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.