What happens to our understanding of functional diversity when we ignore intraspecific trait variability?

Post provided by Mark Wong

Impressive variability sometimes occurs within a species, such as between these sister ants from the same Carebara sp. colony. Credit: Francois Brassard.

Throw a rock at a conference and you’ll likely hit an ecologist who examines the variation among organisms’ functional traits for one reason or another. From understanding the assembly of communities and their responses to environmental change, to the effects of biodiversity on ecosystem functions, and – well, why not – modelling the global spectrum of ecological form and function, assessments of functional diversity have quickly become the bread and butter of community, ecosystem and macro ecology.

In this blog post, Mark Wong discusses his paper ‘Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: lessons from natural assemblages’, recently published in Methods in Ecology & Evolution.

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What Biases Could Your Sampling Methods Add to Your Data?

Post provided by ROGER HO LEE


Have you ever gone fishing? If so, you may have had the experience of not catching any fish, while the person next to you got plenty. If you walked along the pier or bank, you may have seen that other fishermen and -women caught fish of various shapes and sizes. You’d soon realise that each person was using a different set of equipment and baits, and of course, that the anglers differed in their skills and experience. Beneath the water were many fish, but whether you could catch them, or which species could even be caught, all depended on your fishing method, as well as where and how the fish you were targeting lived.

Designing Sampling Protocols

Head view of different ant species found in Hong Kong and further in SE Asia.

Head view of different ant species found in Hong Kong and further in South East Asia.

This is a lot like the situation that ecologists often face when designing sampling protocols for field surveys. While a comprehensive survey will yield the most complete information, few of us have the resources to capture every member of the community we’re studying. So, we take representative samples instead. But the method(s) used for sampling will only allow us to collect a subset of the species which are present. This selection of the species is not random per se – it’s dependent on species’ life history. Continue reading

Overcoming the Challenges of Studying Soil Nematodes: A New Approach with Implications for All (Soil) Organisms

Post provided by Stefan Geisen

(Soil) Nematodes

“…if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes, and oceans represented by a film of nematodes…” (Cobb 1914)

He may have said it more than a century ago but we now, more than ever, realise that Nathan Augustus Cobb was right. Nematodes are by far the most abundant animals soil, freshwater and marine ecosystems. These tiny worms are barely visible to the human eye (if they’re visible at all), hundreds can inhabit a single gram of soil . Their similar shape might lead you to think that they’re all alike, but that’s not the case. More than 25,000 species have been identified and estimates put their entire species diversity in the 100,000s.

Some common nematode species found in most soils. a) Plectus sp; b) Aphelenchus sp; c) Helicotylenchus sp; d) Thonus sp; e) Mononchus sp; © Wageningen University, Laboratory of Nematology, NL; Hanny van Megen

Some common nematode species found in most soils. a) Plectus sp, b) Aphelenchus sp, c) Helicotylenchus sp, d) Thonus sp, e) Mononchus sp. © Wageningen University, Laboratory of Nematology, NL; Hanny van Megen

This taxonomic and functional diversity has boosted nematodes to become useful bioindicators for soil quality. Nematodes perform many different functions in both terrestrial and aquatic ecosystems. These are mainly defined by what they eat:

  • Bacteria/Fungi: Many nematode groups eat bacteria and fungi. They control the population of these organisms and keep them active.
  • Plants: Plant feeders are the unwanted guests in agricultural systems as well as in our gardens. They can destroy entire harvests by piercing into or infiltrating roots.
  • Omnivores/Predators: Many nematode species prey on other smaller organisms including smaller nematodes and control their abundances.
  • Parasites: These species inhabit other larger organisms and can act as biocontrol agents.

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Issue 9.1: Qualitative Methods for Eliciting Judgements for Decision Making

Issue 9.1 is now online!

Our first issue of 2018, which includes our latest Special Feature – “Qualitative methods for eliciting judgements for decision making” – is now online!

This new Special Feature is a collection of five articles (plus an Editorial from Guest Editors Bill Sutherland, Lynn Dicks, Mark Everard and Davide Geneletti) brings together authors from a range of disciplines (including ecology, human geography, political science, land economy and management) to examine a set of qualitative techniques used in conservation research. They highlight a worrying extent of poor justification and inadequate reporting of qualitative methods in the conservation literature.

As stated by the Guest Editors in their Editorial “these articles constitute a useful resource to facilitate selection and use of some common qualitative methods in conservation science. They provide a guide for inter-disciplinary researchers to gauge the suitability of each technique to their research questions, and serve as a series of checklists for journal editors and reviewers to determine appropriate reporting.”

All of the articles in the ‘Qualitative methods for eliciting judgements for decision making‘  Special Feature are all freely available.
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When Measuring Biodiversity, Do Individuals Matter?

Post provided by Samuel RP-J Ross

Close up of a black-capped babbler (Pellorneum capistratum), one of the species included in our study.

Close up of a black-capped babbler (Pellorneum capistratum), one of the species in our study.

Our newly-developed method simulates intraspecific trait variation when measuring biodiversity. This gives us an understanding of how individual variation affects ecosystem processes and functioning. We were able to show that accounting for within-species variation when measuring functional diversity can reveal details about ecological communities which would otherwise remain unseen. Namely, we found a negative impact of selective-logging on birds in Borneo when accounting for intraspecific variation which we could not detect when ignoring intraspecific variation.

Why Biodiversity Matters

Biodiversity is important for many reasons. One of the main reasons is its contribution to the range of goods and services provided by ecosystems (i.e. ecosystem services) that we can take advantage of, such as natural food resources or climatic regulation. It’s generally believed that biodiversity contributes to these services by increasing and maintaining ‘ecosystem functioning’ – often defined as the rate at which ecosystems are turning input energy (e.g. sunlight) into outputs (e.g. plant biomass). Continue reading

My Entropy ‘Pearl’: Using Turing’s Insight to Find an Optimal Estimator for Shannon Entropy

Post provided by Anne Chao (National Tsing Hua University, Taiwan)

Shannon Entropy

Not quite as precious as my entropy pearl

Not quite as precious as my entropy pearl ©Amboo Who

Ludwig Boltzmann (1844-1906) introduced the modern formula for entropy in statistical mechanics in 1870s. Since its generalization by Claude E. Shannon in his pioneering 1948 paper A Mathematical Theory of Communication, this entropy became known as ‘Shannon entropy’.

Shannon entropy and its exponential have been extensively used to characterize uncertainty, diversity and information-related quantities in ecology, genetics, information theory, computer science and many other fields. Its mathematical expression is given in the figure below.

In the 1950s Shannon entropy was adopted by ecologists as a diversity measure. It’s interpreted as a measure of the uncertainty in the species identity of an individual randomly selected from a community. A higher degree of uncertainty means greater diversity in the community.

Unlike species richness which gives equal weight to all species, or the Gini-Simpson index that gives more weight to individuals of abundant species, Shannon entropy and its exponential (“the effective number of common species” or diversity of order one) are the only standard frequency-sensitive complexity measures that weigh species in proportion to their population abundances. To put it simply: it treats all individuals equally. This is the most natural weighing for many applications. Continue reading

New Associate Editor: Anne Chao

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Anne Chao joins us from the National Tsing Hua University in Taiwan and you can find out a little more about her below.

Anne Chao

Anne Chao

“I am 60% statistician, 30% mathematician and 10% ecologist. Mathematical and statistical problems in ecology and evolution fascinate me. My current research interests include statistical inferences of biodiversity measures (for example taxonomic, phylogenetic, and functional diversities along with related similarity/differentiation indices), and statistical analysis of ecological and environmental survey data (such as standardising biological samples and rarefaction/extrapolation techniques).”

Anne has been very engaged with the journal over the past few years as a regular reviewer and as an author. Her first article in Methods, Entropy and the species accumulation curve‘ (written with YT Wang and Lou Jost) was published in 2013 and is now freely available. Continue reading

Advances in Phylogenetic Methods – The Applications Papers

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

On Friday, we gave some more information about the research articles in this Virtual Issue. In this post, we will be focusing on the Applications papers.

Applications papers introduce new tools for research, which provide practitioners with an important source of information and background on the tools they use. In this Virtual Issue we have highlighted the newest Applications papers that describe how phylogenetic methods are contributing to the fields of ecology and evolution. These include tools with aims as diverse as phylogenetic tree reconstruction and analysing phylogenetic diversity in communities. All Applications papers, not just those in the Virtual Issue, are free to access.

You can see a little more information on each of the Applications Papers below.

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Virtual Issue: Advances in Phylogenetic Methods

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

An understanding of the tree of life contributes to many facets of biology. This Virtual Issue has assembled studies that showcase the breadth of the utility of phylogenetic trees, including phylogenetic beta diversity, trait evolution, diversification, biodiversity studies, phylogenetic signal, biogeography, ecosystem functioning, and host-pathogen dynamics.

The Research papers included are excellent examples of new ways that phylogenies can be applied to central questions in ecology, evolution and biodiversity, such as measuring niche conservatism, trait evolution and diversification rates. The issue also has articles on barcoding methods, which increasingly are used to understand phylogenetic and functional diversity.

You can see a little more information on each of the articles below.

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International Day for Biological Diversity 2015

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:

Methods Cover - August 2012Biodiversity Soup

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.

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