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

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

Teaching Evolutionary Concepts in Elementary School

Charles Darwin would be pleased to know that elementary school children in states that have adopted the Next Generation Science Standards (NGSS) are expected to demonstrate their understanding of several core evolutionary concepts, including trait variation and inheritance, fossils and extinct organisms, common ancestry, natural selection, and adaptation. However, he might also wonder how this is accomplished in the demanding 21st-century science curriculum. In files linked to this article, we provide four lesson plans – with engaging examples, natural selection games, and other interactive activities – that were designed to cover the NGSS Disciplinary Core Ideas in evolutionary biology for grades 3–5, in two one-hour lessons. The lesson plans were developed by college students under the guidance of evolutionary biologists and in consultation with elementary school teachers, and then field tested in elementary school classrooms, as described in an accompanying research article

Search for high-energy neutrinos from gravitational wave event GW151226 and candidate LVT151012 with ANTARES and IceCube

The Advanced LIGO observatories detected gravitational waves from two binary black hole mergers during their first observation run (O1). We present a high-energy neutrino follow-up search for the second gravitational wave event, GW151226, as well as for gravitational wave candidate LVT151012. We find two and four neutrino candidates detected by IceCube, and one and zero detected by Antares, within �500s around the respective gravitational wave signals, consistent with the expected background rate. None of these neutrino candidates are found to be directionally coincident with GW151226 or LVT151012. We use nondetection to constrain isotropic-equivalent high-energy neutrino emission from GW151226, adopting the GW event�s 3D localization, to less than 2�10^51�2�10^54??ergby Anand Sengupta et al