Mapping phylogenetic endemism in R using georeferenced branch extents

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dc.contributor.authorGuerin, G.
dc.contributor.authorLowe, A.
dc.date.issued2015
dc.description.abstractApplications 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.
dc.description.statementofresponsibilityGreg R. Guerin, Andrew J. Lowe
dc.identifier.citationSoftwareX, 2015; 3-4:22-26
dc.identifier.doi10.1016/j.softx.2015.10.002
dc.identifier.issn2352-7110
dc.identifier.issn2352-7110
dc.identifier.orcidGuerin, G. [0000-0002-2104-6695]
dc.identifier.orcidLowe, A. [0000-0003-1139-2516]
dc.identifier.urihttp://hdl.handle.net/2440/106626
dc.language.isoen
dc.publisherElsevier BV
dc.relation.grantARC
dc.rights© 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/).
dc.source.urihttps://doi.org/10.1016/j.softx.2015.10.002
dc.subjectPhylogenetic diversity; phylogenetic endemism; area of occupancy; extent of occurrence; minimum convex polygon; R function; non-parametric statistics; interquartile range
dc.titleMapping phylogenetic endemism in R using georeferenced branch extents
dc.typeJournal article
pubs.publication-statusPublished

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