Habitat mediates coevolved but not novel species interactions.

Ongoing recovery of native predators has the potential to alter species interactions, with community and ecosystem wide implications. We estimated the co-occurrence of three species of conservation and management interest from a multi-species citizen science camera trap survey. We demonstrate fundamental differences in novel and coevolved predator-prey interactions that are mediated by habitat. Specifically, we demonstrate that anthropogenic habitat modification had no influence on the expansion of the recovering native pine marten in Ireland, nor does it affect the predator's suppressive influence on an invasive prey species, the grey squirrel. By contrast, the direction of the interaction between the pine marten and a native prey species, the red squirrel, is dependent on habitat. Pine martens had a positive influence on red squirrel occurrence at a landscape scale, especially in native broadleaf woodlands. However, in areas dominated by non-native conifer plantations, the pine marten reduced red squirrel occurrence. These findings suggest that following the recovery of a native predator, the benefits of competitive release are spatially structured and habitat-specific. The potential for past and future landscape modification to alter established interactions between predators and prey has global implications in the context of the ongoing recovery of predator populations in human-modified landscapes.

The evolutionary pathways for local adaptation in mountain hares.

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome-wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area-specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression-driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares' adaptive variants appear predominantly species-specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post-glacial dynamics of species.

Regime shift tipping point in hare population collapse associated with climatic and agricultural change during the very early 20th century.

Animal populations at northern latitudes may have cyclical dynamics that are degraded by climate change leading to trophic cascade. Hare populations at more southerly latitudes are characterized by dramatic declines in abundance associated with agricultural intensification. We focus on the impact of historical climatic and agricultural change on a mid-latitude population of mountain hares, Lepus timidus hibernicus. Using game bag records from multiple sites throughout Ireland, the hare population index exhibited a distinct regime shift. Contrary to expectations, there was a dynamical structure typical of northern latitude hare populations from 1853 to 1908, during which numbers were stable but cyclic with a periodicity of 8 years. This regime was replaced by dynamics more typical of southern latitude hare populations from 1909 to 1970, in which cycles were lost and numbers declined dramatically. Destabilization of the autumn North Atlantic Oscillation (NAO) led to the collapse of similar cycles in the hare population, coincident with the onset of agricultural intensification (a shift from small-to-large farms) in the first half of the 20th century. Similar, but more recent regime shifts have been observed in Arctic ecosystems and attributed to anthropogenic climate change. The present study suggests such shifts may have occurred at lower latitudes more than a century ago during the very early 20th century. It seems likely that similar tipping points in the population collapse of other farmland species may have occurred similarly early but went undocumented. As northern systems are increasingly impacted by climate change and probable expansion of agriculture, the interaction of these processes is likely to disrupt the pulsed flow of resources from cyclic populations impacting ecosystem function.

Detection of a novel gammaherpesvirus (genus Rhadinovirus) in wild muntjac deer in Northern Ireland.

This study represents the initial part of an investigation into the potential for non-native, wild, free-living muntjac deer (Muntiacus reevesi) to carry viruses that could be a threat to livestock. A degenerate PCR assay was used to screen a range of tissues from muntjac deer culled in Northern Ireland for the presence of herpesviral nucleic acids. This was followed by sequencing of PCR amplicons and phylogenetic analysis. We report the detection of a novel gammaherpesvirus most closely related to a type 2 ruminant rhadinovirus from mule deer. It remains to be determined if this new virus is pathogenic to deer or presents a risk to food security through the susceptibility of domestic livestock.

Development of a novel immunochromatographic lateral flow assay specific for Mycobacterium bovis cells and its application in combination with immunomagnetic separation to test badger faeces.

BACKGROUND: The European badger is an important wildlife reservoir of Mycobacterium bovis implicated in the spread of bovine tuberculosis in the United Kingdom and Ireland. Infected badgers are known to shed M. bovis in their urine and faeces, which may contaminate the environment. To aid bovine tuberculosis control efforts novel diagnostic tests for detecting infected and shedding badgers are needed. We proposed development of a novel, rapid immunochromatographic lateral flow device (LFD) as a non-invasive test to detect M. bovis cells in badger faeces. Its application in combination with immunomagnetic separation (IMS) to detect Mycobacterium bovis cells in badger faeces is reported here. RESULTS: A novel prototype LFD for M. bovis cells was successfully developed, with unique specificity for M. bovis and a limit of detection 50% (LOD50%) of 1.7 × 104 M. bovis cells/ml. When IMS was employed to selectively capture and concentrate M. bovis cells from badger faeces prior to LFD testing, the LOD50% of the IMS-LFD assay was 2.8 × 105 M. bovis cells/ml faecal homogenate. Faeces samples collected from latrines at badger setts in a region of endemic bovine tuberculosis infection were tested; 78 (18%) of 441 samples tested IMS-LFD assay positive, whereas 140 (32%) tested IMS-qPCR positive (Kappa agreement -0.009 ± 0.044, p = 0.838). Subsequently, when 130 faeces samples from live captured, or captive, badgers of known infection status (on the basis of StatPak, interferon-γ and/or culture results) were tested, the IMS-LFD assay had higher relative diagnostic specificity (Sp 0.926), but poorer relative diagnostic sensitivity (Se 0.081), than IMS-qPCR (Sp 0.706, Se 0.581) and IMS-culture (Sp 0.794, Se 0.436). CONCLUSIONS: The novel IMS-LFD assay, although very specific for M. bovis, has low analytical sensitivity (indicated by the LOD50%) and would only detect badgers shedding high numbers of M. bovis (>104-5 cells/g) in their faeces. The novel LFD would, therefore, have limited value as a non-invasive test for badger TB surveillance purposes but it may have value for alternative veterinary diagnostic applications.

Stress related to wild canid predators near dairy sheep farms associated with increased somatic cell counts in bulk-tank milk.

We investigated the association between wild canid predators reported near sheep farms throughout Greece and somatic cell counts in bulk-tank milk as a reflection of milk quality. The study included 325 dairy sheep flocks, where bulk-tank milk somatic cell counts and total bacterial counts were measured and staphylococci were isolated. Farms were divided into three groups: Cohort A (farms with no reports of wild canid predators nearby), B (farms with canid predators (golden jackal and grey wolf) nearby yet with no experience of livestock losses to predation) and C (farms with canid predators nearby and livestock losses to predation). Somatic cell counts in bulk-tank milk of Cohort C farms were significantly higher, + 43% and + 29%, compared to those for Cohorts A and B, respectively: 0.617 × 106 cells mL-1 versus 0.433 × 106 or 0.477 × 106 cells mL-1, respectively. The presence of wild canid predators near sheep farms was associated with lower quality milk potentially indicative of stress consistent with the potential effects of a landscape of fear. Increasing biosecurity measures at livestock farms, e.g., fencing, and presence of livestock guard dogs could minimise predation risk, whilst also improving livestock welfare by reducing predator-associated stress.

Unprecedented Harmful algal bloom in the UK and Ireland's largest lake associated with gastrointestinal bacteria, microcystins and anabaenopeptins presenting an environmental and public health risk.

Harmful Algal Blooms (HABs) are outbreaks of aquatic toxic microalgae emerging as a global problem driven by nutrient enrichment, global climate change and invasive species. We uniquely describe a HAB of unprecedented duration, extent and magnitude during 2023 in Lough Neagh; the UK and Ireland's largest freshwater lake, using an unparalleled combination of satellite imagery, nutrient analysis, 16S rRNA gene sequencing and cyanotoxin profiling. The causative agent Microcystis aeruginosa accounted for over a third of DNA in water samples though common bacterioplankton species also bloomed. Water phosphate levels were hypertrophic and drove local algal biomass. The HAB pervaded the entire ecosystem with algal mats accumulating around jetties, marinas and lock gates. Over 80 % of bacterial DNA isolated from algal mat samples consisted of species associated with wildfowl or livestock faeces and human-effluent wastewater including 13 potential pathogens that can cause serious human illness including: E. coli, Salmonella, Enterobacter and Clostridium among others. Ten microcystins, nodularin and two anabaenopeptin toxins were confirmed as present (with a further microcystin and four anabaenopeptins suspected), with MC-RR and -LR in high concentrations at some locations (1,137-18,493 µg/L) with MC-LR exceeding World Health Organisation (WHO) recreational exposure guidelines in all algal mats sampled. This is the first detection of anabaenopeptins in any waterbody on the island of Ireland. Notwithstanding the ecological impacts, this HAB represented an environmental and public health risk, curtailing recreational activities in-and-around the lake and damaging local businesses. Reducing agricultural runoff and discharge from human-effluent wastewater treatment to manage nutrient loading, and the public health risk, should be the top priority of stakeholders, especially government. Key recommendations include Nature-based Solutions that avoid conflict with the productivity and profitability of the farming sector enhancing sustainability. We hope this stimulates real-world action to resolve the problems besetting this internationally important ecosystem.

Survival, movements, home range size and dispersal of hares after coursing and/or translocation.

Hare coursing is the pursuit of a hare by dogs for sport. In recent years in Ireland, between 2,900 to 3,700 hares have been caught from the wild (under Government license) and held in captivity for up to 8 weeks. Hares are given a head start and coursed in an enclosed arena by two muzzled greyhounds where the object is not to kill the hare, but judge the dogs on their ability to turn the hare which escapes under a partition through which the dogs cannot follow. Recent licence returns suggest over 99% of hares survive and are released back into the wild. This study aimed to assess survival and behaviour of coursed hares after their release sometimes into unfamiliar territory. Forty hares were tracked using GPS-radio collars for six months after release in a factorial experimental design to test the impact of coursing and translocation on survival, movements, home range size and dispersal. Coursed and uncoursed hares did not differ in observed mortality rates, movements, home range sizes or dispersal distances after release back into the wild though fewer coursed than uncoursed hares were relocated six months after release, due to a combination of collar strap failures and radio silence. Spatial behavior was similar between the cohorts once translocated hares, which moved further and had larger home range sizes during the first four days after release, had settled. Two hares released shortly before sunset were killed in road traffic collisions during their first night. Releasing hares during daylight, preferably as early as possible, may provide time for animals to settle before darkness. Suggestions are made for potential methodological improvements such as the use of cellular (mobile phone) or satellite communication technology mounted on stouter straps to reduce failures and improve relocation rates.

Initial ecological change in plant and arthropod community composition after wildfires in designated areas of upland peatlands.

Wildfires are an increasing concern due to rising temperatures and incidence of droughts associated with changing climate, poor land management, and direct human interference. Most studies of the impact of fire on temperate heathland and bog examined the consequences of controlled or prescribed burning. Less is known about the impacts of uncontrolled wildfires on sites designated for their conservation value. We examined the initial impact and short-term trajectory (3.5 years) of cool temperate peatland plant and arthropod communities on designated upland sites in Northern Ireland following wildfires, that is, unplanned with respect to where and when they occur, severity, and duration. These near simultaneous wildfires were often due to a failure to control prescribed burns. Wildfires were associated with a loss of blanket bog and heath indicator species. Broad vegetation groups showed initial recovery characterized by a decrease in bare ground and increasing cover of shrub species and bryophytes. However, at a species level, Sphagnum spp and bryophyte communities, which are central to peatland ecosystem functioning, showed no sign of recovery to prefire composition. Rather, bryophyte communities became more divergent over the course of the study and were mainly characterized by increased abundance of the alien pioneer acrocarp Campylopus introflexus. Similarly, composition of arthropod communities (ground beetles and spiders) differed between burnt and unburnt areas and showed no evidence of a return to species composition in unburnt areas. The nationally rare beetle Carabus nitens was more common in the aftermath of wildfire. Synthesis. Whilst, long-term recovery was not investigated, these short-term changes suggest enduring detrimental impacts on the distinctive communities associated with peatlands, primarily through the loss of Sphagnum spp., affecting ecosystem services such as carbon sequestration and water and soil retention. It may not be possible to restore exact prefire species composition of plant and animal communities. We suggest a precautionary approach involving management of upland vegetation, public education, and vigilance, to prevent further wildfires and protect these key upland habitats.

Abiotic and biotic correlates of the occurrence, extent and cover of invasive aquatic Elodea nuttallii.

Biological invasions, especially invasive alien aquatic plants, are a major and growing ecological and socioeconomic problem worldwide. Freshwater systems are particularly vulnerable to invasion, where impacts of invasive alien species can damage ecological structure and function. Identifying abiotic and biotic factors that mediate successful invasions is a management priority. Our aim was to determine the environmental correlates of Elodea nuttallii; a globally significant invasive aquatic species. Elodea nuttallii presence/absence (occurrence), extent (patch area) and percentage cover (density) was visually assessed from a boat throughout Lough Erne (approximately 144 km2), County Fermanagh, Northern Ireland during the active summer growth season (July-September). In addition, substrate type and zebra mussel Dreissena polymorpha occurrence was recorded. Fourteen water chemistry variables were collected monthly from 12 recording stations throughout the lake during the 9 years before the survey to spatially interpolate values and establish temporal trajectories in their change. Shoreline land use was derived from CORINE land cover maps. Environmental associations between E. nuttallii, substrate, D. polymorpha, water chemistry and land use were assessed. Elodea nuttallii occurrence was positively associated with water conductivity, alkalinity, suspended solids, phosphorus (both total and soluble) and chlorophyll-a concentrations, but negatively associated with pH and total oxidised nitrogen. E. nuttallii patch extent and proportional cover were positively associated, to varying degrees, with the presence of D. polymorpha, biological oxygen demand, water clarity and soft substrate, but negatively associated with urban development and ammonium. Elodea nuttallii displayed high levels of phenotypic plasticity in response to environmental variation, allowing it to adapt to a wide range of conditions and potentially gain competitive advantage over native or other invasive macrophytes.It is evident that multiple abiotic and biotic factors, including facilitation by co-occurring invasive dreissenid mussels, interact to influence the distribution and abundance of E. nuttallii. Thus, it is necessary to consider a more comprehensive environmental context when planning Elodea management strategies.

Highest densities of mountain hares (Lepus timidus) associated with ecologically restored bog but not grouse moorland management.

Over the last 20 years, ecological restoration of degraded habitats has become common in conservation practice. Mountain hares (Lepus timidus scoticus) were surveyed during 2017-2021 using 830 km of line transects in the Peak District National Park, England. Historically degraded bog areas were previously reported having low hare numbers. Following bog restoration, we found hare densities of 32.6 individuals km-2, notably higher than neighboring degraded (unrestored) bog with 24.4 hares km-2. Hare density on restored peatland was 2.7 times higher than on bogs managed for grouse shooting at 12.2 hares km-2 and 3.3 times higher than on heather moorland managed for grouse shooting at 10.0 hares km-2. Yearly estimates varied most on habitats managed for grouse, perhaps indicative of the impact of habitat management, for example, heather burning and/or possible hare culling to control potential tick-borne louping ill virus in gamebirds. Acid grassland used for sheep farming had a similar density to grouse moorland at 11.8 hares km-2. Unmanaged dwarf shrub heath had the lowest density at 4.8 hares km-2. Hare populations are characterized by significant yearly fluctuations, those in the study area increasing by 60% between 2017 and 2018 before declining by ca. 15% by 2020 and remaining stable to 2021. During an earlier survey in 2002, total abundance throughout the Peak District National Park was estimated at 3361 (95% CI: 2431-4612) hares. The present study estimated 3562 (2291-5624) hares suggesting a stable population over the last two decades despite fluctuations likely influenced by weather and anthropogenic factors. Mountain hares in the Peak District favored bog habitats and were associated with restored peatland habitat. Wildlife management should be cognizant of hare density variation between habitats, which may have implications for local extinction risk.

Rabbit Haemorrhagic Disease Virus 2 (RHDV2; GI.2) in Ireland Focusing on Wild Irish Hares (Lepus timidus hibernicus): An Overview of the First Outbreaks and Contextual Review.

Rabbit haemorrhagic disease virus 2 (RHDV2; GI.2) is a pathogenic lagovirus that emerged in 2010, and which now has a global distribution. Outbreaks have been associated with local population declines in several lagomorph species, due to rabbit haemorrhagic disease (RHD)-associated mortality raising concerns for its potential negative impact on threatened or vulnerable wild populations. The Irish hare (Lepus timidus hibernicus) is endemic to Ireland, and is of conservation interest. The first cases of RHDV2 in Ireland were reported in domestic rabbits (Oryctolagus cuniculus) in 2016, soon followed by the first known case in a wild rabbit also in 2016, from a population reported to be experiencing high fatalities. During summer 2019, outbreaks in wild rabbits were confirmed in several locations throughout Ireland. Six cases of RHDV2 in wild hares were confirmed between July and November 2019, at four locations. Overall, 27 cases in wildlife were confirmed in 2019 on the island of Ireland, with a predominantly southern distribution. Passive surveillance suggests that the Irish hare is susceptible to lethal RHDV2 infection, and that spillover infection to hares is geographically widespread in eastern areas of Ireland at least, but there is a paucity of data on epidemiology and population impacts. A literature review on RHD impact in closely related Lepus species suggests that intraspecific transmission, spillover transmission, and variable mortality occur in hares, but there is variability in reported resistance to severe disease and mortality amongst species. Several key questions on the impact of the pathogen in Irish hares remain. Surveillance activities throughout the island of Ireland will be important in understanding the spread of infection in this novel host.

Case Report of Puffinosis in a Manx Shearwater (Puffinus puffinus) Suggesting Environmental Aetiology.

Puffinosis is a disease of a range of seabirds characterised by dorsal and ventral blistering of their webbed feet, conjunctivitis, dry necrosis, leg spasticity, head shaking, loss of balance, tremors, and death. It is associated with Manx shearwaters (Puffinus puffinus), frequently affecting chicks within their underground nesting burrows. The aetiology of the disease is unclear but has been attributed to a type-2 coronavirus associated with Neotombicula mites as a potential vector. However, there is some uncertainty given potential laboratory contamination with mouse hepatitis virus and failure to fulfil Koch's postulates, with birds injected with isolates remaining healthy. We describe a detailed case report of puffinosis in a Manx Shearwater covering necropsy, histology, bacteriology, and metagenomics including viral sequencing. We found no evidence of viral infection or parasites. Our results are consistent with an entirely environmental aetiology, with caustic faecal ammonia in damp nesting burrows causing conjunctivitis and foot dermatitis breaking the skin, allowing common soil bacteria (i.e., Flavobacterium, Staphylococcus and Serratia spp., Clostridia perfringens and Enterococcus faecalis) to cause opportunistic infection, debilitating the bird and leading to death. A similar condition (foot pad dermatitis or FPD) has been reported in broiler chickens, attributed to caustic faeces, high humidity, and poor environmental conditions during indoor rearing, preventable by adequate ventilation and husbandry. This is consistent with puffinosis being observed in Shearwater nesting burrows situated in tall, dense, vegetation (e.g., bracken Pteridium aquilinum) but rarely reported in burrows situated in well-ventilated, short coastal grasslands. This proposed environmental aetiology accounts for the disease's non-epizootic prevalence, spatial variation within colonies, and higher frequency in chicks that are restricted to nesting burrows.

Combining spawn egg counts, individual photo-ID and genetic fingerprinting to estimate the population size and sex ratio of an endangered amphibian.

According to the International Union for Conservation of Nature Red List, 41% of the world's amphibian species are threatened with extinction, making them more threatened than any other vertebrate group nowadays. Given the global amphibian crisis, comprehensive understanding of demographics and population trends of declining and threatened species is essential for effective management and conservation strategies. Counting egg spawns is widely used to assess population abundance in pond breeding anurans. However, it is unknown how such counts translate into robust population size estimations. We monitored the breeding activity of the Natterjack toad (Epidalea calamita), combining egg string counts and individual photo-identification with Capture-Mark-Recapture population size and operational sex ratio estimation. Male Natterjack toads were identified by the pattern of natural markings with repeated ID of the same individual confirmed for 10% of the samples using genetic fingerprinting. We identified 647 unique individuals within a closed study population at Caherdaniel, Co Kerry. Population estimates derived from egg string counts estimated a breeding population of 368 females (95% CI 353-384) and Capture-Mark-Recapture estimated a breeding population of 1698 males (95% CI 1000-2397). The female:male sex ratio was conservatively estimated at 1:5 (95% CI 1:3-1:6) where 62% ± 6% of females were assumed to spawn. These substantially departed from any priori assumption of 1:1 which could have underestimated the breeding population by up to 72%. Where amphibian absolute population size estimation is necessary, methods should include empirical survey data on operational sex ratios and not rely on assumptions or those derived from the literature which may be highly population and/or context-dependent.

Will predicted positive effects of climate change be enough to reverse declines of the regionally Endangered Natterjack toad in Ireland?

The global amphibian crisis is driven by a range of stressors including disease, habitat loss, and environmental contamination. The role of climate change remains poorly studied and is likely to influence environmental suitability, ranges, reproduction, and phenology. This study aimed to characterize the bioclimatic-habitat niche space of the Natterjack toad (Epidalea calamita) throughout its European range and to assess the impact of climate on the toad's environmental suitability and breeding behavior in Ireland, where declines in recent decades have resulted in it being regionally Red-Listed as Endangered. To address these questions, we first identified which climate variables best predict the current bioclimatic niche, fecundity (number of eggs deposit), and phenology. We then used future climate projections for two time periods (2041-2060 and 2061-2080) and two greenhouse gas emission scenarios (RCP 4.5 and RCP 8.5) to predict how the species range, fecundity, and phenology would change. The European range of the species was found to be limited by winter temperatures while its bioclimatic niche varied markedly throughout its range. Species distribution models suggested projected climate change will increase environmental suitability for the species throughout its range, including Ireland, but most notably in Scandinavia and the Baltic. Fecundity in Ireland was greatest during the cool temperatures of spring and after wet winters associated with ephemeral breeding pool availability. Warm, dry summers in the preceding year influenced fecundity the following spring indicative of carryover effects. Initiation of spawning was driven by spring temperatures, not rainfall. Projections suggested future climate change may increase fecundity in Ireland while spawning may commence earlier throughout the 21st century especially under a high greenhouse gas emission scenario (RCP 8.5). Despite recent range contraction and population declines due to habitat deterioration, the Natterjack toad, if subject to a suitable species conservation strategy, has the potential to be a climate change winner, notwithstanding unpredictable habitat and land-use change, sea-level rise inducing coastal erosion, changes in invertebrate prey abundance, and disease.

First detected case of rabbit Haemorrhagic disease virus 2 (RHDV2) in the Irish hare (Lepus timidus hibernicus).

BACKGROUND: Rabbit haemorrhagic disease virus (RHDV) is a Lagovirus, a subgroup of the family Caliciviridae. RHDV2 is a variant first described in France in 2010, and has since spread globally. It has been reported in several Lagomorph species (rabbits, hares, and their relatives) as well as other mammals including voles and shrews. The disease has raised international concerns for its potential impact on population abundance trajectories, particularly as 25% of Lagomorphs are currently Red-Listed by the International Union for the Conservation of Nature (IUCN). The Irish hare (Lepus timidus hibernicus) is a subspecies of the mountain hare, L. timidus, and is endemic to Ireland, making it an Evolutionarily Significant Unit of intrinsic value. CASE PRESENTATION: The first case of RHDV2 was detected in a wild Irish hare in July 2019. The individual exhibited atypical neurological behaviour (running in circles) prior to death. On necropsy, pink tinged foam was seen in the trachea and congestion was noted in the lungs, but there was no evidence of haemorrhages in any other organ. Both the liver and spleen were tested by reverse transcription real time qPCR confirming high levels of RHDV2 RNA. Histopathology confirmed multifocal necrotising hepatitis. CONCLUSION: The Irish hare is susceptible to RHDV2 infection. Further investigation is warranted to explore the clinical, epidemiological, and population biology implications.

Bovine tuberculosis breakdown duration in cattle herds: an investigation of herd, host, pathogen and wildlife risk factors.

BACKGROUND: Despite rigorous controls placed on herds which disclose ante-mortem test positive cattle to bovine tuberculosis, caused by the infection of Mycobacterium bovis, many herds in Northern Ireland (NI) experience prolonged breakdowns. These herds represent a considerable administrative and financial burden to the State and farming community. METHODS: A retrospective observational study was conducted to better understand the factors associated with breakdown duration, which was modelled using both negative binomial and ordinal regression approaches. RESULTS: Six explanatory variables were important predictors of breakdown length in both models; herd size, the number of reactors testing positive in the initial SICCT test, the presence of a lesioned animal at routine slaughter (LRS), the count of M. bovis genotypes during the breakdown (MLVA richness), the local herd-level bTB prevalence, and the presence of herds linked via management factors (associated herds). We report that between 2008 and 2014, mean breakdown duration in NI was 226 days (approx. seven months; median: 188 days). In the same period, however, more than 6% of herds in the region remained under movement restriction for more than 420 days (13 months); almost twice as long as the mean. The MLVA richness variable was a particularly important predictor of breakdown duration. We contend that this variable primarily represents a proxy for beef fattening herds, which can operate by purchasing cattle and selling animals straight to slaughter, despite prolonged trading restrictions. For other herd types, the model supports the hypothesis that prolonged breakdowns are a function of both residual infection within the herd, and infection from the environment (e.g. infected wildlife, contiguous herds and/or a contaminated environment). The impact of badger density on breakdown duration was assessed by including data on main sett (burrow) density. Whilst a positive association was observed in the univariate analysis, confounding with other variables means that the contribution of badgers to prolonged breakdowns was not clear from our study. We do not fully reject the hypothesis that badgers are implicated in prolonging bTB breakdowns via spillback infection, but given our results, we posit that increased disease risk from badgers is unlikely to simply be a function of increasing badger density measured using sett metrics.

An Annotated Draft Genome of the Mountain Hare (Lepus timidus).

Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.

Quantifying intraherd cattle movement metrics: Implications for disease transmission risk.

There are a paucity of data quantifying on-farm management practices such as the frequency of intraherd cattle movements, use of consolidated or spatially fragmented grazing pastures, and duration of time cattle spend at grass with respect to biosecurity and disease transmission. Such movement dynamics are important when attempting to understand the maintenance of chronic infectious disease, such as bovine tuberculosis (bTB). We captured empirical data on daily cattle movements for a sample of eighteen farms throughout one complete grazing season (n = 18,988 grazing days) and assessed these attributes in relation to herd bTB risk. Dairy herds were stocked at significantly higher densities compared to beef production systems (6.6 animals/ha, 95 % confidence intervals (CI) 6.5-6.7 and 4.1 animals/ha, 95 %CI 4.1 - 4.1 respectively, p < 0.001). Most notably milking cows, were grazed at higher densities than other life stages (e.g. calves, heifers and bullocks) (p < 0.001) and experienced four times the number of movements between pastures. Beef cattle were more likely to be grazed across multiple (rather than single) fields (p < 0.001), with greater time spent on fragmented land away from the main/home farm (p < 0.001). None of the farm or herd attributes analysed (e.g. stocking density, frequency of movement, movement distances or land fragmentation) were associated with herd bovine tuberculosis (bTB) breakdowns during this study. However, there was a weak positive association between bTB breakdowns during the 3 years prior to the study and cattle movement distances (p = 0.05) and time spent on fragmented land (p = 0.08). After a bTB breakdown occurs, restrictions on animals moving out of these herds are implemented to control disease spread, yet we argue that more attention is needed on the role of intraherd grazing patterns in modelling disease transmission risk between herds.