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

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]

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

Priorities for synthesis research in ecology and environmental science

ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD

Priorities for synthesis research in ecology and environmental science

ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD

DataSheet_1_Evolutionary lability underlies drought adaptation of Australian shrubs along aridity gradients.docx

Leaf drought tolerance traits influence plant survival in water deficit conditions, and these traits are influenced by both the plant’s evolutionary history and the environment in which the plant is currently growing. However, due to the substantial phenotypic plasticity in leaf traits, we still do not know to what degree variation in leaf traits is governed by species’ phylogenetic history or by their environment. To explore this question, we re-examined a drought tolerance dataset from 37 native Australian shrub species with varying climate origins growing in a common garden located in Melbourne, Australia. We previously measured seven leaf morphophysiological traits, and here, we estimated how phylogenetically conserved these traits are. We quantified phylogeny and the strength of correlation between the morphological traits and physiological traits before and after accounting for shared phylogenetic history. We also evaluated the relationship between species’ leaf traits and the climate of their native ranges. We present three main findings: (a) most leaf drought tolerance traits had weak phylogenetic signals, which is consistent with the convergent evolution of these traits. (b) There is weak but consistent coordination between distinct leaf drought tolerance traits, which can be masked due to species’ phylogenetic histories. (c) Leaf drought tolerance traits show strong correlations with the climate of species’ origins, and this relationship is only weakly impacted by phylogenetic signals. Therefore, the role of phylogeny on the coordination among leaf functional traits and their links to climate were limited. A better understanding of trait–environment relationships might be more pivotal than understanding the evolution of these traits for improving the predictions of species’ response to climate change–type drought, especially for shrub species that span substantial aridity gradients.</p

A competition–defence trade-off both promotes and weakens coexistence in an annual plant community

13 páginas.-- 5 figuras.-- 1 tabla.-- 53 referencias.-- Additional supporting information may be found online in the Supporting Information section at the end of the article. https://doi.org/10.1111/1365-2745.13028Competition–defence trade-offs have long been thought to promote plant coexistence and increase species diversity. However, insights from modern coexistence theory clarify that such trade-offs alone cannot sustain coexistence. Coexistence also requires stabilising niche differences and the ability of competitor populations to persist under consumer pressure. Despite the breadth of potential consequences of competition–defence trade-offs, we have little mechanistic understanding of how they affect diversity in natural communities. We investigated the effects of seed harvesting by ants on coexistence in an annual plant community. We parameterised a model of plant competitive population dynamics with data from two field experiments: (a) plant demographic rates and competition coefficients determined by growing plants alone and against intra- and interspecific competitor density gradients; (b) plant fitness losses to ant consumers determined by measuring seed removal from experimental depots. We tested for a trade-off between a plant species’ demographic potential and its susceptibility to consumption and then determined the bounds of ant effects on pairwise and multispecies coexistence by comparing model projections with and without seed consumption. Ants harvested seeds of all plant species, but they strongly preferred the competitively superior large seeded species, inducing a competition–defence trade-off. Unequal seed loss to ants changed competition-based fitness hierarchies, affecting both the number and identities of plant species pairs that were predicted to coexist compared to a scenario without ants. The trade-off most often prevented coexistence by severely disadvantaging the superior competitor or excluding species directly through overconsumption, and a simulated reduction in the overall consumption rate opened few additional opportunities for coexistence. Ant exacerbation of average fitness differences was particularly disruptive to multispecies coexistence, where niche differences were insufficient to stabilise the coexistence of plant triplets and quadruplets. Synthesis. Our results show that the presence of a competition–defence trade-off in a community with stabilising niche differences does not always increase diversity. Instead, the full range of diversity outcomes—positive and negative changes in species number and changes in the identity of the dominant—are possible. Taken together, our results support the emerging paradigm that consumers have wide-ranging impacts on plant diversity and suggest that variation in consumer pressure may be an important driver of large-scale diversity patternsH2020 Marie Skłodowska‐Curie Actions, Grant/Award Number: 661118‐BioFUNC; National Science Foundation, Division of Environmental Biology, Grant/Award Number: 1644641Peer reviewe

Data_Sheet_1_Behavioral mechanisms underlying trait-mediated survival in a coral reef fish.PDF

Fast growth and large size generally increase survivorship in organisms with indeterminate growth. These traits frequently covary, but where they do not, trade-offs often exist in the behavioral choices of organisms. Juvenile bicolor damselfish Stegastes partitus that settle on coral reefs at larger sizes generally experience enhanced survivorship but have slower juvenile growth rates. We hypothesized that differences in behavior may mediate this trade-off. To test whether it is trait-related behaviors or the traits themselves that enhance early survival, we combined individual behavioral observations with otolith (ear stone)-based daily growth measurements for juvenile S. partitus in the Florida Keys. Foraging, sheltering, and chasing behaviors of 256 fish were measured during 5 different months (2008–2009), and patterns of differential survival were similar to those from a 6-year (2003–2008) recruitment time series. We found a trade-off between sheltering and foraging that significantly explained patterns in size-at-settlement: damselfish that settled at larger sizes spent less time sheltered and more time feeding high in the water column. Juvenile growth rates were unrelated to any of the sheltering–foraging behaviors but instead were inversely related to adult conspecific density. Damselfish that settled near higher densities of conspecifics were subjected to increased territorial chasing. Chasing intensity interacted with settlement size such that large juveniles who were chased more frequently exhibited slower growth rates, whereas smaller settlers did not experience this energetic cost. Thus, the dominant survival strategy of S. partitus is to settle at a large size and spend more time foraging high in the water column while dodging conspecifics at an energetic cost to their growth rates. Size-at-settlement is determined during the larval period and after settlement, this trait is key to subsequent behaviors and the strength of trait-mediated survival. Understanding how somatic growth, body size, and survival are intertwined in early life is necessary to help explain population dynamics.</p

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