Data and code for "Predicting high pathogenicity avian influenza H5N1 susceptibility in wild birds"

Full description

We analyse outbreak notifications of high pathogenicity avian influenza (HPAI) in wild birds to understand the impacts of species’ ecologies and phylogeny on HPAI notifications and predict host susceptibility to HPAI H5N1 for Australia, as the only continent thus far unaffected by this virus. We found a significant family-level phylogenetic signal in HPAI notifications in wild birds. Furthermore, we found that adding ecological traits to this phylogenetic information does not improve explanatory power of HPAI notifications. Using the family-level phylogenies to predict HPAI H5N1 susceptibility in Australian birds, we predict that families of Australian seabirds, shorebirds, and waterbirds will be most susceptible to HPAI H5N1 once it arrives on the continent.

The HPAI_Feb26 dataset contains the columns: AvesLatin (bonimal name), Species (binomial name), EnglishName (species common name), Genus (taxonomic genus), Family (taxonomic family), Order (taxonomic order), event_start_date (onset of notification event), latitude and longitude (coordinates of event location), and country_name (name of country where outbreak occured).

HPAI_traits_2 dataset contains the columns: Species (binomial name), EnglishName (species common name), Genus (taxonomic genus), Family (taxonomic family), Order (taxonomic order), CongregateTrue (whether the species is known to congregate or not; Y/N) Habitat_Groupings (habitat the species uses: Marine/Coastal, Freshwater, or Terrestrial), and Feb26.New.Diet (diet the species eats: Vertebrate predator, Scavenger, Piscivore, Plant-based diet, Omnivore and Invetebrate Predator: see code for how these are grouped in analyses).

The AusBirds dataset contains the columns: Species (binomial name), TaxonName (species common name), FamilyCommonName (family common name), Family (taxonomic family), Order (taxonomic order), CongregateTrue (whether the species is known to congregate or not; Y/N) Habitat_Groupings (habitat the species uses: Marine/Coastal, Freshwater, or Terrestrial), and Feb.2026.Diet (diet the species eats: Vertebrate predator, Scavenger, Piscivore, Plant-based diet, Omnivore and Invetebrate Predator: see code for how these are grouped in analyses).

prunedtree contains the family-level phylogenetic tree used in analyses.

R scrip contains the code used to analyse the data.