The effective number of species ( We used simulations of five stream macroinvertebrate assemblages and spatially extensive field data of stream fishes and mussels to show (a) how different Values of The amount of variation in
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“
- NSF-PAR ID:
- 10045854
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 26
- Issue:
- 21
- ISSN:
- 0962-1083
- Page Range / eLocation ID:
- p. 5872-5895
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Weighting effective number of species measures by abundance weakens detection of diversity responses
Abstract ENS ) has been proposed as a robust measure of species diversity that overcomes several limitations in terms of both diversity indices and species richness (SR). However, it is not yet clear ifENS improves interpretation and comparison of biodiversity monitoring data, and ultimately resource management decisions.ENS formulations respond to stress and (b) how diversity–environment relationships change with values ofq , which weightENS measures by species abundances.ENS derived from whole simulated assemblages with all species weighted equally (true SR) steadily decreased as stress increased, andENS ‐stress relationships became weaker and more different among assemblages with increased weighting.ENS across the fish and mussel assemblages that was associated with environmental gradients decreased with increasingq .Synthesis and applications . Species diversity is valued by many human societies, which often have policies designed to protect and restore it. Natural resources managers and policy makers may use species richness and diversity indices to describe the status of ecological communities. However, these traditional diversity measures are known subject to limitations that hinder their interpretation and comparability. The effective number of species (ENS ) was proposed to overcome the limitations. Unfortunately, our analyses show thatENS does not improve interpretability of how species diversity responds to either stress or natural environmental gradients. Moreover, incorporating the relative abundance of individuals in different species (evenness) into diversity measures as implemented inENS can actually weaken detection of diversity responses. Natural resources managers and policy makers therefore need to be cautious when interpreting diversity measures, includingENS , whose values are jointly influenced by richness and evenness. We suggest that both researchers and practitioners measure and report three aspects of diversity (species richness, evenness, and composition) separately when assessing and monitoring the diversity of ecological communities. -
Premise The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated
DNA sequencing (ddRAD seq) protocol usingDNA s from four genera extracted from both silica‐dried and herbarium tissue.Methods DNA s fromDraba ,Boechera ,Solidago , andIlex were processed with a ddRAD seq protocol. The effects ofDNA degradation, taxon, and specimen age were assessed.Results Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.
Discussion These results suggest that herbarium samples can be incorporated into dd
RAD seq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRAD seq projects that minimize the expenses associated with fieldwork and sample evaluation. -
Abstract Aim Quantifying abundance distributions is critical for understanding both how communities assemble, and how community structure varies through time and space, yet estimating abundances requires considerable investment in fieldwork. Community‐level population genetic data potentially offer a powerful way to indirectly infer richness, abundance and the history of accumulation of biodiversity within a community. Here we introduce a joint model linking neutral community assembly and comparative phylogeography to generate both community‐level richness, abundance and genetic variation under a neutral model, capturing both equilibrium and non‐equilibrium dynamics.
Location Global.
Methods Our model combines a forward‐time individual‐based community assembly process with a rescaled backward‐time neutral coalescent model of multi‐taxa population genetics. We explore general dynamics of genetic and abundance‐based summary statistics and use approximate Bayesian computation (
ABC ) to estimate parameters underlying the model of island community assembly. Finally, we demonstrate two applications of the model using community‐scale mtDNA sequence data and densely sampled abundances of an arachnid community on La Réunion. First, we use genetic data alone to estimate a summary of the abundance distribution, ground‐truthing this against the observed abundances. Then, we jointly use the observed genetic data and abundances to estimate the proximity of the community to equilibrium.Results Simulation experiments of our
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