phyr: Anrpackage for phylogenetic species-distribution modelling in ecological communities

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 a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. To fill this gap, therpackagephyr(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. Thephyrworkhorse functions are implemented in C++ making all calculations and model estimations fast. phyrcan fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models.phyralso 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. Allphyrmethods 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 inphyrprovide an easy-to-use collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions

Coevolution, diversification and alternative states in two-trophic communities

Single-trait eco-evolutionary models of arms races between consumers and their resource species often show inhibition rather than promotion of community diversification. In contrast, modelling arms races involving multiple traits, we found that arms races can promote diversification when trade-off costs among traits make simultaneous investment in multiple traits either more beneficial or more costly. Coevolution between resource and consumer species generates an adaptive landscape for each, with the configuration giving predictable suites of consumer and resource species. Nonetheless, the adaptive landscape contains multiple alternative stable states, and which stable community is reached depends on small stochastic differences occurring along evolutionary pathways. Our results may solve a puzzling conflict between eco-evolutionary theory that predicts community diversification via consumer–resource interactions will be rare, and empirical research that has uncovered real cases. Furthermore, our results suggest that these real cases might be just a subset of alternative stable communities

Presence of Breeding Birds Improves Body Condition for a Crocodilian Nest Protector.

Ecological associations where one species enhances habitat for another nearby species (facilitations) shape fundamental community dynamics and can promote niche expansion, thereby influencing how and where species persist and coexist. For the many breeding birds facing high nest-predation pressure, enemy-free space can be gained by nesting near more formidable animals for physical protection. While the benefits to protected species seem well documented, very few studies have explored whether and how protector species are affected by nest protection associations. Long-legged wading birds (Pelecaniformes and Ciconiiformes) actively choose nesting sites above resident American alligators (Alligator mississippiensis), apparently to take advantage of the protection from mammalian nest predators that alligator presence offers. Previous research has shown that wading bird nesting colonies could provide substantial food for alligators in the form of dropped chicks. We compared alligator body condition in similar habitat with and without wading bird nesting colonies present. Alligator morphometric body condition indices were significantly higher in colony than in non-colony locations, an effect that was statistically independent of a range of environmental variables. Since colonially nesting birds and crocodilians co-occur in many tropical and subtropical wetlands, our results highlight a potentially widespread keystone process between two ecologically important species-groups. These findings suggest the interaction is highly beneficial for both groups of actors, and illustrate how selective pressures may have acted to form and reinforce a strongly positive ecological interaction

phyr:Anrpackage for phylogenetic species-distribution modelling in ecological communities

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 a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. 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. 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. The functions and model formula syntax we propose in phyr provide an easy‐to‐use collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions.Funding for this work was provided by the National Science Foundation (US-NSF-DEB Dimensions of Biodiversity, 1240804)

Morphometric body condition for colony and non-colony alligators.

<p>Comparison of morphometric body condition (Fulton’s factor, <i>K</i>, and scaled mass index, ) for adult female alligators caught near Everglades tree islands with and without wading bird nesting colonies present. Error bars are CI_95% via bias-corrected and accelerated bootstrapping, and crossed points indicate the individual caught with a broken tail. Beanplots represent values from the reference population of alligators caught in our study area between 1999–2014, filtered for those within the range of snout-vent lengths from our captured females (<i>n</i> = 387); dashed and dotted lines are located at the mean values for colony and non-colony alligators, respectively.</p

Map of the study area.

<p>Locations of Water Conservation Area 3A (WCA 3A) and Arthur R. Marshall Loxahatchee National Wildlife Refuge (LOX) in the Everglades of Florida, USA, and inset maps of adult female alligator capture sites. In capture-site maps, habitat type shows the densities of tree islands (clusters of trees / shrubs) and locations of canals near capture sites; white areas in the LOX inset are non-habitat. Open-source data for habitat type were obtained from the Ecological Modeling Team at Everglades National Park: <a href="http://simglades.org/" target="_blank">http://simglades.org/</a>.</p

Intermediary plasma metabolites (IPMs) for colony and non-colony alligators.

<p>Comparison of the IPMs glucose, triglycerides, β-hydroxy-butyrate (BHB), and uric acid for adult female alligators caught near Everglades tree islands with and without wading bird nesting colonies present. Error bars are CI_95% via bias-corrected and accelerated bootstrapping; crossed points indicate the individual caught with a broken tail. For triglycerides and BHB, censored values were replaced with model estimates from separate regressions on order statistics for colony and non-colony subpopulations.</p

Model selection on RLMs predicting alligator body condition (Fulton’s factor, <i>K</i>).

<p>Model selection on RLMs predicting alligator body condition (Fulton’s factor, <i>K</i>).</p

Mass versus length for the reference population.

<p>Plot of mass against snout-vent length for a reference population of alligators caught in the study area from 1999–2014 (<i>n</i> = 565). Regression lines are for standardized major axis (dashed) and ordinary least squares (solid) regressions, and rug plots along vertical and horizontal axes represent masses and snout-vent lengths respectively for alligators in this study.</p