What About Winter? Accounting for the Snow Season When We Simulate Climate Warming

Post provided by Rebecca Sanders-DeMott and Pamela Templer

Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos

Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos

The climate is changing throughout the globe with consequences for the biogeochemical processes and ecological relationships that drive ecosystems. Scientists have been conducting manipulative experiments to determine the effect of climate warming on ecosystems for several decades. These experiments allow us to observe ecosystem responses before the climate changes occur and have yielded invaluable insight that has expanded our understanding of the natural world.

There is a wide range of creative approaches to mimicking climate warming that have been used, for example open-topped chambers which passively heat small areas of soil and small stature plants (like the ITEX global network), burying heating cables in the soil to directly increase soil temperatures (e.g. Harvard Forest experiments), infrared heating lamps (like Jasper Ridge), or even large scale chambers that can encompass taller stature plants like trees and actively warm the air (like the SPRUCE experiment). The focus of much of these inquiries has been on changes that occur during the growing season, when biological activity is at its peak. Continue reading

Advertisements

Two More New Associate Editors

Today we are welcoming two more Associate Editors to the Methods in Ecology and Evolution who were invited to work with the journal following our open call earlier this year. Jessica Royles joins from the University of Cambridge, UK and Simon Blomberg is coming to us from the University of Queensland, Australia. You can find out more about both of them below.

Simon Blomberg

“I am a statistician who started out as a lizard demographer. I am interested in all applications of statistics in evolutionary biology and systematics. It is my passion to see that good science gets done by everybody, and sound statistical methods are essential to reach that goal. My research involves the application of stochastic process models (predominantly Itoh diffusions) to the macroevolution of quantitative traits. I believe that evolution can be described by beautiful mathematics but theory must be tested with data. I have published widely on phylogenetic comparative methods. I use Bayesian methods, data augmentation, regularisation and other modern and traditional statistical methods. I am interested in how to treat missing data. I still like lizards. Also jazz.”

Simon has been working on stochastic process models for a couple of years. His most recent article ‘Beyond Brownian motion and the Ornstein-Uhlenbeck process: Stochastic diffusion models for the evolution of quantitative characters‘ is now available on BioRxiv and he would welcome comments on it from the Methods community.

Jessica Royles

“I am interested in the impact of climate change on plant physiology and specialise in using stable isotopes as environmental markers. Having worked in Antarctica I have strong interests in polar biology, high latitude peatlands and fieldwork techniques. My current work focusses on  temperate bryophytes and I am interested in using techniques including gas exchange and chlorophyll fluorescence at different spatial scales to link the leaf level to the ecosystem level.”

Jessica’s most recently published article – ‘Widespread Biological Response to Rapid Warming on the Antarctic Peninsula‘ – describes how she and her co-authors used moss cores to study Antarctic warming due to climate change. The article builds on her previous paper ‘Plants and Soil Microbes Respond to Recent Warming on the Antarctic Peninsula‘. Jessica is currently working on a Moss Ecophysiology project which aims to investigate the value of mosses as tools to understand past climate.

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

Issue 8.8

Issue 8.10 is now online!

The October issue of Methods is now online!

This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

 Phylogenetic TreesThe fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.

 Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.

 Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

Continue reading

Birds and Climate in Space and Time: Separating Spatial and Temporal Effects of Climate Change on Wildlife

Post provided by Cornelia Oedekoven

The Standard Method

When trying to understand how wildlife, for example a bird species, may react to climate change scientists generally study how species numbers vary in relation to climatic or weather variables (e.g. Renwick et al. 2012, Johnston et al. 2013). The way this tends to be done is by gathering information (data!) about bird numbers as well as the weather variables (for example temperature) in several locations (i.e. in space) and fitting a regression model to these data to detect and illustrate how bird numbers go up or down with temperature.

Data on bird numbers and temperatures in several locations lets researchers see the relationship between the two.

Data on bird numbers and temperatures in several locations lets researchers see the relationship between the two.

This relationship is then used to forecast how bird numbers may change along with potential temperature changes in the future (i.e. in time), for example due to climate change.

Relationships between bird numbers and temperature in a given location are often used to forecast changes in bird numbers with expected changes in temperatures over time.

Relationships between bird numbers and temperature in a given location are often used to forecast changes in bird numbers with expected changes in temperatures over time.

Continue reading

Britain’s Smallest Bird Affected by Cold Winters: New Analysis Methods Relate Wildlife Abundance to Weather

Below is a press release about the Methods paper ‘Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds‘ taken from the University of St Andrews.

©CJ Hughson

The goldcrest is being hit hard by cold winters. ©CJ Hughson

Britain’s smallest bird species, the goldcrest, is being hit hard by cold winters, new analysis methods developed by researchers at the University of St Andrews have revealed.

The data analysis techniques, published today in Methods in Ecology and Evolution, take a longer term view over multiple locations and for a period of several years, compared to previous studies.

They showed that the cold temperatures strongly affected breeding numbers of the goldcrest, while in contrast, the song thrush was not affected by the cold, but benefited from wet and mild summers. Continue reading

Tiny Grains, Big Data: The Global Pollen Project

Post Provided by Andrew Martin

A drawer from the Oxford Long-Term Ecology Lab (OxLEL) pollen reference collections, which has been digitised into the Global Pollen Project reference set.

A drawer from the Oxford Long-Term Ecology Lab (OxLEL) pollen reference collections, which has been digitised into the Global Pollen Project reference set.

The Global Pollen Project is a new, online, freely available tool developed to help people identify and disseminate palynological resources. Palynology – the study of pollen grains and other spores – is used across many fields of study modern and fossil vegetation dynamics, forensic sciences, pollination, beekeeping, and much more. This platform helps to facilitate cross/multi-disciplinary integration and discussion, outsourcing identifications, expertise and the sharing of knowledge.

Pollen’s Role in Plant Conservation

Successful conservation of rare, threatened, and valuable plants is dependent on an understanding of the threats that they face. Also, conservationists must prioritise species and populations based on their value to humans, which may be cultural, economic, medicinal, etc. The study of fossil pollen (palaeoecology), deposited through time in sediments from lakes and bogs, can help inform the debate over which species to prioritise: which are native, and when did they arrive? How did humans impact species richness? By establishing such biodiversity baselines, policymakers can make more informed value judgements over which habitats and species to conserve, especially where conservation efforts are weighted in favour of native and/or endemic flora. Continue reading

Capturing the Contribution of Rare and Common Species to Turnover: A Multi-Site Version of Generalised Dissimilarity Modelling

Post provided by Guillaume Latombe and Melodie A. McGeoch

Understanding how biodiversity is distributed and its relationship with the environment is crucial for conservation assessment. It also helps us to predict impacts of environmental changes and design appropriate management plans. Biodiversity across a network of local sites is typically described using three components:

  1. alpha (α) diversity, the average number of species in each specific site of the study area
  2. beta (β) diversity, the difference in species composition between sites
  3. gamma (γ) diversity, the total number of species in the study area.
Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Despite the many insights provided by the combination of alpha, beta and gamma diversity, the ability to describe species turnover has been limited by the fact that they do not consider more than two sites at a time. For more than two sites, the average beta diversity is typically used (multi-site measures have also been developed, but suffer shortcomings, including difficulties of interpretation). This makes it difficult for researchers to determine the likely environmental drivers of species turnover.

We have developed a new method that combines two pre-existing advances, zeta diversity and generalised dissimilarity modelling (both explained below). Our method allows the differences in the contributions of rare versus common species to be modelled to better understand what drives biodiversity responses to environmental gradients. Continue reading

Carson’s Call: An Inspiration for Ecologists Working in a Post-Truth World

Post provided by Will Pearse

Rachel Carson (1940) Fish & Wildlife Service employee photo.

Rachel Carson (1940) Fish & Wildlife Service employee photo.

I can’t think of a more inspirational and influential ecologist than Rachel Carson. Nearly fifty years ago she released a book called Silent Spring, which argued that pesticides such as DDT were cascading up through food chains causing the death or sterilisation of birds and other animals. The publication of her book provoked public debate, likely in part because it was serialised in The New Yorker, and led to a paradigm shift in US and (arguably) global pest control policy.

With the full support of the scientific community to verify her facts and arguments, she was able to defeat the chemical industry’s backlash and galvanise public opinion in her favour. The 2005 Stockholm Convention, in which DDT was banned from agricultural use, would likely have never happened if it were not for her work.

“In a post-truth world where trust in the scientific process is being eroded almost daily, Rachel Carson is a perfect example of how we can speak out and be heard while still being scientists.”

Continue reading

Sounding Them Out: A Unique Conservation Tool for Monitoring Bush-Crickets

Below is a press release about the Methods paper ‘Potential for coupling the monitoring of bush-crickets with established large-scale acoustic monitoring of bats‘ taken from the British Trust for Ornithology.

Speckled Bush-cricket © Tom Housley

Speckled bush-cricket © Tom Housley

New research led by British Trust for Ornithology (BTO) and published today in the international journal Methods in Ecology and Evolution, shows how existing bat monitoring could improve our understanding of bush-crickets.

Bush-crickets are a little-known group of insects that inhabit our marshes, grasslands, woods, parks and gardens. Some may be seen in the summer when they are attracted to artificial lights, but as most produce noises that are on the edge of human hearing, we know little about their status. There are suggestions that some bush-crickets may be benefiting from climate change, while others may be affected by habitat changes. But how to survey something that is difficult to see and almost impossible to hear? Continue reading

Lichens and the “health” of ecosystems: we are closer to a global ecological indicator

Below is a press release about the Methods paper ‘Tracking global change using lichen diversity: towards a global-scale ecological indicator‘ taken from the University of Lisbon.

Candelaria pacifica. © Paula Matos

Candelaria pacifica. © Paula Matos

For the first time, it is possible to integrate at the global scale the results obtained with the most widely used methods to evaluate the “health” of ecosystems using lichens. This is the result of a study now published in the journal Methods in Ecology and Evolution, and represents a fundamental step for this indicator to be considered at the global scale and included in the list of indicators of the United Nations.

Lichens have long been successfully used by scientists as ecological indicators – a kind of environment health thermometer. These complex organisms – the yellow or green taints we often see on the surface of tree trunks – are very sensitive to pollution and changes in temperature and humidity. Evaluating how many lichens, of what kind, and their abundance in a certain ecosystem allows scientists to understand the impact that problems like climate change or pollution have on those ecosystems.  Continue reading