DOI: 10.5061/dryad.0rxwdbs37
title: Habitat availability alters the relative risk of a bovine tuberculosis breakdown in the aftermath of a commercial forest clearfell disturbance

description: 1. Human modification of landscapes and associated disturbances may
 facilitate the emergence and spread of zoonotic diseases. Policy-makers
 need better understanding of the link between anthropogenic disturbances
 and wildlife disease hosts at the interface of human society and the
 natural environment, e.g. agriculture, forestry and aquaculture. Empirical
 research is strongly needed for the control of novel zoonoses which might
 emerge, as well as the management of existing zoonoses with significant
 economic repercussions such as bovine tuberculosis (bTB). 2. We aimed to
 examine the link between ecological disturbance and relative bTB risk
 using Ireland as a case study. We analysed clearfell forestry operations
 and assessed bTB breakdowns within cattle farms across different
 spatio-temporal scales over multiple years, examining how ecological
 conditions may modulate this relationship using conditional logistic
 regression models. 3. We found a significant effect of the interaction
 between the extent of clearfell forestry removed and the extent of natural
 grassland and mixed forestry present on relative bTB risk. This
 interaction was dynamic, leading to an increase or decrease of the
 relative bTB risk depending on where (between 2 and 6 km from the farm)
 and when (between 0 and 36 months prior to the bTB outbreak) the clearfell
 operations occurred. 4. Our study provides empirical evidence of the link
 between mechanised forestry operations and fluctuating relative bTB risk
 in cattle farms, although the mechanism behind it is yet to be elucidated.
 Given our data, we hypothesise that wildlife hosts may abandon the area
 subjected to clearfell when disturbance is highest (during active
 operations and shortly afterward) but are subsequently attracted back to
 the site as they regenerate, potentially affecting the contact rates with
 livestock and thus, relative bTB risk. 5. Our analysis demonstrates that
 landscape modification is correlated with a change in relative bTB risk
 that is dynamic in time and space, allowing managers to understand the
 risk in landscape modification and inform policy accordingly.
 Landscape-level studies are necessary to unveil subtle ecological
 processes, shifting research and management efforts away from cattle
 herd-centric and toward macroecological surveillance of wildlife hosts and
 longitudinal assessment of bTB risk.
description: The relevant bTB testing and breakdown
 history data for all farms in Ireland was collected from the Department of
 Agriculture, Food and the Marine (DAFM) in collaboration with UCD Centre
 for Veterinary Epidemiological Risk Analysis (CVERA). Every cattle herd in
 Ireland has at least one herd test per year. All cattle present on the
 farm on the day of the test are tested, with the exception of calves aged
 under 6 weeks which were born on the farm. The test used is the single
 intradermal comparative tuberculin test (SICTT). The SICTT test is the
 main diagnostic test used in Ireland, though it is imperfect. The 
 sensitivity and specificity of the test is known to vary with estimates of
 52.9-60.8% and 99.2-99.8% respectively from field trials in Ireland (Clegg
 et al, 2011).  The animals showing a positive reaction to the test are
 known as reactors - due to the imperfections of the SICCT test it is
 possible for false positives to be detected in herds showing only one
 reactor (see below for more details on how we took this bias into account
 during modelling). Spatial and
 administrative data for these farms were also provided by DAFM-CVERA via
 the Land Parcel Information System (LPIS). All relevant spatial and
 administrative forestry data including private forestry, public forestry,
 clearfell sites and forest boundaries were collected from Coillte,
 Ireland's semi-state forest custodian. Coillte manage 57% (440,000
 hectares) of Ireland's forestry, which is predominantly conifer high
 forest in clearfell rotations. We collected data on the date of each
 forest clearfell event, the administrative boundary of the forest and the
 ID of each forest subplot felled within the property.
 We collected habitat data relevant to known bTB hosts in Ireland
 from the Corine Land Cover (2018) dataset (© European Union, Copernicus
 Land Monitoring Service , European Environment Agency). We removed all
 habitat classifications which did not meet our <em>a priori
 </em>expectation of influencing resource selection by bTB disease
 hosts in Ireland. We used mixed forestry, which is defined as coniferous
 tree species mixed with broad-leaved deciduous tree species with height
 &gt; 5-7 m and canopy closure around 30 % (always &gt; 15 %). We
 used natural grassland, which is defined as areas with herbaceous
 vegetation (maximum height is 150 cm and gramineous species are
 prevailing) covering at least 50 % of the surface. The term ”natural”
 indicates that vegetation is developed under a minimum human interference
 i.e not mowed, drained, irrigated, sown, fertilised or stimulated by
 chemicals, which might influence production of biomass. We also used
 broad-leaved forest, defined as vegetation formation composed principally
 of trees, including shrub and bush understorey, where broad-leaved species
 predominate. The predominant classifying parameter for this class is a
 crown cover density of &gt; 30 % or a minimum 500 subjects/ha density,
 with broad-leaved trees representing &gt; 75 % of the formation. The
 minimum tree height is 5 m. These data then underwent
 geospatial analysis to create the databases needed for modelling. We
 computed a spatial buffer for each scale (ranging from 1km - 6km) and
 extracted the summary statistics which we would use as covariates in the
 models, such as the number of land parcels on the farm, the elevation and
 the area of habitats available in the buffer. See Supplementary Material 1
 for further information on the geospatial data analysis and full list of
 data extracted from the buffers.
description: All necessary data to re-run the analysis included here.