The Field Guide to Sequence-Based Identification of Biodiversity: An Interview with Simon Creer

In a new Methods in Ecology and Evolution podcast, Georgina Brennan (Bangor University) interviews Simon Creer (Bangor University) about his article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘. They talk about about where the idea for the paper came from, what it’s aim are and who will benefit from it. We hear how new sequences can improve and enhance current biomonitoring programmes (and make them quicker and cheaper).

To find out more about Sequence-based Identification of Biodiversity, read the Open Access Methods in Ecology and Evolution article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘.

 

A Homage to EC Pielou: One of the 20th Century’s Most Accomplished Scientists

Post provided by Daniel Simberloff, Nathan Sanders and Pedro Peres-Neto

Evelyn Chrystalla ‘E.C.’ Pielou. © Sharon Niscak

Evelyn Chrystalla ‘E.C.’ Pielou. © Sharon Niscak

Evelyn Chrystalla ‘E.C.’ Pielou (February 20, 1924 – July 16, 2016) – a towering figure in ecology – was a key pioneer in the incorporation of statistical rigor into biogeography and ecology. She devised many important statistical hypotheses tests for spatial arrangements and patterns ranging in scale from individual plants in a field through to elevational zonation of vegetation to ranges of groups of species distributed over regional through to continental-scale ranges. Her research has provided the impetus for biogeographical analyses for generations.

She published ten books, including several long after her formal retirement in 1988. Her book Biogeography (1979) is a masterpiece. It covers historical biogeography (including inferences from cladograms, which were just beginning to be a hot topic at that time) and ecological biogeography with keen insight and treats topics like long-distance dispersal (that had largely been the subject of just-so stories) with her characteristic statistical rigor. Her books on mathematical ecology have a strong emphasis on models of spatial pattern and ways to estimate biodiversity, and her methods – including the famous Pielou‘s evenness index – are still widely used. Continue reading

How Should Biologists Measure Climate Change?

Post provided by Christopher Nadeau

Climate change could cause the extinction of one in six species and change the abundance and distribution of those that remain (Urban, 2015). This doesn’t necessarily mean that one in six species in your backyard will go extinct though. Climate change impacts will vary greatly around the globe, with some regions seeing disproportionate effects.

The degree to which climate change will affect species in your region depends on many factors (e.g., land use and species traits), but the amount of climate change that species experience in your region – known as climate change exposure – will certainly be important. For that reason, measuring and mapping climate change exposure is critical for predicting where climate change will have the biggest impacts. Yet, biologists have no agreed upon method to measure exposure and different methods can produce dramatically different results.

A Simple Measure of Exposure and its Limitations

Climate can be defined as a statistical description of weather (e.g., temperature, precipitation) over the course of a long time period, usually 30 years. Most often climate is reduced to the average value of a particular weather variable over a 30-year period of interest. Climate change is then measured as the difference between the averages in two time periods; say the predicted average between 2070-2099 minus the average between 1971-2000.

Projected changes in annual average temperature between 1971-2000 and 2070-2099

Projected changes in annual average temperature between 1971-2000 and 2070-2099.

For example, the map to the left shows projected exposure to changes in average annual temperature. This map suggests that species in the arctic will be exposed to the most temperature change while species in the southern hemisphere will experience the least change. However, there are many problems with this interpretation. Continue reading

Why Do We Need Digital Elevation Models to Infer the Local Adaptation of Alpine Plants?

Post provided by Kevin Leempoel

dsc_4214-crest-flight-27-06-11It’s not easy to characterise the local environment of species living in mountains because these habitats are highly heterogeneous. At a large scale, we typically assume that temperature varies with altitude, but at a local scale, we understand that exposure to wind or being in the shade has a great influence on climatic conditions. If you go from the south-facing to the north-facing side of a mountain, it can be easily 5°C colder. If we can feel that, so can the organisms that live up there. Plants in particular are submitted to tremendous climatic variations over a year. What we want to know is: how did they adapt to these climatic variations and how localised is their adaptation?

Overcoming the Challenges of Measuring Local Adaptation

We don’t know much about how organisms adapt locally because it’s so difficult to measure the environmental conditions that these plants are facing. Existing weather stations can’t capture micro-habitat conditions because they are few and far between. What we can do instead, is use topographic models of mountains to model their environment. After all, if orientation, slope or shade have an impact on climatic conditions, why couldn’t we use them to model local variations in temperature for example? Continue reading

Biogeography at a Global Scale: The Benefits of Distributed Experimental Networks

Post provided by Elizabeth Borer

©NASA

©NASA

I have always loved the Blue Marble image of Earth from the Apollo 17 mission, yet a large part of my science is focused on experimental responses at the scale of meter squared grassland plots or even individual grass plants. While I spent my early career wanting to be able to say something important about regional or global processes, I found myself feeling like generating any experimental insights into processes and ecosystem responses at larger scales would be an impossible fiction.

As a postdoc, I had the opportunity to do a multi-site study across a north-south precipitation gradient in California and jumped at it. Among other questions, I decided to ask about whether plants and insects varied similarly across sites in response to replicated experimental treatments. Yet, the idea of actually sampling – and then processing samples from – more than about four sites for more than a year or two was utterly daunting. Continue reading

Biogeography Virtual Issue

Photo © An-Yi Cheng

© An-Yi Cheng

To coincide with the International Biogeography Society’s 2017 conference in Tuscon, Arizona, we have compiled a Virtual Issue that shows off new Methods in Ecology and Evolution articles in the field from a diverse array of authors.

To truly understand how species’ distributions vary through space and time, biogeographers often have to make use of analytical techniques from a wide array of disciplines. As such, these papers cover advances in fields such as evolutionary analysis, biodiversity definitions, species distribution modelling, remote sensing and more. They also reflect the growing understanding that biogeography can include experiments and highlight the increasing number of software packages focused towards biogeography.

This Virtual Issue was compiled by Methods in Ecology and Evolution Associate Editors Pedro Peres-Neto and Will Pearse (both of whom are involved in the conference). All of the articles in this Virtual Issue are free for a limited time and we have a little bit more information about each of the papers included here: Continue reading

New Associate Editors

Today we are welcoming two new Associate Editors to Methods in Ecology and Evolution: Samantha Price (University of California, Davis, USA) and Andrés Baselga (University of Santiago de Compostela, Spain).

Samantha Price

Samantha Price

Samantha Price

“My research seeks to answer the question ‘What regulates biodiversity?’. I use phylogenetic and comparative methods to investigate the abiotic and biotic drivers of global patterns of ecomorphological and lineage diversity over long periods of time and across large clades of vertebrates. To work at this macro-scale I tap the reserves of scientific data in museum collections, published literature, as well as online databases using data and techniques from across ecology, evolution, organismal biology, palaeobiology and data science. ”

Samantha will be joining the Board as our sixth Applications Editor. In July, she had an article titled ‘The Impact of Organismal Innovation on Functional and Ecological Diversification‘ published in Integrative and Comparative Biology. The paper introduces a framework for studying biological innovations in an evolutionary context. Earlier in the year, Sam was the first author of the article ‘A promising future for integrative biodiversity research: An increased role of scale-dependency and functional biology‘, published in Philosophical Transactions of The Royal Society B Biological Sciences. In this article, the authors argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research.

Andrés Baselga

Andres Baselga

Andres Baselga

“I am broadly interested in biodiversity. My background includes a PhD on beetle taxonomy. Later on I focused on biogeography and macroecology, particularly on beta diversity patterns and their underlying processes. This has led me to develop novel methods to quantify the dissimilarity between assemblages, aiming to improve our ability to infer the driving processes. With this objective, I am also interested in the integration of phylogenetic information to quantify macroecological patterns at multiple hierarchical levels (from genes to species, i.e. multi-hierarchical macroecology).”

Andrés has been an active author and reviewer for Methods in Ecology and Evolution over the past few years. He was the lead author of the article ‘Comparing methods to separate components of beta diversity‘,  which tested whether the replacement components derived from the BAS and POD frameworks are independent of richness difference. This article was also the basis for one of the most popular posts we have ever had on this blog: ‘What is Beta Diversity?‘. In addition to this, Andrés was the lead author of ‘Multi-hierarchical macroecology at species and genetic levels to discern neutral and non-neutral processes‘, published in Global Ecology and Biogeography in 2015. The paper proposed that the patterns emerging across multiple hierarchical levels can be used to discern the effects of neutral and non-neutral macroecological processes, which otherwise have proven difficult to separate.

We are thrilled to welcome Samantha and Andrés to the Associate Editor Board and we look forward to working with them over the coming years.

Evolution MegaLab

Modern technology offers some really exciting new opportunities for the use of citizen science, and in our newest video Jonathan Silvertown, Open University, gives a demonstration of Evolution MegaLab, a huge collaboration exploring the use of citizen science methods to undertake high-quality surveys of polymorphism in a wild species.


Jonathan demonstrates the site’s display of historical polymorphism data, some features designed to enable researchers to assess the reliability of volunteer-gathered data, and the process by which anyone can add newly gathered data to the project database.

In a paper recently published in Methods, the authors detail  the methodology used in setting up the Evolution MegaLab, analyse its more and less successful components, and provide a clear set of guidelines for any designer of future citizen science projects.

Related

 

Methods in Biogeography

The International Biogeography Society has just held their 5th meeting in Crete and I thought I would pick some highlights that are methods relevant.  This meeting brings together a range of researchers from the intersection of ecology, evolutionary biology, geography, geology and systematics: a truly diverse grouping.

Biogeography is, in essence concerned with the distributions of species and how these change with time. It is no surprise then that phylogenetic analysis was the focus of many talks. Indeed, if there is one thing that sets the talks I saw at this meeting apart from those at more ‘ecological’ meetings, it is the heavy reliance on phylogenetic methods. Relatively recently developed methods for looking at phylogenetic structure in ecological communities were particularly in evidence.

Three talks were particularly methods focussed and described really interesting new approaches and perspectives.

Andy Purvis of Imperial College, UK, looked at how macroevolutionary questions could be tested using different methods and data. His talk emphasised that evolutionary models can be varied and that broad-scale analyses that assume single models could be misleading. For example, using data on all mammal species he showed that the evolution of body mass could be described using an ‘early burst’ model; however when broken up into individual orders, the picture was a highly variable one with different models fitting best to some orders rather than others, and very different rates across groups.

Andy also dealt with niche conservatism, another big theme at this meeting. Niche conservatism is the idea that closely related species share their niches because they inherit them from ancestors. If niches are generally conserved then this is important because, for example, changes to climate or habitat may affect taxonomic groups of species that share similar requirements, or that are historically slow to adapt. Andy made the good point that current definitions are sometimes at odds with each other, and that notions of niche conservatism need to be clearly spelled out.

Also from Imperial, Ally Phillimore took a different perspective. The aim in his research is to link small-scale ecological processes with macroevolution. He described an elegant method for linking within and between population spatial and temporal variation to explore the degree to which adaptation and plasticity drive phenological responses to climate change. Using data on data gathered by the public on egg laying dates in frogs in the UK, Ally showed how his approach could be used to predict how fast populations need to evolve in order to keep up with climate change.

A major issue in the analyis of biogeographical and macroecological data is how to deal with spatialautocorrelation. Pedro Peres Neto from the University of Quebec and Montréal described simulation results that showed how autocorrelation affects the outcomes of statistical tests, and provided some guidelines on the expected outcome of methods. He pointed out that the strength of a relationship between two variables and the source of dependency (whether in the residuals or the predictors) could be factors. One point well made was that spatial and phylogenetic methods for trait data analysis share a lot of similarity and there is a lot of potential for interchange.

These are just three talks I have highlighted as I found them particularly stimulating (and methods relevant), overall the meeting was really enjoyable interesting. And, following the coldest UK December in 100 years, I really do have to congratulate the organisers on their choice of Crete a venue!

Methods Digest – January 2010

A belated happy new year! Here is this month’s round-up of methods papers published in the last month. Do let me know if there are any papers that I have missed that could be featured.

In Systematic Biology Brian O’Meara presents new heuristics for joint species delimitation and tree inference. A new comparative method for logistic regression controlling for phylogeny is outlined by Ives & Garland, and Wertheim et al. publish an analysis of the use of relaxed clocks in phylogenetic inference.

Marc Cadotte and colleagues outline in the latest issue of Ecology Letters new metrics for measuring phylogenetic diversity in ecological communities.

In the Journal of Applied Ecology Len Thomas and colleagues present a review of distance sampling and its use in estimating population size; Marc Kéry and co-workers illustrate a method for estimating trends from replicated count data when detection is imperfect; Deanna Dawson and Murray Efford demonstrate a new method for estimating bird densities from acoustic data. William Kendall and Gary White have a cautionary note on substituting spatial subnits for temporally replicated sampling in estimating site occupancy.

A ‘how to’ paper in Journal of Animal Ecology by Alastair Wilson et al. presents a review and guide to using the ‘animal model’ in quantitative genetics.

In Global Ecology and Biogeography Cabral & Schurr have a paper illustrating a method for linking range dynamics and demographic models in the Fynbos. Andrés Baselga has a paper in the same issue illustrating a method for disentangling the contributions of spatial turnover and nestedness to beta diversity.

Tommaso Zillion and Fangliang He publish in Oikos a new method for linking species abundance distributions across scales.

In Journal of Ecology Damgaard & Fayolle present a new method for estimating the influence of competition in plants.

A mini-review by Gavin Stewart and colleagues in Conservation Letters reviews the design of temperate marine reserves from a analytic perspective. In the same issue Kyle Van Houtan et al. look at the effectiveness of translocations in conserving endangered species.