenen Arten zu bekommen, haben wir deshalb Kamerafallendaten und molekulargenetische Nachweise aus Umwelt-DNA-Proben (Blutegeln) kombiniert (Kapitel 3). Mittels multi-species occupancy Modellen konnten wir dann die räumliche Verteilung der Arten großflächig über fünf benachbarte Untersuchungsgebiete modellieren. Unsere Ergebnisse zeigten, dass trotz der starken Wilderei einige hochgradig bedrohte Arten noch immer im Untersuchungsgebiet vorkommen. Bedrohte und endemische Arten wurden vor allem in höheren Lagen und in entlegenen Gebieten gefunden. Unsere Ergebnisse lieferten unseren Naturschutzpartnern wichtige Informationen, um ihre Schutzpatrouillen gezielter einsetzen zu können. Für die Entwicklung wirksamer Arterhaltungsstrategien ist es zudem wichtig zu verstehen, wie sich die Defaunation auf einzelne Arten auswirkt. Solche Informationen sind besonders für Arten wichtig, die nur wenig erforscht sind, jedoch in Gebieten vorkommen die besonders von Wilderei bedroht sind. Wir nutzten Kamerafallendaten des zentralen Truong-Son Gebirges, um die Ökologie und Verbreitung des Annamiten-Streifenkaninchens Nesolagus timminsi zu untersuchen (Kapitel 4). Es zeigte sich, dass sich das Vorkommen des Annamiten-Streifenkaninchens wahrscheinlich mit dem vergangenem Jagddruck erklären lässt und die Population durch diese intensive Wilderei mit Drahtschlingen bereits negativ beeinflusst wurde. Unsere Ergebnisse stellen den ersten großflächigen Referenzdatensatz über die Verbreitung des Annamiten-Streifenkaninchens dar und geben Hinweise auf Gebiete in denen bevorzugt und gezielt Drahtschlingen beseitigt werden sollten

How the loss of forest fauna undermines the achievement of the SDGs

The human-driven loss of biodiversity has numerous ecological, social, and economic impacts at the local and global levels, threatening important ecological functions and jeopardizing human well-being. In this perspective, we present an overview of how tropical defaunation—defined as the disappearance of fauna as a result of anthropogenic drivers such as hunting and habitat alteration in tropical forest ecosystems—is interlinked with four selected Sustainable Development Goals (SDGs). We discuss tropical defaunation related to nutrition and zero hunger (SDG 2), good health and well-being (SDG 3), climate action (SDG 13), and life on land (SDG 15). We propose a range of options on how to study defaunation in future research and how to address the ongoing tropical defaunation crisis, including but not limited to recent insights from policy, conservation management, and development practice

Camera-trapping reveals new insights in the ecology of three sympatric muntjacs in an overhunted biodiversity hotspot

The Annamites ecoregion harbors exceptional levels of species richness and endemism, but intensive snaring has decimated populations of terrestrial mammals. Ungulates, such as muntjacs, are susceptible to snaring, and in need of effective conservation action. At least three muntjacs occur sympatrically in the region: the Annamite dark muntjac species complex Muntiacus rooseveltorum/truongsonensis, the northern red muntjac Muntiacus vaginalis, and the large-antlered muntjac Muntiacus vuquangensis. We conducted a landscape-scale systematic camera-trapping survey in Nakai-Nam Theun National Park to gather information on the ecology and distribution of these muntjacs. We analyzed camera-trap records within an occupancy framework to evaluate responses to environmental and anthropogenic variables, and to predict distributions across the protected area. We found varying responses to the covariates, indicating complex drivers of occurrence, though all three muntjac had higher occupancies in more inaccessible areas. Mean (95%) PAO in the protected area was higher for large-antlered muntjac (0.33 [0.22–0.49]), followed by Annamite dark muntjac (0.28 [0.18–0.39]), and then northern red muntjac (0.27 [0.15–0.42]). Large-antlered muntjac and northern red muntjac were widespread, while dark muntjac was restricted to a single high elevation area. Overall, our results provide new insights into muntjac ecology, distribution, and population status, and we discuss how this information can be used to inform conservation efforts. Given the high occupancies that we found for the Critically Endangered large-antlered muntjac, we argue that Nakai-Nam Theun National Park may be vital for the long-term survival of the species

Using terrestrial leeches to assess the genetic diversity of an elusive species: The Annamite striped rabbit Nesolagus timminsi

Information on geographic patterns of species genetic diversity is often needed to inform conservation strategies. Obtaining data over large geographic areas can be difficult, especially for rare or elusive species. Here, we explore the use of invertebrate-derived DNA (iDNA) obtained from terrestrial leeches to assess genetic diversity of the Annamite striped rabbit Nesolagus timminsi, a little-known and highly threatened lagomorph endemic to the Annamites ecoregion of Vietnam and Laos. We collected 4,877 leeches pooled into 651 leech bulk samples from eight study areas across the northern and central Annamites. Using metabarcoding, we detected Annamite striped rabbit DNA in 11 leech bulk samples from five of the study areas. We amplified up to 3,000 bp of six mitochondrial DNA loci of Annamite striped rabbit from nine of the 11 bulk samples. Haplotype network analyses showed five shared haplotypes among these samples. Phylogenetic trees constructed using maximum likelihood and Bayesian inference showed little geographic structuring among the Annamite striped rabbit populations across the five study areas. Our results provide information that can be directly used to inform planned ex situ conservation measures for the Annamite striped rabbit. We discuss our results within the context of using iDNA to noninvasively obtain data to assess species genetic diversity, and the potential of this approach to be applied to other species and systems

Getting the big picture: Landscape‐scale occupancy patterns of two Annamite endemics among multiple protected areas

The Annamite mountains of Vietnam and Laos are a global biodiversity hotspot harboring several threatened endemic species. Conservation efforts to protect these endemics are hampered by a lack of knowledge on their ecology and distribution. We conducted landscape scale camera-trapping across six study areas in the Annamites to assess distribution patterns of two endemics: the Annamite dark muntjac species complex Muntiacus rooseveltorum/ truongsonensis and the Annamite striped rabbit Nesolagus timminsi. We used a Bayesian single-species occupancy framework to estimate occupancy as a function of ecological and anthropogenic factors. Our study showed that Annamite dark muntjac was predominantly found at higher elevations (&gt;1000 m) and in areas that were more inaccessible to people and had lower surrounding village density. Annamite striped rabbit exhibited both positive and negative responses to elevation among study areas, with no clear response to the anthropogenic covariates. Our results showed that covariate responses varied among the study areas when random effects were included on study areas. We discuss the application of random effects to investigate species occupancies across large spatial scales, and the risk of not accounting for variation among study areas. Our prediction maps provide the first comprehensive overview of the distribution of these endemic species across a substantial part of their range and can be used to help stakeholders focus conservation efforts on priority areas