Laffan, S. W. | bioRxiv Science

bioRxiv2022

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

O_LIBiodiversity 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. C_LIO_LIHere, we present canaper, a new R package 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. C_LIO_LIOur 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). C_LIO_LIcanaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby averting 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. C_LI

evolutionary biology↗

bioRxiv2020

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.

ecology↗