Phylogenetic and species distribution data
This protocol is extracted from research article:
Multiple macroevolutionary routes to becoming a biodiversity hotspot
Sci Adv, Feb 6, 2019; DOI: 10.1126/sciadv.aau8067

The maximum clade credibility (MCC) tree for mammals was estimated with 100 random trees from the pseudoposterior provided by Kuhn et al. (38) using TreeAnnotator v.1.8.2 (39). Following Rolland et al. (40), we recalibrated the dates in this MCC tree and in the initial 100 trees from the pseudoposterior with alternative dates from Meredith et al. (41) using PATHd8 (42). For birds, we used 100 random trees from the updated version of the posterior distribution of trees in Jetz et al. (26), and we obtained the MCC tree as above.

Species distribution data were obtained from the International Union for Conservation of Nature (IUCN) Red List for mammals (version 5.2) (24) and BirdLife (version 6.0) (25) for birds. Marine species were not analyzed. Hotspots were defined using all species with distribution data—5302 and 11,093 species of mammals and birds, respectively. Species names in the phylogenetic trees were standardized with the IUCN (version 5.2) and BirdLife (version 6.0) taxonomies and collated with the distributional data. In total, 4633 and 9622 species of mammals and birds, respectively, representing 83.3 and 86.5% of the described species were present in the phylogenetic trees and were used in downstream analyses. We followed the definition of the World Wildlife Fund Simplified Biogeographical Realms (version 2.0) (43) for the different biogeographic realms. By definition, the areas in each realm share a common evolutionary and biogeographic history, so comparing them provides a framework for generalization across realms with distinct biotas (43). The Oceanic realm was much smaller than the rest, so we did not include it in our analyses.

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