Mammal Communities Research Articles

Selective impacts of subsistence hunting on mammal communities in Manu National Park, Peru

AbstractResearch on impacts of subsistence hunting on habitat use and species communities of forest wildlife is limited. Subsistence hunting of mammals in one of the world's most biodiverse region, Manu National Park, Peru, is considered sustainable, but this is based on sparse evidence. We analyzed change in species relative abundance and functional composition of mammal communities, including non‐hunted species along a hunting pressure gradient. We used camera trap data and tested for confounding effects of environmental and disturbance gradients (distances to rivers, lakes, settlements, and trails; NDVI at survey point). We found that sites with no hunting or at further distances from settlements harbor relatively more species with a larger body mass, long generation lengths, and small litters (primarily carnivores: 36% at non‐hunted site vs. 13%–29% at hunted sites), indicating selective impacts of hunting pressure on mammal communities. However, all carnivore species still occurred at all sites. Species with a smaller body mass, short generation lengths, and large litters were more prevalent at the hunted sites (mostly rodents: 23%–31% at hunted sites vs. 20% at non‐hunted site). Surprisingly, large herbivores appeared unaffected by hunting despite being one of the most hunted mammals in Manu (25% at non‐hunted site vs. 23%–27% at hunted sites). Our findings suggest that current hunting pressure is largely sustainable with only local depletion of a few sensitive species. Habitat is more important for some species than hunting pressure (e.g., distance to lake), further emphasizing the importance of local forest management.

Recovering connectivity through restoration corridors in a fragmented landscape in the magdalena river’s valley in Colombia

Forest fragmentation is one of the main drivers of global biodiversity loss leading to the isolation of wildlife populations. This study focuses on understanding the role of restoration corridors as a strategy promoting resilience and viability of mammal and bird populations in a fragmented landscape in Colombia. We installed 98 camera-trap stations − 8497 camera-trap days - in four different land cover categories: (1) forest fragments, (2) natural corridors, (3) stablished corridors and (4) pastures. We evaluated if restoration corridors do promote connectivity for large vertebrates and recover species richness and functional diversity lost in anthropogenically transformed pastures. We used indices of taxonomic and functional diversity and a non-metric multidimensional scaling to evaluate the influence of land cover over mammal and bird communities. Both, species richness and functional diversity have higher values in forests, followed by natural corridors and corridors and lower values in open pastures. Differences in species composition were greater between forests and pastures, and species composition of restoration corridors begins to resemble that of riparian forests and forest fragments. Our results provide initial evidence on the role of restoration corridors as an efficient strategy aimed to recover biodiversity and functional diversity in pervasively fragmented landscapes.

Mammal responses to human recreation depend on landscape context.

Rapid growth in outdoor recreation may have important and varied effects on terrestrial mammal communities. Few studies have investigated factors influencing variation in observed responses of multiple mammal species to recreation. We used data from 155 camera traps, in western Alberta (Canada), and a hierarchical Bayesian community modelling framework to document 15 mammal species responses to recreation, test for differential responses between predators and prey, and evaluate the influence of local context. Factors characterizing context were trail designation (i.e., use by motorized vs non-motorized), management type, forest cover, landscape disturbance, and season. We used three measures to characterize variation in recreation pressure: distance to trail, trail density, and an index of recreation intensity derived from the platform Strava. We found limited evidence for strong or consistent effects of recreation on mammal space use. However, mammal space use was better explained by an interaction between recreation and the influencing factors than by either on their own. The strongest interaction was between trail density and management type; mammals were more likely to avoid sites near a higher density of trails in areas with more restrictive management. We found that responses to recreation varied with the trail designation, although there were not clear or consistent differences between responses to trails designated for motorized vs. non-motorized use. Overall, we found that responses were species- and context-dependent. Limiting the density of trails may be important for reducing negative impacts to mammals within conservation areas. We show that using multiple measures of recreation yields more insight into the varied effects of human disturbances on wildlife. We recommend investigating how different characteristics of recreation (noise, speed, and visibility) influence animal behaviors. Multispecies monitoring and modelling across multiple landscapes that vary in recreation pressure can lead to an adaptive management approach to ensuring outdoor recreation coexistence with wildlife.

Crop-land simplification impacts differently on small mammal communities: evidence from diversity/dominance plots using Barn Owl (Tyto alba) pellets

Crop-land simplification impacts differently on small mammal communities: evidence from diversity/dominance plots using Barn Owl (Tyto alba) pellets

The nature of vegetation cover and small mammal community structure (on the example of Nizhny Novgorod)

The spatial distribution of Apodemus species (yellow-necked, field, and small forest mice) was studied on the example of the protected area «Oak forest of National Research Lobachevsky State University of Nizhny Novgorod Botanical Garden». Twelve plant associations with non-moral character and representing derivatives of the indigenous type of vegetation were studied. Environmental conditions assessed by the Ellenberg phytoindication method affect the distribution of small mammals in space indirectly. The nature of vegetation cover is more significant. When projective cover increases, the abundance of both small woodland and field mice increases. The strategy of Apodemus agrarius appears to be similar to that of Apodemus uralensis, a species that shows stenobiontic traits in the studied PA. At the same time, insignificant anthropogenic load, a marker of which is the presence of Urtica dioica ruderal species, leads to an increase in the mosaic of vegetation cover, which has a positive effect on the abundance of these small mammal species. A moderate increase in the Berger-Parker dominance index for vegetation cover is positively associated with the confinement of micromammals. In addition, in the conditions of the recreational zone of the upland part of N. Novgorod, Apodemus agrarius prefers areas of old-growth broadleaved forest, not showing the features of anthropophily.

Effects of Seasonality on the Large and Medium-Sized Mammal Community in Mountain Dry Forests

Seasonality drives natural processes, impacting environmental factors like temperature and resource availability, leading to shifts in wildlife communities. The Andean dry forests exhibit a marked seasonality, with a dry and cold season (May–September) and a warm, wet season (October–April). In a year-long remote camera survey in Southern Bolivia, we identified 29 medium to large mammal species, 18 outside their known distribution ranges. While overall species richness remained stable, photographic records varied between seasons. Capture rates, reflecting species richness and abundance, were more influenced by season and habitat. Wet season rates were lower, but higher in all other habitats compared to the mountain bush and grasslands. Rates increased with altitude and distance to hiking trails, but decreased with increasing distance from main roads. Medium to large mammals were more active during the dry season, indicating adjustments in response to seasonal changes. Our results suggest a cumulative impact of various factors beyond mere seasonality, and call for adjustments in global species distributions. Moreover, emphasize the need for biodiversity monitoring in dry forest habitats, particularly regarding responses to environmental shifts and human-induced alterations.

Assessing the role of habitat, climate, and anthropization gradients on terrestrial mammal diversity in the western Mediterranean basin.

Mammal species globally exhibit distribution patterns conditioned by environmental conditions and human impact. The Mediterranean basin provides an ideal system to study these effects due to its diverse climate, and habitat conditions. In this work, we aim to assess the impact of landscape heterogeneity and anthropization degree on terrestrial mammal diversity in this region. Accordingly, we deployed over 300 camera traps across 28 sites for 3 months. Detected mammal species (weighing more than 1kg) were classified as domestic carnivores, domestic ungulates, wild carnivores, wild ungulates, lagomorphs, and large rodents. Alpha and beta diversity were calculated for each group and all wild mammals. Simple linear regressions and multimodal analysis were conducted between mammal diversities and climate, environmental conditions, landscape heterogeneity, and anthropization degree variables. Redundancy analyses were performed to identify variables and species determining the mammalian community composition. Indexes measuring landscape heterogeneity, anthropization degree, and its 30-year change did not correlate with mammal diversity. However, the difference in elevation within sites and domestic carnivore abundance showed a significant positive correlation with some of the diversity indexes. Nonetheless, rainfall and mean elevation factors generally showed the highest correlation with mammal diversity. Instead, a few influential species, including generalists and open-habitat specialists, highlighted the importance of conserving open areas, as well as the importance of the Pyrenees region as a key habitat for certain species. Therefore, climatic variables emerged as the key determinants of mammal diversity, highlighting climate change as a potential threat to mammal diversity in this area.

Identifying remnant biodiversity hotspots in Southern Asia reveals disequilibrium in mammalian communities

Identification of highly biodiverse areas has become a crucial step in protecting species richness, especially considering the rapid collapse of biodiversity and the limited funds available to avert, far less to reverse, these trends. Therefore, we aimed to identify the most important areas for the conservation of specified mammalian groups in Southern Asia, a region rich in biodiversity hotspots threatened by increasing rates of habitat loss and other anthropogenic activities. To achieve this, we modelled the occupancy of ungulates and of small, medium and large carnivorans at 20 study sites across the region and identified hotspots of species richness. We analysed the variation of estimated space use between different species groups and ranked areas according to their predicted importance for mammalian species conservation. Our results reveal a significant positive correlation in the spatial utilization patterns of competitive carnivores, yet no correlation among carnivores and their prey species, suggesting that anthropogenic impacts in the region are constraining species to coexist in only the few remaining suitable areas, superseding interactions between species guilds. Although the rank of site importance varied amongst species groups, we were able to identify a consensus on sites that are crucial for the conservation of all groups considered. Most of these top-ranking sites were located in the peninsular region of Thailand. We argue that, of the areas assessed, these sites represent the most important refuges for species conservation in the region, and their protection is critical for the maintenance of the biodiversity in Southern Asia.

Establishing Silphids in the invertebrate DNA toolbox: a proof of concept.

Environmental DNA (eDNA) analyses are an increasingly popular tool for assessing biodiversity. eDNA sampling that uses invertebrates, or invertebrate DNA (iDNA), has become a more common method in mammal biodiversity studies where biodiversity is assessed via diet analysis of different coprophagous or hematophagous invertebrates. The carrion feeding family of beetles (Silphidae: Coleoptera, Latreille (1807)), have not yet been established as a viable iDNA source in primary scientific literature, yet could be useful indicators for tracking biodiversity in forested ecosystems. Silphids find carcasses of varying size for both food and reproduction, with some species having host preference for small mammals; therefore, iDNA Silphid studies could potentially target small mammal communities. To establish the first valid use of iDNA methods to detect Silphid diets, we conducted a study with the objective of testing the validity of iDNA methods applied to Silphids using both Sanger sequencing and high throughput Illumina sequencing. Beetles were collected using inexpensive pitfall traps in Alberta, Michigan in 2019 and 2022. We successfully sequenced diet DNA and environmental DNA from externally swabbed Silphid samples and diet DNA from gut dissections, confirming their potential as an iDNA tool in mammalian studies. Our results demonstrate the usefulness of Silphids for iDNA research where we detected species from the genera Anaxyrus, Blarina, Procyon, Condylura, Peromyscus, Canis, and Bos. Our results highlight the potential for Silphid iDNA to be used in future wildlife surveys.

Quantifying heterogeneity of hominin environments in and out of Africa using herbivore dental traits

Our own species, Homo sapiens, has been able to invade near-all global ecosystems through a unique form of ecological plasticity. To understand how Homo sapiens have been able to disperse to such a wide range of environments, we need to understand the origins of the characteristic which enabled this, plasticity. Growing evidence indicates that Homo species were already able to occupy a diverse set of environments in the Early Pleistocene, suggesting that the origins of human ecological plasticity have deeper roots than previously anticipated. We analysed the distribution of two dental traits, mean ordinated hypsodonty of large herbivores and proboscidean mesowear, across the mammalian communities at Early Pleistocene hominin sites, to infer the vegetation and climate contexts of these locations. The global distribution of community-level dental traits suggests that, while open grassy vegetation made up a large proportion of the sites, mixed and wooded vegetation was also represented. From our analysis we conclude that Early Pleistocene Homo species were able to exploit habitats with different vegetation types and occupied a range of different environments. In addition to this we found that the distribution of dental traits of mammalian communities in the Eurasian sample was notably different from that of the African sample, suggesting that Homo's dispersal into Eurasia resulted in a niche expansion. Together these findings suggest that Homo in the Early Pleistocene was ecologically plastic and occupied a wide environmental niche space.

Species Composition of a Small Mammal Community and Prevalence of Echinococcus spp. in the Alpine Pastoral Area of the Eastern Tibetan Plateau.

We aimed to investigate the species composition of a small mammal community and the prevalence of Echinococcus spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014-2019. Detection of Echinococcus DNA in tissue samples from small mammal specimens revealed that Ochotona curzoniae (pika, total prevalence: 6.02%, 26/432), Neodon fuscus (5.91%, 38/643), N. leucurus (2.50%, 3/120), and Alexandromys limnophilus (21.74%, 10/46) were infected by both E. multilocularis and E. shiquicus; Cricetulus longicaudatus (16.67%, 1/6) was infected by E. shiquicus; and no infection was detected in N. irene (0/15). Neodon fuscus and O. curzoniae were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three Neodon species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.

Comparison of soil eDNA to camera traps for assessing mammal and bird community composition and site use.

Species detections often vary depending on the survey methods employed. Some species may go undetected when using only one approach in community-level inventory and monitoring programs, which has management and conservation implications. We conducted a comparative study of terrestrial mammal and bird detections in the spring and summer of 2021 by placing camera traps at 30 locations across a large military installation in northern Michigan, USA and testing replicate soil samples from these sites for environmental DNA (eDNA) using an established vertebrate metabarcoding assay. We detected a total of 48 taxa from both survey methods: 26 mammalian taxa (excluding humans, 24 to species and two to genus) and 22 avian taxa (21 to species and one to genus). We detected a relatively even distribution of mammalian taxa on cameras (17) and via eDNA analysis (15), with seven taxa detected from both methods. Most medium-to-large carnivores were detected only on cameras, whereas semi-fossorial small mammals were detected only via eDNA analysis. We detected higher bird diversity with camera traps (18 taxa) compared to eDNA analysis (eight taxa; four taxa were detected with both methods), but cameras alone were most effective at detecting smaller birds that frequently occupy arboreal environments. We also used Bayesian spatial occupancy models for two widely distributed game species (white-tailed deer, Odocoileus virginianus, and ruffed grouse, Bonasa umbellus) that were moderately detected with both survey methods and found species-specific site use (occupancy) estimates were similar between cameras and eDNA analysis. Concordant with similar studies, our findings suggest that a combination of camera trap and eDNA surveys could be most useful for assessing the composition of terrestrial mammal communities. Camera traps may be most efficient for assessing bird diversity but can be complemented with eDNA analysis, particularly for species that spend considerable time on the ground.

Impact of environmental factors on small mammals and their fleas

Abstract Small mammals in the Horšianska dolina-Valley were researched first in 1984–86 and later in 2016–19. This paper seeks to identify and assess the species composition and dynamics of fleas (Siphonaptera) found in the valley on small mammals of Rodentia and Eulipotyphla and to compare findings from these two periods separated by thirty years. The results indicated deviations in small mammal and flea community similarity as well as in the small mammal indicator species for each habitat and flea indicator species for the small mammal species. A total 12 different species of small mammals were captured, and 12 flea species were collected. Eight flea species were detected in 1984–86 and ten species were found in 2016–19. In both periods A. penicilliger, C. assimilis, C. solutus, D. dasycnema, N. fasciatus were captured. The differences were that in the earlier period, the species uncovered were C. congener, P. bidentata, and P. soricis, while in the later period they were C. agyrtes, C. bisoctodentatus, M. turbidus, and R. integella. In the relationship between fleas and small mammals, C. solutus was the specific species for Apodemus flavicollis, while A. penicilliger and C. agyrtes were for Clethrionomys glareolus, and C. assimilis was for Microtus arvalis.

Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here, we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalayas to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87%) and human presence (83%) compared to those located in habitats with lower human modification (64%) and human presence (65%) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance, corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences.

Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species.

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here, we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalayas to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87%) and human presence (83%) compared to those located in habitats with lower human modification (64%) and human presence (65%) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance, corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences.

Unique functional diversity during early Cenozoic mammal radiation of North America.

Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects have probably altered mammalian community structure, raising the question of how past perturbations have done so. We used functional diversity (FD) to describe how the structure of North American mammal palaeocommunities changed over the past 66 Ma, an interval spanning the radiation following the K/Pg and several subsequent environmental disruptions including the Palaeocene-Eocene Thermal Maximum (PETM), the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examined three aspects of ecological function: functional evenness, functional richness and functional divergence. We found that shifts in FD were associated with major ecological and environmental transitions. All three measures of FD increased immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of FD were decoupled and responded differently to environmental changes over the last ~56 Myr.

Activity responses of a mammal community to a 17-year cicada emergence event

Abstract During a limited period in the summer of 2021, 17-year cicada species (Magicicada cassini, M. septendecula, M. septendecim) represented a large pulse of easily accessible food unique to forest ecosystems in the eastern United States. Using trail cameras and acoustic recorders, we tested whether the activity levels of 8 mammal species in northwestern Indiana shifted in response to spatial and temporal variation in cicada densities from 18 May to 20 June 2021. Cicada densities varied temporally and spatially across all study sites. Most mammal species with sufficient data showed no response to cicada emergence, including 2 tree squirrel species, Peromyscus mice, Eastern Chipmunks (Tamias striatus), and 2 species of bats. Raccoons (Procyon lotor), likely cicada predators, showed a quadratic or more complex activity response to cicada abundance, indicating a potential saturation point at densities near 1 cicada per m2. Surprisingly, White-tailed Deer (Odocoileus virginianus) activity decreased to almost 0 at the same cicada densities when we expected no change in activity. While size or accessibility may exclude cicadas as prey for small and volant mammals, our results suggest predation and satiation by Raccoons. In contrast, deer may be avoiding areas of cicada abundance due to other stimuli, such as high noise output, which may decrease their ability to detect predators.

Dynamics of species diversity of the small mammal community in slope larch forests of Northern Coast of the Sea of Okhotsk

Dynamics of species diversity of the small mammal community in slope larch forests of Northern Coast of the Sea of Okhotsk

Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana)

Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.

Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes.

Unravelling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. Individual physiology and metabolism are often studied to understand the response of individual animals to environmental change. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behaviour in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.