Mammal Communities Research Articles

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.

Disturbance-mediated changes to boreal mammal spatial networks in industrializing landscapes.

Compound effects of anthropogenic disturbances on wildlife emerge through a complex network of direct responses and species interactions. Land-use changes driven by energy and forestry industries are known to disrupt predator-prey dynamics in boreal ecosystems, yet how these disturbance effects propagate across mammal communities remains uncertain. Using structural equation modeling, we tested disturbance-mediated pathways governing the spatial structure of multipredator multiprey boreal mammal networks across a landscape-scale disturbance gradient within Canada's Athabasca oil sands region. Linear disturbances had pervasive direct effects, increasing site use for all focal species, except black bears and threatened caribou, in at least one landscape. Conversely, block (polygonal) disturbance effects were negative but less common. Indirect disturbance effects were widespread and mediated by caribou avoidance of wolves, tracking of primary prey by subordinate predators, and intraguild dependencies among predators and large prey. Context-dependent responses to linear disturbances were most common among prey and within the landscape with intermediate disturbance. Our research suggests that industrial disturbances directly affect a suite of boreal mammals by altering forage availability and movement, leading to indirect effects across a range of interacting predators and prey, including the keystone snowshoe hare. The complexity of network-level direct and indirect disturbance effects reinforces calls for increased investment in addressing habitat degradation as the root cause of threatened species declines and broader ecosystem change.

Forest composition shapes seed‐rodent interactions in a gradient of broadleaves and conifers

Abstract Non‐native tree species and mixed forests have been increasingly employed in forestry practice as a safeguard against climate change and as a tool to foster biodiversity while providing economic benefits. Though these changes in forest composition may affect animal communities and ecosystem processes, they are seldom studied through a plant–animal interaction perspective. Here we investigated how forests with varying proportions of a native broadleaf (Fagus sylvatica) and two conifers (introduced Pseudotsuga menziesii and native Picea abies) affect rodents and their interactions with seeds. We surveyed terrestrial small mammal communities, estimated species' densities, assessed seed preference by rodents, collected data on environmental variables (understory density and tree basal area), measured Fagus sylvatica seed production and tracked 1200 seeds of Fagus sylvatica in 20 different forest plots in northern Germany in a mast and non‐mast year for Fagus sylvatica. Forest composition influenced the interactions between rodents and seeds. In forests with a lower proportion of broadleaves, beech seeds were harvested faster and in greater quantities, had diminished survival and were less often cached. These results are in agreement with three other findings: (a) seed fate responded to the proportion of broadleaves and conifers irrespective of conifer tree identity, (b) rodents preferred nutritious beech seeds over small conifer seeds, and (c) higher proportions of seeds were harvested during the period when beech seeds were scarce (non‐mast year). Synthesis and applications: This work provides evidence of how forest composition can affect plant–animal interactions without necessarily altering animal communities or population densities. Specifically, we found no differences between forests with native and non‐native conifer trees regarding small mammal community, seed‐rodent interactions or seed fate. Furthermore, rodents may provide a service in mixed forests by primarily preying upon seeds of Fagus sylvatica, a superior‐competitive species, and thus mitigate beech dominance over conifer species.

Small mammal assemblages in heterogeneous landscapes at the Southern tip of Italian peninsula evidence clear eco-biogeographic patterns

We investigated the frequencies of sympatric small mammal species in 12 habitat-types located in the extreme south of the Italian peninsula (Calabria) using trapping techniques. Ten species were detected with Apodemus sylvaticus, the most abundant species. The assemblages of small mammal species recorded in the 12 selected habitat types revealed clear ecological and biogeographical patterns in the extreme southern tip of the Italian peninsula. Ecologically, we observed a clear dissimilarity between a guild of species linked to thermo-xerophilous habitat types and a comparable guild of mesophilous species linked to forest and sciaphilous habitat types. The differences among communities inhabiting in different habitat types also emerged in rarefaction curves, DCA analysis and Whittaker plots. Thus, all these sets of analyses were consistent in their interpretation of the variation of small mammal community structure along the gradient (β-diversity) among habitat types. From a biogeographical point of view, this is an apparent expression of a clear North–South gradient pattern that was already observed at the species level with Calabria being characterized by a strong impoverishment in species’ richness and diversity (“peninsula effect”). However, this rationale has been based so far on indirect data of small mammals preyed upon and recorded in owl’s pellets: the fact that a similar pattern was obtained also using small mammals recorded by traps indicates that the results were robust and generalizable. Ecological factors at the local scale and biogeographical factors at the peninsular scale could explain the community patterns that we observed in the present study.

Disentangling the Effects of Climate and Land Uses on Small Mammals in Agroecosystems of NE Spain

We analyzed the two main drivers (climate and land uses) shaping the composition of small mammal communities at 16 localities situated in the confluence of the Mediterranean and Eurosiberian regions (Barcelona, Spain). The study area represents a land use and land cover gradient showing urbanization and crop intensification in the lowlands and forest encroachment in mountain areas. We identified 2458 small mammal individuals of 12 different species from barn owl (Tyto alba) pellets. Three open-land species (Microtus duodecimcostatus, Crocidura russula, and Mus spretus) and one forest/generalist species (Apodemus sylvaticus) were dominant in the diet, accounting for 93% of prey. In order to disentangle the effects of both main drivers on the small mammal community, we used partial constrained ordination techniques, which allowed us to determine the pure effects (and shared effects) of the environmental factors. Land use predictors explained 33.4% of the variance (mostly crops), followed by 23.4% of the variance explained by the geo-climatic variables (mostly rainfall), and an additional 24.8% of the variance was shared by both groups of predictors, totaling 81.6% of environmental variance. The remaining 18.4% of variance was unexplained by environmental matrices. This pattern was consistent with expected associations of species and biotic influences at small spatial scales and highlighted that the number of species increased from the crops in the lowlands towards the highlands covered by deciduous and coniferous forests.

Dynamics of Species Diversity in Small Mammal Communities in Slope Larch Forests on the Northern Coast of the Sea of Okhotsk

Dynamics of Species Diversity in Small Mammal Communities in Slope Larch Forests on the Northern Coast of the Sea of Okhotsk

Community of medium and large-sized mammals and functional diversity in a tropical rainforest of Southern México under different degrees of human pressure

Community of medium and large-sized mammals and functional diversity in a tropical rainforest of Southern México under different degrees of human pressure

Limited herbivore migration during the Last Glacial Period of Kenya.

Eastern Africa is home to the largest terrestrial migrations on Earth. Though these migratory systems have been well studied for decades, little is known of their antiquity and evolutionary history. Serially sampled strontium stable isotopes (87Sr/86Sr) from tooth enamel can be used to track migration in mammals. Here we analyse 87Sr/86Sr for 79 bovid and equid individuals representing 18 species from four localities in Kenya to characterize prehistoric migratory systems during the Last Glacial Period (115-11.7 ka). Of the species analysed, 16 lack definitive evidence for migration, including blue wildebeest (Connochaetes taurinus), Thomson's gazelle (Eudorcas thomsonii) and plains zebra (Equus quagga), which are long-distance migrants today in the Greater Serengeti Ecosystem and historically in the Athi-Kapiti Plains. Only two species, the extinct wildebeests Rusingoryx atopocranion and Megalotragus sp., were migratory. These findings suggest a possible alternative narrative about ecosystem dynamics during the Last Glacial Period and shed light on the behaviour of both extant and extinct species at this time. In particular, these results indicate that migratory behaviour in extant species either emerged during the Holocene or was more spatiotemporally constrained in the past. Our results contribute to a growing body of evidence suggesting that the structure and function of geologically recent large mammal communities in eastern Africa differed considerably from those observed in the present day.

Mammalian community responses in relation to anthropogenic disturbances and resource gradients in the shade coffee forest ecosystem of Southwestern Ethiopia

Understanding the effects of variation in resource availability and habitat disturbance on the ecology of mammals is vital for successful conservation management. In this study, we examined how human disturbances, resource availability and elevation gradients influence mammal assemblages in both managed coffee forest and natural forest of the Belete-Gera National Forest Priority Area, southwestern Ethiopia. We surveyed mammals using motion-detecting infrared camera traps in 90 locations for a total of 4142 camera days. We measured distance from main roads and settlements as disturbance factors, and distance from water sources, key grazing sites, and forest edges and woody plant diversity as resource variables. We assessed the mammal assemblages in coffee forest and natural forests using generalized linear models. Further, we used linear modelling to compare the relationships of mammal detection rates by feeding guilds and body size to resource variables. In total, we recorded 8815 videos identifying 23 different mammal species. The mammal assemblages in coffee forests were negatively associated with increasing distances from key grazing sites, water sources, and elevation. In contrast, the association with increasing distance from the road and woody plant diversity was positive. In addition, herbivores and large (25–200 kg) and very large (≥200 kg) mammals, were all negatively associated with increasing distance from the natural forest edges. With the conversion of natural forest to coffee forest and the intensification of coffee forest management, sustainable management of key grazing sites, water sources, and diverse woody plant species will be essential to the conservation of mammals. In addition, to ensure mammal conservation, adjacent natural forests around coffee forests should also be protected.

A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa).

The family Bovidae [Mammalia: Artiodactyla] is speciose and has extant representatives on every continent, forming key components of mammal communities. For these reasons, bovids are ideal candidates for studies of ecomorphology. In particular, the morphology of the bovid humerus has been identified as highly related to functional variables such as body mass and habitat. This study investigates the functional morphology of the bovid distal humerus in isolation due to its increased likelihood of preservation in the fossil record, and the resulting opportunity for a better understanding of the ecomorphology of extinct bovids. A landmark scheme of 30 landmarks was used to capture the 3D distal humerus morphology in 111 extant bovid specimens. We find that the distal humerus has identifiable morphologies associated with body mass, habitat preference and tribe affiliation and that some characteristics are shared between high body mass bovids and those living on hard, flat terrain which is likely due to the high stress on the bone in both cases. We directly apply our findings regarding extant bovids to the extinct alcelaphine bovid, Rusingoryx atopocranion from the mid to late Pleistocene (>33-45 ka) Lake Victoria region of Kenya. This species is known for some peculiar morphologies including a domed cranium with hollow nasal crests, and having small hooves for a bovid of its size. Another interesting aspect of Rusingoryx's skeletal morphology which has not been addressed is an unusual protrusion on the lateral epicondyle of the distal humerus. Despite considerable individual variation in the Rusingoryx specimens, we find evidence to support its historical assignment to the tribe Alcelaphini, and that it likely preferred open grassland habitats, which is consistent with independent reconstructions of the palaeoenvironment. We also provide the most accurate body mass estimate for Rusingoryx to date, based on distal humerus centroid size. Overall, we are able to conclude that the distal humerus in extant bovids is highly informative regarding body mass, habitat preference and tribe, and that this can be applied directly to a fossil taxon with promising results.

On the Dynamics of Mortality and the Ephemeral Nature of Mammalian Megafauna.

AbstractEnergy flow through consumer-resource interactions is largely determined by body size. Allometric relationships govern the dynamics of populations by impacting rates of reproduction as well as alternative sources of mortality, which have differential impacts on smaller to larger organisms. Here we derive and investigate the timescales associated with four alternative sources of mortality for terrestrial mammals: mortality from starvation, mortality associated with aging, mortality from consumption by predators, and mortality introduced by anthropogenic subsidized harvest. The incorporation of these allometric relationships into a minimal consumer-resource model illuminates central constraints that may contribute to the structure of mammalian communities. Our framework reveals that while starvation largely impacts smaller-bodied species, the allometry of senescence is expected to be more difficult to observe. In contrast, external predation and subsidized harvest have greater impacts on the populations of larger-bodied species. Moreover, the inclusion of predation mortality reveals mass thresholds for mammalian herbivores, where dynamic instabilities may limit the feasibility of megafaunal populations. We show how these thresholds vary with alternative predator-prey mass relationships, which are not well understood within terrestrial systems. Finally, we use our framework to predict the harvest pressure required to induce mass-specific extinctions, which closely align with previous estimates of anthropogenic megafaunal exploitation in both paleontological and historical contexts. Together our results underscore the tenuous nature of megafaunal populations and how different sources of mortality may contribute to their ephemeral nature over evolutionary time.

Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Ticks are obligate hematophagous ectoparasites of vertebrates and are relevant worldwide due to the number of bacterial and other pathogens they can transmit. To date, the knowledge about the microorganisms that ticks harbor and transmit to their hosts is incipient. In this study, 24 samples of mammals belonging to four taxonomic orders and ticks of the genera Amblyomma and Rhipicephalus from the Orinoco region of Colombia were analyzed to described and compare the bacterial microbiome. Genetic extraction was performed, and the V3–V4 region of the 16S rRNA gene was amplified by PCR. Libraries were created, and those samples with adequate quality indices were sequenced using Illumina MiSeq technology. Bacterial taxonomic assignment analyses were conducted through Amplicon Sequence Variants (ASVs) and Operational Taxonomic Units (OTUs). The results correspond to 16 samples that passed the quality filters, with 3218 OTUs (415 families). Although a considerable number of unknown bacteria was found, Enterobacteriaceae, Beijerinckiaceae, Moraxellaceae, and Burkholderiaceae are the most prevalent families, and the presence of the genera Coxiella, Escherichia-Shigella, Enterobacter, which can harbor pathogenic species was confirmed. In individuals of Amblyomma mixtum found actively feeding on Hydrochoerus hydrochaeris, bacteria of the genera Escherichia-Shigella and Enterobacter were documented. Similarly, Rhipicephalus microplus found actively feeding on Odocoileus virginianus cariacou shared Escherichia-Shigella. Ralstonia was shared among the blood samples of H. hydrochaeris, while Anaplasma and Eubacterium were shared in blood and liver samples of O. v. cariacou. Shared bacteria between A. mixtum and R. microplus included Bacillus, Coxiella, and Escherichia-Shigella. The results highlight the need of additional studies in other natural regions of Colombia and other American countries where tick-borne diseases have been detected. Likewise, the recorded data are the first at the level of bacterial communities in ticks of the family Ixodidae and provide valuable knowledge for the understanding host-tick and pathogen interactions.