phyr: An R package for phylogenetic species-distribution modelling in ecological communities

Abstract

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to lack of accessible tools allowing ecologists to t phylogenetic species distribution models easily. . To ll this gap, the R package phyr (pronounced re) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. The phyr workhorse functions are implemented in C++ making all calculations and model estimations fast. . phyr can t a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models. phyr also estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. All phyr methods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution and phylogenetic terms are modelled as phylogenetic covariance matrices.. The functions and model formula syntax we propose in phyr serves as a simple and uni ed framework that ignites the use of phylogenies to address a variety of ecological questions.

Ecological interactions shape the evolution of flower color in communities across a temperate biodiversity hotspot

“…We used the implementation of APGLMM in the R package phyr (version 1.1.0; Li et al. 2020) to fit the model (using function pglmm). This implementation uses a Bayesian approach, fit using integrated nested Laplace approximation, and so we examine the 95% credible intervals for inference.…”

Beta and phylogenetic diversities tell complementary stories about ecological networks biogeography

“…We used the resulting trees to measure the phylogenetic community dissimilarity (PCD) of both hosts and parasites metacommunities using the function pcd of the package phyr, in R (R Core Team, 2019; Li et al, 2020). To do that, we discarded sites with no correspondents taxa in the phylogenetic trees.…”

Beta and phylogenetic diversities tell complementary stories about ecological networks biogeography

“…The authors also used molecular and morphological traits of species to retrieve the phylogenetic relationships between species. We used the resulting trees to measure the phylogenetic community dissimilarity (PCD) of both hosts and parasites metacommunities using the function pcd of the package phyr, in R (Li et al 2020; R Core Team 2018). To do that, we discarded sites with no correspondents taxa in the phylogenetic trees.…”