Data from: Life-history and ecological variables as drivers of the evolution of avian innate immune defences
Data files
Oct 27, 2025 version files 856.97 KB
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20250316_birdtree_consensus.newick
6.78 KB
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20251010_correlation_HA_HL_one_observation_per_species.R
1.80 KB
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20251010_HA_BPMM_multiple_observations_per_species.R
101.32 KB
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20251010_HA_evolution_one_observation_per_species.R
9.22 KB
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20251010_HA_nested_ANOVA_multiple_observations_per_species.R
1.98 KB
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20251010_HL_BPMM_multiple_observations_per_species.R
100.98 KB
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20251010_HL_evolution_one_observation_per_species.R
9.05 KB
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20251010_HL_nested_ANOVA_multiple_observations_per_species.R
1.98 KB
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20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx
181.64 KB
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20251010_Peng_et_al_one_observation_per_species_dataset.xlsx
41.24 KB
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20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv
348.06 KB
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20251010_R_Peng_et_al_one_observation_per_species_dataset.csv
37.56 KB
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README.md
15.35 KB
Abstract
Dataset DOI: 10.5061/dryad.gxd25480n
Description of the data and file structure
The file ‘20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx’ contains the raw data for haemagglutination and haemolysis obtained from all (sub)populations included in the selected HLHA studies. It also includes all explanatory variables required for the Bayesian phylogenetic mixed models (BPMMs).
The file ‘20251010_Peng_et_al_one_observation_per_species_dataset.xlsx’ contains the within-species means for haemagglutination and haemolysis. These data were calculated from those in 20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx. This file also includes the species-level explanatory variables.
The file ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ is a reformatted version of ‘20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx’ prepared specifically for data analysis in RStudio.
The file ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ is a reformatted version of ‘20251010_Peng_et_al_one_observation_per_species_dataset.xlsx’ prepared specifically for data analysis in RStudio.
The file ‘20250316_birdtree_consensus.newick’ contains the consensus tree including all collected avian species.
The file ‘20251010_correlation_HA_HL_one_observation_per_species.R’ calculates the correlation between species-level haemagglutination and haemolysis using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HA_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemagglutination in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HL_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemolysis in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HA_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemagglutination across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HL_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemolysis across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HA_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemagglutination at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
The file ‘20251010_HL_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemolysis at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
Files and variables
File: 20250316_birdtree_consensus.newick
Description: The file ‘20250316_birdtree_consensus.newick’ contains the consensus tree including all collected avian species.
File: 20251010_correlation_HA_HL_one_observation_per_species.R
Description: The file ‘20251010_correlation_HA_HL_one_observation_per_species.R’ calculates the correlation between species-level haemagglutination and haemolysis using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_evolution_one_observation_per_species.R
Description: The file ‘20251010_HA_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemagglutination across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_BPMM_multiple_observations_per_species.R
Description: The file ‘20251010_HA_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemagglutination in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_nested_ANOVA_multiple_observations_per_species.R
Description: The file ‘20251010_HA_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemagglutination at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_nested_ANOVA_multiple_observations_per_species.R
Description: The file ‘20251010_HL_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemolysis at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_evolution_one_observation_per_species.R
Description: The file ‘20251010_HL_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemolysis across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_BPMM_multiple_observations_per_species.R
Description: The file ‘20251010_HL_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemolysis in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_R_Peng_et_al_one_observation_per_species_dataset.csv
Description: The file ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ is a reformatted version of ‘20251010_Peng_et_al_one_observation_per_species_dataset.xlsx’ prepared specifically for data analysis in RStudio.
Variables
- row_no:
- Order:
- Order_code:
- Family:
- Family_code:
- Genus:
- Common_name:
- Latin2:
- Subspecies:
- alternative_Latin:
- notes_Latin:
- Diet_Type:
- Diet_notes:
- Diet_Ref:
- Social_Structure:
- Social_Structure_Ref:
- migration:
- flight_distance_(km):
- water_type:
- Water_Ref:
- Clutch_size:
- CS_Mean:
- Clutch_size_Ref:
- mass:
- Mass_notes:
- Mass_Ref:
- Max_Lifespan:
- Max_Lifespan_notes:
- source_type:
- Max_Lifespan_ref:
- breeding_latitude:
- abs_breeding_latitude:
- HL_value_mean:
- HA_value_mean:
- n_for_species_HL:
- n_for_species_HA:
File: 20251010_Peng_et_al_one_observation_per_species_dataset.xlsx
Description: The file ‘20251010_Peng_et_al_one_observation_per_species_dataset.xlsx’ contains the within-species means for haemagglutination and haemolysis. These data were calculated from those in 20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx. This file also includes the species-level explanatory variables.
Variables
- Order:
- Order_code:
- Family:
- Family_code:
- Genus:
- Common_name:
- Latin2:
- Subspecies:
- alternative_Latin:
- notes_Latin:
- Diet_Type:
- Diet_notes:
- Diet_Ref:
- Social_Structure:
- Social_Structure_Ref:
- migration:
- flight_distance_(km):
- water_type:
- Water_Ref:
- Clutch_size:
- CS_Mean:
- Clutch_size_Ref:
- mass:
- Mass_notes:
- Mass_Ref:
- Max_Lifespan:
- Max_Lifespan_notes:
- source_type:
- Max_Lifespan_ref:
- breeding_latitude:
- abs_breeding_latitude:
- HL_value_mean:
- HA_value_mean:
- n_for_species_HL:
- n_for_species_HA:
File: 20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx
Description: The file ‘20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx’ contains the raw data for haemagglutination and haemolysis obtained from all (sub)populations included in the selected HLHA studies. It also includes all explanatory variables required for the Bayesian phylogenetic mixed models (BPMMs).
Variables
- Order:
- Order_code:
- Family:
- Family_code:
- Genus:
- Common_name:
- Latin2:
- Subspecies:
- alternative_Latin:
- notes_Latin:
- Diet_Type:
- Diet_notes:
- Diet_Ref:
- Social_Structure:
- Social_Structure_Ref:
- migration:
- flight_distance:
- water_type:
- Water_Ref:
- Clutch_size:
- CS_Mean:
- Clutch_size_Ref:
- mass:
- Mass_notes:
- Mass_Ref:
- Max_Lifespan:
- Max_Lifespan_notes:
- source_type:
- Max_Lifespan_ref:
- breeding_latitude:
- abs_breeding_latitude:
- seasonal_stage:
- seasonal_stage_notes:
- moulting:
- Free_or_captive:
- captivity_status_notes:
- Sampling_season_or_month:
- sex:
- age_group:
- Sampling_location_country_or_region:
- Sampling_location_specific:
- Sampling_location_lat1:
- Sampling_location_long1:
- average_temperature1:
- precipitation1:
- solar_radiation1:
- water_vapor_pressure1:
- wind_speed1:
- Bird_origin_location_lat2:
- Bird_origin_location_long2:
- average_temperature2:
- precipitation2:
- solar_radiation2:
- water_vapor_pressure2:
- wind_speed2:
- Habitat_type:
- Other_measurements:
- HL_value:
- HL_value_type:
- HL_variation:
- HL_variation_type:
- HA_value:
- HA_value_type:
- HA_variation:
- HA_variation_type:
- Notes_for_value_and_variation:
- Number_of_birds_per_(sub)pop:
- notes_number:
- n_for_species_HL:
- n_for_species_HA:
- ref_number:
- Reference:
File: 20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv
Description: The file ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ is a reformatted version of ‘20251010_Peng_et_al_multiple_observations_per_species_dataset.xlsx’ prepared specifically for data analysis in RStudio.
Variables
- no.row:
- Order:
- Order_code:
- Family:
- Family_code:
- Genus:
- Common_name:
- Latin2:
- Subspecies:
- alternative_Latin:
- notes_Latin:
- Diet_Type:
- Diet_notes:
- Diet_Ref:
- Social_Structure:
- Social_Structure_Ref:
- migration:
- flight_distance:
- water_type:
- Water_Ref:
- Clutch_size:
- CS_Mean:
- Clutch_size_Ref:
- mass:
- Mass_notes:
- Mass_Ref:
- Max_Lifespan:
- Max_Lifespan_notes:
- source_type:
- Max_Lifespan_ref:
- breeding_latitude:
- abs_breeding_latitude:
- seasonal_stage:
- seasonal_stage_notes:
- moulting:
- Free_or_captive:
- captivity_status_notes:
- Sampling_season_or_month:
- sex:
- age_group:
- Sampling_location_country_or_region:
- Sampling_location_specific:
- Sampling_location_lat1:
- Sampling_location_long1:
- average_temperature1:
- precipitation1:
- solar_radiation1:
- water_vapor_pressure1:
- wind_speed1:
- Bird_origin_location_lat2:
- Bird_origin_location_long2:
- average_temperature2:
- precipitation2:
- solar_radiation2:
- water_vapor_pressure2:
- wind_speed2:
- Habitat_type:
- Other_measurements:
- HL_value:
- HL_value_type:
- HL_variation:
- HL_variation_type:
- HA_value:
- HA_value_type:
- HA_variation:
- HA_variation_type:
- Notes_for_value_and_variation:
- Number_of_birds_per_(sub)pop:
- notes_number:
- n_for_species_HL:
- n_for_species_HA:
- ref_number:
- Reference:
Code/software
All analyses were conducted in R version 4.4.2 (R Core Team, 2024).
The packages include: MCMCglmm, dplyr, ape, moments, nlme, geiger, phytools, plotly, ggplot2, viridis, RColorBrewer, tidyr, coda.
File: 20251010_correlation_HA_HL_one_observation_per_species.R
Description: The file ‘20251010_correlation_HA_HL_one_observation_per_species.R’ calculates the correlation between species-level haemagglutination and haemolysis using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_evolution_one_observation_per_species.R
Description: The file ‘20251010_HA_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemagglutination across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_BPMM_multiple_observations_per_species.R
Description: The file ‘20251010_HA_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemagglutination in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HA_nested_ANOVA_multiple_observations_per_species.R
Description: The file ‘20251010_HA_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemagglutination at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_nested_ANOVA_multiple_observations_per_species.R
Description: The file ‘20251010_HL_nested_ANOVA_multiple_observations_per_species.R’ performs nested analyses of haemolysis at different taxonomic levels using (sub)population-level data. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_evolution_one_observation_per_species.R
Description: The file ‘20251010_HL_evolution_one_observation_per_species.R’ builds the macro-evolutionary models and related analyses for haemolysis across species, mainly using ‘20251010_R_Peng_et_al_one_observation_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
File: 20251010_HL_BPMM_multiple_observations_per_species.R
Description: The file ‘20251010_HL_BPMM_multiple_observations_per_species.R’ establishes the Bayesian phylogenetic mixed models (BPMMs) explaining variation in haemolysis in relation to life-history traits and ecological variables. It uses ‘20251010_R_Peng_et_al_multiple_observations_per_species_dataset.csv’ and ‘20250316_birdtree_consensus.newick’.
Access information
Other publicly accessible locations of the data:
- none
Data was derived from the following sources:
- see References in data files