Abstract
Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot.com/biogeobears.
Highlights
The methods employed in historical biogeography are very diverse and include historical narrative, panbiogeography (Heads 2012, Waters et al 2013), cladistic biogeography, multistate charac‐ ter methods, and ancestral state methods special‐ ized for biogeography
I have created an R package, “BioGeoBEARS” (Matzke 2013b) that implements in a likelihood framework several popular models, such as the LAGRANGE Dispersal‐Extinction Cladogenesis (DEC) model, a likelihood version of Dispersal‐Vicariance Analysis (DIVA), and a likelihood version of the range evolution model assumed by methods such as BayArea program and the Bayesian Binary Model (BBM) of RASP (Yu et al 2013)
BayArea and BBM have no special range evolution process occurring at cladogenesis, and this assumption is implemented in Bio‐ GeoBEARS in the “BAYAREA” model
Summary
The methods employed in historical biogeography are very diverse and include historical narrative, panbiogeography (Heads 2012, Waters et al 2013), cladistic biogeography, multistate charac‐ ter methods, and ancestral state methods special‐ ized for biogeography. Cladogenesis, DIVA, founder‐event speciation, historical biogeography, jump dispersal, LA‐ GRANGE, phylogenetics Far there has been no method to determine which processes are most important, nor to determine which available model best fits the geographical and phylogenetic data for any particular clade.
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