Mammal phylogenetic tree (example)

A 5,987-tip subset of the Upham, Esselstyn & Jetz (2019) VertLife mammal phylogeny, used by the db-assembly-workflow_mammals vignette to demonstrate reconciling species names from multiple trait sources against a tree. Tip labels use underscores (Genus_species); 76 tips carry an X_ prefix, denoting Mesozoic stem-mammal fossils grafted onto the molecular backbone via the Upham et al. "backbone-and-patch" framework.

Usage

mammal_tree_example

Format

An object of class phylo (from the ape package), with 5,987 tips and 5,986 internal nodes.

Source

Upham, N.S., Esselstyn, J.A. & Jetz, W. (2019) Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology 17(12):e3000494. doi:10.1371/journal.pbio.3000494 . Full credible sets at https://vertlife.org/phylosubsets/.

Details

Source confirmed by Santiago Ortega, who contributed the data, on issue #11.

If you use this tree in published work, please cite Upham et al. (2019) directly. The bundled object is a subset used for examples only — for analysis-grade trees, download the full credible set from https://vertlife.org/phylosubsets/.

References

Other published mammal phylogenies suitable for comparative analysis (alternatives to Upham et al. 2019):

Faurby, S. & Svenning, J.-C. (2015) A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach. Molecular Phylogenetics and Evolution 84:14–26. doi:10.1016/j.ympev.2014.11.001

Bininda-Emonds, O.R.P. et al. (2007) The delayed rise of present-day mammals. Nature 446:507–512. doi:10.1038/nature05634