EcoEvoApps: Interactive apps for theoretical models in ecology and evolutionary biology.

The integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. A promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. To promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source, and multilingual R/Shiny apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interactions, and landscape ecology. These apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students' interest and confidence in working with mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology.

Multiple routes to interspecific territoriality in sister species of North American perching birds.

Behavioral interference between species can influence a wide range of ecological and evolutionary processes. Here, we test foundational hypotheses regarding the origins and maintenance of interspecific territoriality, and evaluate the role of interspecific territoriality and hybridization in shaping species distributions and transitions from parapatry to sympatry in sister species of North American perching birds (Passeriformes). We find that interspecific territoriality is pervasive among sympatric sister species pairs, and that interspecifically territorial species pairs have diverged more recently than sympatric noninterspecifically territorial pairs. None of the foundational hypotheses alone explains the observed patterns of interspecific territoriality, but our results support the idea that some cases of interspecific territoriality arise from misdirected intraspecific aggression while others are evolved responses to resource competition. The combination of interspecific territoriality and hybridization appears to be an unstable state associated with parapatry, whereas species that are interspecifically territorial and do not hybridize are able to achieve extensive fine- and coarse-scale breeding range overlap. In sum, these results suggest that interspecific territoriality has multiple origins and impacts coexistence at multiple spatial scales.

Competition and hybridization drive interspecific territoriality in birds.

Costly interactions between species that arise as a by-product of ancestral similarities in communication signals are expected to persist only under specific evolutionary circumstances. Territorial aggression between species, for instance, is widely assumed to persist only when extrinsic barriers prevent niche divergence or selection in sympatry is too weak to overcome gene flow from allopatry. However, recent theoretical and comparative studies have challenged this view. Here we present a large-scale, phylogenetic analysis of the distribution and determinants of interspecific territoriality. We find that interspecific territoriality is widespread in birds and strongly associated with hybridization and resource overlap during the breeding season. Contrary to the view that territoriality only persists between species that rarely breed in the same areas or where niche divergence is constrained by habitat structure, we find that interspecific territoriality is positively associated with breeding habitat overlap and unrelated to habitat structure. Furthermore, our results provide compelling evidence that ancestral similarities in territorial signals are maintained and reinforced by selection when interspecific territoriality is adaptive. The territorial signals linked to interspecific territoriality in birds depend on the evolutionary age of interacting species, plumage at shallow (within-family) timescales, and song at deeper (between-family) timescales. Evidently, territorial interactions between species have persisted and shaped phenotypic diversity on a macroevolutionary timescale.

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.