1. 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 modelbased 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 a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. 2. To fill this gap, the r package phyr (pronounced fire) 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. 3. phyr can fit 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. 4. The functions and model formula syntax we propose in phyr provide an easy-touse collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions.

A candidate malaria vaccine promoted the evolution of more virulent malaria parasites in mice.

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.

Pulsed fluxes of organisms across ecosystem boundaries can exert top‐down and bottom‐up effects in recipient food webs, through both direct effects on the subsidized trophic levels and indirect effects on other components of the system. While previous theoretical and empirical studies demonstrate the influence of allochthonous subsidies on bottom‐up and top‐down processes, understanding how these forces act in conjunction is still limited, particularly when an allochthonous resource can simultaneously subsidize multiple trophic levels. Using the Lake Mývatn region in Iceland as an example system of allochthony and its potential effects on multiple trophic levels, we analyzed a mathematical model to evaluate how pulsed subsidies of aquatic insects affect the dynamics of a soil–plant–arthropod food web. We found that the relative balance of top‐down and bottom‐up effects on a given food web compartment was determined by trophic position, subsidy magnitude, and top predators’ ability to exploit the subsidy. For intermediate trophic levels (e.g., detritivores and herbivores), we found that the subsidy could either alleviate or intensify top‐down pressure from the predator. For some parameter combinations, alleviation and intensification occurred sequentially during and after the resource pulse. The total effect of the subsidy on detritivores and herbivores, including top‐down and bottom‐up processes, was determined by the rate at which predator consumption saturated with increasing size of the allochthonous subsidy, with greater saturation leading to increased bottom‐up effects. Our findings illustrate how resource pulses to multiple trophic levels can influence food web dynamics by changing the relative strength of bottom‐up and top‐down effects, with bottom‐up predominating top‐down effects in most scenarios in this subarctic system.