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Species relative abundance (SRA) is an essential attribute of biotic communities, which can provide an accurate description of community structure. However, the sampling method used may have a direct influence on SRA quantification, since the use of attractants (e.g., baits, light, and pheromones) can introduce additional sources of variation in trap performance. We tested how sampling aided by baits affect community data and therefore alter derived metrics. We tested our hypothesis on dung beetles using data from flight interception traps (FITs) as a baseline to evaluate baited pitfall trap performance. Our objective was to assess the effect of bait attractiveness on estimates of SRA and assemblage metrics when sampled by pitfall traps baited with human feces.Dung beetles were sampled at three terra firme primary forest sites in the Brazilian Amazon. To achieve our objective, we (i) identified species with variable levels of attraction to pitfall baited with human feces; (ii) assessed differences in SRA; and (iii) assessed the effect of bait on the most commonly used diversity metrics derived from relative abundance (Shannon and Simpson indices). We identified species less and highly attracted to the baits used, because most attracted species showed greater relative abundances within baited pitfall traps samples compared with our baseline. Assemblages sampled by baited pitfall traps tend to show lower diversity and higher dominance than those sampled by unbaited FITs. Our findings suggest that for ecological questions focused on species relative abundance, baited pitfall traps may lead to inaccurate conclusions regarding assemblage structure. Although tested on dung beetles, we suggest that the same effect could be observed for other insect taxa that are also sampled with baited traps. We highlight a need for further studies on other groups to elucidate any potential effects of using baits.

The rise in species richness with area is one of the best-studied patterns in ecology. Yet, little is known about the spatial scaling of alternate dimensions of diversity. Here, we provide empirical evidence for a relationship between the richness of acoustic traits emanating from the landscape, or soundscape richness, and the island area, which we term the Soundscape Area Relationship (SSAR). We show a positive relationship between the gamma soundscape richness and island area, with slope and R2-values of comparable magnitude to those reported in the literature. This relationship breaks down at the smallest spatial scales, indicating a small-island effect. Moreover, we demonstrate a positive spatial scaling of the plot-scale alpha soundscape richness, but not the beta soundscape turnover, suggesting disproportionate effects are an important underlying mechanism. We conclude that the scaling of biodiversity can be extended to the realm of ecoacoustics, implying soundscape metrics are sensitive to fundamental ecological patterns and useful to disentangle the complex mechanisms that drive them.

Habitat conversion is a major driver of tropical biodiversity loss, but its effects are poorly understood in montane environments. While community-level responses to habitat loss display strong elevational dependencies, it is unclear whether these arise via elevational turnover in community composition and interspecific differences in sensitivity or elevational variation in environmental conditions and proximity to thermal thresholds. Here we assess the relative importance of inter- and intraspecific variation across the elevational gradient by quantifying how 243 forest-dependent bird species vary in sensitivity to landscape-scale forest loss across a 3000-m elevational gradient in the Colombian Andes. We find that species that live at lower elevations are strongly affected by loss of forest in the nearby landscape, while those at higher elevations appear relatively unperturbed, an effect that is independent of phylogeny. Conversely, we find limited evidence of intraspecific elevational gradients in sensitivity, with populations displaying similar sensitivities to forest loss, regardless of where they exist in a species' elevational range. Gradients in biodiversity response to habitat loss thus appear to arise via interspecific gradients in sensitivity rather than proximity to climatically limiting conditions.

Soundscape studies are increasingly used to capture landscape-scale ecological patterns. Yet, several aspects of soundscape diversity remain unexplored. Although some processes influencing acoustic niche usage may operate in the 24-hr temporal domain, most acoustic indices only capture the diversity of sounds co-occurring in sound files at a specific time of day. Moreover, many indices do not consider the relationship between the spectral and temporal traits of sounds simultaneously. To provide novel insights into landscape-scale patterns of acoustic niche usage at broader temporal scales, we present a workflow to quantify soundscape diversity through the lens of trait-based ecology. Our workflow quantifies the diversity of sound in the 24-hr acoustic trait space. We introduce the Operational Sound Unit (OSU), a unit of diversity measurement that groups sounds by their shared acoustic properties. Using OSUs and building on the framework of Hill numbers, we propose three metrics that capture different aspects of acoustic trait space usage: (i) soundscape richness, (ii) soundscape diversity and (iii) soundscape evenness. We demonstrate the use of these metrics by (a) simulating soundscapes to assess whether the indices possess a set of desirable behaviours and (b) quantifying soundscape richness and evenness along a gradient in species richness. We demonstrate that (a) the indices outlined herein have desirable behaviours and (b) the soundscape richness and evenness are positively correlated with the richness of sound-producing species. This suggests that more acoustic niche space is occupied when the species richness is higher. Additionally, species-poor acoustic communities have a higher proportion of rare sounds and use the acoustic space less evenly. Our workflow generates novel insights into acoustic niche usage at a landscape scale and provides a useful tool for biodiversity monitoring. Moreover, Hill numbers can also be used to measure the taxonomic, functional and phylogenetic diversity. Using a common framework for diversity measurement gives metrics a common behaviour, interpretation and standardised unit, thus ensuring comparisons between soundscape diversity and other metrics represent real-world ecological patterns rather than mathematical artefacts stemming from different formulae.

The wildlife trade is worth billions of dollars annually and affects most major taxonomic groups. Despite this, a global understanding of the trade's impacts on species populations is lacking. We performed a quantitative meta-analysis of the wildlife trade that synthesized 506 species-level effect sizes from 31 studies, estimating trade-driven declines in mammals (452 effect sizes), birds (36) and reptiles (18). Overall, species declined in abundance by 62% (95% confidence interval (CI), 20 to 82%) where trade occurs. Reductions involving national or international trade were greatest, driving declines of 76% (95% CI, 36 to 91%) and 66% (95% CI, 12 to 87%), respectively. The impacts of trade were pervasive, requiring over 102 hours of travel time from settlements for trade to have no mean effect. Current protective measures fail species, with significant declines even where the harvesting for trade occurs in protected areas. Population declines tracked species threat status, indicating heightened extirpation and extinction risk in traded species. Critically, for such a severe global threat to wildlife, our analysis unearthed a limited number of studies using treatment versus control comparisons, and no studies on amphibians, invertebrates, cacti or orchids. Improved management, tackling both unsustainable demand and trade reporting, must be a conservation priority to prevent rampant trade-induced declines.

Summary The ‘Critically Endangered’ Black-winged Trumpeter Psophia obscura is endemic to the Belém Centre of Endemism in extreme eastern Amazonia and has a declining population and range. Here we report on a five-year (2016–2020) systematic camera-trap (n = 61) study of the species in Gurupi Biological Reserve, one of its most important conservation areas. We used a multi-season occupancy model to identify factors affecting occupancy rates and to assess occupancy trends in the reserve. Occupancy was negatively related to elevation and site-level tree density, and was positively related to post-logging recovery times. Average annual occupancy rates remained stable throughout the study period (ranging between 0.57 and 0.67) and this stability was largely driven by high between-year survival rates. Results confirm that the Black-winged Trumpeter is an interior-forest specialist that is highly sensitive to forest disturbance, which underlines the importance of the Gurupi Biological Reserve as a core site for the conservation of the species. However, the species is long-lived, so continuous monitoring is needed to further clarify population trends. We also recommended that the status of the species in other forest remnants, most of which remain unprotected, is assessed.

The seasonal flood pulse in Amazonia can be considered a primary driver of community structure in floodplain environments. Although this natural periodic disturbance is part of the landscape dynamics, the seasonal inundation presents a considerable challenge to organisms that inhabit floodplain forests. The present study investigated the effect of seasonal flooding on fruit-feeding butterfly assemblages in different forest types and strata in central Amazonia. We sampled fruit-feeding butterflies in the canopy and the understory using baited traps in adjacent upland (unflooded forests

Soundscape studies are increasingly common to capture landscape-scale ecological patterns. Yet, several aspects of soundscape diversity quantification remain unexplored. Although some processes influencing acoustic niche usage may operate in the 24h domain, most acoustic indices only capture the diversity of sounds co-occurring in sound files at a specific time of day. Moreover, many indices do not consider the relationship between the spectral and temporal traits of sounds simultaneously. To provide novel insights into landscape-scale patterns of acoustic niche usage at broader temporal scales, we present a workflow to quantify soundscape diversity through the lens of functional ecology.Our workflow quantifies the functional diversity of sound in the 24-hour acoustic trait space. We put forward an entity, the Operational Sound Unit (OSU), which groups sounds by their shared functional properties. Using OSUs as our unit of diversity measurement, and building on the framework of Hill numbers, we propose three metrics that capture different aspects of acoustic trait space usage: (i) soundscape richness; (ii) soundscape diversity; (iii) soundscape evenness. We demonstrate the use of these metrics by (a) simulating soundscapes to assess if the indices possess a set of desirable behaviours; and (b) quantifying the soundscape richness and evenness along a gradient in species richness to illustrate how these metrics can be used to shed unique insights into patterns of acoustic niche usage.We demonstrate that: (a) the indices outlined herein have desirable behaviours; and (b) the soundscape richness and evenness are positively correlated with the richness of soniferous species. This suggests that the acoustic niche space is more filled where taxonomic richness is higher. Moreover, species-poor acoustic communities have a higher proportion of rare sounds and use the acoustic space less effectively. As the correlation between the soundscape and taxonomic richness is strong (>0.8) and holds at low sampling intensities, soundscape richness could serve as a proxy for taxonomic richness.Quantifying the soundscape diversity through the lens of functional ecology using the analytical framework of Hill numbers generates novel insights into acoustic niche usage at a landscape scale and provides a useful proxy for taxonomic richness measurement.

The domestic cat (Felis catus) is the most popular companion animal and the most abundant carnivore globally. It is also a pet with an immense ecological footprint, because even non-feral and food-subsidized cats are prolific predators. Whereas knowledge about the spatial behavior of individual domestic cats is growing, we still know little about how a local population of free-ranging pet cats occupies the landscape. Using a citizen science approach, we GPS-tagged 92 pet cats with outdoor access living in a residential area in southern Norway. The resulting position data allowed us to construct both individual home range kernels and a population-level utilization distribution. Our results reveal a dense predatory blanket that outdoor cats drape over and beyond the urban landscape. It is this population-level intensity surface - the “catscape” - that potential prey have to navigate. There were almost no gaps in the catscape within our residential study area and therefore few terrestrial refuges from potential cat predation. However, cats spent on average 79% of their outdoor time within 50 meters to their owner’s home, which suggests that the primary impact is local and most acute for wildlife in the vicinity to homes with cats. We discuss the catscape as a conceptual and quantitative tool for better understanding and mitigating the environmental impact of domestic cats.

Ecologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously.We show how this challenge can be overcome by incorporating pre-existing range information into MSOMs, yielding a ‘biogeographic multi-species occupancy model’ (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey, and entire avian communities in forests and pastures of Colombia’s West Andes.Compared to traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species.Incorporating pre-existing range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false-absences are modeled in an occupancy framework.

Made available in DSpace on 2022-04-28T19:41:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-10-01 Animal coloring serves several functions, including camouflage and thermoregulation. However, some individuals have anomalous coloring patterns due to excess (melanism) or deficiency (albinism, leucism, or piebaldism) in melanin production. Although these anomalies occur in several species, there are few cited cases. Here, we report the occurrence of color anomalies in three Neotropical deer species. Data were obtained from wildlife inventories, through direct observation, camera-traps, and/or deer carcasses, between 2011 and 2020, in three biomes—the Brazilian Savanna (Cerrado), and the Atlantic and Amazon Rain Forests. We registered 10 individuals with anomalous coloring from Minas Gerais, São Paulo, Amazonas and Rondônia states; seven Mazama gouazoubira (six piebalds and one leucistic), two piebald M. americana, and one piebald M. nemorivaga. Of the registered individuals, five were males, two females, and three of undetermined sex. To our knowledge, this is the largest set of anomalous coloring data for Neotropical deer. Even with the increasing reports of anomalous coloring, little is known about the factors that may cause this and how it influences the survival of individuals and consequently wild populations. Programa de Pós-Graduação em Conservação dos Recursos Naturais do Cerrado Instituto Federal Goiano-IFG Programa de Conservação Mamíferos do Cerrado-PCMC Departamento de Ciências Biológicas Universidade Federal de Catalão-UFCAT, Campus II/sala 06, Rua Terezinha Margon Vaz, s/n-Residencial Barka II Instituto Latino-Americano de Ciências da Vida e da Natureza Universidade Federal da Integração Latino-Americana-UNILA Deer Research and Conservation Center (NUPECCE)/São Paulo State University Muriqui Instituto de Biodiversidade Technical Director at Ecologic-Centro de Avaliações e Perícias Ambientais FURNAS Centrais Elétricas S.A. Biodiversity Research Centre-Universidade Federal de Roraima-CBio-UFRR University of East Anglia-UEA Norwegian University of Life Sciences-NMBU Department of Wildlife Fish and Conservation Biology Graduate Group in Ecology University of California Grupo de Ecologia e Conservação de Felinos na Amazônia Instituto de Desenvolvimento Sustentável Mamirauá Deer Research and Conservation Center (NUPECCE)/São Paulo State University

Finding new pathways for reconciling socioeconomic well-being and nature sustainability is critically important for contemporary societies, especially in tropical developing countries where sustaining local livelihoods often clashes with biodiversity conservation. Many projects aimed at reconciling the goals of biodiversity conservation and social aspirations within protected areas (PAs) have failed on one or both counts. Here, we investigate the social consequences of living either inside or outside sustainable-use PAs in the Brazilian Amazon, using data from more than 100 local communities along a 2,000-km section of a major Amazonian river. The PAs in this region are now widely viewed as conservation triumphs, having implemented community comanagement of fisheries and recovery of overexploited wildlife populations. We document clear differences in social welfare in communities inside and outside PAs. Specifically, communities inside PAs enjoy better access to health care, education, electricity, basic sanitation, and communication infrastructure. Moreover, living within a PA was the strongest predictor of household wealth, followed by cash-transfer programs and the number of people per household. These collective cobenefits clearly influence life satisfaction, with only 5% of all adult residents inside PAs aspiring to move to urban centers, compared with 58% of adults in unprotected areas. Our results clearly demonstrate that large-scale “win–win” conservation solutions are possible in tropical countries with limited financial and human resources and reinforce the need to genuinely empower local people in integrated conservation-development programs.

Amazonia comprises a mosaic of contrasting habitats, with wide environmental heterogeneity at local and regional scales. In central Amazonia, upland forest (terra firme) is the predominant forest type and seasonally flooded forests inundated by white- and black-water rivers (várzea and igapó, respectively) represent around 20% of the forested areas. In this work, we took advantage of a natural spatial arrangement of the main vegetation types in central Amazonia to investigate butterfly assemblage structure in terra firme, várzea and igapó forests at the local scale. We sampled in the low- and high-water seasons, combining active and passive sampling with traps placed in both the understory and canopy. Terra firme supported the highest number of butterfly species, whereas várzea forest provided the highest number of butterfly captures. The high species richness in terra firme may reflect that this forest type is floristically richer than várzea and igapó. Várzea is a very productive environment and may thus support a higher number of butterfly individuals than terra firme and igapó. Most butterfly species (80.2%) were unique to a single forest type and 17 can be considered forest type indicator species in this landscape. Floodplain forest environments are therefore an important complement to terra firme in terms of butterfly species richness and conservation in Amazonia.

The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) regulates international legal trade to prevent the detrimental harvest of wildlife. We assess the volumes of threatened and non-threatened bird, mammal, amphibian, and reptile species in the CITES-managed trade and how this trade responded to category changes of species in the IUCN Red List between 2000 and 2018. In this period, over a thousand wild-sourced vertebrate species were commercially traded. Species of least conservation concern had the highest yearly trade volumes (excluding birds), whereas species in most Red List categories showed an overall decrease in trade reoccurrence and volume through time, with most species unlikely to reoccur in recent trade. Charismatic species with populations split-listed between Appendices I and II were traded in substantially lower yearly volumes when sourced from the more-threatened Appendix I populations. Species trade volumes did not systematically respond to changes in the Red List category, with 31.0% of species disappearing from trade before changing category and the majority of species revealing no difference in trade volumes from pre- to post-change. Just 2.7% (12/432) of species volumes declined and 2.1% (9/432) of volumes increased after a category change. Our findings highlight that non-threatened species dominate trade but reveal small numbers of highly threatened species in trade and a disconnect between species trade volumes and changing extinction risk. We highlight potential drawbacks in the current regulation of trade in listed species and urgently call for open and accessible assessments-non-detriment findings-robustly evidencing the sustainable use of threatened and non-threatened species alike.

Amazonia encompasses forests that grow in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain, creating a flooding gradient. This gradient directly affects the biota, but the effect on soil organisms remains elusive. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity from soil and litter samples in a seasonally flooded forest and its adjacent unflooded forest in central-western Amazonia using 16S and 18S gene sequences, respectively. We characterize the below-ground diversity and community composition based on Amplicon Sequence Variants (ASVs) along the flooding gradient. We test for the relationship of soil biota with the flooding gradient, soil properties and above-ground woody plant diversity. The flooding gradient did not explain below-ground biodiversity. Nor was the below-ground diversity explained by the above-ground woody plant diversity. However, we found taxonomic groups not previously reported in Amazonian seasonally flooded forests. Also, the flooding gradient and woody plant diversity did, in part, explain the community composition of soil bacteria. Although the effects of the flooding gradient, soil properties and above-ground woody plant diversity is hard to quantify, our results thus indicate that flood stress could influence below-ground bacterial community composition.

Research Highlights: Rare, or sparsely distributed, species drive the floristic diversity of upland, terra firme and seasonally flooded forests in the central Juru&aacute, &mdash, a remote and hitherto floristically poorly known area in the Brazilian Amazon. Background and Objectives: Floristic inventories are critical for modelling and understanding the role of Amazonian forests in climate regulation, for sustainable management of forest resources and efficient conservation planning. Yet, detailed information about the often complex spatial distributions of many Amazonian woody plants is limited. Here, we provide information about forest structure and species composition from a remote terra firme forest and an adjacent floodplain forest in the western Brazilian Amazon. More specifically, we ask (1) how floristically different are the terra firme and floodplain forests? and (2) how variable is species composition within the same forest type? Materials and Methods: Between September 2016 and October 2017, we inventoried 97 plots (each 0.1 ha, 100 &times, 10 m) placed at least 800 m apart, with 46 plots in terra firme forest and 51 in seasonally flooded forest. We included all trees, hemi-epiphytes and palms with diameter at breast height (dbh) &gt, 10 cm and woody lianas &gt, 5 cm dbh. We examine forest structure, family- and species-level floristic composition and species diversity within and between forest types using family and species importance values, rarefaction curves and dissimilarity matrices. Results: Terra firme forest and seasonally flooded forest woody plant communities differ both in structure and species composition, which was highly variable within forest types. Many species were shared between terra firme and seasonally flooded forests, but most species were forest type-specific. Whereas species richness was greatest in the terra firme forest, floodplain species richness was among the highest regionally. Conclusions: Floodplain forests are a crucial complement to terra firme forests in terms of Amazonian woody plant diversity.

The wildlife trade is worth billions of dollars annually and affects most major taxonomic groups. Despite this, a global understanding of the trade's impacts on species populations is lacking. We performed a quantitative meta-analysis of the wildlife trade that synthesized 506 species-level effect sizes from 31 studies, estimating trade-driven declines in mammals (452 effect sizes), birds (36) and reptiles (18). Overall, species declined in abundance by 62% (95% confidence interval (CI), 20 to 82%) where trade occurs. Reductions involving national or international trade were greatest, driving declines of 76% (95% CI, 36 to 91%) and 66% (95% CI, 12 to 87%), respectively. The impacts of trade were pervasive, requiring over 102 hours of travel time from settlements for trade to have no mean effect. Current protective measures fail species, with significant declines even where the harvesting for trade occurs in protected areas. Population declines tracked species threat status, indicating heightened extirpation and extinction risk in traded species. Critically, for such a severe global threat to wildlife, our analysis unearthed a limited number of studies using treatment versus control comparisons, and no studies on amphibians, invertebrates, cacti or orchids. Improved management, tackling both unsustainable demand and trade reporting, must be a conservation priority to prevent rampant trade-induced declines.

For tropical tree species, wood density can vary greatly both within and between species depending on environmental conditions. In Amazonian seasonally flooded forests, yearly flood pulses influence tree growth and floodplain trees have developed specialised strategies to cope with prolonged submersion during flooding. We therefore hypothesised that seasonal floods significantly affect the capacity of trees to store carbon as woody biomass per unit volume and that forest hydrology would be an important factor in determining above-ground woody biomass and carbon stocks across the Amazon Basin. To test these hypotheses, we collected and analysed wood cores from 44 species occurring in both seasonally flooded (varzea) forests and adjacent unflooded (terra firme) forests along the Jurua River, western Brazilian Amazon. We used wood specific gravity (WSG) as a proxy of woody biomass and carbon. We compared WSG values within species, genera and families and found higher WSG in unflooded forest trees compared to their conspecifics in seasonally flooded varzea. Moreover, the effect of forest type on WSG was strongest at the family level and weakest at the species level. We further assessed the implications of WSG accuracy on above-ground woody tree biomass and found significant differences in AGWB as a function of WSG. Again, the differences became greater with lower taxonomic specificity, but also increased with lower site-specificity and greater tree dimensions. In conclusion, habitat specific WSG is important to quantify and map the spatial distribution of above-ground woody biomass and carbon in Amazonian forests.

Effectively managing farming to meet food demand is vital for the future of biodiversity. Increasing yields on existing farmland can allow the abandonment (sparing) of low-yielding areas that subsequently recover as secondary forest. A key question is whether such “secondary sparing” conserves biodiversity more effectively than retaining wildlife-friendly habitat within farmland (“land sharing”). Focusing on the Colombian Choco-Andes, a global hotspot of threatened biodiversity, and on cattle farming, we examined the outcomes of secondary sparing and land sharing via simulated scenarios that maintained constant landscape-wide production and equal within-pasture yield: (1) for species and functional diversity of dung beetles and birds; (2) for avian phylogenetic diversity; and (3) across different stages of secondary forest regeneration, relative to spared primary forests. Sparing older secondary forests (15–30 years recovery) promotes substantial species, functional, and phylogenetic (birds only) diversity benefits for birds and dung beetles compared to land sharing. Species of conservation concern had higher occupancy estimates under land-sparing compared to land-sharing scenarios. Spared secondary forests accumulated equivalent diversity to primary forests for dung beetles within 15 years and within 15–30 years for birds, highlighting the need for longer term protection to maximize the biodiversity gains of secondary sparing. Promoting the recovery and protection of large expanses of secondary forests under the land-sparing model provides a critical mechanism for protecting tropical biodiversity, with important implications for concurrently assisting in the delivery of global targets to restore 350 million hectares of forested landscapes. Edwards et al. use landscape simulations from bird and dung beetle field data to reveal functional, phylogenetic, and species diversity benefits of secondary forest sparing outweigh land sharing. Sparing tracks of secondary forest recovers similar biodiversity to primary sparing in 15–30 years, assisting global restoration and conservation goals.

Production forests are a dominant feature of most tropical forest landscapes and it is therefore important to understand the effects of timber extraction on the resident fauna. Here we investigate the effects of reduced-impact logging (RIL) on medium- to large-sized terrestrial mammals in two Jamari National Forest logging concessions, south-western Brazilian Amazonia. We used camera traps to survey the terrestrial mammal fauna. Bayesian multi-species occupancy models (MSOMs) were performed to assess the effect of logging intensity and density of logging roads on site-level species richness, occupancy and detection rates. Species richness was negatively affected by logging status and by increasing logging intensity, and positively affected by road density. Occupancy and detection rates of individual species were largely unrelated to model predictors, although responses across species tended to be consistent with that observed for species richness. Despite negative effects of logging on species richness, no individual species were lost at the landscape level, suggesting that concessions managed under RIL techniques may be a reasonable compromise between economic and conservation interests.

For arboreal primates, ground use may increase dispersal opportunities, tolerance to habitat change, access to ground-based resources, and resilience to human disturbances, and so has conservation implications. We collated published and unpublished data from 86 studies across 65 localities to assess titi monkey (Callicebinae) terrestriality. We examined whether the frequency of terrestrial activity correlated with study duration (a proxy for sampling effort), rainfall level (a proxy for food availability seasonality), and forest height (a proxy for vertical niche dimension). Terrestrial activity was recorded frequently for Callicebus and Plecturocebus spp., but rarely for Cheracebus spp. Terrestrial resting, anti-predator behavior, geophagy, and playing frequencies in Callicebus and Plecturocebus spp., but feeding and moving differed. Callicebus spp. often ate or searched for new leaves terrestrially. Plecturocebus spp. descended primarily to ingest terrestrial invertebrates and soil. Study duration correlated positively and rainfall level negatively with terrestrial activity. Though differences in sampling effort and methods limited comparisons and interpretation, overall, titi monkeys commonly engaged in a variety of terrestrial activities. Terrestrial behavior in Callicebus and Plecturocebus capacities may bolster resistance to habitat fragmentation. However, it is uncertain if the low frequency of terrestriality recorded for Cheracebus spp. is a genus-specific trait associated with a more basal phylogenetic position, or because studies of this genus occurred in pristine habitats. Observations of terrestrial behavior increased with increasing sampling effort and decreasing food availability. Overall, we found a high frequency of terrestrial behavior in titi monkeys, unlike that observed in other pitheciids.

The annual flooding in the Amazon basin transforms the understory of floodplain forests into an aquatic environment. However, a great number of non-aquatic bird species occupy the understory and midstory of these forests. In general, these birds are thought to be sedentary and territorial, but the way they adapt to this dramatic seasonal transformation has never been described in detail. In this study, we describe avifaunal strategies to cope with seasonal flooding in the lower Purus region, central Amazonia, Brazil. We conducted focal observations of five insectivorous species occupying the lowest forest strata in two types of floodplain forest (black- and whitewater) during the low- and high-water seasons. For each observation, the height of the bird above the substrate (ground or water), its vertical position in the forest, and vegetation density around the bird were noted. All species remained present in the floodplain forests during the two seasons and were not recorded in adjacent unflooded (terra firme) forest. In general, birds migrated vertically to higher forest strata and most species (three of the five) occupied similar vegetation densities independent of water level. Despite the tendency of all species to rise in relative vertical position at high water, there was a reduction in height above substrate for four of the five species, suggesting that their position relative to water was not an important microhabitat element for them. Responses were similar in the two floodplain forest types. It is likely that the decrease in available space during the flood, combined with similar vertical displacement in arthropods, leads to increased prey density for understory insectivorous birds and permits year-round territoriality without major habitat shifts.

Meeting rising demand for oil palm whilst minimizing the loss of tropical biodiversity and associated ecosystem functions is a core conservation challenge. One potential solution is focusing the expansion of high-yielding crops on presently low-yielding farmlands alongside protecting nearby tropical forests that can enhance provision of ecosystem functions. A key question is how this solution would impact invertebrate functional diversity. We focus on oil palm in the Colombian Llanos, where plantations are replacing improved cattle pastures and forest fragments, and on dung beetles, which play key functional roles in nutrient cycling and secondary seed dispersal. We show that functional richness and functional diversity of dung beetles is greater in oil palm than in cattle pasture, and that functional metrics did not differ between oil palm and remnant forest. The abundance-size class profile of dung beetles in oil palm was more similar to forest than to pasture, which had lower abundances of the smallest and largest dung beetles. The abundance of tunneling and rolling dung beetles did not differ between oil palm and forest, while higher forest cover increased the abundance of diurnal and generalist-feeding beetles in oil palm landscapes. This suggests that prioritizing agricultural development on low-yielding cattle pasture will have positive effects on functional diversity and highlights the need for forest protection to maintain ecosystem functioning within agricultural landscapes.

Most terrestrial species on Earth are ectothermic and track temperature at small spatial scales, from sun flecks to cool shaded spots. Current assessments of thermal heterogeneity in complex environments are predominately characterized by ambient temperature. This omission of solar radiation may lead to inaccurate conclusions regarding thermoregulation and distribution of species. We use thermal cameras to gather data on temperature heterogeneity in structurally complex rain forest environments. Using thermographic photographs, we capture the multidimensionality of climate created by vegetation by collecting over 76,000 temperature samples within approximately 1 m2 quadrats. The method was tested against three standard methods that record air temperature to determine possible omissions in capturing thermal heterogeneity in four geographic locations—Colombia, Borneo, Madagascar, and Australia. Across all locations, there was greater thermal heterogeneity in surface temperature than captured from ambient temperature technologies. Spatial variability in surface temperature on 1 d was greater than temporal variability of ambient temperature across the entire month, with extreme deviation from ambient temperatures. Importantly, when compared to the lower bounds for optimal performance for five tropical Anolis species, this technology captured thermal regimes that support the thermoregulatory needs of these species, whereas ambient air temperature methods suggested that these species would be in thermal debt. Sampling surface temperature at high resolutions across space in combination with intensive sampling of ambient temperature and informed spatial modeling should improve our understanding of the distribution of ectothermic species living within thermally heterogeneous environments.

Rural populations in the tropics frequently rely on game vertebrates and fish to supply their daily protein requirements. However, few studies have quantified the environmental and socioeconomic drivers of hunting and fishing effort and the potential compensatory relationship between these extractive activities. Here, we assessed game and fish extraction by 222 semi-subsistence households from 28 villages along a major white-water tributary of Brazilian Amazonia. During the 44 months study, a total of 32,114 kg of game and 261,752 kg of fish were harvested, amounting to an average extraction rate of 30.5 ± 109.9 g person− 1 day− 1 and 1519.4 ± 1037.6 g person− 1 day− 1 for game and fish, respectively. While 97.93 ± 0.03% of all fishing trips resulted in fish catches, only 77.12 ± 27.02% of the hunting forays successfully obtained at least one forest vertebrate. The flood pulse had a strong effect on both fishing and hunting activities. However, the seasonally rising floodwaters had a negative effect on fish yield and catch per unit effort (CPUE), but had a positive effect on game yields. Game yield was also an important variable explaining fish yield, indicating a strong compensatory interaction between these two forms of protein acquisition. Our results highlight the importance of considering different modes of animal protein harvesting in conservation planning and management of both forest vertebrates and aquatic organisms.

Anuran frogs are often considered generalist predators in rice fields and feed upon a variety of invertebrates. They may thus provide an invaluable ecosystem service, as many species belonging to the orders coleoptera, lepidoptera, orthoptera, homoptera and hemiptera are regarded as notorious rice pests, inflicting significant losses on rice production. In this study, we surveyed frogs in rice paddies of lowland Nepal during the dry and rainy seasons, approximately 3–4 weeks after rice had been planted. We used stomach flushing to study the dietary habits of anuran species encountered, and provide empirical evidence of the ecological service provided by frogs in this agricultural landscape. We found that frogs included a high proportion of crop pests in their diet, but consumption of pests varied between the rainy and dry seasons, frog species and even individual frogs. The ecosystem services provided by frogs are not limited to crop pest control, but, as our observations revealed, include consumption of a large number insects known to be important vectors of zoonotic diseases. We encourage both farmers and conservation planners to consider frogs as important biological pest controllers during the development of pest management and strategies in agricultural landscapes.

Tropical land-use change is a key driver of global declines in biodiversity and a major source of anthropogenic carbon emissions, yet there is a substantial shortfall in the funding available to tackle these issues. We urgently need mechanisms that can simultaneously tackle both biodiversity and carbon losses, with carbon-based payments for ecosystem services (e.g. REDD+) of particular interest. A critical question is whether such payments offer strong carbon–biodiversity co-benefits via the regrowth of forests on abandoned farmlands (carbon enhancements) for amphibians, which are the most threatened vertebrate group and reach the greatest richness of threatened and small-ranged species in the montane tropics (>1000 m a.s.l.). Here, we study changes in amphibian communities across a typical Andean habitat transition from cattle pasture through secondary forests (8–35 years) to primary forest. As secondary forests mature, they recovered the abundance, species richness, species composition and Red-listed (near threatened and threatened) species typically found in primary forest. By contrast, cattle pasture contained much lower richness of Red-listed species and a different species composition compared to forest. We then reveal positive relationships between carbon stocks and amphibian species richness and abundance, Red-listed species richness and abundance and the similarity of communities to primary forests, confirming significant carbon–biodiversity co-benefits. Our results underscore the high conservation value of secondary forests and the strong potential for carbon and biodiversity recovery. Using carbon-based funding initiatives to support the regrowth of forests on marginal agricultural land is therefore likely to conserve threatened biodiversity in the Tropical Andes.

Selective logging is a major form of land use in tropical rainforests, with more than half of the world’s tropical forest already explored. In the Brazilian Amazon, most logging operations are illegal and highly damaging to forests. However, the effects of illegal logging on wildlife are poorly studied. Here we investigate the effects of illegal logging on the assemblage of medium- to large-bodied terrestrial vertebrates at the Gurupi Biological Reserve, a protected area in extreme eastern Amazonia that has been subjected to three decades of illegal logging. We used camera traps to survey the terrestrial vertebrate assemblage and visual interpretation of Landsat time series data (1984–2016) to assess the history of illegal logging (number of logging bouts and recovery time) for each camera trap site. Hierarchical Modelling of Species Communities (HMSC) indicates that logging had a minor effect on both the assemblage composition and individual species abundance. At the local level, the study demonstrates that the reserve effectively safeguards a significant portion of the regional biodiversity even though it suffered degradation by illegal logging. At a wider scale, the results suggest that illegally logged forests can retain much of their conservation value, if they are protected from further anthropogenic impacts such as hunting, fragmentation and fires. However, our study represents a best-case scenario, unlikely to be met in most other illegally logged areas in the tropics, where logging is usually followed by secondary effects that amplify its impacts.

Analysis of movement patterns at fine temporal scales may suggest how animals interact with their surrounding habitat. This is particularly useful in determining not only where animals may spend their time, but when and how likely they may be to interact with or utilize specific habitat resources. While previous studies demonstrate various methods seeking to address this concern, most apply for a single individual or a single point pair in a trajectory. However, for practical conservation concerns, information on animal-habitat interactions should be considered at the group level. This paper applies two approaches from movement analysis, the probabilistic voxel-based space-time prism and the comprehensive probability surface, to construct utilization distributions corresponding to specific intervals in time. Utilization distributions are processed towards summary quantification of diel habitat interaction probabilities for multiple individuals. We evaluate this approach using primary tracking data collected from Black skimmers (Rynchops niger cinerascens) traversing Manu National Park, Peru and surrounding areas. Habitat interaction graphs were constructed summarizing animal interaction by habitat type and time of day for all individuals tracked. This information was used to corroborate known black skimmer habitat use behaviors. Habitat interaction results were generally consistent with skimmers’ known foraging patterns for dawn, dusk and overnight hours. Results also raised a noteworthy use pattern for urban areas at dusk and early evening otherwise unobserved. Findings suggest applicability of this approach for cryptic species where direct observation is difficult, but trajectory data are available. Utility of this method for the practical work of conservationists and related researchers is discussed.

Natural regeneration of abandoned farmland provides an important opportunity to contribute to global reforestation targets, including the Bonn Challenge. Of particular importance are the montane tropics, where a long history of farming, frequently on marginal soils, has rendered many ecosystems highly degraded and hotspots of extinction risk. Ants play crucial roles in ecosystem functioning, and a key question is how time since abandonment and elevation (and inherent temperature gradients therein) affect patterns of ant recovery within secondary forest systems. Focusing on the Colombian Andes across a 1300 m altitudinal gradient and secondary forest (2–30 years) recovering on abandoned cattle pastures, we find that over time ant community composition and species richness recovered towards that of primary forest. However, these relationships are strongly dependent on elevation with the more open and warmer pasturelands supporting more ants than either primary or secondary forest at a particular elevation. The loss of species richness and change in species composition with elevation is less severe in pasture than forests, suggesting that conditions within pasture and its remaining scattered trees, hedgerows and forest fragments, are more favourable for some species, which are likely in or near thermal debt. Promoting and protecting natural regenerating forests over the long term in the montane tropics will likely offer significant potential for returning ant communities towards primary forest levels. Electronic supplementary material The online version of this article (10.1007/s00442-019-04497-8) contains supplementary material, which is available to authorized users.

Flying foxes play keystone ecological roles in plant reproduction. Yet, they face numerous threats, including persecution for eating commercial fruits. This human-wildlife conflict has recently escalated to culling campaigns of a threatened flying fox on Mauritius. Finding non-lethal solutions to this human-wildlife conflict on the island is therefore extremely important. We hypothesized that invasive alien plants may reduce native fruit availability through competition and that weeding alien plants could improve the native foraging habitat quality of flying foxes – in turn, reducing their consumption of commercially important fruits. We compared native fruit production and foraging intensity of the Mauritian flying fox (Pteropus niger) in forests weeded of alien plants a decade previously and adjacent non-weeded forests. Fruits and ejecta were collected weekly during five months under 144 randomly chosen native trees of two canopy species whose fruits are eaten by flying foxes. Intraspecific variations in tree and fruit traits were used to examine flying fox foraging preference. Native fruit production was significantly higher in weeded forests for both tree species, and this was matched by higher flying fox foraging intensity. Flying foxes preferred large trees and fed predominantly on large and ripe fruits. The predominant consumption of ripe fruits emphasizes the importance of flying foxes as seed dispersers. Our results indicate that alien plant invasion substantially reduces native fruit production and that weeded forests provide a much better habitat for flying foxes. Our findings lend support to invasive alien plant control as a management strategy in mitigating such human-wildlife conflicts.