README.md

# 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.
	# 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.