SynopsisRecent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals. However, these studies are relatively limited in the scope of species that have been examined. Here we present a dataset that includes paired wild and captive samples from mammalian taxa across six Orders to investigate generalizable patterns of the effects captivity on mammalian gut bacteria. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the taxa surveyed, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that demonstrated larger shifts in relative abundance between the captive and wild states included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.

No abstract

Context. The expansive grassland biome is one of the most extensively transformed in South Africa, yet no strategy for monitoring its integrity is in place. A grassland health program, incorporating different ecosystem levels, was recently initiated. The suitability of three taxonomic groups as indicators has been tested so far: vegetation (by calculating an ecological index value, El), insects (using the South African grassland scoring system, SAGraSS) and small mammals (this study). All of these methods aim to be rapid and easy to perform. Whereas SAGraSS still needs further refinement, several factors already indicate the importance of including small mammal community parameters in integrity assessments.Aims. This contribution reports on more than 12 years of results from various studies on small mammals in the Free State Grasslands, with the aim of exploring the utility of small mammal survey for assessment of ecosystem integrity.Methods. The hypothesis was based on the outcomes of several short-term studies conducted in the grassland biome. Combining all previous results, this paper re-evaluates the parameters of trap success, species richness, diversity, evenness and individual species as bio-indicators.Key results. By combining data from many sites and years, the effect of seasonal and inter-annual variations in habitat and population parameters was diminished, and a more general picture of small mammal community structure revealed. New insights were gleaned into the status of several indicator species. By providing a summary of small mammal community parameter scores and indices, the study establishes a benchmark for future small mammal assessments and monitoring. To be effective, small mammal surveys in the grassland biome of southern Africa should be carried out in autumn and early winter.Conclusions. This study suggests that small mammal species richness and diversity decline with habitat degradation; that the generalist rodent Mastomys coucha dominates community numbers at low ecological integrity; that the number of specialist species increases towards ecological climax; and that specific species act as indicators during the successional process.Implications. This study should benefit the monitoring, conservation and management of grassland ecosystems, make environmental impact assessments more effective, and identify new topics for ecological research.

Coexistence often involves niche differentiation either as the result of environmental divergence, or in response to competition. Disentangling the causes of such divergence requires that environmental variation across space is taken into account, which is rarely done in empirical studies. We address the role of environmental variation versus competition in coexistence between two rodent species: Rhabdomys bechuanae (bechuanae) and Rhabdomys dilectus dilectus (dilectus) comparing their habitat preference and home range (HR) size in areas with similar climates, where their distributions abut (allopatry) or overlap (sympatry). Using Outlying Mean Index analyses, we test whether habitat characteristics of the species deviate significantly from a random sample of available habitats. In allopatry, results suggest habitat selection: dilectus preferring grasslands with little bare soil while bechuanae occurring in open shrublands. In sympatry, shrubland type habitats dominate and differences are less marked, yet dilectus selects habitats with more cover than bechuanae. Interestingly, bechuanae shows larger HRs than dilectus, and both species display larger HRs in sympatry. Further, HR overlaps between species are lower than expected. We discuss our results in light of data on the phylogeography of the genus and propose that evolution in allopatry resulted in adaptation leading to different habitat preferences, even at their distribution margins, a divergence expected to facilitate coexistence. However, since sympatry occurs in sites where environmental characteristics do not allow complete species separation, competition may explain reduced inter-species overlap and character displacement in HR size. This study reveals that both environmental variation and competition may shape species coexistence.

Rodents form a vital component of Free State ecosystems and monitoring them may be a relatively quick and inexpensive method of indicating healthy or unhealthy ecosystem functioning. Using removal trapping, we have studied rodent seasonal abundance, species richness, Shannon diversity, and evenness of rodents in four habitats in the Tussen-die-Riviere Nature Reserve, inspected the most successful sampling method for these habitats, and report on their community structure and how it is related to an Ecological Index (≈ EI value of grassland). Both species richness and Shannon diversity increased significantly with EI value. The indicator species Mastomys coucha occurred at all plots, but contributed the largest proportion of the total captures (ca. 80%) at the plot with lowest EI value. Other results important for small mammal monitoring and collecting are that trap success and species richness was highest in autumn. This study also confirms that four days and nights continuous trapping is essential for the effective sampling of rodent communities in Free State grasslands. Our results partially support expectations that the number of specialist species increases with succession, M. coucha dominance acts as an indicator of habitat disturbance, rodent species richness conforms to Tilman's hump-shaped curve model, and adds to a baseline of diversity indices in a variety of grassland habitats.

Two male and three female caracal Felis caracal were radio‐tracked over a 1‐year period in arid shrub on the west coast of South Africa, by day and night over at least 130 days for each caracal, and uninterrupted for up to 120 h at a time. These results, on short‐term use of space, were related to concurrent availability of prey. The use by caracal of specific plant communities showed a significant positive correlation to prey biomass of rodents. Males had much larger home‐ranges (26.9±0.75 km2) than females (7.39±1.68 km2). Male home‐ranges overlapped completely with those of females, whereas female ranges overlapped between 0 and 19%. Caracal were active by night and day; onset of activity was affected more by ambient temperature (TA) than photoperiod. Caracal were active significantly longer on nights colder than 20°C. Females ceased activity at TA > 20°C, males at TA > 22°C. Males foraged faster than females (667 vs. 312 m h−1) and moved more than twice the distance of females during an active period. Calculated density of caracal was between 0.23 and 0.47 km−2.

No abstract

Species’ partitioning of resources remains one of the most integral components for understanding community assembly. Analysis of stable carbon and nitrogen isotopes in animal tissues has the potential to help resolve patterns of partitioning because these proxies represent the individual’s diet and trophic niche, respectively. Using free-ranging rodents in a southern African savanna as a model community, we find that syntopic species within habitats occupy distinct isotope niches. Moreover, species with strongly overlapping isotope niches did not overlap in their spatial distribution patterns, suggesting an underlying effect of competitive exclusion. Niche conservatism appears to characterize the behaviour of most species in our sample - with little or no observed changes across habitats - with the exception of one species, Mastomys coucha. This species displayed a generalist distribution, being found in similar abundances across a variety of habitats. This spatial pattern was coupled with a generalist isotope niche that shifted across habitats, likely in response to changes in species composition over the same spatial gradient. The case for M. coucha supports contentions that past competition effects played a significant evolutionary role in shaping community structures of today, including the absence of strong interspecific niche overlaps within particular habitats. Our study highlights the value of stable isotope approaches to help resolve key questions in community ecology, and moreover introduces novel analytical approaches to quantifying isotope niche breadths and niche overlaps that are easily comparable with traditional metrices.