piecewiseSEM: Exploring Nature’s Complexity through Statistics

Post provided by Jonathan S. Lefcheck

Nature is complicated. As a scientist, you might say, “Well, duh,” but as students of nature, this complexity is probably the single greatest challenge we must face in trying to dissect the hows and whys of the natural world.

History is a Set of Lies Agreed Upon: Moving beyond ANOVA

For a long time, we tried to strip this complexity away by conducting very controlled experiments adhering to rigid designs. The ‘two-way fully-crossed analysis of variance’ will be familiar to anyone who has taken even the most basic stats class, because, for many decades, it was the gold standard for any experiment.

It might be tough to manipulate this whole reef.

The problem is: the real world doesn’t adhere to an ANOVA design. By this, I mean that by their very nature, manipulative experiments are artificial. It’s hard—if not impossible—to manipulate an entire forest or a coral reef, and as such, we retreat to more tractable, smaller investigations. There is certainly a lot of value in determining whether the phenomenon can occur, but these tightly regulated designs say nothing about whether they are likely to occur, particularly at the scales most relevant to humanity.

To get at the latter point, we must leave the safety of the greenhouse. However, our trusty ANOVA toolbox isn’t very useful anymore, because real-world data often violate the most basic statistical assumptions, not to mention the presence of numerous additional influences that may drive spurious relationships. Continue reading

Advertisements

Googling for Ecological Answers: Using the Morphic Web Application

Post provided by Gabriella Leighton

Online Images: A Treasure Trove of Ecological Data

In the proclaimed ‘information age’, where answers are available at the click of a button or a swipe of a finger, we have become accustomed to the ability to get an almost instant grasp of any topic. Other fields are already making use of this wealth of easily accessible online data, but biologists and ecologists tend to let it slip by. However, this attitude is slowly beginning to change. Some ecological and evolutionary studies are emerging that have used the internet to gather data – through online citizen science projects (e.g. Evolution MegaLab) or databases (e.g. using Google Trends) – but few have used existing data, particularly publicly available data from image repositories.

We were curious to apply the concept of using existing images on the internet to a fascinating visual biological phenomenon: colour polymorphism (or the occurrence of multiple discrete colour phenotypes). To do this, we planned to exploit an existing penchant people have for uploading photographs of animals to the Internet.

Our search phrases included the common and scientific name of the species, as well as a location-specific term

Our search phrases included the common and scientific name of the species, as well as a location-specific term

Continue reading

2016 Robert May Prize Winner: Gabriella Leighton

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2016 winner is Gabriella Leighton, for her article ‘Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms.

‘Just Google it’ marks an important step in converting ecology to an armchair science. Many species (e.g. owls, hawks, bears) are difficult, time-consuming, expensive and even dangerous to observe. It would be a lot easier if we didn’t have to spend time, energy and risk lives having to observe organisms in the field! Continue reading

2015 Robert May Prize Winner: Kim Calders

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2015 winner is Kim Calders, for his article ‘Nondestructive estimates of above-ground biomass using terrestrial laser scanning.

Kim led the work on this article and had an international team of co-authors. They have developed a way to harness laser technology for use in measurements of vegetation structure of forests. The study is an important development in the monitoring of carbon stocks for worldwide climate policy-making. Continue reading

2014 Robert May Prize Winner: Laure Gallien

The Robert May Prize is awarded annually for the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2014 winner is Laure Gallien, for her article ‘Identifying the signal of environmental filtering and competition in invasion patterns – a contest of approaches from community ecology.

Today, biological invasions are of major concern for maintaining biodiversity. However, understanding what drives the success of invasive species at the scale of the community remains a challenge. Two processes have been described as main drivers of the coexistence between invasive and native species: environmental filtering and competitive interactions. However, recent reviews have shown that competitive interactions are rarely detected, and thus their importance as drivers of invasion success placed under question. But can this be due to pure methodological issues? Using a simulation model of community assembly, Laure and co-authors (Marta Carboni and Tamara Münkemüller) show that the infrequent detection of competition can arise from three important methodological shortcomings, and provide guidelines for future studies of invasion drivers at the scale of the community.

Continue reading

2013 Robert May Prize Winner

YIP 2013 - Will PearseThe Robert May Prize is awarded annually for the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2013 winner is Will Pearse, for his Application article “phyloGenerator: an automated phylogeny generation tool for ecologists”.

Although ecologists frequently want to make use of phylogenies, they often lack the skills to create detailed phylogenies of their study taxa. phyloGenerator greatly simplifies the process of creating a phylogeny, automating the download of DNA data and the use of modern phylogenetic software to produce a dated, defensible phylogeny. By linking together a number of existing tools into a single command-line interface and providing an extendable Python library, phyloGenerator is also a useful tool for phylogeneticists wishing to use an open, reproducible phylogenetic workflow. The Editors commented that, “this is an exciting idea that makes phylogenies almost immediately accessible to any researcher needing to use them. It is also a terrific example of the power of what we can achieve when data are made open and accessible.”

Will studied Zoology as an undergraduate at the University of Cambridge, then completed an MSc in Ecology, Evolution and Conservation, and later a PhD at Imperial College London supervised by Andy Purvis and David Roy (Centre for Ecology and Hydrology, Wallingford). His PhD focused on how the phylogeny of species in a community can be used to understand the ecological assembly of that community, and how phylogeny informs our understanding of communities undergoing change. Will is now a post-doc in Jeannine Cavender-Bares’ lab at the University of Minnesota, where he studies urban plant communities.

In addition to Will, the following young authors have been highly commended for their innovative articles:
Emily Dennis from the University of Kent, for her co-authored paper IndexiVI cover - YIP 2013ng butterfly abundance whilst accounting for missing counts and variability in seasonal pattern.
Joost Keuskamp and Bas Dingemans from Utrecht University, for their co-authored paper Tea Bag Index: a novel approach to collect uniform decomposition data across ecosystems. There is also an interview with the Tea Bag Index team to accompany this article.

The above 3 articles are included in a free virtual issue, along with all of the winning and highly commended articles from the other 4 British Ecological Society journals young investigator prizes.

Virtual Issue – BES Young Investigator Prize Winners 2012

YIP VI 2012 cover imageEvery year the British Ecological Society awards a prize for the best paper in each of its 5 journals, by an author at the start of their research career. This freely available Virtual Issue entitled “Young Investigator Prize Winners 2012” brings together the winning papers from each journal, in addition to 2 highly commended papers from each journal, all of which were published in an issue in 2012. The issue is available to read here.

Congratulations to all concerned!

2012 Robert May Prize Winner

YIP 2012 - Sarah Papworth

Sarah Papworth

The Robert May Prize is awarded annually to the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2012 winner is Sarah Papworth from Imperial Collage London, for her article “Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilization functions to quantify hunter and gatherer behaviour”. Although GPS trackers can rapidly collect vast amounts of data on animal movement, appropriate methods for analysing this data are still being developed. The paper describes a methodological framework for the analysis of GPS track records of foragers which routinely return to a central place after foraging, such as a den or nest. The framework combines three existing methods in a flexible method for the accurate description of resource use and movement in humans and animals. This approach will be particularly useful for our understanding of human resource extraction and conservation planning.

Sarah studied a BA Honours in Anthropology at the University of Durham, which focused on human and primate behaviour. This lead to an interest in field biology in the tropics, and she went on to study blue monkeys in Uganda. She then completed an MSc in Ecology, Evolution and Conservation, and a PhD in Conservation Science, at Imperial College London, supervised by E.J. Milner-Gulland and Katie Slocombe (University of York). Her PhD focused on human and primate behaviour within the context of hunting by the Waorani of Amazonian Ecuador, and involved extensive fieldwork. Data collected for her PhD were used to illustrate the methodological framework developed in the Robert M. May prize-winning paper. She has just moved to Singapore, where she is currently a research fellow focusing on poverty and biodiversity at the National University of Singapore.

In addition to the above winner, the following young authors have been highly commended for their innovative articles:
– Brett Favaro from the Marine Ecology Lab,  for his article “TrapCam: an inexpensive camera system for studying deep-water animals“, which is accompanied by a video demonstrating the construction of the TrapCam apparatus.
– David Jacoby from the Marine Biological Association of the United Kingdom, for his article “Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses“.

The above 3 articles will be included in a free virtual issue this year, along with all of the winning and short-listed articles from the other 4 British Ecological Society journals young investigator prizes.

Robert May Prize 2011

Tyler Kuhn

Robert May Prize winner 2011, Tyler Kuhn

Each year our editors select the best paper published in Methods by a young researcher. We are delighted to announce that this year’s winner of the Robert May Prize is Tyler Kuhn for his paper co-authored with Arne Ø. Mooers and Gavin H. Thomas A simple polytomy resolver for dated phylogenies published in vol. 2.5 of the journal.

Tyler and co-authors present a simple approach to polytomy resolution (polytomy, i.e. unresolved nodes in phylogenetic trees), using biologically relevant models of diversification using free available software, BEAST and R. The paper should be useful for many future analyses of the mammalian supertree.

Raised in a small town in Canada’s far north, Tyler has always had a passion for understanding the natural world. This passion led him to the University of Victoria, where he completed his B.Sc. Honours in Earth Sciences in 2004. It was there that he discovered the world of paleontology. He returned to academia after spending several years working as a geologist to pursue his M.Sc in Quaternary paleontology. He completed this degree in 2010, focussing on the use of aDNA to improve our understanding of imperilled northern species, and to help inform management practices. During this time, he and his supervisor, Arne Mooers, became involved in a “side project” aimed at improving the useability of incompletely resolved phylogenies in conservation decision making processes. This work has since expanded far beyond his M.Sc. thesis to include several published papers, including the Robert May Prize winning paper on resolving polytomies of dated supertrees. Tyler currently lives in Canada’s frigid north and works as a government biologist, paleontologist and independent researcher.