Animal density and track counts: understanding the nature of observations based on animal movements

Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics

Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.

Djaffa Mountains guereza (Colobus guereza gallarum) abundance in forests of the Ahmar Mountains, Ethiopia

The size and density of a population are essential parameters in primate ecology and conservation. Such information, however, is still scarce for many forest primate species. The Djaffa Mountains guereza (Colobus guereza gallarum) is an endemic Ethiopian taxon for which data about its distribution and population size are missing. Therefore, we aimed to estimate the abundance and population size of the Djaffa Mountains guereza in four forests in the Ahmar Mountains southeast of the Ethiopian Rift Valley. We conducted line-transect surveys in the forests. Within an area of 183 km2 , we sampled 19 transects covering a distance of 75.9 km. We encountered 73 guereza clusters which most likely represent social groups. Since the detection distances and cluster sizes did not differ among the four forests, we applied a conventional distance sampling (CDS) model and estimated a population density of 20.6 clusters per square kilometer, i.e., 109.6 individuals per square kilometer or 20 061 individuals within the complete study area. This abundance is relatively high compared to other C. guereza taxa. However, given that the habitat and population of C . g . gallarum are already highly fragmented, further monitoring of the population and exploration of the possibilities of reconnecting its habitat should be priorities for the conservation of this taxon.

Eurasian beaver - A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter

There is increasing awareness of the ecosystem engineering services provided by recovering populations of Eurasian beaver. By modifying aquatic environments, this species has a significant, positive influence on biodiversity. Beaver activity affects not only aquatic ecosystems but also terrestrial habitats and organisms. Our study compares and evaluates the species richness and activity of terrestrial mammals in winter at beaver ponds (N = 65) and randomly-selected reference sites along nearby watercourses unmodified by beavers (N = 65) in Poland (central Europe). Mammal assemblages were investigated near pond/watercourse edges, and also at some distance from them. The species richness of mammal and numbers of their tracks were respectively 25% and 33% greater on the beaver than on the reference sites. The higher species richness on beaver sites extended to areas 40-60 m distant from ponds, devoid any signs of beaver activity. Twenty-three mammal species were recorded on beaver sites (mean species richness 3.8 ± 1.6 SD), and 20 on reference ones (3.0 ± 1.5 SD). The numbers of tracks of grey wolf, least weasel and European polecat were higher on beaver than reference sites. Mammal species richness and activity were related to the existence of beaver ponds, but were also correlated with the numbers of snags and coverage of grass, bramble and coniferous saplings in neighbouring terrestrial habitats. Large and small carnivores occurred more frequently and were more active on beaver sites. The frequencies of occurrence of mesocarnivores, mesoherbivores and small herbivores were correlated with habitat characteristics, regardless of whether beavers were present or not. Our results highlight the fact that both pond creation and the habitat changes resulting from the presence of beavers rearrange the occurrence and activity of the terrestrial mammal assemblage.

A preliminary survey of medium and large-sized mammals from Lebu Natural Protected Forest, Southwest Showa, Ethiopia

This study was conducted to determine the species composition and diversity of medium and large-sized mammals from Lebu Natural Protected Forest, Ethiopia. Surveys were conducted to record mammals through direct observation and indirect evidence from three habitat types, namely: natural forest, bushland, and riverine forest. A total of 15 mammalian species were recorded. The species recorded were Papio anubis, Chlorocebus aethiops, Tragelaphus scriptus, Canis aureus, Crocuta crocuta, Panthera pardus, Procavia capensis, Colobus guereza, Sylvicapra grimmia, Orycteropus afer, Helogale parvula, Hystrix cristata, Lepus fagani, Potamochoerus larvatus, and Phacochoeus africanus. A total of 223 records of observations were compiled. About 74% of these records (N = 167) were obtained from direct sight, whereas the rest was recorded through indirect evidence. The dominant order recorded was order Primates (57.4%) followed by order Artiodactyla (17.5%) while the least record was order Lagomorpha (1.34%). The species richness varied across the stratified habitat types. However, there is no significant difference in Shannon-Wiener Index values between the habitat types. The species diversity of the study area was H' = 2.119. The present study area is of great potential area for the conservation of the species. Long-term detailed studies should be carried out for effective conservation and management initiatives in the study area.

Visual encounters on line transect surveys under-detect carnivore species: Implications for assessing distribution and conservation status

We compared the distribution and occurrence of 15 carnivore species with data collected monthly over three years by trained native trackers using both sign surveys and an encounter-based, visual-distance method in a well-preserved region of southern Guyana (Amazon / Guiana Shield). We found that a rigorously applied sign-based method was sufficient to describe the status of most carnivore species populations, including rare species such as jaguar and bush dog. We also found that even when accumulation curves for direct visual encounter data reached an asymptote, customarily an indication that sufficient sampling has occurred to describe populations, animal occurrence and distribution were grossly underestimated relative to the results of sign data. While other researchers have also found that sign are better than encounters or camera traps for large felids, our results are important in documenting the failure of even intensive levels of effort to raise encounter rates sufficiently to enable statistical analysis, and in describing the relationship between encounter and sign data for an entire community of carnivores including felids, canids, procyonids, and mustelids.

BOARD INVITED REVIEW: Immunocontraception as a possible tool to reduce feral pig populations: recent and future perspectives

The feral pig populations of many countries continue to increase. Scientific studies on population size are scarce, while the numbers of reported observations on presence of and damage caused by feral pigs are increasing. Feral pigs can carry and spread several diseases (including zoonotic), but African Swine Fever (ASF) is of most concern. It is a highly transmissible viral disease associated with an extremely high mortality rate. Since 2009 ASF has appeared in several European countries, with cases being identified first among local feral pigs and consequently in domestic pig production units, indicating a clear linkage with the movement of the feral pig population and the spread of the disease across national boundaries. Control of feral pig populations is currently under discussion. Because massive culling raises questions of animal welfare and ethics, fertility control could represent an important and effective means to control feral pig populations. Contraceptive vaccines have been used with some degree of success in many wild species because they are able to provide a long-term effect without any consequent health problems. However, extensive and efficacious use of vaccines to control feral pig populations is not simple. The aim of this article was to review the progress in immunocontraception use in feral pigs, providing an account of the current status and future perspectives.

A camera-based method for estimating absolute density in animals displaying home range behaviour

The measurement of animal density may take advantage of recent technological achievements in wildlife video recording. Fostering the theoretical links between the patterns depicted by cameras and absolute density is required to exploit this potential. We explore the applicability of the Hutchinson-Waser's postulate (i.e. when animal density is stationary at a given temporal and spatial scale, the absolute density is given by the average number of animals counted per frame), which is a counter-intuitive statement for most ecologists and managers who are concerned with counting the same individual more than once. We aimed to reconcile such scepticism for animals displaying home range behaviour. The specific objectives of this paper are to generalize the Hutchinson-Waser's postulate for animals displaying home range behaviour and to propose a Bayesian implementation to estimate density from counts per frame using video cameras. Accuracy and precision of the method was evaluated by means of computer simulation experiments. Specifically, six animal archetypes displaying well-contrasted movement features were considered. The simulation results demonstrate that density could be accurately estimated after an affordable sampling effort (i.e. number of cameras and deployment time) for a great number of animals across taxa. The proposed method may complement other conventional methods for estimating animal density. The major advantages are that identifying an animal at the individual level and precise knowledge on how animals move are not needed, and that density can be estimated in a single survey. The method can accommodate conventional camera trapping data. The major limitations are related to some implicit assumptions of the underlying model: the home range centres should be homogeneously distributed, the detection probability within the area surveyed by the camera should be known, and animals should move independently to one another. Further improvements for circumventing these limitations are discussed.

Simplified large African carnivore density estimators from track indices

BACKGROUND

The range, population size and trend of large carnivores are important parameters to assess their status globally and to plan conservation strategies. One can use linear models to assess population size and trends of large carnivores from track-based surveys on suitable substrates. The conventional approach of a linear model with intercept may not intercept at zero, but may fit the data better than linear model through the origin. We assess whether a linear regression through the origin is more appropriate than a linear regression with intercept to model large African carnivore densities and track indices.

METHODS

We did simple linear regression with intercept analysis and simple linear regression through the origin and used the confidence interval for ß in the linear model y = αx + ß, Standard Error of Estimate, Mean Squares Residual and Akaike Information Criteria to evaluate the models.

RESULTS

The Lion on Clay and Low Density on Sand models with intercept were not significant (P > 0.05). The other four models with intercept and the six models thorough origin were all significant (P < 0.05). The models using linear regression with intercept all included zero in the confidence interval for ß and the null hypothesis that ß = 0 could not be rejected. All models showed that the linear model through the origin provided a better fit than the linear model with intercept, as indicated by the Standard Error of Estimate and Mean Square Residuals. Akaike Information Criteria showed that linear models through the origin were better and that none of the linear models with intercept had substantial support.

DISCUSSION

Our results showed that linear regression through the origin is justified over the more typical linear regression with intercept for all models we tested. A general model can be used to estimate large carnivore densities from track densities across species and study areas. The formula observed track density = 3.26 × carnivore density can be used to estimate densities of large African carnivores using track counts on sandy substrates in areas where carnivore densities are 0.27 carnivores/100 km2 or higher. To improve the current models, we need independent data to validate the models and data to test for non-linear relationship between track indices and true density at low densities.

A Spatio-Temporally Explicit Random Encounter Model for Large-Scale Population Surveys

Random encounter models can be used to estimate population abundance from indirect data collected by non-invasive sampling methods, such as track counts or camera-trap data. The classical Formozov–Malyshev–Pereleshin (FMP) estimator converts track counts into an estimate of mean population density, assuming that data on the daily movement distances of the animals are available. We utilize generalized linear models with spatio-temporal error structures to extend the FMP estimator into a flexible Bayesian modelling approach that estimates not only total population size, but also spatio-temporal variation in population density. We also introduce a weighting scheme to estimate density on habitats that are not covered by survey transects, assuming that movement data on a subset of individuals is available. We test the performance of spatio-temporal and temporal approaches by a simulation study mimicking the Finnish winter track count survey. The results illustrate how the spatio-temporal modelling approach is able to borrow information from observations made on neighboring locations and times when estimating population density, and that spatio-temporal and temporal smoothing models can provide improved estimates of total population size compared to the FMP method.

Proxies in Practice: Calibration and Validation of Multiple Indices of Animal Abundance

The abundance of individuals in a population is a fundamental metric in basic and applied ecology, but sampling protocols yielding precise and unbiased estimates of abundance are often cost-prohibitive. Proxies of abundance are therefore common, but require calibration and validation. There are many ways to calibrate a proxy, and it is not obvious which will perform best. We used data from eight populations of Chinook salmon Oncorhynchus tshawytscha on the Oregon coast where multiple proxies of abundance were obtained contemporaneously with independent mark–recapture estimates. We combined multiple proxy values associated with a single level of abundance into a composite index and then calibrated the composite index to mark–recapture estimates using several different techniques. We tested our calibration methods using leave-one-out cross-validation and simulation. Our cross-validation analysis did not definitively identify a single best calibration technique for all populations, but we could identify consistently inferior approaches. The simulations suggested that incorporating the uncertainty associated with mark–recapture estimates into the calibration technique reduced precision and introduced bias when mark–recapture estimate uncertainty increased with point estimate values. Cross-validation techniques can be used to test multiple methods of calibrating multiple proxies to an estimate of abundance. Critical uncertainties with the application of calibrated proxies still exist, and cost-benefit analysis should be performed to help identify optimal monitoring designs.