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Deer (Cervidae) are key components of many ecosystems and estimating deer abundance or density is important to understanding these roles. Many field methods have been used to estimate deer abundance and density, but the factors determining where, when, and why a method was used, and its usefulness, have not been investigated. We systematically reviewed journal articles published during 2004–2018 to evaluate spatio‐temporal trends in study objectives, methodologies, and deer abundance and density estimates, and determine how they varied with biophysical and anthropogenic attributes. We also reviewed the precision and bias of deer abundance estimation methods. We found 3,870 deer abundance and density estimates. Most estimates (58%) were for white‐tailed deer (Odocoileus virginianus), red deer (Cervus elaphus), and roe deer (Capreolus capreolus). The 6 key methods used to estimate abundance and density were pedestrian sign (track or fecal) counts, pedestrian direct counts, vehicular direct counts, aerial direct counts, motion‐sensitive cameras, and harvest data. There were regional differences in the use of these methods, but a general pattern was a temporal shift from using harvest data, pedestrian direct counts, and aerial direct counts to using pedestrian sign counts and motion‐sensitive cameras. Only 32% of estimates were accompanied by a measure of precision. The most precise estimates were from vehicular spotlight counts and from capture–recapture analysis of images from motion‐sensitive cameras. For aerial direct counts, capture–recapture methods provided the most precise estimates. Bias was robustly assessed in only 16 studies. Most abundance estimates were negatively biased, but capture–recapture methods were the least biased. The usefulness of deer abundance and density estimates would be substantially improved by 1) reporting key methodological details, 2) robustly assessing bias, 3) reporting the precision of estimates, 4) using methods that increase and estimate detection probability, and 5) staying up to date on new methods. The automation of image analysis using machine learning should increase the accuracy and precision of abundance estimates from direct aerial counts (visible and thermal infrared, including from unmanned aerial vehicles [drones]) and motion‐sensitive cameras, and substantially reduce the time and cost burdens of manual image analysis. [ABSTRACT FROM AUTHOR]

Introduced ungulates are an important management issue on New Zealand's public conservation land (PCL). Ungulates are harvested by recreational and commercial hunters, with some government-funded culling. A robust monitoring system is needed to reliably report trends in occupancy and abundance, and to evaluate management effectiveness. We first describe the design and implementation of a monitoring programme enabling ungulate occupancy and relative abundances to be estimated on New Zealand's PCL. Monitoring sites are located at the vertices of an 8-km grid superimposed over PCL on North, South and Stewart/Rakiura islands (i.e. a spatially representative sampling network). At each site, intact ungulate pellets are counted on four transects radiating from a 400 m2 vegetation plot, with each 150 m transect containing 30 1-m radius plots. We next report an analysis of the first such data collected at 1346 sites during 2012-2018. Nationally, ungulate occupancy and abundance were higher at woody than at non-woody sites, and overall were higher in the North Island than in the South Island. Occupancy odds increased by 34% and 21% per annum in the North Island and South Island, respectively. Abundance (conditional on sites being occupied) increased 11% annually in the North Island, but did not change in the South Island. These increases in occupancy and abundance indicate that ungulate populations are recovering from the lows of the 1980s, likely due to reduction in both commercial harvesting and government-funded control. The data from the monitoring reported here establish a baseline against which future estimates of ungulate occupancy-abundance, and the effectiveness of management activities, can be assessed. Five-yearly remeasurements at the sites, coupled with more comprehensive recording of information on government control and commercial/recreational harvesting activities, should enable the drivers of future changes in ungulate occupancy and abundance to be better understood. [ABSTRACT FROM AUTHOR]

Exposure of scavenging wildlife to lead from ammunition is a worldwide problem for wildlife management, but there has been little research on this topic in Australia. To examine which species of scavenging birds are potentially at risk of harmful exposure to lead, we deployed camera-traps to observe avian scavenger behaviour on carcasses of non-native and native mammals shot with lead-based bullets in two different locations in Victoria. We monitored 30 Sambar Deer Rusa unicolor carcasses in temperate eastern Victoria and 48 kangaroo Macropus spp. carcasses in semi-arid north-western Victoria. At least eight avian taxa scavenged from carcasses, including Wedge-tailed Eagles Aquila audax, Little Eagles Hieraaetus morphnoides, Brown Goshawks Accipiter fasciatus, Whistling Kites Haliastur sphenurus, ravens/crows Corvus spp., and three species belonging to the family Artamidae. Fifty-six percent of all carcasses were visited by birds. Corvids visited the most carcasses and typically arrived first, whereas Wedge-tailed Eagles arrived second but individually spent more time feeding. Our results indicate that a diverse avian scavenger community consumes carcasses of shot mammals in Australia, and consequently could be exposed to lead from bullet fragments. [ABSTRACT FROM AUTHOR]

Identifying landscape features and processes that facilitate the persistence of populations is particularly important for invasive mammal species, because it can focus management interventions on relatively small areas. We used camera traps to test predictions concerning the relative abundance of invading chital deer (Axis axis) on seven cattle ranches in northern Australia: that abundance of chital deer would be highest near permanent water and near homesteads, and that dingoes (Canis dingo) reduce abundance of chital deer. Distance from the nearest homestead determined deer abundance (as indexed by images per camera-day), with negligible abundance > 4 km from homesteads. In contrast, distance from homestead did not predict abundance of feral pigs (Sus scrofa), macropods, or dingoes. Abundance of chital deer also declined with increasing distance from water, as did feral pig abundance. There was no relationship between either macropod or dingo abundance and distance to water. The abundance of chital deer was unaffected by dingo abundance, but 75–100% of dingo scats collected within 1 km of homesteads contained chital deer. The high abundances of chital deer near homesteads are likely due to increased food quality or quantity, or protection from dingoes, but these hypotheses require further testing. We conclude that homesteads and permanent water are important determinants of the distribution and abundance of invasive chital deer in northern Australia (i.e. they are "invasion hubs" for this species). Our results suggest that, during the dry season, managers should survey for and attempt to control chital deer within 4 km of homesteads and within 3 km of water. [ABSTRACT FROM AUTHOR]

Although fecal pellet counts have been widely used to index changes in deer abundance in forests, few studies have modeled the relationship between the indices and deer density. We examined the relationships between 3 fecal pellet indices (total pellets, pellet groups, and pellet frequency) and the density of deer (primarily red deer [Cervus elaphus scoticus]) in 20 enclosures in the North and South islands of New Zealand. In each enclosure we estimated the 3 indices on 30 randomly located 150-m transects, with each transect having 30 circular plots of 3.14 m². We developed 4 candidate models (1 linear and 3 nonlinear) to describe the relationship between the indices and deer density. We used a Bayesian analysis to account for uncertainty in the estimates of deer abundance and to facilitate fitting models that included random transect effects. The 4 models explained the relationship between the 3 indices and deer density similarly well. The slopes of the linear relationships between the 3 indices and deer density were positive. Our results suggest that fecal pellet counts may be useful indices of deer abundance. [ABSTRACT FROM AUTHOR]

Avoiding the undesirable impacts of invasive species requires robustly evaluating the effects of alternative management scenarios. Such evaluations depend on reliable spatio‐temporal projections of changes in the distribution and abundance of the invasive species under different scenarios. However, commonly used modelling approaches are constrained for this purpose because they do not incorporate demographic processes and are seldom validated.We develop a spatially and temporally explicit grid‐based population model for invasive fallow deer Dama dama in Tasmania, Australia, validated against observed distribution and abundance 'targets' using a pattern‐oriented approach. We use this validated model to project the future invasion patterns of deer, including encroachment into areas of high conservation value, under eight harvest and habitat suitability scenarios.Projected population sizes of deer differ greatly depending on harvest and habitat suitability scenarios. Without harvest, the population grows sixfold, from about 80,000 deer in 2019 to over 500,000 by 2100. In contrast, the population stabilises at 32,000–41,000 deer with 25% annual harvest. Abundance in the environmentally sensitive Tasmanian Wilderness World Heritage Area (TWWHA), a region of high conservation value, increases in all scenarios. We identify likely areas in the expanding range of deer where targeted removal should be most effective at minimising deer numbers in the TWWHA.Synthesis and applications: Using a pattern‐oriented model validated with spatio‐temporal data, we show how the future distribution and abundance of invasive fallow deer in Tasmania can be substantially reduced by targeted increases in harvest and prioritising areas for removal around high conservation value regions. Our approach can be used to project likely effects of management interventions on future distributions and abundances for a range of invasive taxa. [ABSTRACT FROM AUTHOR]

Invasive deer have undesirable impacts on native ecosystems. Culling is commonly used to reduce those impacts, but is expensive and sometimes controversial. It is therefore important to robustly assess how culling reduces the impacts of invasive deer.We conducted a Before‐After Control‐Impact (BACI) experiment to determine how culling affects the impacts of invasive sambar deer Cervus unicolor in an endangered alpine peatland ecosystem in south‐eastern Australia. We established two blocks, each with four 4300‐ha experimental units, in which two units were randomly assigned to a treatment of deer culling and the other two were non‐treatment areas. Sambar deer relative abundance (faecal pellet count) and three impacts (ground degradation, pugging intensity and water turbidity) in three peatland features (peatlands, natural pools and sambar deer wallows) were surveyed before and after culling was implemented. We used four metrics to quantify the culling intensity in each treatment unit: treatment versus non‐treatment, number of deer culled on each unit, deer culled within a 500‐m buffer of impact monitoring sites and local probability of use by the cullers (1‐ha grid). The effects of culling on deer abundance and impacts were estimated using Bayesian generalised linear mixed models.Our analysis revealed that the effect of culling differed between the two experimental blocks. In one block, culling reduced deer abundance and three impacts. In the other block, culling did not reduce deer abundance but reduced three impacts and increased two impacts. The effects of culling were generally stronger when culling was estimated using finer‐scale (500‐m) than coarser‐scale (experimental unit) culling metrics.Synthesis and applications. Our study provides experimental evidence that culling invasive sambar deer reduces some of their undesirable impacts on endangered peatlands. That not all impacts were reduced by culling suggests that some effects of invasive species are slow to recover or require higher culling intensities to be reversed. [ABSTRACT FROM AUTHOR]

Infections with the coccidian parasite Neospora caninum affect domestic and wild animals worldwide. In Australia, N. caninum infections cause considerable losses to the cattle industry with seroprevalence of 8.7% in beef and 10.9% in dairy cattle. Conversely, the role of wild animals, in maintaining the parasite cycle is also unclear. It is possible that native or introduced herbivorous species could be reservoir hosts of N. caninum in Australia, but to date, this has not been investigated. We report here the first large-scale screening of N. caninum antibodies in Australian wild deer, spanning three species (fallow, red and sambar deer). Consequently, we also assessed two commercial cELISA tests validated for detecting N. caninum in cattle for their ability to detect N. caninum antibodies in serum samples of wild deer. N. caninum antibodies were detected in 3.7% (7/189, 95% CI 1.8 – 7.45) of the wild deer serum samples collected in south-eastern Australia (n = 189), including 97 fallow deer (Dama dama), 14 red deer (Cervus elaphus), and 78 sambar deer (Rusa unicolor). Overall, our study provides the first detection of N. caninum antibodies in wild deer and quantifies deer's potential role in the sylvatic cycle of N. caninum. [ABSTRACT FROM AUTHOR]

Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host's germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV β1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV β1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV β1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV β1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids. [ABSTRACT FROM AUTHOR]

Since deer were introduced into Australia in the mid-1800s, their wild populations have increased in size and distribution, posing a potential risk to the livestock industry, through their role in pathogen transmission cycles. In comparison to livestock, there are limited data on viral infections in all wildlife, including deer. The aim of this study was to assess blood samples from wild Australian deer for serological evidence of exposure to relevant viral livestock diseases. Blood samples collected across eastern Australia were tested by ELISA to detect antigens and antibodies against Pestivirus and antibodies against bovine herpesvirus 1. A subset of samples was also assessed by RT-PCR for Pestivirus, Simbu serogroup, epizootic hemorrhagic disease virus and bovine ephemeral fever virus. Our findings demonstrated a very low seroprevalence (3%) for ruminant Pestivirus, and none of the other viruses tested were detected. These results suggest that wild deer may currently be an incidental spill-over host (rather than a reservoir host) for Pestivirus. However, deer could be a future source of viral infections for domestic animals in Australia. Further investigations are needed to monitor pathogen activity and quantify possible future infectious disease impacts of wild deer on the Australian livestock industry. [ABSTRACT FROM AUTHOR]

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as "Bopivirus C". Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8–15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species. [ABSTRACT FROM AUTHOR]

Picobirnaviruses (PBVs) have been detected in several species of animals worldwide; however, data pertaining to their presence in Australian wild and domestic animals are limited. Although PBVs are mostly found in faecal samples, their detection in blood and respiratory tract samples raises questions concerning their tropism and pathogenicity. We report here PBV detection in wild deer and cattle from southeastern Australia. Through metagenomics, the presence of PBV genogroups I (GI) and II (GII) were detected in deer serum and plasma. Molecular epidemiology studies targeting the partial RNA-dependent RNA polymerase gene were performed in a wide range of specimens (serum, faeces, spleen, lung, nasal swabs, and trachea) collected from wild deer and cattle, with PCR amplification obtained in all specimen types except lung and spleen. Our results reveal the predominance of GI and concomitant detection of both genogroups in wild deer and cattle. In concordance with other studies, the detected GI sequences displayed high genetic diversity, however in contrast, GII sequences clustered into three distinct clades. Detection of both genogroups in the upper respiratory tract (trachea and nasal swab) of deer in the present study gives more evidence about the respiratory tract tropism of PBV. Although much remains unknown about the epidemiology and tropism of PBVs, our study suggests a wide distribution of these viruses in southeastern Australia. [ABSTRACT FROM AUTHOR]