Data from: The release of non-native gamebirds is associated with amplified zoonotic disease risk
Data files
Feb 06, 2025 version files 429.17 KB
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distance_matrix.csv
14.34 KB
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README.md
4.02 KB
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tick_abundance_2024.csv
126.88 KB
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tick_borrelia_genospecies_prev.csv
59.81 KB
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tick_borrelia.sp_broadleaf_prev.csv
106.45 KB
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tick_borrelia.sp_prev.csv
117.67 KB
Feb 06, 2025 version files 429.36 KB
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distance_matrix.csv
14.34 KB
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README.md
4.20 KB
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tick_abundance_2024.csv
126.88 KB
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tick_borrelia_genospecies_prev.csv
59.81 KB
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tick_borrelia.sp_broadleaf_prev.csv
106.45 KB
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tick_borrelia.sp_prev.csv
117.67 KB
Abstract
Spillback – where non-native species increase native pathogen prevalence – is potentially an important mechanism by which non-natives contribute to zoonotic disease emergence. However, spillback has not yet been directly demonstrated because it is difficult to disentangle from confounding factors which correlate with non-native species abundance and native pathogen prevalence. Here, we capitalise on replicated, quasi-experimental releases of non-native pheasants (Phasianus colchicus) to compare vector abundance and native pathogen prevalence between sites with similar local conditions but different non-native densities. Prevalence of Borrelia sp. (the causative agent of Lyme disease) in questing ticks was almost 2.5x higher in woods where pheasants are released compared to control woods, with a particularly strong effect on Borrelia garinii, a bird specialist genospecies. Furthermore, adult (but not nymphal) ticks tended to be more abundant at pheasant-release woods. This work provides evidence that non-native species can impact zoonotic pathogen prevalence via spillback in ecologically relevant contexts.
https://doi.org/10.5061/dryad.d7wm37q9d
Code can be found in the 'related works' box on right of the DRYAD landing page. Or via the DOI https://doi.org/10.5281/zenodo.13919564
Description of the data and file structure
I.ricinus tick abundance and Borrelia prevalence data from 89 woods across the southwest of England. Including woods in which pheasants were released, and woods in which pheasants were not released.
Files and variables
File: distance_matrix.csv
Description: pairwise distances for the 25 shoots included in the present study.
File: tick_abundance_2024.csv
Description:
Variables
- area: a unique identity number attributed to each shoot
- edge: distance from woodland edge, either 'interior' (-0.5) or 'edge' (0.5)
- temp: temperature, already scaled
- tree_sp: the species of the tree closest to a given transect
- herb_sp: the most common under-story plant species during a transect
- herb_sp2: the second most common under-story plant species during a transect
- bare: % cover of bare-ground during a transect
- n: tick nymph count on a given transect
- a: adult tick count on a given transect
- size: the area of a wood in meters squared, scaled to have a mean of 0 and sd of 1
- xcoord: longitudinal coordinate of a given shoot
- ycoord: latitudinal coordinate of a given shoot
- id: a unique identity number attributed to each transect (referred to in the main text as a 'drag')
- dys3: date, the number of days since the first survey day, scaled to vary from 0 to 1, where 1 is the last day of surveying and 0 the first.
- depth_scaled: vegetation depth, already scaled
- rank: a unique identity number attributed to each wood
- tr: pheasant-release, 0.5 is attributed to each transect conducted in a wood where pheasants are released, -0.5 for each transect conducted where pheasants are not released.
- cn: conifer, 0.5 is attributed to each transect where the nearest tree species is was broadleaf, -0.5 where the nearest tree species is was conifer.
- pheas_scale: the number of pheasants released, scaled to have a standard deviation of 1 and a mean of 0
File: tick_borrelia.sp_prev.csv
Description: borrelia sp. infection status for all ticks sampled in this study
Variables
- edge: distance from woodland edge, either 'interior' (2), or 'edge' (1)
- size : the area of a wood in meters squared
- area: a unique identitiy number attributed to each shoot
- pos: Borrelia positive, tick from positive pools are attributed '1'
- treat: pheasant-release, 2 is attributed to ticks collected from wood where pheasants are released, 1 to ticks collected from woods where pheasants are not released.
- adult: tick life stage, nymphs = 1, adults = 2
- sday: julian day scaled to have a standard deviation of 1 and mean of 0.
- pheas_standard: The number of pheasants released at a shoot, scaled to have a mean of 0 and standard deviation of 1.
- rank: a unique identitiy number attributed to each wood
- iii: a code fed into missclassification models, 1 for negative ticks were borrelia screened individually, 2 for positive ticks screened infividually, 3 for negative ticks screened with another tick, and 4 for positive ticks screened with another tick.
File: tick_borrelia.sp_broadleaf_prev.csv
Description: as above but also including:
Variables
- per_cent_broadleaf: percentage of trees in a given wood which were broadleaf, expressed as a ratio
File: tick_borrelia_genospecies_prev.csv
Description: as above but also including:
Variables
- best_match: borrelia genospecies 1 = garinii, 2 = afzelii, 3 = valaisiana, 4 = undescribed/finlandensis, 5 = unresolved
Code/software
Analysis is conducted using R versions 4+. Models are built using the packages 'rethinking' and 'brms' which are wrappers for the free statistics program 'Stan'. Installation instructions can be found in the markdown file as well as a list of any other required packages.