Mapping phylogenetic endemism in R using georeferenced branch extents
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2015
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Guerin, G.
Lowe, A.
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SoftwareX, 2015; 3-4:22-26
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Greg R. Guerin, Andrew J. Lowe
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Abstract
Applications are needed to map biodiversity from large-scale species occurrence datasets whilst seamlessly integrating with existing functions in R. Phylogenetic endemism (PE) is a biodiversity measure based on range-restricted phylogenetic diversity (PD). Current implementations use area of occupancy (AOO) or frequency to estimate the spatial range of branch-length (i.e. phylogenetic range-rarity), rather than extent of occurrence (EOO; i.e. georeferenced phylogenetic endemism), which is known to produce different range estimates.We present R functions to map PD or PE weighted by AOO or EOO (new georeferenced implementation), taking as inputs georeferenced species occurrences and a phylogeny. Non-parametric statistics distinguish PD/PE from trivial correlates of species richness and sampling intensity.
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© 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/ by/4.0/).