New Tool to Assess Effects of Powerful Man-Made Underwater Sounds

Below is a press release about the Methods paper ‘An interim framework for assessing the population consequences of disturbance‘ taken from the University of St Andrews:

A team of scientists from the University of St Andrews has developed a new desktop tool for assessing the impact of noise from human disturbance, such as offshore wind development on marine mammal populations.

PCOD_PR_imageThe team, led by Prof. John Harwood, have developed the interim Population Consequences of Disturbance (PCoD) framework for assessing the consequences of human induced noise disturbance on animal populations. The study was published yesterday in the journal Methods in Ecology and Evolution.

Changes in natural patterns of animal behaviour and physiology resulting from animals being disturbed may alter the conservation status of a population if the activity affects the ability of individuals to survive, breed or grow. However, information to forecast population-level consequences of such changes is often lacking. The project team developed an interim framework to assess impacts when empirical information is sparse. Crucially, the model shows how daily effects of being disturbed, which are often straightforward to estimate, can be scaled to the duration of disturbance and to multiple sources of disturbance.

“We have developed a novel framework that can be used to broadly forecast the consequences of anthropogenic disturbance on animal populations, which in principal can be applied to a range of marine and terrestrial species and different types of disturbance.” – Dr Stephanie King

One important application for the interim PCoD framework is in the marine industry. Many industries use practices that involve the generation of underwater noise. These include shipping, oil and gas exploration, defence activities and port, harbour and renewable energy construction. 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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The Methods in Ecology and Evolution 5th Anniversary Impact Factor

Thomson-Reuters have just released this year’s Impact Factors. The Methods in Ecology and Evolution Impact Factor is now an astounding 6.554, up from a truly dismal 5.322 last year. We now have enough years of Impact Factors to make it worthwhile drawing a graph.

Zoooom!

The Methods in Ecology and Evolution Impact Factor goes up and up (…except when it doesn’t).

This puts us ninth in Ecology, and we would be fifth in Evolutionary Biology if Thomson-Reuters thought we published stuff in Evolutionary Biology. We would also be top in Statistics and Substance Abuse if we could get ourselves into either of those categories. Continue reading

Issue 6.6

Issue 6.6 is now online!

The June issue of Methods is now online!

This month’s issue contains one Applications article and one Open Access article.

VirtualCom: A simple and readily usable tool that will help to resolve theoretical and methodological issues in community ecology. VirtualCom simulates the evolution of the pool of regionally occurring species, the process-based assembly of native communities and the invasion of novel species into native communities. One of the authors of this Application is the 2014 Robert May Young Investigator Prize Winner, Laure Gallien.

Calibrating animal-borne proximity loggers, this month’s only Open Access article, comes from Christian Rutz et al. The authors calibrated a recently developed digital proximity-logging system (‘Encounternet’) for deployment on a wild population of New Caledonian crows. They show that, using signal-strength information only, it is possible to assign crow encounters reliably to predefined distance classes, enabling powerful analyses of social dynamics. Their study demonstrates that well-calibrated proximity-logging systems can be used to chart social associations of free-ranging animals over a range of biologically meaningful distances.

Our June issue also features articles on Phylogenetic MethodsPhysiological Ecology, Biomonitoring and Conservation, Species Distribution Monitoring and Bioinformatics. Continue reading

What fish ears can tell us about sex, surveillance and sustainability

Below is a press release about the Methods paper, ‘Quantifying physiological influences on otolith microchemistry, from the University of Southampton:

Dr Anna Sturrock blood sampling plaice ©Anna Sturrock

Dr Anna Sturrock blood sampling plaice ©Anna Sturrock

Scientists at the University of Southampton have found a way to pry into the private lives of fish – by looking in their ears!

By studying ear stones in fish, which act as tiny data recorders, scientists can now reveal migration patterns and even provide insights into their sex life.

Managing fish stocks in a sustainable way is a major challenge facing scientists, conservationists, policy makers and fishermen. To get the best results, accurate information about the movements of fish in the wild is needed but gathering this information is extremely difficult. Continue reading

In Defence of Satellite Data: The Perfect Companion to Ground-Based Research

Post provided by Dr Nathalie Pettorelli

Nathalie is an Institute Research Fellow at the Zoological Society of London. She heads the Environmental Monitoring and Conservation Modelling (EMCM) team and her main research involves assessing and predicting the impacts of global environmental change on biodiversity and ecosystem services. Nathalie was one of the presenters at the UK half of the Methods in Ecology and Evolution 5th Anniversary Symposium in April. You can watch her talk, ‘Harnessing the Potential of Satellite Remote Research’ here.

If there is one question I hear over and over again, it’s this: “why, oh why, do you use satellite data instead of ground-based data in your research?” People seem to think that I believe satellite data are better than ground-based data. Do I not value fieldwork? Do I not trust ground-based data? My answer to all of this is: you’ll never catch me preaching that satellite remote sensing can solve the entire data collection gap in ecological monitoring.

I use satellite data because a lot of my work happens at relatively large spatial and temporal scales, targets regions where ground-based data are simply unavailable or extremely difficult to gather and relies on being able to access data that have been collected in a systematic and scalable manner.

Yes, satellite-based techniques can address spatial and temporal domains inaccessible to traditional, on-the-ground, approaches, but I am the first to acknowledge that satellite remote sensing cannot match the accuracy, precision and thematic richness of in-situ measurement and monitoring.

©Clare Duncan

The New Generation of Ecologists in Action: Clare Duncan conducting field measurements in the Philippines to be combined with satellite remote sensing information to monitor ecosystem services delivery. ©Clare Duncan

In spite of this, data collected on the ground are currently difficult to use for mapping and predicting regional or global changes in the spatio-temporal distribution of biodiversity (a problem for those of us trying to tackle these kinds of issues). Ground-based data can also be expensive and tend to come from a single annual time period. This makes it difficult to gather information on temporal changes and phenology. Continue reading

Ten Top Tips for Reviewing Statistics: A Guide for Ecologists

post provided by Dr Mark Brewer.

Mark is a statistician with Biomathematics & Statistics Scotland, based in Aberdeen. His main statistical research interests are Species Distribution Modelling, Compositional Data Analysis, Bayesian Mixture Modelling and Bayesian Ordinal Regression. Mark was one of the presenters at the UK half of the Methods in Ecology and Evolution 5th Anniversary Symposium in April. You can watch his talk, ‘Model Selection and the Cult of AIC’ here.

The level of statistical analysis in ecology journals is far higher than in most other disciplines. Ecological journals lead the way in the development of statistical methodology, necessitated by challenging practical problems involving complex data sets. As a statistician, publishing also in hydrology, soil science, social science and forensic science journals, I’ve found papers in those areas are much more likely to only use well-established methods than papers in ecology.

Here’s the big question though: why then do I have the most difficulty with ecological journals when it comes to statistical analyses? Let’s be clear here: when I say “difficulty”, I mean I receive reviews which are just plain wrong. Most statisticians I’ve spoken to who work in ecology have anecdotes from reviews which demonstrate a lack of understanding by the non-statistician reviewer (including the all-too-frequent “perhaps you should consult a statistician”). So, why the apparent disconnect?

The difference seems to be in how non-statisticians in different disciplines treat the statistics in a paper. In many subject areas, reviewers are almost deferential to the statistical analysis; in ecology, reviewers can be forthright in their condemnation, often without justification. Reviewers have every right to question the statistical analysis in a paper, but the authors have the exact same right to expect a high quality review from a genuine expert in the field. Has ecology become blasé about statistics? Continue reading

What is Beta Diversity?

Post provided by Dr Andrés Baselga

Dr Andrés Baselga

A key property of biodiversity is that it is not evenly distributed around the world. In other words, different sites are usually  home to different biological communities. Quantifying the differences among biological communities is a major step towards understanding how and why biodiversity is distributed in the way it is.

The term beta diversity was introduced by R.H. Whittaker in 1960. He defined it as “the extent of change in community composition, or degree of community differentiation, in relation to a complex-gradient of environment, or a pattern of environments”. In his original paper, Whittaker proposed several ways to quantify beta diversity. In its simplest form (which we will call strict sense or multiplicative beta diversity), beta diversity is defined as the ratio between gamma (regional) and alpha (local) diversities (Whittaker, 1960; Jost, 2007). Therefore, it is the effective number of distinct compositional units in the region (Tuomisto, 2010). Essentially, beta diversity quantifies the number of different communities in the region. So it’s clear that beta diversity does not only account for the relationship between local and regional diversity, but also informs about the degree of differentiation among biological communities. This is because alpha and gamma diversities are different if (and only if) the biological communities within the region are different.

It’s easy to demonstrate how beta diversity varies from the minimum to the maximum differentiation of local assemblages in a region. For simplicity, we will quantify biological diversity as species richness (number of species), but it’s important to remember that alpha, beta and gamma diversities can also be defined to account for richness and relative abundances (see Jost, 2007 for a detailed explanation). When local assemblages are all identical (minimum differentiation), alpha diversity equals gamma diversity, and beta diversity equals 1 (figure below).

beta1

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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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