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MultiHostPrediction/README.md

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MultiHostPrediction Database Analyses
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MultiHostPrediction

Database

The input folder contains the mammal-mites database file: mammal_mite_db.v11.xlsx.

Mammal super treefile MamPhy_BDvr_Completed_5911sp_topoCons_NDexp_v2_tree0001.tre is obtained from Upham, N. S., Esselstyn, J. A. & Jetz, W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol. 17, e3000494, doi:10.1371/journal.pbio.3000494 (2019)

Mammal range maps were obtained from https://mol.org/datasets/ec694c34-bddd-4111-ba99-926a5f7866e8, curated by experts from the paper: Marsh, C. J. et al. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. J. Biogeogr. 49, 979-992, doi:10.1111/jbi.14330 (2022). The total size the maps exceed 10GB, we therefore do not provide the original dataset on this github folder.

Analyses

  • Fig2&3_model_building: scripts that predict multi-host risk based on predictors from mites morphology, mites biogeographic properties, host traits, and hosts' mites sharing probability

  • Fig4_mitesSharing_calculation: scripts that build the model of mites sharing among hosts as a function of phylogenetic distances and geographic overlaps.

  • Fig2&3_model_building/generatingHostPD&GO: scripts that calculate pairwise range overlap between hosts using the expert mammal range maps, and PD using the mammal super tree.