DOI: 10.5061/dryad.8kprr4xt1
title: Data from: Investigating the association between diet and infection with <em>Trichomonas gallinae</em> in the European turtle dove (<em>Streptopelia turtur</em>)

description: Trichomonas gallinae, a protozoan parasite infecting a wide range of
 birds, has been a cause for conservation concern since its recognition as
 an emerging infectious disease, having had notable impacts on several
 avian species, including causing widespread mortality in greenfinches
 (Chloris chloris), and chaffinches (Fringilla coelebs), and hindering the
 recovery of the endangered pink pigeon (Nesoenas mayeri). Horizontal
 transmission between birds congregating at feeding sites, such as those
 provided for conservation and species management purposes, is an important
 driver in the spread of T. galliane. Supplementary feeding is a key
 conservation intervention for the European turtle dove (Streptopelia
 turtur), which is declining across its range, driven at least partially by
 a loss of natural food resources. Due to the link between T. gallinae
 transmission and supplementary feeding, we consider the prevalence of this
 parasite amongst European turtle doves in relation to diet in the first
 study to analyse these two factors in the decline of this species
 together. Using birds sampled from breeding and wintering grounds, the
 dietary composition of individuals was compared to the presence of T.
 gallinae, and specific T. gallinae strains. Dietary variation was
 summarised into two axes using detrended correspondence analysis; neither
 was associated with the presence of T. gallinae, or any specific strains.
 The proportion of diet accounted for by cultivated seeds did not affect
 parasite presence, despite the spread of this parasite being associated
 with supplementary feeding due to an increase in contact between
 potentially infected and uninfected birds gathering at high densities at
 feeding sites. Significant dietary overlap was observed between infected
 and uninfected individuals in all sites, with almost complete dietary
 overlap being observed in one breeding site. The level of dietary overlap
 between individuals infected with specific strains fluctuated between
 sampling seasons, indicating no consistent relationship between diet and
 infection status.
description: Faecal samples and buccal cavity swab samples were collected from
 wild-caught European Turtle Doves <em>(Streptopelia</em>
 <em>turtur</em>). DNA was extracted from these samples,
 amplified by PCR, then sequenced using High-Throughput Sequencing.
 Bioinformatic data processing was completed to identify dietary items
 consumed by birds sampled (faecal samples) and the status of infection
 with the protozoan parasite <em>Trichomonas galliane</em>
 (buccal swab samples). Statistical analysis was carried out using
 R. 
description: # Investigating the association between diet and infection with
 Trichomonas gallinae in the European turtle dove (Streptopelia turtur)
 [https://doi.org/10.5061/dryad.8kprr4xt1](https://doi.org/10.5061/dryad.8kprr4xt1) ## Description of the data and file structure These data sets contain both dietary and parasite infection data collected from European turtle dove (*Streptopelia turtur*) on both the breeding and wintering grounds. Data sets used in analysis are post-bioinformatic processing. Dietary data is obtained from faecal samples, using high throughput sequencing. Data on *Trichomonas galliane* infection and strains were obtained from DNA isolated from swabs of the oral cavity, oesophagus, and crop. High-throughput sequencing was used to detect strains present in samples. The results of this study look at infection with *T. gallinae* in relation to diet. ### Files and variables #### File: 1._Detrended_correspondence_analysis_and_GLM_including_DCA_variables_script.R **Description:** To assess the relationship between diet and infection status, detrended correspondence analysis (DCA) was first carried out to summarise dietary data, based on the presence or absence of dietary taxa within each bird sampled, to capture the source of dietary variation in a small number of variables, to be included in a Generalised Linear Model (GLM). A high proportion of dietary items occur in a very low number of samples, which may mask co-occurrence patterns of plant taxa in dietary samples, therefore DCA was conducted on a subset of data, containing only frequently consumed taxa. Four different thresholds representing how frequently items occurred in the diet were tested (taxa occurring in the diet of at least 3%, 5%, 7% and 10% of birds sampled), to determine the most appropriate threshold for defining ‘frequently occurring taxa’. A Generalised Linear Model was then fitted with the presence or absence of *T. gallinae* as the dependent variable and season, body condition index, and the coordinate scores for DCA1 and DCA2 as the independent variables. #### Data sets used:  #### File: 1._For_CorAna_3.csv **Description:** Taxa (by genus) occurring in at least 3% of birds sampled.  ##### Variables: * Sample: Bird ring number - unique identifier for each sample * All other columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample. #### File: 1._For_CorAna_5.csv **Description:** Taxa (by genus) occurring in at least 5% of birds sampled.  ##### Variables: * Sample: Bird ring number - unique identifier for each sample * All other columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample. #### File: 1._For_CorAna_7.csv **Description:** Taxa (by genus) occurring in at least 7% of birds sampled.  ##### Variables: * Sample: Bird ring number - unique identifier for each sample * All other columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 1._For_CorAna_10.csv **Description:** Taxa (by genus) occurring in at least 10% of birds sampled.  ##### Variables: * Sample: Bird ring number - unique identifier for each sample * All other columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 1._CA_GLM_7.csv and 1._CA_GLM_7_strains.csv **Description:** Data for fitting Generalised Linear Model with the presence or absence of *T. gallinae* infection (1._CA_GLM_7.csv), or of specific *T. gallinae* strains (1._CA_GLM_7_strains.csv) as the dependent variable and season, body condition index, and the coordinate scores for DCA1 and DCA2 as the independent variables. ##### Variables * Sample: Bird ring number - unique identifier for each sample * Sample_: Bird ring number - unique identifier for each sample DCA1 and DCA2 explained the majority of the variation observed in the data set when correspondence analysis was used, therefore were included as explanatory variables in GLM analysis. * DCA1: Score from correspondence analysis * DCA2: Score from correspondence analysis * Condition: Body condition index score * Infection: Presence (1) or Absence (0) of *Trichomonas galliane* infection * GEO: Presence (1) or Absence (0) of specific *Trichomonas galliane* strain * Tcl-1: Presence (1) or Absence (0) of specific *Trichomonas galliane* strain * Type C: Presence (1) or Absence (0) of specific *Trichomonas galliane* strain * Type IIIc: Presence (1) or Absence (0) of specific *Trichomonas galliane* strain * Wi.Br: Wintering or breeding season * Country: Country from which sample was collected (Senegal, France, or Hungary) * Season: Coded to correspond to the year and country samples were collected. * All remaining columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  | Country | Year | Sampling season | | :------ | :-------- | :-------------- | | Senegal | 2014/2015 | Winter 1 (W1) | | Senegal | 2015/2016 | Winter 2 (W2) | | Senegal | 2016/2017 | Winter 3 (W3) | | Senegal | 2017/2018 | Winter 4 (W4) | | France | 2018 | Spring 1 (S1) | | Hungary | 2019 | Spring 2 (S2) | Table 1: coding of sampling seasons #### File: 2._GLM_infection_and_proportion_wild_food_in_diet.R **Description:** The effect of different food sources was assessed by considering dietary items categorised as ‘wild’ or ‘cultivated’ based on the likely source of food items. The effect of the proportion of wild seeds in the diet upon the infection probability by *T. gallinae* was assessed using a binomial GLM.  Presence of *T. gallinae* infection was the dependent variable, and the independent variables were season and proportion of the diet accounted for by wild seeds. This model was repeated to assess individual strains, modelling the presence/absence of GEO, Tcl-1, Type C, and Type IIIc in turn as the dependent variable. #### Data sets used: #### File: 2._Diet_infection_GLM.csv ##### Variables * Sample: Bird ring number - unique identifier for each sample * Julian_date: Number of days since November 1st (start of wintering season) * Infection: Infected or uninfected with *T. galliane* * Infaction_status:  Presence (1) or Absence (0) of *T. galliane* infection. * Strain: the dominant strain detected in infected individuals. Sequencing of some samples failed, and no dominant strain could be reliably identified. These cells (11 samples) are left empty. * Condition: Value of body condition index. Some samples did not have the morphometric data collected allowing the calculation of body condition. In these instances (3 individuals) these cells are left empty. * Country: Sampling country (Senegal, France, Hungary) * Dom_type: The dominant food classification in the diet (natural (wild), unnatural (cultivated), or even if the same number of natural and unnatural genera appeared in the diet) * Prop_wild: The proportion of dietary items consumed which were classified as wild. * Season: Coded to correspond to the year and country samples were collected (see Table 1). * Age: Ad = Adult, Juv= juvenile * All remaining columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 2._wild_cult_glm.csv ##### Variables * Sample, Julian_date, Infection, Infaction_status, Strain, Condition, Country, Dom_type, Prop_wild, Season, Age as in file 2._Diet_infection_GLM.csv * Tcl-1: Presence (1) or Absence (0) of this strain of *T. galliane* * GEO: Presence (1) or Absence (0) of this strain of *T. galliane* * Type C: Presence (1) or Absence (0) of this strain of *T. galliane* * Type IIIc: Presence (1) or Absence (0) of this strain of *T. galliane* * GEO-TD: Presence (1) or Absence (0) of this strain of *T. galliane* * Ttl-TD: Presence (1) or Absence (0) of this strain of *T. galliane* * Co-infected: Presence (1) or Absence (0) of con-infection with multiple strains of *T. galliane* #### File: 3.*NMDS_and_spider_plots*-_comparing_breeding_and_wintering_grounds.R **Description:** Dietary overlap between infected and uninfected birds, and birds infected with different strains of *T. gallinae,* was visualised using non-metric multidimensional scaling (NMDS). Ordination of multidimensional data condenses information into two-dimensional axes, representing variation in the diet. Separate figures were generates to visualise the diets of breeding birds and wintering birds independently.  Plots generated to compare the diet of infected versus uninfected birds, and to compare the diets of bird infected with different strains.  #### Data sets used: #### File: 3._NMDS_breeding.csv and File: 3._NMDS_winter.csv **Description:** Visualising dietary overlap between infected and uninfected birds on the breeding grounds and on the wintering grounds.  ##### Variables * Sample: Bird ring number - unique identifier for each sample * Infection: Presence (1) or Absence (0) of *T. galliane* infection.  * Status: Infected or uninfected with *T. galliane* * Condition: Value of body condition index. Some samples did not have the morphometric data collected allowing the calculation of body condition. In these instances, these cells are left empty. * Country: Sampling country (Senegal, France, Hungary) * Wi.Br: Wintering or breeding season * Dominant food type in diet: The dominant food classification in the diet (natural (wild), unnatural (cultivated), or even if the same number of natural and unnatural genera appeared in the diet) * Season: Sampling season (see Table 1) * Age: Ad = Adult, Juv= juvenile * All remaining columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 3._NMDS_strains2_breeding.csv and File: 3._NMDS_strains2_winter.csv **Description**: Visualising dietary overlap between birds infected with different strains of *T. gallaine* on the breeding grounds and on the wintering grounds.   ##### Variables * Sample: Bird ring number - unique identifier for each sample * Julian_date: Number of days since November 1st (start of wintering season) * Infection:  Infected or uninfected with *T. galliane* * Strain: strain of *T. gallinae* infected individuals (GOT, Tcl-1, Type C, Type IIIc, Uninfected) * Condition: Value of body condition index. Some samples did not have the morphometric data collected allowing the calculation of body condition. In these instances these cells are left empty. * Country: Sampling country (Senegal, France, Hungary). * Br.wi: Breeding or wintering season * Dominant food type in diet: The dominant food classification in the diet (natural (wild), unnatural (cultivated), or even if the same number of natural and unnatural genera appeared in the diet) * Season: Sampling season (see Table 1). * Age: Ad = Adult, Juv= juvenile * All remaining columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 4.*NMDS_and_spider_plots*-_comparing_between_seasons.R **Description:** Dietary overlap between infected and uninfected birds, and birds infected with different strains of *T. gallinae,* was visualised using non-metric multidimensional scaling (NMDS). Ordination of multidimensional data condenses information into two-dimensional axes, representing variation in the diet. Separate plots were generated to visualise the diets of birds infected with different T. galliane strains in different sampling seasons.  #### Data sets used: #### File: 4._NMDS_strains2.csv **Description:** Visualising dietary overlap between birds infected with different strains of *T. gallaine* on in different seasons.   ##### Variables * Sample: Bird ring number - unique identifier for each sample * Julian_date: Number of days since November 1st (start of wintering season) * Infection:  Infected or uninfected with *T. galliane* * Strain: Strain of *T. gallinae* infected individuals (GOT, Tcl-1, Type C, Type IIIc, Uninfected) * Condition: Value of body condition index. Some samples did not have the morphometric data collected allowing the calculation of body condition. In these instances these cells are left empty. * Country: Sampling country (Senegal, France, Hungary). * Br.wi: Breeding or wintering season * Dominant food type in diet: The dominant food classification in the diet (natural (wild), unnatural (cultivated), or even if the same number of natural and unnatural genera appeared in the diet) * Season: Sampling season (see Table 1). * Age: Ad = Adult, Juv= juvenile * All remaining columns are genera detected in the diet, with 0 or 1 indicating if they are absent or present in the sample.  #### File: 5._Pianksa_d_niche_overlap.R **Description:** Pianka’s measure of overlap was used to assess the extent to which diet overlapped for uninfected and infected birds, and in birds infected with different strains. This measure is given as a value from 0, indicating no dietary overlap, to 1, indicating complete dietary overlap. #### Data sets used #### File: 5._Pianka_counts_breeding.csv, File: 5._Pianka_counts_breeding_status.csv, File: 5._Pianka_counts_Senegal.csv, File: 5._Pianka_counts_Senegal_status.csv, File: 5._Pianka_counts_UK_status.csv, File: 5._S1_status.csv, File: 5._W1_strains.csv, File: 5._W3_strains.csv, File: 5._W3_status.csv, File: 5._W4_status.csv, File: 5._W4_strains.csv **Description:** Table gives the number of individuals infected/infected with the specified strain (row) that had consumed the specified genus (column). Data sets are divided based on if they are the breeding or wintering grounds and the specific sampling season.  ##### Variables * Status: infection status (infected or uninfected with *T. gallinae*) * Strain: strain of *T. gallinae* present. * All remaining columns are genera detected in the diet. #### ## Code/software All data files are .csv file,s and all statistical analyses were carried out in R, version 4.0.1 (R Core Team 2020). Packages used:  * *vegan* (Oksanen et al. 2020) * *ggplot2* (Wickham 2016) * *EcoSimR* (Gotelli & Ellison, 2013)  ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * Samples collected from the field, DNA extracted and sequenced by authors.