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Phylogenetic occupancy models integrate imperfect detection and phylogenetic signal to analyze community structure
Author(s) -
Frishkoff Luke O.,
Valpine Perry,
M'Gonigle Leithen K.
Publication year - 2017
Publication title -
ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.144
H-Index - 294
eISSN - 1939-9170
pISSN - 0012-9658
DOI - 10.1002/ecy.1631
Subject(s) - phylogenetic tree , occupancy , community structure , taxon , phylogenetic comparative methods , biology , ecology , community , phylogenetics , evolutionary biology , imperfect , habitat , biochemistry , linguistics , philosophy , gene
Biological communities are structured phylogenetically—closely related species are typically more likely to be found at the same sites. This may be, in part, because they respond similarly to environmental gradients. Accurately surveying biological communities is, however, made difficult by the fact that detection of species is not perfect. In recent years, numerous statistical methods have been developed that aim to overcome deficiencies in the species detection process. However, these methods do not allow investigators to assess phylogenetic community structure. Here, we introduce the phylogenetic occupancy model (POM), which accounts for imperfect species detection while assessing phylogenetic patterns in community structure. Using simulated data sets we show that the POM grants less biased estimates of phylogenetic structure than models without imperfect detection, and can correctly ascertain the effects of species traits on community composition while accounting for evolutionary non‐independence of taxa. Integrating phylogenetic methods into widely used occupancy models will help clarify how evolutionary history influences modern day communities.