Mapping phylogenetic endemism in R using georeferenced branch extents | Zendy

Greg R. Guerin | Zendy; Andrew J. Lowe | Zendy

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Mapping phylogenetic endemism in R using georeferenced branch extents

Author(s) -

Greg R. Guerin,

Andrew J. Lowe

Publication year - 2015

Publication title -

softwarex

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.528

H-Index - 21

ISSN - 2352-7110

DOI - 10.1016/j.softx.2015.10.002

Subject(s) - georeference , endemism , phylogenetic tree , occupancy , biodiversity , range (aeronautics) , species richness , phylogenetics , phylogenetic diversity , geography , biology , ecology , evolutionary biology , physical geography , biochemistry , materials science , composite material , gene

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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