canaper: Categorical analysis of neo‐ and paleo‐endemism in R

Abstract

Biodiversity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of biodiversity. CANAPE (categorical analysis of neo‐ and paleo‐endemism) is one such method that can provide insight into the evolutionary processes generating biodiversity. The only currently available software implementing CANAPE is Biodiverse, which is written in Perl and can be used either through a graphical user interface (GUI) or user‐developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. Here, we present canaper, a new R package (www.r‐project.org) that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility; CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. Our case study shows that canaper produces equivalent results to Biodiverse and can complete computations on moderately sized datasets quickly (<10 min to reproduce a canonical study). canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby obviating the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing biodiversity in R.

Effects of climate and environmental heterogeneity on the phylogenetic structure of regional angiosperm floras worldwide

“…A positive value of PD ses or MPD ses reflects relative phylogenetic overdispersion of species, while a negative value reflects relative phylogenetic clustering of species. We used the package PhyloMeasures 72 to calculate PD, MPD, PD ses , and MPD ses , and the package canaper 73 to calculate RPD. We used a Mollweide (equal-area) projection to map each of the five phylogenetic metrics (Fig.…”

Machine learning approaches to assess microendemicity and conservation risk in cave-dwelling arachnofauna

“…To assess the conservation priority of Israeli Tegenaria we conducted Categorical Analysis of Neo- and Paleo-Endemism (CANAPE) on our full dataset (Mishler et al, 2014). We used canaper, a package which allows for the running of CANAPE in its entirety in R (Nitta et al, 2023). As inputs for canaper, we used our 50% taxon occupancy phylogeny and a data frame consisting of a column with each terminal name and 2 columns with the latitude and longitude from which the corresponding samples were collected.…”