An R package for detecting in situ speciation and providing a clearer picture of how biodiversity emerged on isolated systems.
Overview
A speciation event is considered to be in situ when it occurs within a specific geographical range, as opposed to a lineage colonizing a location from elsewhere. The importance of in situ speciation for understanding diversity patterns has been emphasized by decades of work, much of which discusses how in situ speciation contributes to species richness on islands.
The insitu R package provides a suite of functions that allows the user to estimate in situ speciation events and quantify their contribution to biodiversity in discrete geographical units, with a primary focus on island systems and island-like environments. This vignette will cover the functions from the insitu package that are necessary to perform a basic analysis that classifies nodes on a phylogeny as in situ speciation, colonization, or dispersal events, as well as computing diversity decomposition metrics and visualizing results.
Installation
The insitu R package can be installed using remotes:
remotes::install_github("datadiversitylab/insitu")Getting Started
Please find our vignette describing the main functions of insitu and how to get started using it for your analyses on our pkgdown website linked here.