Data from: Diverse hosts, diverse immune systems: evolutionary variation in bat immunology
Data files
May 02, 2025 version files 581.41 KB
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Becker_et_al_2025_ANYAS_data.csv
567.80 KB
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Becker_et_al_2025_ANYAS_R_script.R
4.94 KB
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README.md
8.66 KB
Jun 09, 2025 version files 560.62 KB
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Becker_et_al_2025_ANYAS_data.csv
545.88 KB
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Becker_et_al_2025_ANYAS_R_script.R
5.93 KB
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README.md
8.81 KB
Abstract
The ability of multiple bat species to host zoonotic pathogens without often showing disease has fostered growing interest in bat immunology, indicating ways immune systems may differ between bats and other vertebrates. However, interspecific variation in immunological diversity among bats has only begun to be recognized. The order Chiroptera accounts for over 20% of all mammal species and shows extreme diversity in a suite of correlated ecological traits, such that bats should not be expected to be immunologically homogenous. Here, we review the ecological and evolutionary diversity of chiropteran hosts and highlight case studies emphasizing the range of immune strategies thus far observed across bat species, including responses to SARS-CoV-2. Next, we synthesize and propose hypotheses to explain this immunological diversity, focused on pathogen exposure, biogeography, host energetics, and environmental stability. We then analyze immunology-related citations per species across bats to motivate discussion of key research priorities. Broad sampling is needed to remedy current biases, as only a fraction of bat species has been immunologically studied. Such work should integrate methodological advancements, in vitro and in vivo studies, and phylogenetic comparative methods to robustly test evolutionary hypotheses and understand the drivers and consequences of immunological diversity among bats.
Dataset DOI: 10.5061/dryad.ksn02v7gj
Description of the data and file structure
The data CSV contains species-level data across bats from the COMBINE, PanTHERIA, and VIRION databases, standardized to the mammalian taxonomy of Upham et al. 2019. The R script contains code for downloading VIRION data, matching to the bat taxonomy above, and aggregating bat–virus interactions to viral family richness. The R script also aggregates total and immunology-related citation counts per bat species.
Files and variables
File: Becker_et_al_2025_ANYAS_R_script.R
Description:
File: Becker_et_al_2025_ANYAS_data.csv
Description: Blank cells are coded as NA
Variables
- tip: bat species name
- clade: bat clade label from Upham et al. 2019
- fam: bat family from Upham et al. 2019
- gen: bat genus from Upham et al. 2019
- vfams: number of viral families (derived from VIRION)
- adult_mass_g: adult body mass in grams from COMBINE
- adult_brain_mass_g: adult brain mass in grams from COMBINE
- adult_body_length_mm: adult body length in mm from COMBINE
- adult_forearm_length_mm: adult forearm length in mm from COMBINE
- max_longevity_d: maximum longevity in days from COMBINE
- maturity_d: age of sexual maturity in days from COMBINE
- female_maturity_d: age of female sexual maturity in days from COMBINE
- male_maturity_d: age of male sexual maturity in days from COMBINE
- age_first_reproduction_d: age of first reproduction in days from COMBINE
- gestation_length_d: duration of gestation period in days from COMBINE
- teat_number_n: number of teats from COMBINE
- litter_size_n: number of offspring per female from COMBINE
- litters_per_year_n: numbers of litters per year from COMBINE
- interbirth_interval_d: time between reproductive events in days from COMBINE
- neonate_mass_g: mass of neonates in grams from COMBINE
- weaning_age_d: age at which weaning ends in days from COMBINE
- weaning_mass_g: weight at weaning in grams from COMBINE
- generation_length_d: average age of parents in days from COMBINE
- dispersal_km: distance from natal origin in km from COMBINE
- density_n_km2: population density in km2 from COMBINE
- hibernation_torpor: binary for whether the species hibernates or undergoes torpor (1) from COMBINE
- fossoriality: binary for ground dwelling or fossorial (1) from COMBINE
- home_range_km2: home range size in km from COMBINE
- social_group_n: number of individuals per social group from COMBINE
- dphy_invertebrate: percent of invertebrates in diet from COMBINE
- dphy_vertebrate: percent of vertebrates in diet from COMBINE
- dphy_plant: percent of plants in diet from COMBINE
- det_inv: percent of invertebrates in diet from COMBINE
- det_vend: percent of endotherms in diet from COMBINE
- det_vect: percent of ectotherms in diet from COMBINE
- det_vfish: percent of fish in diet from COMBINE
- det_vunk: percent of unknown in diet from COMBINE
- det_scav: percent of scavenge/carcasses in diet from COMBINE
- det_fruit: percent of fruit in diet from COMBINE
- det_nect: percent of nectar in diet from COMBINE
- det_seed: percent of seeds in diet from COMBINE
- det_plantother: percent of other plants in diet from COMBINE
- det_diet_breadth_n: number of dietary categories from COMBINE
- trophic_level: herbivore (1), omnivore (2), or carnivore (3) from COMBINE
- foraging_stratum: assignment to one of five foraging strata from COMBINE (M: marine, G: ground, S: scansorial, Ar: arboreal, A: aerial)
- activity_cycle: nocturnal (1), mix (2), or diurnal (3) from COMBINE
- freshwater: binary for spending significant time in freshwater (1) from COMBINE
- marine: binary for spending significant time in marine habitats (1) from COMBINE
- terrestrial_non.volant: binary for spending significant time on land (1) from COMBINE
- terrestrial_volant: binary for capable of powered flight (1) from COMBINE
- upper_elevation_m: upper elevation of species range in meters from COMBINE
- lower_elevation_m: lower elevation of species range in meters from COMBINE
- altitude_breadth_m: difference in elevation of species range in meters from COMBINE
- island_dwelling: binary for dwelling on islands (1) from COMBINE
- island_endemicity: score of island endemicity from COMBINE
- disected_by_mountains: binary for range being dissected by mountains (1) from COMBINE
- glaciation: binary for historical exposure to glaciation (1) from COMBINE
- biogeographical_realm: biogeographic realm categories
- habitat_breadth_n: number of habitat categories from the IUCN from COMBINE
- X1.1_ActivityCycle: nocturnal only (1), mixed (2), or diurnal only (3) from PanTHERIA
- X5.1_AdultBodyMass_g: adult body mass in grams from PanTHERIA
- X8.1_AdultForearmLen_mm: adult forearm length in mm from PanTHERIA
- X13.1_AdultHeadBodyLen_mm: adult head to base of tail length in mm from PanTHERIA
- X2.1_AgeatEyeOpening_d: age of eye opening in days from PanTHERIA
- X3.1_AgeatFirstBirth_d: age at first birth in days from PanTHERIA
- X18.1_BasalMetRate_mLO2hr: basal metabolic rate from PanTHERIA
- X5.2_BasalMetRateMass_g: mass of individuals from BMR measures from PanTHERIA
- X6.1_DietBreadth: number of dietary categories from PanTHERIA
- X7.1_DispersalAge_d: age of dispersal in days from PanTHERIA
- X9.1_GestationLen_d: length of gestation period in days from PanTHERIA
- X12.1_HabitatBreadth: number of habitat layers used from PanTHERIA
- X22.1_HomeRange_km2: home range size (individuals or groups) in km2 from PanTHERIA
- X22.2_HomeRange_Indiv_km2: home range size of individuals in km2 from PanTHERIA
- X14.1_InterbirthInterval_d: days between births in days from PanTHERIA
- X15.1_LitterSize: individuals per litter from PanTHERIA
- X16.1_LittersPerYear: numbers of litters per year from PanTHERIA
- X17.1_MaxLongevity_m: maximum lifespan in months from PanTHERIA
- X5.3_NeonateBodyMass_g: body mass of neonates in grams from PanTHERIA
- X13.2_NeonateHeadBodyLen_mm: neonate head to base of tail length in mm from PanTHERIA
- X21.1_PopulationDensity_n.km2: population size in km2 from PanTHERIA
- X10.1_PopulationGrpSize: population group size from PanTHERIA
- X23.1_SexualMaturityAge_d: age of sexual maturity in days from PanTHERIA
- X10.2_SocialGrpSize: social group size from PanTHERIA
- X24.1_TeatNumber: number of teats from PanTHERIA
- X12.2_Terrestriality: binary terrestrial (1) or not (0) from PanTHERIA
- X6.2_TrophicLevel: herbivore (1), omnivore (2), or carnivore (3) from PanTHERIA
- X25.1_WeaningAge_d: age when weaning ends in days from PanTHERIA
- X5.4_WeaningBodyMass_g: body mass when weaning in grams from PanTHERIA
- X13.3_WeaningHeadBodyLen_mm: weaning head to base of tail length in mm from PanTHERIA
- X5.5_AdultBodyMass_g_EXT: extrapolated adult body mass in grams from PanTHERIA
- X16.2_LittersPerYear_EXT: extrapolated litters per year from PanTHERIA
- X5.6_NeonateBodyMass_g_EXT: extrapolated neonate body mass in grams from PanTHERIA
- X5.7_WeaningBodyMass_g_EXT: extrapolated weaning body mass in grams from PanTHERIA
- X26.1_GR_Area_km2: geographic range size in km2 from PanTHERIA
- X26.2_GR_MaxLat_dd: maximum latitude of geographic range in decimal degrees from PanTHERIA
- X26.3_GR_MinLat_dd: minimum latitude of geographic range in decimal degrees from PanTHERIA
- X26.4_GR_MidRangeLat_dd: median latitudinal extent of range in decimal degrees from PanTHERIA
- X26.5_GR_MaxLong_dd: maximum longitude of geographic range in decimal degrees from PanTHERIA
- X26.6_GR_MinLong_dd: minimum longitude of geographic range in decimal degrees from PanTHERIA
- X26.7_GR_MidRangeLong_dd: median longitudinal extent of range in decimal degrees from PanTHERIA
- X27.1_HuPopDen_Min_n.km2: minimum human population density in range in km2 from PanTHERIA
- X27.2_HuPopDen_Mean_n.km2: mean human population density in range in km2 from PanTHERIA
- X27.3_HuPopDen_5p_n.km2: 5th percentile human population density in range in km2 from PanTHERIA
- X27.4_HuPopDen_Change: mean rate of increase in human population density in range (km2) from PanTHERIA
- X28.1_Precip_Mean_mm: mean monthly rainfall (mm) from PanTHERIA
- X28.2_Temp_Mean_01degC: mean monthly temperature (0.1°C) from PanTHERIA
- X30.1_AET_Mean_mm: mean actual evapotranspiration (AET) rate in mm from PanTHERIA
- X30.2_PET_Mean_mm: mean potential evapotranspiration (PET) rate in mm from PanTHERIA
- cites: citation count per species binomial from PubMed
- icites: immunology-related citation count per species binomial from PubMed
Version changes
- 6/9/2025: Updated virus family richness with up-to-date VIRION data (see https://github.com/viralemergence/virion)
