Happy International Day for Biological Diversity everyone!
As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).
If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.
Without further ado though, here are a few of the best Methods papers on Biological Diversity:
We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.
The August 2014 issue included a wonderful article from Nadine Sandau et al. on the importance of including community composition in biodiversity-productivity models. The authors begin by reviewing previous approaches that use species richness as an explanatory variable and propose modifications to improve their performance. Next, a new method, in which composition is included as a similarity matrix affecting the residual variance–covariance, is outlined. This new method is very well-suited to observational or manipulative studies where plant diversity is not kept constant by weeding.
Our next highlighted paper is an Application (which means that it has been free to everyone since it was published) and was part of the June 2011 issue. In this article, Fernando Casanoves et al. describe FDiversity: a free, user-friendly, open source-based software package for the calculation and integrated statistical analysis of most functional diversity indices and metrics. Their R package greatly facilitates the analysis of functional diversity patterns and also the links of different dimensions of functional diversity with environmental factors and ecosystem properties and services.
At the beginning of this year, in the January issue of Methods in fact, we had an Open Access article from Olga Chernomor et al. titled ‘Split diversity in constrained conservation prioritization using integer linear programming’. The authors discuss several optimization problems related to the use phylogenetic diversity in conservation prioritization. Using two data sets (one from South Africa and one from the Caribbean) they show how optimization routines that incorporate various conservation constraints can be used to select sets of species for conservation action.
Ecological communities are composed of populations connected in tangled networks of interactions. The extinction of a single species can reverberate through the network and cause other species to go extinct as well. In this article from our August 2013 issue, Anna Eklöf et al. advance the study of secondary extinctions using Bayesian networks. The authors show how this approach can account for different extinction responses using binary and quantitative data. They test their method using simulated ecological networks from the Allometric Trophic Network model.
If you keep up-to-date with our articles published through Early View, you will have seen this article just a couple of weeks ago. Andrés Baselga and Fabien Leprieur compare two frameworks that partition compositional dissimilarity: BAS and POD. In a systematic comparison, they test whether the replacement components are independent of richness difference. The authors also evaluate whether previously reported tests of monotonicity between indices and ecological processes are informative to assess the performance of indices and illustrate the consequences of differences between the two frameworks using freshwater fish.
Detecting and Interpreting Biodiversity
From an article which has just been published, we move on to a classic from our very first issue. In ‘A new method for detecting and interpreting biodiversity and ecological community thresholds’ Metthew Baker and Ryan King introduce the Threshold Indicator Taxa ANalysis (TITAN). TITAN detects changes in taxa distributions along an environmental gradient over space or time and helps to assess synchrony among taxa change points as evidence for community thresholds. Using simulated data sets to test it, the authors were able to correctly identify taxon and community thresholds in more than 99% of 500 unique versions of each simulation.
Interspecific and Intraspecific Biodiversity
Most diversity measures concentrate on how functionally or phylogenetically dissimilar species are from each other (the interspecific components of biodiversity). However, components that concern only the current features of the individuals of a species or the history of the species regardless of the other extant species of the community (the intraspecific components) can also be important. In this 2014 article, Sandrine Pavoine and Janos Izsák introduce a new measure which encompasses both inter- and intraspecific components. They demonstrate their method using both a theoretical phylogenetic tree and real-world data.
Sharing Biodiversity Data
Our second issue of 2013 included an excellent article on BEFdata: an open source web platform for the upload, validation and storage of data related to the field of biodiversity–ecosystem functioning (BEF). Karin Nadrowski et al. explain the uses of this platform and highlight its key features. Throughout the paper they are able to show that this is a great tool for researchers in a cross-disciplinary field.
Diversity Decision Framework
This year’s final International Day for Biological Diversity article comes from Kristofor Voss et al. and is currently available in Early View. The authors present a new modelling approach, the hierarchical diversity decision framework (HiDDeF), that explicitly communicates the sensitivity of water quality benchmarks to implicit judgments about the degree of biodiversity loss that some people are willing to accept. HiDDeF allows users to investigate both individual and community level responses to environmental gradients and generates output that includes a summary of uncertainty in model parameters.