The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database

There is an urgent need for largeâ scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling humanâ biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and coâ occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an r package that provides easy access to these data.The bien r package allows users to access the multiple types of data in the BIEN database. Functions in this package query the BIEN database by turning user inputs into optimised PostgreSQL functions. Function names follow a convention designed to make it easy to understand what each function does. We have also developed a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the bien r package.The development of the BIEN database represents a significant achievement in biological data integration, cleaning and standardization. Likewise, the bien r package represents an important tool for open science that makes the BIEN database freely and easily accessible to everyone.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142458/1/mee312861_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142458/2/mee312861.pd

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

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits : A Multi-Ethnic Meta-Analysis of 45,891 Individuals

J. Kaprio, S. Ripatti ja M.-L. Lokki työryhmien jäseniä.Peer reviewe

Data from: A structural approach for understanding multispecies coexistence

Although observations of species-rich communities have long served as a primary motivation for research on the coexistence of competitors, the majority of our empirical and theoretical understanding comes from two-species systems. How much of the coexistence observed in species rich communities results from indirect effects among competitors that only emerge in diverse systems remains poorly understood. Resolving this issue requires simple, scalable, and intuitive metrics for quantifying the conditions for coexistence in multispecies systems, and how these conditions differ from those expected based solely on pairwise interactions. To achieve these aims, we develop a structural approach for studying the set of parameter values compatible with n-species coexistence given the geometric constraints imposed by the the matrix of competition coefficients. We derive novel mathematical metrics analogous to stabilizing niche differences and fitness differences that measure the range of conditions compatible with multispecies coexistence, incorporating the effects of indirect interactions emerging in diverse systems. We show how our measures can be used to quantify the extent to which the conditions for coexistence in multispecies systems differ from those that allow pairwise coexistence, and apply the method to a field system of annual plants. We conclude by presenting new challenges and empirical opportunities emerging from our structural metrics of multispecies coexistence

Disentangling the functional trait correlates of spatial aggregation in tropical forest trees

Environmental filtering and dispersal limitation can both maintain diversity in plant communities by aggregating conspecifics, but parsing the contribution of each process to community assembly has proven difficult empirically. Here we assess the contribution of filtering and dispersal limitation to the spatial aggregation patterns of 456 tree species in a hyperdiverse Amazonian forest and find distinct functional trait correlates of interspecific variation in these processes. Spatial point process model analysis revealed that both mechanisms are important drivers of intraspecific aggregation for the majority of species. Leaf drought tolerance was correlated with species topographic distributions in this aseasonal rainforest, showing that future increases in drought severity could significantly impact community structure. In addition, seed mass was associated with the spatial scale and density of dispersal‐related aggregation. Taken together, these results suggest variation in environmental filtering and dispersal limitation act in concert to influence the spatial and functional structure of diverse forest communities

A Common Toolbox to Understand, Monitor or Manage Rarity? A Response to Carmona et al.

International audienc

Sustaining ecosystem functions in a changing world: a call for an integrated approach

With ever-increasing human pressure on ecosystems, it is critically important to predict how ecosystem functions will respond to such human-induced perturbations. We define perturbations as either changes to abiotic environment (e.g. eutrophication, climate change) that indirectly affects biota, or direct changes to biota (e.g. species introductions). While two lines of research in ecology, biodiversity-ecosystem function (BDEF) and ecological resilience (ER) research, have addressed this issue, both fields of research have nontrivial shortcomings in their abilities to address a wide range of realistic scenarios. We outline how an integrated research framework may foster a deeper understanding of the functional consequences of perturbations via simultaneous application of (i) process-based mechanistic predictions using trait-based approaches and (ii) detection of empirical patterns of functional changes along real perturbation gradients. In this context, the complexities of ecological interactions and evolutionary perspectives should be integrated into future research. Synthesis and applications. Management of human-impacted ecosystems can be guided most directly by understanding the response of ecosystem functions to controllable perturbations. In particular, we need to characterize the form of a wide range of perturbation-function relationships and to draw connections between those patterns and the underlying ecological processes. We anticipate that the integrated perspectives will also be helpful for managers to derive practical implications for management from academic literature. Management of human-impacted ecosystems can be guided most directly by understanding the response of ecosystem functions to controllable perturbations. In particular, we need to characterize the form of a wide range of perturbation-function relationships and to draw connections between those patterns and the underlying ecological processes. We anticipate that the integrated perspectives will also be helpful for managers to derive practical implications for management from academic literature

Functional trait space and the latitudinal diversity gradient

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory