Movement-Based Estimation and Visualization of Space Use in 3D for Wildlife Ecology and Conservation

Advances in digital biotelemetry technologies are enabling the collection of bigger and more accurate data on the movements of free-ranging wildlife in space and time. Although many biotelemetry devices record 3D location data with x, y, and z coordinates from tracked animals, the third z coordinate is typically not integrated into studies of animal spatial use. Disregarding the vertical component may seriously limit understanding of animal habitat use and niche separation. We present novel movement-based kernel density estimators and computer visualization tools for generating and exploring 3D home ranges based on location data. We use case studies of three wildlife species – giant panda, dugong, and California condor – to demonstrate the ecological insights and conservation management benefits provided by 3D home range estimation and visualization for terrestrial, aquatic, and avian wildlife research.     

Computational Reproducibility in The Wildlife Society's Flagship Journals

Scientific progress depends upon the accumulation of empirical knowledge via reproducible methodology. Although reproducibility is a main tenet of the scientific method, recent studies have highlighted widespread failures in adherence to this ideal. The goal of this study was to gauge the level of computational reproducibility, or the ability to obtain the same results using the same data and analytic methods as in the original publication, in the field of wildlife science. We randomly selected 80 papers published in the Journal of Wildlife Management and Wildlife Society Bulletin between 1 June 2016 and 1 June 2018. Of those that were suitable for reproducibility review (n = 74), we attempted to obtain study data from online repositories or directly from authors. Forty-two authors did not respond to our requests, and we were further unable to obtain data from authors of 13 other studies. Of the 19 studies for which we were able to obtain data and complete our analysis, we judged that 13 were mostly or fully reproducible. We conclude that the studies with publicly available data or data shared upon request were largely reproducible, but we remain concerned about the difficulty in obtaining data from recently published papers. We recommend increased data-sharing, data organization and documentation, communication, and training to advance computational reproducibility in the wildlife sciences. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Effects of Point Pattern Shape on Home-Range Estimates

Abstract: Home-range estimators are commonly tested with simulated animal locational data in the laboratory before the estimators are used in practice. Although kernel density estimation (KDE) has performed well as a home-range estimator for simulated data, several recent studies have reported its poor performance when used with data collected in the field. This difference may be because KDE and other home-range estimators are generally tested with simulated point locations that follow known statistical distributions, such as bivariate normal mixtures, which may not represent well the space-use patterns of all wildlife species. We used simulated animal locational data of 5 point pattern shapes that represent a range of wildlife utilization distributions to test 4 methods of home-range estimation: 1) KDE with reference bandwidths, 2) KDE with least-squares cross-validation, 3) KDE with plug-in bandwidths, and 4) minimum convex polygon (MCP). For the point patterns we simulated, MCP tended to produce more accurate area estimates than KDE methods. However, MCP estimates were markedly unstable, with bias varying widely with both sample size and point pattern shape. The KDE methods performed best for concave distributions, which are similar to bivariate normal mixtures, but still overestimated home ranges by about 40–50% even in the best cases. For convex, linear, perforated, and disjoint point patterns, KDE methods overestimated home-range sizes by 50–300%, depending on sample size and method of bandwidth selection. These results indicate that KDE does not produce home-range estimates that are as accurate as the literature suggests, and we recommend exploring other techniques of home-range estimation.     

Does land use within the home range drive the exposure of roe deer (Capreolus capreolus) to two abortive pathogens in a rural agro-ecosystem?

The recent increase in interactions between wildlife and domestic animals has heightened the risks of transmission of pathogens between wildlife, livestock, and humans. Our objective was to better understand how the spatial behavior of wildlife impacts their exposure to pathogens. We carried out a 5-year serological survey of Toxoplasma gondii and Chlamydia abortus in a roe deer population (Capreolus capreolus) living in a rural landscape and monitored using GPS technology. We tested whether the apparent seroprevalence of these pathogens was related to the characteristics of roe deer’s home range, indirectly reflecting the probability of contact between deer and domestic hosts (cats for T. gondii and ruminants for C. abortus). We controlled for the effects of temperature and rainfall, as local weather can affect pathogen survival in the environment. Overall, apparent seroprevalences were 43.7 and 15.8 % for T. gondii (N?=?135) and C. abortus (N?=?133), respectively. The apparent seroprevalence to T. gondii increased with the proportion of human dwellings (a proxy of cat presence) within the roe deer’s core home range and was higher during mild and wet years. This result illustrates how the spatial behavior of wild animals can modulate their exposure to pathogens through the degree of spatial overlap with a domestic host. By contrast, apparent seroprevalence to C. abortus increased with the annual number of frosty days but not with the proportion of meadows occupied by domestic ruminants within the core home range. This suggests that the cycle of C. abortus in wild animals could be somewhat independent from that in livestock.     

Socio-spatial ecology of pine marten (Martes martes) in conifer forests,Ireland

Understanding the social organisation and spacing patterns of wildlife populations is an important aspect of conservation management and applied science. The present study investigated the spatial ecology of pine marten (Martes martes) inhabiting conifer forests in Ireland, the largest habitat resource available for the species. It represented the first study of pine marten spacing patterns in Irish conifer forests. Pine marten (n?=?7; five males and two females) were live-trapped and radio-tracked for between 4 and 10 months from March 2008 to March 2009. Mean annual home-range estimates (95 % fixed kernel) for males (150.7 ha) were generally larger than those of females (90.2 ha). There was considerable inter-seasonal overlap in home ranges (approx 85 %) with less inter-sexual (12.0 %) or intra-sexual (11.8 %) overlap, although the sample size of individuals for comparison was small. Pine marten home ranges were stable from season to season. Core ranges varied in size from 10.6 to 104.1 ha, and as a mean percentage of home-range area were 22.9 and 42.5 % for males and females, respectively. In terms of forest management, potential under occupancy of available space by pine marten and vulnerability of very small core ranges to clear felling practices needs further research to determine any impacts on individuals and populations.     

Standardising Home Range Studies for Improved Management of the Critically Endangered Black Rhinoceros

Comparisons of recent estimations of home range sizes for the critically endangered black rhinoceros in Hluhluwe-iMfolozi Park (HiP), South Africa, with historical estimates led reports of a substantial (54%) increase, attributed to over-stocking and habitat deterioration that has far-reaching implications for rhino conservation. Other reports, however, suggest the increase is more likely an artefact caused by applying various home range estimators to non-standardised datasets. We collected 1939 locations of 25 black rhino over six years (2004–2009) to estimate annual home ranges and evaluate the hypothesis that they have increased in size. A minimum of 30 and 25 locations were required for accurate 95% MCP estimation of home range of adult rhinos, during the dry and wet seasons respectively. Forty and 55 locations were required for adult female and male annual MCP home ranges, respectively, and 30 locations were necessary for estimating 90% bivariate kernel home ranges accurately. Average annual 95% bivariate kernel home ranges were 20.4 ± 1.2 km², 53 ±1.9% larger than 95% MCP ranges (9.8 km² ± 0.9). When home range techniques used during the late-1960s in HiP were applied to our dataset, estimates were similar, indicating that ranges have not changed substantially in 50 years. Inaccurate, non-standardised, home range estimates and their comparison have the potential to mislead black rhino population management. We recommend that more care be taken to collect adequate numbers of rhino locations within standardized time periods (i.e., season or year) and that the comparison of home ranges estimated using dissimilar procedures be avoided. Home range studies of black rhino have been data deficient and procedurally inconsistent. Standardisation of methods is required.     

Extreme home range sizes among Eurasian lynx at the northern edge of their biogeographic range

Eurasian lynx (Lynx lynx) have a wide distribution across Eurasia. The northern edge of this distribution is in Norway, where they reach up to 72 degrees north. We conducted a study of lynx space use in this region from 2007 to 2013 using GPS telemetry. The home range sizes averaged 2,606 (± 438 SE) km² for males (n = 9 ranges) and 1,456 (± 179 SE) km² for females (n = 24 ranges). These are the largest home ranges reported for any large felid, and indeed are only matched by polar bears, arctic living wolves, and grizzly bears among all the Carnivora. The habitat occupied was almost entirely treeless alpine tundra, with home ranges only containing from 20% to 25% of forest. These data have clear implications for the spatial planning of lynx management in the far north as the current management zones are located in unsuitable habitats and are not large enough to encompass individual lynx movements.     

野放普氏野马(Equus przewalskii)家域面积及其影响因素

采用MCP方法研究了2011年至2012年新疆卡拉麦里山有蹄类自然保护区野放普氏野马家域的变化。通过方差分析验证了年间、季节间不同群体家域及其两两重叠无差异。以家族群大小为协变量进行了野放野马家域协方差分析。利用野放野马家族大小为协变量的协方差分析分析检验了野放野马家族大小与家域关系。结果表明:(1)野马平均家域面积由2011年的(20±2)km~2/匹扩大到2012年的(30±2)km~2/匹。对部分野放群体中头马未发生更替的野马群的研究表明,随着野马群体增大,其家域面积显著增大(P0.05)。(2)单因素方差分析显示,不同野马群的家域面积在不同年份差异显著,且春季家域秋季家域夏季家域。(3)2011年不同群家域两两间相互重叠面积与群大小无显著相关(r=0.256,P=0.5800.05)。而2012年野马群家域两两之间重叠面积有显著差异(F=4.521,df=8,P0.001)。家域两两相互重叠面积与群大小显著相关(r=0.706,P=0.0330.05)。(4)不同季节间野马群家域重叠面积有显著差异(F=5.695,df=8,P0.001)。5号群、7号群和8号群的自身家域重叠面积(P0.05),3号群、6号群和9号群的家域重叠面积(P0.05)。(5)影响野放野马家域面积的生物因子有草本盖度、灌木盖度,非生物因子主要有温度、湿度、风速、最近水源地距离和最近居民点距离等。温度与草本盖度是影响野放野马家域面积大小的主要因素,两者与野放野马家域面积显著相关(P0.01)。     

Life in Unpredictable Environments: First Investigation of the Natural History of Microcebus griseorufus

The dry spiny forest of southern Madagascar is a highly unpredictable environment in terms of the amount and distribution of rainfall. The region is also subject to marked El Niño oscillations. One of the inhabitants of the region is Microcebus griseorufus (Kollman, 1910), the reddish-grey mouse lemur. During the 4 yr of the study, the focal population underwent marked fluctuations in size and exhibited a relatively long reproductive season: September–May. Subjects used daily torpor and expressed opportunistic seasonal fattening when food availability was high. They fed mainly on gum, especially during periods of drought. The estimated sex-ratio of the population is 54% female. Young males dispersed. Females and less frequently, males, associated in same-sex pairs that sometimes joined to form larger sleeping groups. I observed both erratic and resident males, the latter sometimes associated with females in sleeping groups. Mating occurred from September to January and involved mate-guarding. Individual female home ranges (N?=?14) overlapped with, on average, 2.8?±?0.3 male home ranges (range 2–5), whereas individual male home ranges (N?=?12) overlapped with 4.7?±?0.4 female home ranges (range 2–7). Female estrus was not synchronized, even within the female pairs, allowing alloparental care. Gestation lasted 52 d in 1 female, and litter size could be as high as 3; 20 reproductive females out of 37 adult females raised only 1 or 2 young per year.     

Determining Observer Reliability in Counts of River Otter Tracks

ABSTRACT In many research projects, reliability of collected data is dependent on reliability of field observers. However, it is uncommon for observer reliability to be either measured or reported in wildlife research. We tested whether observer skill affected outcomes of a northern river otter (Lontra canadensis) track survey conducted by the Texas Parks and Wildlife Department. Observers recorded presence of tracks at bridge sites (n = 250) throughout a 27-county region in east Texas, USA. Logistic regression indicated that observers were significantly associated with frequency of reported otter tracks. Because observers were not assigned to bridges at random, we tested and found associations between the bridges surveyed by each observer (SURVEY ROUTE) and habitat variables (WATERSHED, VEGETATION-TYPE, WATER-TYPE, BRIDGE-AREA) that may have influenced otter presence and probability of detection. A standardized tracker evaluation procedure indicated that experienced observers (n = 7) misidentified 37% of otter tracks. Additionally, 26% of tracks from species determined to be “otter-like” were misidentified as otter tracks. We recommend that observer skill in identification of animal tracks and other indirect signs be measured to detect and reduce observer errors in wildlife monitoring.     

Time geography and wildlife home range delineation

We introduce a new technique for delineating animal home ranges that is relatively simple and intuitive: the potential path area (PPA) home range. PPA home ranges are based on existing theory from time geography, where an animal's movement is constrained by known locations in space–time (i.e., n telemetry points) and a measure of mobility (e.g., maximum velocity). Using the formulation we provide, PPA home ranges can be easily implemented in a Geographic Information System (GIS). The advantage of the PPA home range is the explicit consideration of temporal limitations on animal movement. In discussion, we identify the PPA home range as a stand-alone measure of animal home range or as a way to augment existing home range techniques. Future developments are highlighted in the context of the usefulness of time geography for wildlife movement analysis. To facilitate the adoption of this technique we provide a tool for implementing this method. © 2011 The Wildlife Society.     

Admixture between released and wild game birds: a changing genetic landscape in European mallards (<Emphasis Type="Italic">Anas platyrhynchos</Emphasis>)

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n?=?171 and n?=?209, respectively) as well as farmed (n?=?211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.     

Thermal acclimation of photosynthesis: on the importance of adjusting our definitions and accounting for thermal acclimation of respiration

While interest in photosynthetic thermal acclimation has been stimulated by climate warming, comparing results across studies requires consistent terminology. We identify five types of photosynthetic adjustments in warming experiments: photosynthesis as measured at the high growth temperature, the growth temperature, and the thermal optimum; the photosynthetic thermal optimum; and leaf-level photosynthetic capacity. Adjustments of any one of these variables need not mean a concurrent adjustment in others, which may resolve apparently contradictory results in papers using different indicators of photosynthetic acclimation. We argue that photosynthetic thermal acclimation (i.e., that benefits a plant in its new growth environment) should include adjustments of both the photosynthetic thermal optimum (T _opt) and photosynthetic rates at the growth temperature (A _growth), a combination termed constructive adjustment. However, many species show reduced photosynthesis when grown at elevated temperatures, despite adjustment of some photosynthetic variables, a phenomenon we term detractive adjustment. An analysis of 70 studies on 103 species shows that adjustment of T _opt and A _growth are more common than adjustment of other photosynthetic variables, but only half of the data demonstrate constructive adjustment. No systematic differences in these patterns were found between different plant functional groups. We also discuss the importance of thermal acclimation of respiration for net photosynthesis measurements, as respiratory temperature acclimation can generate apparent acclimation of photosynthetic processes, even if photosynthesis is unaltered. We show that while dark respiration is often used to estimate light respiration, the ratio of light to dark respiration shifts in a non-predictable manner with a change in leaf temperature.     

A comparison of methods for classifying clinical samples based on proteomics data: a case study for statistical and machine learning approaches

The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called “omics” disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS) and Principal Components Analysis (PCA) followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM). Both PLS and SVM demonstrate strong utility for proteomic classification problems.     

Spacing pattern in a social group of stray cats: effects on male reproductive success

Reproductive consequences of male spacing patterns have received relatively little attention in nonterritorial mammals, in particular in group-living species, where most studies have focused on the relation between social rank and reproductive success. We investigated the effects of spacing pattern on male reproductive success within a social, nonterritorial, promiscuous population of stray cats, Felis catus. Male home ranges overlapped home ranges of many females, consistent with a promiscuous mating system. Furthermore, males with the largest home ranges included the most female home ranges; they successfully reproduced with these females and had the highest reproductive success. Home range size predicted male reproductive success even when controlling for the effect of social rank. However, males also reproduced with females whose home range did not overlap their home range, suggesting that males can make quick excursions outside their home range to find new mating opportunities. We conclude that, in group-living situations, a male's ability to maintain a large home range may be one of the principal causes of variation in mating success in the stray cat.     

Effects of sampling regime on the mean and variance of home range size estimates

1. Although the home range is a fundamental ecological concept, there is considerable debate over how it is best measured. There is a substantial literature concerning the precision and accuracy of all commonly used home range estimation methods; however, there has been considerably less work concerning how estimates vary with sampling regime, and how this affects statistical inferences. 2. We propose a new procedure, based on a variance components analysis using generalized mixed effects models to examine how estimates vary with sampling regime. 3. To demonstrate the method we analyse data from one study of 32 individually marked roe deer and another study of 21 individually marked kestrels. We subsampled these data to simulate increasingly less intense sampling regimes, and compared the performance of two kernel density estimation (KDE) methods, of the minimum convex polygon (MCP) and of the bivariate ellipse methods. 4. Variation between individuals and study areas contributed most to the total variance in home range size. Contrary to recent concerns over reliability, both KDE methods were remarkably efficient, robust and unbiased: 10 fixes per month, if collected over a standardized number of days, were sufficient for accurate estimates of home range size. However, the commonly used 95% isopleth should be avoided; we recommend using isopleths between 90 and 50%. 5. Using the same number of fixes does not guarantee unbiased home range estimates: statistical inferences differ with the number of days sampled, even if using KDE methods. 6. The MCP method was highly inefficient and results were subject to considerable and unpredictable biases. The bivariate ellipse was not the most reliable method at low sample sizes. 7. We conclude that effort should be directed at marking more individuals monitored over long periods at the expense of the sampling rate per individual. Statistical results are reliable only if the whole sampling regime is standardized. We derive practical guidelines for field studies and data analysis.     

Aspects of northern bobwhite ecology on south Florida US pastureland

During 2004 and 2005, we monitored breeding season survival, home range, habitat use, density, and reproduction of northern bobwhite (Colinus virginianus) in the peninsular region of Florida, USA. We radio-tagged 81 birds across a 20-km² cattle ranch consisting predominately of rotationally grazed pastureland. Birds were radio-tracked three to five times per week until mortality or the transition to nonbreeding season. We found no difference in home range size among the sexes, ages, or their interaction. Mean home range size pooled for years, sexes, and age class was 56.28 ha (±7.87 SE). Home ranges of bobwhites were not distributed among habitats randomly (second order: Λ?=?0.10; 7, 35 df; P?=?0.002). In addition, bobwhites did not use the habitats within their home range at random (third order: Λ?=?0.14, 5, 35 df; P?=?0.02). Estimated seasonal survival was 0.28 (±0.12 SE) and was best explained by the time-dependent model. Reproductive metrics indicated adequate reproduction and values consistent with the bobwhite literature. Bobwhite density (birds per hectare) in 2004 was 0.52 (±0.54 95 % confidence interval [CI]) and 0.75 (±0.51 95 % CI) for 2005. These results suggest that pastureland landscapes managed with rotational grazing can support bobwhite populations, albeit at low densities. More conservation attention should be directed towards improving these systems for bobwhite restoration.     

Poor health is associated with use of anthropogenic resources in an urban carnivore

Rates of encounters between humans and wildlife are increasing in cities around the world, especially when wildlife overlap with people in time, space and resources. Coyotes (Canis latrans) can make use of anthropogenic resources and reported rates of conflict have increased in cities across North America. This increase may be linked to individual differences in the use of human food and developed areas. We compared the relationships between coyote age, sex or health and the use of anthropogenic resources, which we defined as using developed areas over large home ranges, being active during the day, and consuming anthropogenic food. To do so, we applied GPS collars to 19 coyotes and sampled hair for stable isotope analysis. Eleven coyotes appeared to be healthy and eight were visibly infested with sarcoptic mange (Sarcoptes scabiei), a mite that causes hair loss. Diseased coyotes used more developed areas, had larger monthly home ranges, were more active during the day, and assimilated less protein than coyotes that appeared to be healthy. We speculate that anthropogenic food provides a low-quality but easily accessible food source for diseased coyotes, which in turn may increase reliance on it and other anthropogenic resources to promote encounters with people.     

Using abundance and habitat variables to identify high conservation value areas for threatened mammals

The present study used abundance and habitat variables to design High Conservation Value Forests for wildlife protection. We considered great apes (Gorilla gorilla gorilla and Pan troglodytes troglodytes) as model species, and we used nest surveys, dietary analysis and botanical inventories to evaluate whether the traditional methods that use abundance data alone were consistent with the survival of the species. We assumed that setting a local priority area for animal conservation can be made possible if at least one variable (abundance or habitat variables) is spatially clustered and that the final decision for a species may depend on the pattern of spatial association between abundance, nesting habitat and feeding habitat. We used Kernel Density Estimation to evaluate the spatial pattern of each biological variable. The results indicate that all three variables were spatially clustered for both gorillas and chimpanzees. The abundance variables of both animal species were spatially correlated to their preferred nesting habitat variables. But while the chimpanzee feeding habitat variable was spatially correlated to the abundance and nesting habitat variables, the same pattern was not observed for gorillas. We then proposed different methods to be considered to design local priority areas for the conservation of each great ape species. Alone, the abundance variable does not successfully represent the spatial distribution of major biological requirements for the survival of wildlife species; we, therefore, recommend the integration of the spatial distribution of their food resources to overcome the mismatch caused by the existence of a biological interaction between congeneric species.     

Effects of high density on spacing behaviour and reproduction in Akodon azarae: A fencing experiment

We studied the short term spacing behavioural responses of Pampean grassland mouse (Akodon azarae) with regard to population density in four 0.25 ha enclosures (two control and two experimental) in the 2011 breeding season. Based on the hypothesis that A. azarae breeding females exhibit spacing behaviour, and breeding males show a fusion spatial response, we tested the following predictions: (1) home range size and intrasexual overlap degree of females are independent of population density values; (2) at high population density, home range size of males decreases and the intrasexual home range overlap degree increases. To determine if female reproductive success decreases at high population density, we analyzed pregnancy rate, size and weight of litters, and period until fecundation in both low and high enclosure population density. We found that both males and females varied their home range size in relation to population density. Although male home ranges were always bigger than those of females in populations with high density, home range sizes of both sexes decreased. Females kept exclusive home ranges independent of density values meanwhile males decreased home range overlap in high breeding density populations. Although females produced litters of similar size in both treatments, weight of litter, pregnant rate and period until fecundation varied in relation to population density. Our results did not support the hypothesis that at high density females of A. azarae exhibit spacing behaviour neither that males exhibit a fusion spatial response.