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Figure 4 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems
Figure 4. Occlusal view of the upper molars of the Sigmodontine rodents from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = Akodon azarae, UFSC-CF 43-2-1, left M1-M3. (B) = Akodon sp., UFSC-CF 32-4-1, left M1-M3. (C) = Bibimys sp., UFSC-CF 32-5-1, left M1-M3. (D) = Calomys sp., UFSC-CF 32-6-1, left M1-M3. (E) = Juliomys sp., UFSC-CF 32-7-1, left M1-M3. (F) = Holochilus sp., UFSC-CF 43-4-1, left M1-M3. (G) = Oligoryzomys sp., UFSC-CF 32-11-1, left M1-M3. (H) = Oxymycterus sp., UFSC-CF 32-12-1, left M1-M3. (I) = Sooretamys angouya, UFSC-CF 32-13-1, right M1-M3. (J) = Wilfredomys oenax, UFSC-CF 32-14-1, left M1-M3. Scale bars: C = 200 µm; A, B, D, E, F, G, H, I, J = 500 µm.
Figure 1 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems
Figure 1. Location of the sampling sites of the Tyto furcata pellets at the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Southern Brazil. BV1 = Boa Vista I; BV2 = Boa Vista II; BOQ = Boqueirão; CGA = Canta Galo; EV1 = Evaristo I; EV2 = Evaristo II; ANT = Picada das Antas; PF1 = Picada Feliz I; PF2 = Picada Feliz II; QV1 = Quevedos I; QV2 = Quevedos II; RES = Reserva. Map modified from MMA (1992).
Figure 3 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems
Figure 3. Chiroptera specimens from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = ventral view of the skull of Sturnira lilium, UFSC-CF 40-5-1. (B) = labial view of the right dentary of Tadarida brasiliensis, UFSC-CF 42-11-1. Scale bars: 1 mm.
Figure 2 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems
Figure 2. Didelphimorphia specimens from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = labial view of the left dentary of Cryptonanus guahybae, UFSC-CF 32-2-1. (B) = labial view of the right dentary of Gracilinanus microtarsus, UFSC-CF 42-10-1. Scale bars: 1 mm.
Figure 6 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems
Figure 6. Occlusal view of the upper and lower molars of the Muridae and Caviidae rodents fromTytofurcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil.(A) = Mus musculus, UFSC-CF 32-15-1, left M1-M3. (B) = Rattus rattus, UFSC-CF 35-9-1, right M1-M3. (C) = Cavia aperea, UFSC-CF 43-8-1, left P4-M3. (D) = M. musculus, UFSC-CF 32-15-2, right m1-m3. (E) = R. rattus, UFSC-CF 35-9-2, right m1-m3. (F) = C. aperea, UFSC-CF 43-8-2, right p4-m3. Scale bars A, D = 200 µm; B, C, E, F = 1 mm.
Data from: Does metabolism constrain bird and mammal ranges and predict shifts in response to climate change?
Mechanistic approaches for predicting the ranges of endotherms are needed to forecast their responses to environmental change. We test whether physiological constraints on maximum metabolic rate and the factor by which endotherms can elevate their metabolism (metabolic expansibility) influence cold range limits for mammal and bird species. We examine metabolic expansibility at the cold range boundary (MECRB) and whether species' traits can predict variability in MECRB and then use MECRB as an initial approach to project range shifts for 210 mammal and 61 bird species. We find evidence for metabolic constraints: the distributions of metabolic expansibility at the cold range boundary peak at similar values for birds (2.7) and mammals (3.2). The right skewed distributions suggest some species have adapted to elevate or evade metabolic constraints. Mammals exhibit greater skew than birds, consistent with their diverse thermoregulatory adaptations and behaviors. Mammal and bird species that are small and occupy low trophic levels exhibit high levels of MECRB. Mammals with high MECRB tend to hibernate or use torpor. Predicted metabolic rates at the cold range boundaries represent large energetic expenditures (>50% of maximum metabolic rates). We project species to shift their cold range boundaries poleward by an average of 3.9° latitude by 2070 if metabolic constraints remain constant. Our analysis suggests that metabolic constraints provide a viable mechanism for initial projections of the cold range boundaries for endotherms. However, errors and approximations in estimating metabolic constraints (e.g., acclimation responses) and evasion of these constraints (e.g., torpor/hibernation, microclimate selection) highlight the need for more detailed, taxa‐specific mechanistic models. Even coarse considerations of metabolism will likely lead to improved predictions over exclusively considering thermal tolerance for endotherms.
Data from: Immune stability predicts tuberculosis infection risk in a wild mammal
Immunity is one of the most variable phenotypic traits in animals; however, some individuals may show less fluctuation in immune traits, resulting in stable patterns of immune variation over time. It is currently unknown whether immune variation has consequences for infectious disease risk. In this study, we identified moderately stable immune traits in wild African buffalo and asked whether the stability of these traits affected bovine tuberculosis (TB) infection risk. We found that adaptive immune traits such as the level of IFN-γ released after white blood cell stimulation, the number of circulating lymphocytes, and the level of antibodies against bovine adenovirus-3 were moderately repeatable (i.e. stable) over time, whereas parameters related to innate immunity either had low repeatability (circulating eosinophil numbers) or were not repeatable (e.g. neutrophil numbers, plasma bacteria killing capacity). Intriguingly, individuals with more repeatable IFN-γ and lymphocyte levels were at a significantly higher risk of acquiring TB infection. In stark contrast, average IFN-γ and lymphocyte levels were poor predictors of TB risk, indicating that immune variability rather than absolute response level better captured variation in disease susceptibility. This work highlights the important and under-appreciated role of immune variability as a predictor of infection risk.
Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small-mammal density. We tested the effects of a diverse LMH community on small-mammal habitat use using 4 years of spatially explicit small-mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi-arid Kenyan savanna. Small-mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small-mammal density associated with LMH exclusion. Our results show that LMH indirectly affect small-mammal behaviour, and that these effects are influenced by climate and can arise via density-independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small-mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East Africa (as predicted in many recent climate-model simulations) may relax constraints on small-mammal distribution where LMH are rare or absent, whereas increased aridity and/or drought frequency may tighten them.
Strandings of marine mammals, sea turtles and seabirds along the central-south coast of São Paulo, Brazil, from 2015 to 2018.
<p><span><span><span>To assess the potential impacts on seabirds, turtles and marine mammals from oil and gas production from the oceanic Pre-Salt province at Brazil's Santos Basin, the Brazilian environmental agency (IBAMA) required PETROBRAS, the main oil company in the basin, to implement the "Programa de Monitoramento de Praias da Bacia de Santos" (Santos Basin Beach Monitoring Program - PMP-BS). Since 2015 PMP-BS has been operating along the states of Santa Catarina, Paraná, São Paulo and Rio de Janeiro, to collect biological data from live and dead stranded animals. This dataset comprises the first three years of monitoring (September 2015 to August 2018) along the central-south São Paulo state coastline, from 24°1'1.248" S 46°23'52.026" W to 24°26'49.147" S 47°4'49.505" W. During this period, 3790 animals of 47 species were recorded, 94.88% of which were dead and 5.12% alive when first observed. This dataset represents the first high-intensity monitoring effort in the area and is essential to establish baselines for future work that seek to better understand the impacts of human activities on marine ecosystems.</span></span></span></p>
Data from: Increasing synergistic effects of habitat destruction and hunting on mammals over three decades in the Gran Chaco
Habitat destruction and overexploitation are the main threats to biodiversity and where they co-occur, their combined impact is often larger than their individual one. Yet, detailed knowledge of the spatial footprints of these threats is lacking, including where they overlap and how they change over time. These knowledge gaps are real barriers for effective conservation planning. Here, we develop a novel approach to reconstruct the individual and combined footprints of both threats over time. We combine satellite-based land-cover change maps, habitat suitability models, and hunting pressure models to demonstrate our approach for the community of larger mammals (48 species >1 kg) across the 1.1 million km² Gran Chaco region, a global deforestation hotspot covering parts of Argentina, Bolivia, and Paraguay. This provides three key insights. First, we find that the footprints of habitat destruction and hunting pressure expanded considerably between 1985 and 2015, across ~40% of the entire Chaco – twice the area affected by deforestation. Second, both threats increasingly acted together within the ranges of larger mammals in the Chaco (17% increase on average, ±20% SD, cumulative increase of co-occurring threats across 465,000 km2), suggesting large synergistic effects. Conversely, core areas of high-quality habitats declined on average by 38%. Third, we identified remaining priority areas for conservation in the northern and central Chaco, many of which are outside the protected area network. We also identify hotspots of high threat impacts in central Paraguay and northern Argentina, providing a spatial template for threat-specific conservation action. Overall, our findings suggest increasing synergistic effects between habitat destruction and hunting pressure in the Chaco, a situation likely common in many tropical deforestation frontiers. Our work highlights how threats can be traced in space and time to understand their individual and combined impact, even in situations where data are sparse.
Data from: Environmental variation is a major predictor of global trait turnover in mammals
Aim: To evaluate how environment and evolutionary history interact to influence global patterns of mammal trait diversity (a combination of 14 morphological and life-history traits). Location: The global terrestrial environment. Taxon: Terrestrial mammals. Methods: We calculated patterns of spatial turnover for mammalian traits and phylogenetic lineages using the mean nearest taxon distance. We then used a variance partitioning approach to establish the relative contribution of trait conservatism, ecological adaptation and clade specific ecological preferences on global trait turnover. Results: We provide a global scale analysis of trait turnover across mammalian terrestrial assemblages, which demonstrates that phylogenetic turnover by itself does not predict trait turnover better than random expectations. Conversely, trait turnover is consistently more strongly associated with environmental variation than predicted by our null models. The influence of clade-specific ecological preferences, reflected by the shared component of phylogenetic turnover and environmental variation, was considerably higher than expectations. Although global patterns of trait turnover are dependent on the trait under consideration, there is a consistent association between trait turnover and environmental predictive variables, regardless of the trait considered. Main conclusions: Our results suggest that changes in phylogenetic composition are not always coupled with changes in trait composition on a global scale and that environmental conditions are strongly associated with patterns of trait composition across species assemblages, both within and across phylogenetic clades.
Disentangling drivers of small mammal diversity in a highly fragmented forest system
<p class="Standard">The Atlantic Forest is the second most diverse forest system in South America and only a fraction of its original distribution remains. In this study, we aim to use robust datasets of small mammals along the entire forest system to disentangle the main drivers for diversity along this gradient. More specifically we aim to disentangle if deforestation (recent), biogeographical variables, including 19 bioclimatic variables (historic), or historical trapping bias best describe patterns of taxonomic, functional, and phylogenetic diversities using small mammal assembles, from northeastern Brazil to eastern Paraguay. For that, we applied regression tree analyses to determine what environmental variables best describe each of the dimensions of diversity. Additionally, we implemented polynomial regression to test non-linear relationships between biodiversity metrics and patch size. We found that patterns of overall taxonomic, functional and phylogenetic diversities; rodent taxonomic diversity; and marsupial functional diversity were better explained by temperature variables. Meanwhile, marsupial taxonomic and phylogenetic diversities; and rodent functional and phylogenetic diversities were best explained by precipitation variables. Furthermore, patch area, trapping, and latitude were never the best descriptors for any of the diversity dimensions. Although all dimensions of biodiversity are correlated, they have unique information and should be considered individually to better understand biodiversity and inform conservation strategies. We found that fragmentation is impactful at a local scale and becomes less important at a biogeographical scale. Therefore, climatic variables drove biogeographical faunal patterns for all clades, probably reflecting important historical assembly process at large spatial scales.</p>
Data from: Maternal oxidative stress and reproduction: testing the constraint, cost and shielding hypotheses in a wild mammal
1. Oxidative stress has been proposed as a central causal mechanism underlying the life history trade-off between current and future reproduction and survival in wild animals. 2. Whereas mixed evidence suggests that maternal oxidative stress may act both as a constraint and a cost to reproduction, some studies have reported a lack of association between reproduction and maternal oxidative stress. 3. The oxidative shielding hypothesis offers an alternative explanation, suggesting that mothers may pre-emptively mitigate the oxidative costs of reproduction by increasing antioxidant defences prior to reproduction. 4. We tested the oxidative constraint, cost, and shielding hypotheses using a longitudinal field study of oxidative stress levels in a species that breeds using daily energy income, the Columbian ground squirrel (Urocitellus columbianus). 5. Elevated maternal oxidative damage prior to reproduction was associated with higher maternal investment in litter mass at birth, but not at weaning. 6. Breeding females increased their antioxidant capacity and decreased their oxidative damage from birth to lactation compared to non-breeding females measured at the same time periods. However, lower maternal oxidative stress during lactation was not associated with higher offspring survival or mass growth over this period. 7. Our results provide little evidence for maternal oxidative stress acting as a constraint on, or cost to, reproduction in Columbian ground squirrels, but partially support the idea that oxidative shielding occurred to buffer potential oxidative costs of reproduction.
Data from: Comparative phylogeography biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland
The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins. This phylogenetic pattern has not been commonly described in mammals, and we found no evidence for this pattern in the greater mouse deer. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reveals dynamic forested connections throughout Sundaland, and reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos.
Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals
The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.
Sex-independent senescence in a cooperatively breeding mammal
<p>1. Researchers studying mammals have frequently interpreted earlier or faster rates of ageing in males as resulting from polygyny and the associated higher costs of reproductive competition.</p> <p>2. Yet few studies conducted on wild populations have compared sex-specific senescence trajectories outside of polygynous species, making it difficult to make generalised inferences on the role of reproductive competition in driving senescence, particularly when other differences between males and females might also contribute to sex-specific changes in performance across lifespan.</p> <p>3. Here, we examine age-related variation in body mass, reproductive output and survival in dominant male and female meerkats, <i>Suricata suricatta</i>. Meerkats are socially monogamous cooperative breeders where a single dominant pair virtually monopolize reproduction in each group and subordinate group members help to rear offspring produced by breeders.</p> <p>4. In contrast to many polygynous societies, we find that neither the onset nor the rate of senescence in body mass or reproductive output show clear differences between males and females. Both sexes also display similar patterns of age-related survival across lifespan, but unlike most wild vertebrates, survival senescence (increases in annual mortality with rising age) was absent in dominants of both sexes, and as a result, the fitness costs of senescence were entirely attributable to declines in reproductive output from mid- to late-life.</p> <p>5. We suggest that the potential for intrasexual competition to increase rates of senescence in females – who are hormonally masculinised and frequently aggressive – is offset by their ability to maintain longer tenures of dominance than males, and that these processes combined lead to similar patterns of senescence in both sexes.</p> <p>6. Our results stress the need to consider the form and intensity of sexual competition as well as other sex-specific features of life history when investigating the operation of senescence in wild populations.</p>
Universal microbial network decomposes mammals despite varied climate, location, and seasonal influence
<p>Microbial breakdown of organic material is one of the most important processes on earth, yet enormous knowledge gaps exist about its controls. We demonstrate that a universal, inter-kingdom microbial network assembles in response to nutrient-rich, terrestrial mammalian decomposition, despite selection effects of location, climate and season. We created the first metagenome-assembled genome library from mammalian decomposition-associated soils and combined it with metabolomics to identify a microbial decomposer network that interacts by cross-feeding to efficiently metabolize labile decomposition products. The key fungal and bacterial decomposers appear unique to the breakdown of terrestrial cadavers, and are rare in relative abundance across non-decomposition environments. Blow flies are suggested as an important decomposer vector and the observed lockstep of microbial interactions underlies a robust microbial forensic tool for predicting the time since death. </p>
Dataset and code: Mammals in the city and animal personality
Open the record for dataset details and reuse information.
FSC-certified forest management benefits large mammals compared to non-FSC
<p><strong>Data for:</strong> <br>Zwerts, J.A., Sterck, E.H.M., Verweij, P.A. <em>et al.</em> FSC-certified forest management benefits large mammals compared to non-FSC. <em>Nature</em> <strong>628</strong>, 563–568 (2024). https://doi.org/10.1038/s41586-024-07257-8</p> <p><strong>Abstract</strong><br>Over a quarter of the world's tropical forests are exploited for timber. This has extensive impacts on biodiversity and ecosystems, primarily through the creation of roads which facilitates hunting for wildlife over extensive areas. Forest management certification schemes such as the Forest Stewardship Council (FSC) are expected to mitigate impacts on biodiversity but to date very little is known about the effectiveness of FSC certification due to research design challenges, predominantly due to limited sample sizes. Here we provide this evidence by using 1.3 million camera trap photos of 55 mammal species in 14 logging concessions in Western Equatorial Africa. We observed higher mammal encounter rates in FSC-certified than in non-FSC logging concessions. The effect was most pronounced for species weighing over 10 kg, and for species of high conservation priority such as the Critically Endangered forest elephant and western lowland gorilla. Across the whole mammal community, non-FSC concessions contained proportionally more rodents and other small species than FSC-certified concessions. Our findings provide convincing data that FSC-certified forest management is less damaging to the mammal community than non-FSC forest management. This study provides strong evidence that FSC-certified forest management, or equivalently stringent requirements and controlling mechanisms, should become the norm for timber extraction to avoid half-empty forests dominated by rodents and other small species. </p> <p><strong>Data collection</strong></p> <p>We set up arrays of camera traps from 2018 to 2021 in 14 logging concessions owned by 11 different companies (5 FSC and 6 non-FSC) in Gabon and the Republic of Congo. Seven FSC-certified concessions were each paired to the closest non-FSC concession that was similar in terms of terrain and forest type1. All concessions are situated in a matrix of connected forests. Within each pair of concessions, camera traps (Bushnell Trophy Cam HD for pairs 1 - 6 and Browning 2018 Spec Ops Advantage for pair 7) were deployed simultaneously to account for seasonal differences, for two to three months. There was one exception where Covid restrictions obliged the cameras to remain in place for longer. Camera trap grid locations within each pair of concessions were chosen based on similarity between potential drivers of mammal abundance, including distance to settlements, roads, rivers, protected areas, elevation and time since logging (2-10 years before our study), although some camera grids overlapped older logging blocks. Camera traps were set out in systematic, one-kilometre spaced grids with a random start point. Upon reaching the predetermined GPS locations, the first potential installation location was used where cameras had at least 4 metres of visibility. This ensured that each grid was representative of environmental heterogeneity: i.e. not specifically targeting nor ignoring trails or other landscape elements that could influence detection2. The one-kilometre inter-camera distance exceeds most species' home range sizes to avoid spatial autocorrelation. Neither were species expected to migrate within the sampling duration of the study. Between 28 to 36 cameras were deployed in each concession, totalling up to 474 camera traps, distributed over 474 km2. Cameras were installed at a height of 30 cm to enable observations of mammals of all sizes while ensuring that each camera had at least four metres visibility in front of it. Cameras were programmed to take bursts of three photos to maximize the chance of detection and to take a photo every 12 hours for correct calculation of active days in the event of a defect before the end of the deployment period. For each camera, we recorded whether there was an elephant path skidder trail, small wildlife trail, or none of the above within each camera's field of view. We also visually estimated forest visibility (0-10m / 11-20m / >20m), slope (0-5° / 5-20° / >20°), presence of fruiting trees within 30 m and presence of small water courses within 50 m. When approaching each predefined camera point, we counted cartridges, snares and hunting camps from 500 m before the camera up to its location. Various field teams were employed in different sites and hence there may be some influence interobserver bias of hunting observations between sites.</p> <p><strong>Photo processing and data analysis</strong></p> <p>Camera trap efforts yielded 1,278,853 photos, including 645,165 photos with animals. All photos were annotated in the program Wild.ID, version 1.0.1. We identified animals up to the species level if photo quality permitted and otherwise designated the species as 'indet'3. As reliable species identification of small mammals is difficult, they were grouped into squirrels, rats and mice and shrews. Rare observations of humans, birds, bats, reptiles and domestic dogs were excluded from the analyses.</p> <p>Observations of the same species that were at least 10 minutes apart were considered as separate detections. We assessed the influence of this threshold by calculating the number of detections for intervals of 10, 30, 60 and 1440 minutes, which all yielded similar numbers of observations. When multiple animals were observed, the number of individuals was determined by taking the highest number of individuals in a photo within the 10-minute threshold. Sampling effort was defined as the number of camera days minus down time due to malfunctioning cameras or obstruction of vision by vegetation. </p> <p>Mammal behaviour may be different in hunted concessions, as mammals may be shyer for non-natural objects like camera traps, which would in turn negatively affect their probability of detection. If this dynamic indeed existed, this shyness was assumed to fade over time with habituation to the materials, resulting in an increase of observations over time. We tested for an interaction between certification status and the number of observations over time using a linear model with a log transformed number of observations for the first 65 days of all deployments, as that was the shortest concession deployment period, ensuring that all concessions were equally represented, but did not find that FSC certification was related to a trend in observations over time. We recognize however that other factors may exist that may have influenced detection probability, such as movement rates, which may be affected by hunting.</p> <p>For each species for each concession, we calculated encounter rate, weighted by group size, as the number of observations divided by the sampling effort and we reported all findings using the metric "Observations / day". Encounter rate was calculated for all species combined, per weight class, per taxonomic group, per IUCN Red List category and within taxonomic groups for large versus small forest antelopes, carnivores, primates and pangolins. Body weight of each species was determined by taking the mean across sexes3. Taxonomic groups Hyracoidea and Tubulidentata were excluded from the taxonomic analysis due to low sample sizes. Shrews were included as rodents in the taxonomy analysis even though they are formally not, because they are difficult to distinguish from mice. We consider this acceptable given that shrews are functionally very similar to rodents in the light of this study. Lastly, to study the impact of certification on total estimated faunal biomass, the encounter rate of each species was multiplied by its average weight divided by the sampling effort.</p> <p>To assess whether encounter rates varied between FSC and non-FSC concessions, we quantified the means of the paired concessions using linear mixed-effects models with concession pairs, concessions and cameras as random effects, whereby cameras were nested within concessions within concession pairs, in a multi-level random effect structure. We allowed the means of concession pairs to vary between weight class, taxonomic group and IUCN Red List category if supported by model selection. We tested whether potential drivers of mammal abundance were important using a model-selection approach based on minimization of Bayesian Information Criterion (BIC) values. We found that the inclusion of geographic covariates did not substantially improve the model for weight classes, taxonomic groups and IUCN categories. Only for all mammals pooled together , the inclusion of elevation and distance to rivers resulted in slightly improved models, but differences were negligible and did not support strong evidence for a significant influence of these covariates4. Quadratic geographic covariate terms and camera trap site covariates did not result in better models. Post hoc comparisons were multivariate t adjusted. We used two-sided Wilcoxon signed-rank tests for all other analyses. Statistical analyses were performed in R version 4.2.2.</p> <p> </p> <p><strong>References</strong></p> <ol> <li>Grantham, H. S. <em>et al.</em> Spatial priorities for conserving the most intact biodiverse forests within Central Africa. <em>Environmental Research Letters</em> <strong>15</strong>, 0940b5 (2020).</li> <li>Zwerts, J. A. <em>et al.</em> Methods for wildlife monitoring in tropical forests: Comparing human observations, camera traps, and passive acoustic sensors. <em>Conserv Sci Pract</em> <strong>3</strong>, e568 (2021).</li> <li>Kingdon, J. <em>The Kingdon field guide to African mammals</em>. (Bloomsbury Publishing, 2015).</li> <li>Anderson, D. R. <em>Model based inference in the life sciences: a primer on evidence</em>. vol. 31 (Springer, 2008).</li> </ol> <p> </p> <p> </p>
Maritime international trade and bioinvasions: a three-year long survey of small mammals in Autonomous Port of Cotonou, Benin
<ol> <li>International trade has been favoring the dissemination of a wide panel of invasive alien species. Upstream prevention through the monitoring of entry points is identified as an appropriate strategy to achieve control of bioinvasions and their consequences. Maritime transports have been responsible for the introduction worldwide of exotic rodents that are major pests for crops and food stocks as well as reservoirs of many zoonotic pathogens. In order to limit further dissemination, the International Health Regulation constrains decision makers and socio-economic stakeholders to manage ship-mediated import/export of rodents within seaports. Unfortunately, eco-evolutionary insights into rodent introduction events that could guide preventive actions in seaports are very scarce.</li> <li>In order to bridge this gap, we here describe the results of a three-year-long survey of small mammals conducted in the Port of Cotonou, Benin, that aims at assessing the spatio-temporal distribution, diversity and relative abundance of invasive and native rodents.</li> <li>960 small mammal individuals were captured in nine within-seaport sites. We found (i) a marked predominance of invasive species (84% of the individuals belonging to <em>Mus</em> <em>musculus</em>, <em>Rattus</em> <em>rattus</em>, <em>R. norvegicus</em>), (ii) with native species (i.e., <em>Mastomys natalensis</em> and the shrew <em>Crocidura olivieri</em>) essentially restricted to peripheral non-industrial areas, as well as (iii) a fine-scale spatial segregation stable over time between the invasive Norway rats and house mice on the one hand, and the black rats and shrews on the other hand.</li> <li>Furthermore, trapping before and after two successive rodent anticoagulant-based control campaigns indicates that they were poorly efficient and that subsequent rodent recolonization occurs 6–12 months following intervention.</li> <li> <em>Synthesis and applications</em>: Our results are discussed in terms of ecological processes at play (e.g., interspecific interactions) and operational actions that may be implemented to improve rodent control (e.g., assessment of proper eradication units, environmental modifications) and to limit re-infestation (e.g., rat-proofing of moors and buildings).</li> </ol>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.