Find research datasets worth reusing

opencc-zeroOct 2020View details →

Data for Body mass-related changes in mammal community assembly patterns during the late Quaternary of North America

The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements, and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) – wherein each species pair was classified as spatially aggregated, segregated, or random – we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40,000 14C - 11,700 14C ybp, Holocene: 11,700 14C - 50 ybp, and Modern: 50 - 0 yrs). In the Late Pleistocene and Holocene, the BMD of both aggregated and segregated species pairs was significantly smaller than the BMD of random pairs. These results are consistent with environmental filtering and competition as important drivers of community structure in both time periods. Modern assemblages showed a breakdown between BMD and co-occurrence patterns: the average BMD of aggregated, segregated, and random species pairs did not differ from each other. Collectively, these results indicate that the late Quaternary mammalian extinctions not only eliminated many large- bodied species but were followed by a re-organization of communities that altered patterns of species coexistence and associated differences in body size.

opencc-zeroDec 2017View details →

Data from: Progressively excluding mammals of different body size affects community and trait structure of ground beetles

Mammalian grazing induces changes in vegetation properties in grasslands, which can affect a wide variety of other animals including many arthropods. However, the impacts may depend on the type and body size of these mammals. Furthermore, how mammals influence functional trait syndromes of arthropod communities is not well known. We progressively excluded large (e.g. red deer, chamois), medium (e.g. alpine marmot, mountain hare), and small (e.g. mice) mammals using size-selective fences in two vegetation types (short- and tall-grass vegetation) of subalpine grasslands. We then assessed how these exclusions affected the community composition and functional traits of ground beetles (Coleoptera, Carabidae), and which vegetation characteristic mediated the observed effects. Total carabid biomass, the activity densities of carabids with specific traits (i.e. small eyes, short wings), the richness of small-eyed species and the richness of herbivorous species were significantly higher when certain mammals were excluded compared to when all mammals had access, regardless of vegetation type. Excluding large and medium mammals increased the activity density of herbivorous carabid species, but only in short-grass vegetation. Similarly, excluding large mammals (ungulates) altered carabid species composition in the short-, but not in the tall-grass vegetation. All these responses were related to aboveground plant biomass, but not to plant Shannon diversity or vegetation structural heterogeneity. Our results indicate that changes in aboveground plant biomass are key drivers of mammalian grazers' influence on carabids, suggesting that bottom-up forces are important in subalpine grassland systems. The exclusion of ungulates provoked the strongest carabid response. Our results, however, also highlight the ecological significance of smaller herbivorous mammals. Our study furthermore shows that mammalian grazing not only altered carabid community composition, but also caused community-wide functional trait shifts, which could potentially have a wider impact on species interactions and ecosystem functioning.

opencc-zeroDec 2015View details →

Data from: Synchrony in small mammal community dynamics across a forested landscape

Long-term studies at local scales indicate that fluctuations in abundance among trophically similar species are often temporally synchronized. Complementary studies on synchrony across larger spatial extents are less common, as are studies that investigate the subsequent impacts on community dynamics across the landscape. We investigate the impact of species population fluctuations on concordance in community dynamics for the small mammal fauna of the White Mountain National Forest, USA. Hierarchical open population models, which account for imperfect detection, were used to model abundance of the most common species at 108 sites over a three year period. Most species displayed individualistic responses of abundance to forest type and physiographic characteristics. However, among species, we found marked synchrony in population fluctuations across years, regardless of landscape affinities or trophic level. Across the region, this population synchrony led to high within-year concordance of community composition and aggregate properties (e.g., richness and diversity) independent of forest type and low among-year similarity in communities, even for years with similar species richness. Results suggest that extrinsic factors primarily drive abundance fluctuations and subsequently community dynamics, although local community assembly may be modified by species dispersal abilities and biotic interactions. Concordant community dynamics across space and over time may impact the stability of regional food webs and ecosystem functions.

opencc-zeroDec 2016View details →

Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared BLAST with the new program PROTAX, and we found that PROTAX improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera-trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by eight years of transect counts and camera-trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys, and has the potential to detect a broader range of species than more commonly used methods.

opencc-zeroDec 2015View details →

Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits: body size (small, medium, large and extra-large) and diet (carnivore, omnivore and herbivore). We photographed 44 species of mammals over 6607 trap nights. Camera station-specific estimates of species richness ranged from 8 to 27 unique species, and species had a mean occurrence probability of 0·32 (95% credible interval = 0·21–0·45). At the community level, our model revealed species richness was generally greatest in floodplains and grasslands and with increasing distances into protected wildlife areas. Variation among species' responses was explained in part by our species groupings. The positive influence of protected areas was strongest for extra-large species and herbivores, while medium-sized species actually increased in the non-protected areas. The positive effect of grassland/floodplain cover, alternatively, was strongest for large species and carnivores and weakest for small species and herbivores, suggesting herbivore diversity is promoted by habitat heterogeneity. Synthesis and applications. Our results highlight the importance of protected areas and grasslands in maintaining biodiversity in southern Africa. We demonstrate the utility of hierarchical Bayesian models for assessing community, group and individual species' responses to anthropogenic and environmental variables. This framework can be used to map areas of high conservation value and predict impacts of land-use change. Our approach is particularly applicable to the growing number of camera trap studies world-wide, and we suggest broader application globally will likely result in reduced costs, improved efficiency and increased knowledge of wildlife communities.

opencc-zeroDec 2014View details →

Data from: Random versus game trail-based camera trap placement strategy for monitoring terrestrial mammal communities

Camera trap surveys exclusively targeting features of the landscape that increase the probability of photographing one or several focal species are commonly used to draw inferences on the richness, composition and structure of entire mammal communities. However, these studies ignore expected biases in species detection arising from sampling only a limited set of potential habitat features. In this study, we test the influence of camera trap placement strategy on community-level inferences by carrying out two spatially and temporally concurrent surveys of medium to large terrestrial mammal species within Tanzania's Ruaha National Park, employing either strictly game trail-based or strictly random camera placements. We compared the richness, composition and structure of the two observed communities, and evaluated what makes a species significantly more likely to be caught at trail placements. Observed communities differed marginally in their richness and composition, although differences were more noticeable during the wet season and for low levels of sampling effort. Lognormal models provided the best fit to rank abundance distributions describing the structure of all observed communities, regardless of survey type or season. Despite this, carnivore species were more likely to be detected at trail placements relative to random ones during the dry season, as were larger bodied species during the wet season. Our findings suggest that, given adequate sampling effort (> 1400 camera trap nights), placement strategy is unlikely to affect inferences made at the community level. However, surveys should consider more carefully their choice of placement strategy when targeting specific taxonomic or trophic groups.

opencc-zeroDec 2015View details →

Data from: Revealing kleptoparasitic and predatory tendencies in an African mammal community using camera traps: a comparison of spatiotemporal approaches

Camera trap data are increasingly being used to characterise relationships between the spatiotemporal activity patterns of sympatric mammal species, often with a view to inferring inter-specific interactions. In this context, we attempted to characterise the kleptoparasitic and predatory tendencies of spotted hyaenas Crocuta crocuta and lions Panthera leo from photographic data collected across 54 camera trap stations and two dry seasons in Tanzania's Ruaha National Park. We applied four different methods of quantifying spatiotemporal associations, including one strictly temporal approach (activity pattern overlap), one strictly spatial approach (co-occupancy modelling), and two spatiotemporal approaches (co-detection modelling and temporal spacing at shared camera trap sites). We expected a kleptoparasitic relationship between spotted hyaenas and lions to result in a positive spatiotemporal association, and further hypothesised that the association between lions and their favourite prey in Ruaha, the giraffe Giraffa camelopardalis and the zebra Equus quagga, would be stronger than those observed with non-preferred prey species (the impala Aepyceros melampus and the dikdik Madoqua kirkii). Only approaches incorporating both the temporal and spatial components of camera trap data resulted in significant associative patterns. The latter were particularly sensitive to the temporal resolution chosen to define species detections (i.e. occasion length), and only revealed a significant positive association between lion on spotted hyaena detections, as well as a tendency for both species to follow each other at camera trap sites, during the dry season of 2013, but not that of 2014. In both seasons, observed spatiotemporal associations between lions and each of the four herbivore species considered provided no convincing or consistent indications of any predatory preferences. Our study suggests that, when making inferences on inter-specific interactions from camera trap data, due regards should be given to the potential behavioural and methodological processes underlying observed spatiotemporal patterns.

opencc-zeroApr 2022View details →

Andean non-volant small mammals: a dataset of community assemblages of non-volant small mammals from the high Andes

Information from diversity inventories is used to study patterns of biodiversity and species distribution; likewise, it may be useful to identify priority areas for conservation, and to guide future sampling efforts. In this context, we compiled information on non-volant small mammal communities from the high Andes (> 2,000 m.). Here we present an open resource data set containing information diversity (species composition, number of individuals captured ), inventory design (type of traps, sampling efforts), and environment (habitat) for both unpublished and published information. This study covers 630 mammalian communities, geographically distributed throughout the Andes in Venezuela, Colombia, Ecuador, Peru, Bolivia, Argentina, and Chile. We compiled a total of 26,412 individual records belonging to 240 species; the order with greatest number of records was Rodentia (n=25,319, 96.06%), followed by Didelphimorphia (n=373, 1.42%), Eulipotyphla (n=358, 1.36%) and Paucituberculata, (n=307, 1.16%). Andean non-volant small mammal communities harbor a range of 1-17 species, with 93.06 % of sites being composed of one to five species, 27.78% of sites ranging in richness from six to ten species, and 4.17% are composed by more than ten species. Multiple sampling methods were used to survey non-volant small mammals; the most representative methods being the use of snap-traps and Sherman traps, or a combination of both, in more than 81% of the studies. The Andean Non-Volant Small Mammals Data Paper represents the first large dataset of faunal species inventories for Andes. There are no copyright restrictions associated with the use of this data set. Please cite this Data Paper when its data are used total or partially in research or teaching.

openother-openMay 2022View details →

Largely independent effects of top predators, including Amur tigers and humans, on mammal communities in a recovering temperate forest region

Data associated with the manuscript "Largely independent effects of top predators, including Amur tigers and humans, on mammal communities in a recovering temperate forest region"

opencc-zeroMay 2022View details →

Altitudinal dispersal process drives community assembly of montane small mammals

Montane small mammals are subjected to strong forces of dispersal limitation and habitat filtering that mainly operate on their community structures along the altitudinal direction. However, so far little is known about the relative contributions of dispersal and niche processes to their community assembly. By applying the newly-proposed PER-SIMPER/DNCI (dispersal–niche continuum index) framework to small mammal occurrence data collected from 21 extensive altitudinal gradients, we quantitatively assess the relative importance of dispersal and niche processes on mammalian community assembly in a large mountainous region of southwest China. We compared the pairwise DNCI values among assemblages from low, middle, and high altitudinal zones and overall DNCI values between glires and insectivores that differ in dispersal abilities to test three explicit (altitudinal connectivity, environmental difference, and dispersal ability) hypotheses. The overall DNCI values for all small mammal species combined (-12.7 ± 0.4, 90 species), glires (-12.8 ± 0.5, 56 species) and insectivores (-13.5 ± 1.4, 34 species) values were all negative, while insectivores showed a lower value than glires. For both all species combined and glires, we found a lower pairwise DNCI value between the low and high altitudinal zones than that between the other two pairs of altitudinal zones. Our study indicated that altitudinal dispersal process dominates the taxonomic composition of small mammal assemblages in this region. Importantly, the results reinforced the idea that community structures of less vagile taxa are more subjected to dispersal limitation, yet another idea that assemblages from further altitudinal areas are more differentiated by dispersal process was only supported in glires and all species combined. Community biologists should therefore pay attention to recent climate-induced upward range shifts by montane species, which may dramatically alter their community structures in different altitudinal zones through dynamics of immigration and mountaintop extinction.

opencc-zeroJan 2023View details →

Glacier Bay National Park mammal and plant community data

1. Disturbance is a key driver of community assembly and patterns of diversity. Whereas successional changes in vegetation have been well studied, post-disturbance successional patterns of wildlife communities remain poorly understood. 2. Here, we investigated the roles of site age and habitat in shaping community assembly and the diversity of terrestrial mammals in Glacier Bay National Park, Alaska (GBNP), which has undergone the most rapid and extensive deglaciation in the world since the Little Ice Age. Deglaciation has extensively altered the landscape, opening up new habitat for recolonization by plants and animals. 3. We used camera traps, small mammal trapping and vegetation surveys to investigate the patterns of mammalian succession and beta diversity following deglaciation, using a space-for-time substitution across 10 sites during summers 2017 and 2018. Site age and habitat characteristics were not strongly correlated (r < 0.46), allowing the influences of time since disturbance and habitat changes to be distinguished. 4. PERMANOVA analyses indicated that mammal community assembly was more strongly influenced by site age than habitat, whereas habitat and age had similar effects on beta (between site) diversity. Beta diversity was higher for smaller, less mobile mammals than larger, more mobile mammals and was primarily driven by species turnover among sites, whereas relative turnover was much lower for larger mammals. A comprehensive review of historic distributions of mammals in GBNP supported our findings that species turnover is a driving influence of community assembly for smaller mammals. 5. Our results indicate that body size of mammals may play an important role in shaping colonization patterns post-disturbance, likely via size-related differences in mobility. Patterns of wildlife community assembly may therefore not track vegetation succession following disturbances if there are barriers to movement or if dispersal ability is limited, highlighting the importance of incorporating landscape connectivity and species traits into wildlife conservation efforts following disturbances. This knowledge may improve predictions of mammalian community assembly following major disturbance events.

Fig. 5 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 5.—Nonparametric multiplicative regression response curves (estimated by kernel functions) for the best model (highest cross-validated xR2) for describing Glaucomys sabrinus abundance given the habitat characteristics at 20 trapping sites in Yosemite National Park, California (2004–2005). The best model included a combination of fire severity (index), shrub species understory cover (%), and oak tree overstory cover (%). The values on the graph are not intended to suggest definitive thresholds or maximum values for any of the habitat variables (see "Materials and Methods").

Fig. 3.—Nonmetric multidimensional scaling ordination for the 4 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 3.—Nonmetric multidimensional scaling ordination for the 4 habitat variables (overstory cover, oak tree cover, shrub cover, and fire severity index) and elevation and the 11 most commonly captured mammal species in 10 burned and 10 unburned sites from April to July 2004 and 2005 in Yosemite National Park, California. Only variables with a r ≥ 0.7 or the environmental variable with the highest r for that axis (i.e., fire severity r = −0.41 and oak tree cover r = 0.51) are listed on each axis. The R2 was 0.09 and 0.77 for axis 1 and 2, respectively, for a cumulative total of 0.86. The mammal species codes represent the following: CALA, Callospermophilus lateralis; GLSA, Glaucomys sabrinus (r = 0.73 on axis 1); MIXX, Microtus sp.; NEQU, Neotamias quadrimaculatus (r = −0.71 on axis 2); NESP, N. speciosus (r = −0.67 on axis 1); OTBE, Otospermophilus beecheyi; PEBO, Peromyscus boylii; PEMA; P. maniculatus (r = −0.88 on axis 2); SCGR, Sciurus griseus (r = 0.68 on axis 1); SOXX, Sorex sp.; TADO, Tamiasciurus douglasii.

Fig. 4 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 4.—Nonparametric multiplicative regression response curves (estimated by kernel functions) for the best model (highest cross-validated xR2) describing Neotamias quadrimaculatus abundance given the habitat characteristics at 20 trapping sites in Yosemite National Park, California (2004–2005). The best model was the full model. The values on the graph are not intended to suggest definitive thresholds or maximum values for any of the habitat variables (see "Materials and Methods").

Fig. 2 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 2.—Nonmetric multidimensional scaling ordination results for overstory cover (%), oak tree cover (%), and shrub cover (%) at 10 burned and 10 unburned small mammal trapping sites in Yosemite National Park, California, 2004 and 2005. Only the variables with a Pearson correlation coefficient (r) ≥ 0.7 are listed on each axis with overstory canopy and oak tree cover on axis 1 (r = −0.90 and 0.82, respectively) and shrub cover (r = 0.85) on axis 2. The R2 was 0.58 and 0.38 for axis 1 and 2, respectively, for a cumulative total of 0.96.

Fig. 6 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 6.—Nonparametric multiplicative regression response curves (estimated by kernel functions) for the best model (highest crossvalidated xR2) describing Neotamias speciosus abundance given the habitat characteristics at 20 trapping sites in Yosemite National Park, California (2004–2005). The best model included a combination of fire severity (index) and elevation (m). The values on the graph are not intended to suggest definitive thresholds or maximum values for any of the habitat variables (see "Materials and Methods").

Fig. 1 in Effects of fire on small mammal communities in frequent-fire forests in California

Fig. 1.—Locations of 10 burned and 10 unburned small mammal trapping sites (April to July, 2004 and 2005) in Yosemite National Park, California. Burned trapping areas were completely within the boundary of either wildfire or prescribed fire between 1990 and 2004.