The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.     

Chronic Wasting Disease: Transmission Mechanisms and the Possibility of Harvest Management

We develop a model of CWD management by nonselective deer harvest, currently the most feasible approach available for managing CWD in wild populations. We use the model to explore the effects of 6 common harvest strategies on disease prevalence and to identify potential optimal harvest policies for reducing disease prevalence without population collapse. The model includes 4 deer categories (juveniles, adult females, younger adult males, older adult males) that may be harvested at different rates, a food-based carrying capacity, which influences juvenile survival but not adult reproduction or survival, and seasonal force of infection terms for each deer category under differing frequency-dependent transmission dynamics resulting from environmental and direct contact mechanisms. Numerical experiments show that the interval of transmission coefficients β where the disease can be controlled is generally narrow and efficiency of a harvest policy to reduce disease prevalence depends crucially on the details of the disease transmission mechanism, in particular on the intensity of disease transmission to juveniles and the potential differences in the behavior of older and younger males that influence contact rates. Optimal harvest policy to minimize disease prevalence for each of the assumed transmission mechanisms is shown to depend on harvest intensity. Across mechanisms, a harvest that focuses on antlered deer, without distinguishing between age classes reduces disease prevalence most consistently, whereas distinguishing between young and older antlered deer produces higher uncertainty in the harvest effects on disease prevalence. Our results show that, despite uncertainties, a modelling approach can determine classes of harvest strategy that are most likely to be effective in combatting CWD.     

Genetic assessment of environmental features that influence deer dispersal: implications for prion-infected populations

The landscape can influence host dispersal and density, which in turn, affect infectious disease transmission, spread, and persistence. Understanding how the landscape influences wildlife dispersal and pathogen epidemiology can enhance the efficacy of disease management in natural populations. We applied landscape genetics to examine relationships among landscape variables, dispersal of white-tailed deer hosts and transmission/spread of chronic wasting disease (CWD), a fatal prion encephalopathy. Our focus was on quantifying movements and population structure of host deer in infected areas as a means of predicting the spread of this pathology and promoting its adaptive management. We analyzed microsatellite genotypes of CWD-infected and uninfected deer from two disease foci (Southern Wisconsin, Northern Illinois). We quantified gene flow and population structure using F _ST, assignment tests, and spatial autocorrelation analyses. Gene flow estimates were then contrasted against a suite of landscape variables that potentially mediate deer dispersal. Forest fragmentation and grassland connectivity promoted deer movements while rivers, agricultural fields and large urbanized areas impeded movement. Landscape variables, deer dispersal, and disease transmission covaried significantly and positively in our analyses. Habitats with elevated host gene flow supported the concept of dispersal-mediated CWD transmission by reflecting a concomitant, rapid CWD expansion. Large, interrelated social groups isolated by movement barriers overlapped disease foci, suggesting that philopatry exacerbated CWD transmission. Our results promote adaptive management of CWD by predicting patterns of its spread and identifying habitats at risk for invasion. Further, our landscape genetics approach underscores the significance of topography and host behavior in wildlife disease transmission.     

Antibodies to bluetongue and epizootic hemorrhagic disease viruses in a barrier island white-tailed deer population.

From 1981 through 1989, serum samples from 855 white-tailed deer (Odocoileus virginianus) from Ossabaw Island, Georgia (USA), were tested for antibodies to bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV). During this period, prevalence of precipitating antibodies to BTV and EHDV as determined by agar gel immunodiffusion (AGID) tests decreased from 74% to 3% and from 34% to 1%, respectively. Antibodies were detected in serum samples from 0.5-yr-old deer only during 1981, 1982, and 1983, and with few exceptions, positive serological results after 1983 were restricted to older age classes. A decrease in prevalence of precipitating antibodies to BTV and EHDV in age classes exposed during 1981 indicates that AGID results from white-tailed deer populations underestimate the extent of previous exposure to these viruses. Serum neutralization test results from AGID-positive deer indicated that BTV 11 was the principal serotype responsible for infections during 1981. Since 1983, this serotype has been replaced by BTV 13; however, there has been a low level of transmission within the herd. Infection with EHDV 2 appeared most prevalent during 1982; as with BTV 13, there has been limited transmission in this high density deer population since 1983.     

Homogenization,sex, and differential motility predict spread of chronic wasting disease in mule deer in southern Utah

Chronic wasting disease (CWD) is an infectious prion disease that affects mule deer, along with other Cervids. It is a slow-developing, fatal disease which is rare in the free-ranging deer population of Utah. We present a sex-structured, spatial model for the spread of CWD over heterogeneous landscapes, incorporating both horizontal and environmental transmission pathways. To connect the local movement of deer to the regional spread of CWD, we use ecological diffusion with motility coefficients estimated from mule deer movement data. Ecological diffusion allows for aggregation of populations in desirable habitats and therefore allows for an interaction between density dependent disease transmission and landscape structure. The major innovation presented is use of homogenization to accelerate simulations of disease spread in southeastern Utah, from the La Sal Mountains near Moab to the Abajo Mountains near Monticello. The homogenized model provides accuracy while maintaining fidelity to small-scale habitat effects on deer distribution, including differential aggregation in land cover types with high residence times, with errors comparable to the order parameter measuring separation of small and large scales ( \(\epsilon \approx .01\) in this case). We use the averaged coefficients from the homogenized model to explore asymptotic invasion speed and the impact of current population size on disease spread in southeastern Utah.     

Interaction among deer in a chronic wasting disease endemic zone

Although it is known that chronic wasting disease (CWD) can be transmitted by both direct animal-to-animal contact and contact with contaminated environments, the relative role of each mechanism in the spread of CWD in free-ranging populations has yet to be defined. We investigated patterns of interaction between mule deer (Odocoileus hemionus) in order to understand how factors such as season and landscape may influence patterns of disease spread in these populations. Using location data from male and female Global Positioning System (GPS)-collared mule deer in 5 study areas located in and around a CWD-endemic zone in southern Saskatchewan, Canada, we quantified close proximity events, or events involving both spatial and temporal overlap of individuals. We defined close proximity events as occurrences in which 2 deer were located <25 m apart at the same point in time. We looked at seasonal variation in the probability of close proximity events, as well as landscape factors associated with these events when compared to areas of shared space use, or spatial overlap alone. Overall probability of an individual GPS-collared deer being located in close proximity to another GPS-collared deer was 0.092 (n = 107). The early gestation (16 Dec–31 Mar) and late gestation (1 Apr–15 May) seasons had the highest probability of close proximity events occurring, and same-sex pairs were more likely to be found in close proximity than between-sex pairs during all seasons aside from the rut (1 Nov–15 Dec). High probability of close proximity events during the gestation seasons agrees with the tendency of mule deer to aggregate into large groups during late winter and suggests that this may be an important time period for CWD transmission to occur. Close proximity events occurred more in cropland and wetland than expected based on availability, whereas close proximity events occurred less than expected in grassland. The opposite was true for spatial overlap between individuals, which occurred more than expected in areas of low elevation and rugged terrain and in grassland or shrub–wood habitats. These results suggest that cropland may be a higher risk habitat for direct and indirect CWD transmission between individuals and that, although coulees and other areas of rugged topography are less likely to be associated with close proximity events, those areas may be more likely to contain environmental contamination in CWD-affected areas due to common use by multiple deer. © 2011 The Wildlife Society.     

海南坡鹿的起源、进化及保护

坡鹿是世界濒危物种,三个亚种分布在东南亚大陆,仅海南坡鹿种群分布在中国海南岛.2003年,国际社会的专家和学者提出了将海南坡鹿引入泰国亚种原分布区,重建已经绝灭野生种群的建议.在此种情况下,明确海南坡鹿的起源、与其它亚种间的系统发生关系、以及遗传多样性水平对有效保护坡鹿具有重要意义.本研究以线粒体DNA D-loop区490 bp基因片段为分子标记,比较分析了海南坡鹿、泰国亚种和缅甸亚种共35个样本的序列差异.我们所测的样本中,总共发现4种单倍型.所有21个海南坡鹿样品共享1种单倍型.利用最大似然法(ML)、最大简约法(MP)、邻接法(NJ)和贝叶斯法(Bayesian)构建的系统进化树表明海南坡鹿种群与泰国亚种的关系较近.但是,二者也发生一定程度的遗传分化.海南坡鹿与泰国亚种的遗传距离均值为0.026.我们推测海南坡鹿可能是在更新世冰期(69万年前)通过陆桥由东南亚大陆迁入中国海南岛.我们的结论说明海南坡鹿的遗传多样性很低,并且已独立进化很长时间.因此,我们不支持将海南坡鹿引入泰国亚种的原分布区,重建已经绝灭的野生种群的设想和建议.我们建议将海南坡鹿与泰国亚种分别作为两个独立的进化显著单元(ESUs)进行管理.     

Assessing deer densities and impacts at the appropriate level for management: a review of methodologies for use beyond the site scale

• 1 Population density alone is unlikely to be a good predictor of the impacts of deer on their environment. The assessment of management requirements should therefore be based on assessment of deer impacts, alongside estimates of density.
• 2 Both density and impacts need to be monitored at a landscape scale, and there is a need to develop appropriate methodologies that allow managers to consider the current and likely future impact of deer.
• 3 The relevant scale for assessment (and management) varies both with deer species and context of impact, but should always encompass at least the estimated biological range of the population of deer present in an area. Some impacts (e.g. deer–vehicle collisions, and risks of disease transmission) may need to be assessed at a wider regional level.
• 4 In this review we consider various approaches available for assessing: absolute or relative animal abundance; impacts of ungulates on agriculture, forestry, amenity woodlands and other conservation sites; impacts on public safety (e.g. through road traffic accidents) and on humans or livestock through potential spread of disease.
• 5 In each case the advantages and disadvantages of a variety of methods are considered, before recommendations are made for methodologies which are sufficiently accurate, sufficiently robust and sufficiently practical to be favoured in a management context.
• 6 To address impacts at the landscape scale requires management policies that integrate information on both positive and negative impacts of deer in order to ensure appropriate and holistic management. We present a decision‐support framework suitable for use within the UK, using inputs from a variety of possible impact types to assist managers and forewarn of situations where current management may need to be modified.

     

Evaluating Spatial Overlap and Relatedness of White-tailed Deer in a Chronic Wasting Disease Management Zone

Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin’s area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.     

Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)

Studies of hybrid zones have revealed an array of evolutionary outcomes, yet the underlying structure is typically characterized as one of three types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary objective was to determine which of these three structures best characterizes a zone of hybridization between two divergent lineages of mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These lineages are morphologically, ecologically and genetically distinct, yet hybridize readily along a zone of secondary contact between the east and west slopes of the Cascade Mountains (Washington and Oregon, USA). Using microsatellite and mitochondrial DNA, we found clear evidence for extensive hybridization and introgression between lineages, with varying degrees of admixture across the zone of contact. The pattern of hybridization in this region closely resembles a hybrid swarm; based on data from 10 microsatellite loci, we detected hybrids that extend well beyond the F1 generation, did not detect linkage disequilibrium at the centre of the zone and found that genotypes were associated randomly within the zone of contact. Introgression was characterized as bidirectional and symmetric, which is surprising given that the zone of contact occurs along a sharp ecotone and that lineages are characterized by large differences in body size (a key component of mating success). Regardless of the underlying mechanisms promoting hybrid swarm maintenance, it is clear that the persistence of a hybrid swarm presents unique challenges for management in this region.     

Variation in the herd composition counts of sika deer

Herd composition counts (HCC) are commonly used to assess population status in deer. We evaluated the reliability of HCC of sika deer (Cervus nippon Temminck) using repeated counts and by comparing estimated sex ratios and calf-to-female ratios of marked deer on Nakanoshima Island, Hokkaido, Japan between April 1999 and October 2000. Although both total counts and sex and age ratios fluctuated greatly by month, seasonal changes showed a relatively small variance. This suggested that seasonal changes in behavior within sex and age classes contributed to biased ratio estimates obtained from HCC. Route counts should be used as a relative population abundance index with estimates of detection probability, especially for females. Adult sex ratios and age ratios from HCC were unbiased during the rutting season (October–November), and age ratios in spring could be used if yearlings are counted as adults.     

Host status of wild roe deer in bovine tuberculosis endemic areas

Rarely found infected, roe deer (Capreolus capreolus) are not considered a bovine tuberculosis (bTB) reservoir. However, serial cases discovered between 2010 and 2014 in one of the bTB endemic regions in France threw doubt on the epidemiological role played by this small wild cervid in ecosystems where cattle and other wild animals are both infected. Our objective was to analyse the bTB host status of roe deer as regards infection prevalence within the population and Mycobacterium bovis-induced pathology in this species. From November 2001 to March 2016, 668 roe deer were analysed (culture and/or PCR) through active surveillance implemented in three bTB endemic areas in France (Brotonne forest, Dordogne and Côte d’Or) and 132 through passive surveillance (presence of macroscopic lesions) in the whole country. Only seven roe deer were found infected by M. bovis, exclusively in bTB endemic areas, one through active surveillance (Brotonne forest; n = 203, apparent prevalence 0.49%). On the basis of these results, observed pathological patterns (mainly pulmonary lesions), species social behaviour (less gregarious than other ungulates) and food behaviour (mainly a selective browser), roe deer does not appear to be a true reservoir of bTB. However, once infected, it develops lesions reflecting a clear ability for bacterial excretion and therefore transmission to other species, most likely by indirect contact. It could thus be a spillover host included in a multi-host component reservoir in endemic areas. Consequently, passive surveillance is essential to detect infection and to implement specific management to limit interactions with cattle, where infected roe deer are found.     

The role of predation in disease control: a comparison of selective and nonselective removal on prion disease dynamics in deer

Effective measures for controlling chronic wasting disease (CWD), a contagious prion disease of cervids, remain elusive. We review theoretic relationships between predation and host-parasite dynamics and describe a mathematical model to evaluate the potential influence of random removal through harvest or culling and selective predation by wolves (Canis lupus) upon CWD dynamics in deer (Odocoileus spp.) populations. Imposing nonselective mortality representing a 15% annual harvest or cull 51 yr after CWD introduction lowered both deer population size and steady state CWD. Selective (4×) mortality at the same 15% predation rate caused a more modest reduction in deer population size accompanied by a relatively rapid decline in CWD prevalence and elimination of the disease from a closed population. The impacts of selective predation on epidemic dynamics were sensitive to assumptions on parameter estimates; however, within expected ranges, the results of selective predation were consistent and robust. We suggest that as CWD distribution and wolf range overlap in the future, wolf predation may suppress disease emergence or limit prevalence.     

基于微卫星位点的人工圈养豚鹿亲子关系鉴定

豚鹿属我国国家I级重点保护动物,目前国内野生种群已经灭绝,人工圈养数量少,已极度濒危。成都动物园是国内最大的豚鹿饲养单位,对该园内豚鹿进行亲子鉴定及遗传谱系建立是我国豚鹿拯救工程中一重要环节。本文利用7个微卫星标记对成都动物园27只豚鹿个体进行了基因分型,在母本已知情况下成功鉴定了13对父子关系,其中排除法鉴定8对,似然法鉴定5对且置信度达95%。将亲子鉴定的结果辅以动物园豚鹿圈养的历史记录,我们构建了该园豚鹿的遗传谱系图。本文的研究成果将为后续人工繁殖中亲本雌雄配对的个体选择以及种群的遗传管理提供参考。     

Modeling routes of chronic wasting disease transmission: environmental prion persistence promotes deer population decline and extinction

Chronic wasting disease (CWD) is a fatal disease of deer, elk, and moose transmitted through direct, animal-to-animal contact, and indirectly, via environmental contamination. Considerable attention has been paid to modeling direct transmission, but despite the fact that CWD prions can remain infectious in the environment for years, relatively little information exists about the potential effects of indirect transmission on CWD dynamics. In the present study, we use simulation models to demonstrate how indirect transmission and the duration of environmental prion persistence may affect epidemics of CWD and populations of North American deer. Existing data from Colorado, Wyoming, and Wisconsin's CWD epidemics were used to define plausible short-term outcomes and associated parameter spaces. Resulting long-term outcomes range from relatively low disease prevalence and limited host-population decline to host-population collapse and extinction. Our models suggest that disease prevalence and the severity of population decline is driven by the duration that prions remain infectious in the environment. Despite relatively low epidemic growth rates, the basic reproductive number, R(0), may be much larger than expected under the direct-transmission paradigm because the infectious period can vastly exceed the host's life span. High prion persistence is expected to lead to an increasing environmental pool of prions during the early phases (i.e. approximately during the first 50 years) of the epidemic. As a consequence, over this period of time, disease dynamics will become more heavily influenced by indirect transmission, which may explain some of the observed regional differences in age and sex-specific disease patterns. This suggests management interventions, such as culling or vaccination, will become increasingly less effective as CWD epidemics progress.     

Mandibular osteomyelitis in red deer (Cervus elaphus hispanicus) and fallow deer (Dama dama): occurrence and associated factors in free-living populations in southern Spain

The prevalence of mandibular osteomyelitis, which results in a condition called lumpy jaw, and factors associated with its occurrence were investigated in syntopic free-living populations of red deer (Cervus elaphus hispanicus) and fallow deer (Dama dama) in Spain. The study material consisted of 3,586 mandibles from 2,548 red deer and 1,038 fallow deer shot during sport hunting, herd management culls, and programs for population control between 1988 and 1997 (period 1) and 2002 and 2009 (period 2) in eastern Sierra Morena, southern Spain. Disease prevalence ranged from 0.36% to 10.91% among age groups. Older animals were significantly more likely to be affected than younger ones. Red deer stags had higher prevalence than other groups. There was a significantly higher prevalence in period 1, probably associated with differences in climatic and population conditions. High population densities of female red deer contributed significantly to occurrence of disease. Intensive herd management and poor environmental conditions were considered risk factors that increased susceptibility to disease. The study of this affliction could be useful for monitoring general herd welfare and ecologic changes in Mediterranean ecosystems.     

Phylogeography and conservation genetics of Eld's deer (Cervus eldi)

Eld's deer (Cervus eldi) is a highly endangered cervid, distributed historically throughout much of South Asia and Indochina. We analysed variation in the mitochondrial DNA (mtDNA) control region for representatives of all three Eld's deer subspecies to gain a better understanding of the genetic population structure and evolutionary history of this species. A phylogeny of mtDNA haplotypes indicates that the critically endangered and ecologically divergent C. eldi eldi is related more closely to C. e. thamin than to C. e. siamensis, a result that is consistent with biogeographic considerations. The results also suggest a strong degree of phylogeographic structure both between subspecies and among populations within subspecies, suggesting that dispersal of individuals between populations has been very limited historically. Haplotype diversity was relatively high for two of the three subspecies (thamin and siamensis), indicating that recent population declines have not yet substantially eroded genetic diversity. In contrast, we found no haplotype variation within C. eldi eldi or the Hainan Island population of C. eldi siamensis, two populations which are known to have suffered severe population bottlenecks. We also compared levels of haplotype and nucleotide diversity in an unmanaged captive population, a managed captive population and a relatively healthy wild population. Diversity indices were higher in the latter two, suggesting the efficacy of well-designed breeding programmes for maintaining genetic diversity in captivity. Based on significant genetic differentiation among Eld's deer subspecies, we recommend the continued management of this species in three distinct evolutionarily significant units (ESUs). Where possible, it may be advisable to translocate individuals between isolated populations within a subspecies to maintain levels of genetic variation in remaining Eld's deer populations.     

Widespread hybridization in the introduced hog deer population of Victoria,Australia, and its implications for conservation

In Australia, many species have been introduced that have since undergone drastic declines in their native range. One species of note is the hog deer (Axis porcinus) which was introduced in the 1860s to Victoria, Australia, and has since become endangered in its native range throughout South‐East Asia. There is increased interest in using non‐native populations as a source for genetic rescue; however, considerations need to be made of the genetic suitability of the non‐native population. Three mitochondrial markers and two nuclear markers were sequenced to assess the genetic variation of the Victorian population of hog deer, which identified that the Victorian population has hybrid origins with the closely related chital (Axis axis), a species that is no longer present in the wild in Victoria. In addition, the mitochondrial D‐loop region within the Victorian hog deer is monomorphic, demonstrating that mitochondrial genetic diversity is very low within this population. This study is the first to report of long‐term persistence of hog deer and chital hybrids in a wild setting, and the continual survival of this population suggests that hybrids of these two species are fertile. Despite the newly discovered hybrid status in Victorian hog deer, this population may still be beneficial for future translocations within the native range. However, more in‐depth analysis of genetic diversity within the Victorian hog deer population and investigation of hybridization rates within the native range are necessary before translocations are attempted.     

Spatial and Temporal Analysis of Contact Rates in Female White-Tailed Deer

Abstract: White-tailed deer (Odocoileus virginianus) are important game mammals and potential reservoirs of diseases of domestic livestock; thus, diseases of deer are of great concern to wildlife managers. Contact, either direct or indirect, is necessary for disease transmission, but we know little about the ecological contexts that promote intrasexual contact among deer. Using pair-wise direct contacts estimated from Global Positioning System collar locations and joint utilization distributions (JUDs), we assessed habitats in which contacts occur to test whether direct contact rates among female white-tailed deer in different social groups differs among land-cover types. We also tested whether contact rates differed among seasons, lunar phases, and times of day. We obtained locations from 27 female deer for periods of 0.5–17 months during 2002–2006. We designated any simultaneous pair of locations for 2 deer <25 m apart as a direct contact. For each season, we used compositional analysis to compare land-cover types where 2 deer had contact to available land-cover weighted by their JUD. We used mixed-model logistic regression to test for effects of season, lunar phase, and time of day on contact rates. Contact rates during the gestation season were greater than expected from random use in forest and grassland cover, whereas contact rates during the fawning period were greater in agricultural fields than in other land-cover types. Contact rates were greatest during the rut and lowest in summer. Diel patterns of contact rates varied with season, and contact rates were elevated during full moon compared to other lunar periods. Both spatial and temporal analyses suggest that contact between female deer in different social groups occurs mainly during feeding, which highlights the potential impact of food distribution and habitat on contact rates among deer. By using methods to associate contacts and land-cover, we have created beneficial tools for more elaborate and detailed studies of disease transmission. Our methods can offer information necessary to develop spatially realistic models of disease transmission in deer.