Methods in Ecology and Evolution Anniversary Symposium - 22 April 2015

The youngest BES journal, Methods in Ecology and Evolution, is now five years old. In celebration of the 5th Anniversary of the journal and its success so far, we held a one-day symposium, spanning two continents, on 22 April 2015. The UK section of the symposium was at Charles Darwin House, London and the Canadian section was held in the University of Calgary’s Alberta Room. There was live streaming of speakers across the two countries to end the UK event and to get things started in Calgary.

We heard what’s in store for the future from young, international researchers including the first winner of the Robert May Young Investigator’s Prize and a number of the journal’s Associate Editors. Topics discussed included model selection, data analysis, R and much more.

 

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Event Overviews

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Event Overviews

Looking Forward to the Next Five Years

Charles Darwin House, London, UK – Wednesday 22 April 2015

To mark the launch of Methodsin Ecology and Evolution back in April 2010, we held a symposium at Charles Darwin House. Five years on, we returned to celebrate the successes of the journal. With talks from a former Robert May Young Investigator Prize Winner and a number of the journal’s Associate Editors, as well as an introduction from the President of the BES, this was a fantastic start to the Symposium.
Sponsored by:

BES Macroecology Special Interest Group The British Ecological Society BES Plant Environmental Physiology Group

 

Next Generation Ecology and Evolution: Genomics Tools for the Study of Ecology, Evolution, and Biomonitoring

The Alberta Room, Calgary – Wednesday 22 April 2015

As the first half of our joint symposium finished in London, the baton was taken up over 4000 miles away in Calgary. The programme in Calgary was packed with exciting speakers and topics. Our Joint Symposium concluded with a Poster Session and a wine reception for all delegates.

Sponsored by:

       

    

OpenData and Reproducibility Workshop: the Good Scientist in the Open Science era

Charles Darwin House, London, UK - Tuesday 21 April 2015

Most ecologists are aware of the open science agenda, but there are few examples of ecological studies that are truly reproducible. This workshop discussed the tools available to the modern scientist and debated priorities and incentives to achieving greater openness in ecology. The program featured talks from leaders in the field and opportunities to learn about best practice in reproducible science. 

 

Looking Forward to the Next Five Years: Confirmed speakers

10.00-10-30: Registration and coffee

10.30-11.00: Bill Sutherland, President of the British Ecological Society
New Methods in Monitoring

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11.00-11.30: Nathalie Pettorelli, Zoological Society of London
Harnessing the potential of satellite remote sensing for supporting ecological research
Over the last few decades, numerous studies have highlighted the potential key role of satellite data in macroecology, plant ecology, animal population dynamics, habitat selection and habitat use studies, as well as movement ecology. This talk will provide an overview of the current opportunities for satellite remote sensing to inform ecological research, discuss existing constraints and limitations, and present possible new avenues and ways forward.

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11.30-12.00: Matt Davey, University of Cambridge
The metabolic phenotype in contrasting habitats
In the plant kingdom alone, there are an estimated 200,000 metabolic products, all of which are controlled by both genetic and environmental factors. The understanding and exploitation of these plant processes is essential for a range of current ecological and environmental topics, such as how climate change may affect plant communities and how plant populations growing at the margin of their range may exhibit traits that indicate genetic adaptation to their local abiotic environment. I use metabolic fingerprinting techniques to investigate the metabolic phenotype of wild species in laboratory and field studies to answer such questions. I will present data of how we can use the metabolic phenotype to study local adaptation and acclimation in a range of plant and algal species growing in three different habitats - Arctic-Alpine, Coastal Sand Dune and Antarctic Peninsula.

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12.00-12.30: Greg McInerny, University of Oxford
Defy the defaults, understand the user: Reproducibility and visualisation in R
Computing has expanded the possibilities of scientific research. However, software defaults will rarely suit every user task or the needs of particular scientific sub-disciplines. I will present two projects that defy the defaults in R. Firstly, BackFilz, a set of new techniques for visual diagnostics in MCMC analysis, and then Zoön, a framework for reproducible and shareable ‘Species Distribution Modelling’ (SDM). Both projects aim to increase how understandable, open and interactive basic activities are by developing an understanding of users, their tasks and their research communities.

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12.30-13.30: Lunch

13.30-14.00: Mark Brewer, Biomathematics & Statistics Scotland
Model selection and the cult of AIC
Model selection is difficult. Even in the apparently straightforward case of choosing between linear regression models, there does not yet appear to be consensus in the statistical ecology literature as to what to do. A series of Forum articles in the journal Ecology last year dealt with part of the issue: the distinction between AIC and p-values. There are, however, more fundamental concerns with regard to types of model comparison and to why models are being compared. In this talk, works seeking to evangelise AIC in the context of model selection will be criticised, and it will be argued that AIC and p-values are just different points on the same curve. Differences from using AIC, BIC and p-values (the last via either Likelihood Ratio Tests or stepwise regression) will be explored, and a strategy proposed which differentiates between explanation and prediction, a key distinction in model selection.

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14.00-14.30: Elena Ieno, Highland Statistics
Common mistakes in data analysis and strategies to address them
The pressure to publish is one of the greatest demands on scientific researchers: academic success depends on publications. Despite the large number of journals, competition to publish is particularly great in the areas of life science and ecology. When teaching statistics to ecologists, we identify common errors that may result in incorrect ecological conclusions. We sometimes encounter students and scientists who lack sufficient training in statistics; others may be determined to apply certain techniques they have only read about or seen used in a paper. In this presentation we discuss a series of pitfalls that may seriously impact the results of a statistical analysis and consequently decrease the likelihood of publishing a paper in a good quality journal. Such problems often can be avoided if the researcher applies methodical data exploration before embarking on the analysis.

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14.30-15.00: Louise Johnson, University of Reading
Experimental evolution in cancer cell lines
The field of experimental evolution has provided a hugely successful set of methods for testing evolutionary hypotheses. Cancer cell lines, taken from human tumours, can be grown in vitro much like microbes, and subjected to selection pressure in replicated experiments. We describe our cancer experimental evolution model system, which uses techniques adapted from those used in microbes, and we present data from our first cancer evolution experiment, on the evolution of motility / dispersal under different nutrient conditions.

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15.00-15.30: Iain Stott, University of Exeter
Methods put to good use: Advances in population ecology through studies of transient demography
We publish methods in the hope that our peers will notice them and use them, and in doing so advance the field. In population ecology, interest in transient demography is steadily increasing, with a proliferation of methodological advances in the past decade. Transient demography concerns short-term population response to environmental and anthropogenic disturbances and perturbations, and studying transients may be key to managing populations effectively, and understanding eco-evolutionary processes. This talk provides a retrospective of studies of transient demography, including many studies employing methods published in Methods in Ecology and Evolution.

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15.30-16.00: Coffee break

16.00-16.30: Natalie Cooper, Trinity College Dublin
Limitations of phylogenetic comparative methods
Phylogenetic Comparative Methods make numerous assumptions and suffer from biases in the same way as any statistical method, but these issues are often inadequately assessed in empirical studies. Such issues are the responsibility of end users but also of methods developers: the tools and approaches used to fit models are often far more user-friendly and better documented than the methods used to to assess whether that model fit is reasonable. I will discuss these issues, along with new research on detecting and accounting for them, and suggest ways of encouraging better dialogue between method developers and method users.

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16.30-17.00 Live Streamed from the Canadian Symposium: Janneke Wit, University of Calgary
Exploring population genomic approaches to identify genetic loci associated with anthelmintic drug resistance in parasitic nematodes
See below for details.

17.00-17.30: Kate Jones, University College London
Impact of global change on the emergence and spread of zoonotic infectious diseases
There is growing interest in the role of ecosystems and the goods and services they provide in governing human health and well-being. In particular, intact habitats may act to regulate diseases emerging into human populations. If true, this powerful idea would provide a critical argument for the protection of biodiversity because global emerging infectious diseases are a huge burden to human health and economies. However supporting evidence for this link is contradictory and controversial. Empirical statistical analyses of human infectious diseases has been successful in understanding the spatial environmental correlates of initial outbreaks but a mechanistic understanding of these patterns is lacking at a global scale. Here I present some latest research attempting to merge both empirical and mechanistic approaches at a global scale using data from a poorly understood disease, Lassa fever. I show that macro-scale environmental conditions play an important role in driving the spatial extent of Lassa virus and that any future habitat change to agricultural systems may facilitate a range expansion. I also expand this approach to model zoonotic diseases more generally and examine the impact of future environmental and habitat change on the emergence and spread of zoonotic diseases.

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17.30-17.30 Live Streamed from the Canadian Symposium: Jason de Koning, University of Calgary
New Tools for Identifying Convergent Molecular Evolution across Entire Phylogenies
See below for details.

18.00-20.00: Drinks Reception

 

Next Generation Ecology and Evolution: Confirmed Speakers

08.30-09.00: Registration and coffee

09.00-09.30 Live streamed from the UK symposium: Natalie Cooper, Trinity College Dublin
Limitations of Phylogenetic Comparative Methods
See above.

09.30-10.00: Janneke WitUniversity of Calgary
Exploring population genomic approaches to identify genetic loci associated with anthelmintic drug resistance in parasitic nematodes
Understanding the evolutionary consequences of anthelmintic resistance is key to strategies that aim to identify putative mutations and mitigate the spread of resistant parasitic nematodes. We are employing a population genomic approach to elucidate genomic signatures of selection in the parasitic nematode Haemonchus contortus. Initially, genome-wide scans are conducted between four populations isolated in the field that have been exposed to varying anthelmintic drug treatment regimes. Two of those populations have a history of regular drug treatment, while the other two populations have not received treatment. A polymorphism in the drug target locus known to be involved in resistance (isotype-1 ß-tubulin P200Y) has already been shown to be present at high frequency (90-100%) in the former populations, but at much lower frequencies in the latter (0-15%). We are investigating the nature of the signature of selection at this known benzimidazole resistance locus and aiming to identify additional areas of the genome under selection. We are using a ddRAD-seq approach (double-digest Restriction-site Associated DNA sequencing), in association with the H. contortus reference genome, to identify loci conferring resistance. The detection and monitoring of drug resistant parasites will be a key step to study the evolutionary mechanisms associated with anthelmintic drug action.

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10.00-10.30 Live streamed from the UK symposiumKate JonesUniversity College London.
Impact of global change on the emergence and spread of zoonotic infectious diseases
See above.


10.30-11.00: Jason de KoningUniversity of Calgary
New Tools for Identifying Convergent Molecular Evolution across Entire Phylogenies
Recent studies have identified surprising cases of convergent evolution at the molecular level. While both neutral sequence convergence (homoplasy) and non-neutral convergence can cause errors in phylogenetic inferences, we view selection-driven convergence as a particularly interesting and important phenomenon. I will discuss our recent work on accelerated algorithms and software for the discovery of non-random sequence convergence across entire phylogenies. Recently developed tools for large-scale inference will be discussed and demonstrated.

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11.00-11.30: Coffee

11.30-12.00: James WasmuthUniversity of Calgary
The trials and celebrations of working with genomes from non-model eukaryotes
The genome sequences of nearly 1800 eukaryotic species and their subspecies/strains are available through the NCBI. Of these, 30% were released in 2014. This wealth of data presents wonderful opportunities to deepen our understanding of these species’ biology. However, the process to generate these data – the sequencing, assembly and annotation – is often an interest only for those bioinformaticians at sequencing centres. Once published and released, the use of the genomes and their annotations by the research community typically assumes a high level of accuracy. Our work in nematode and protozoan genomes has highlighted cases where assembly and annotation errors can have a large and negative impact on the analysis and biological interpretation. I will describe examples of these errors and discuss practices and software that will help make the most from the genome of your favourite organism.

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12.00-12.30: Mason KulbabaUniversity of Calgary
Single nucleotide polymorphisms for the study of plant sexual systems
The development of single nucleotide polymorphism (SNP) markers provides access to fundamental questions of the ecology and evolution of plant reproduction. Studies that employ SNPs possess power to fully describe differential rates of genome introgression during hybridization, describe genome-wide inbreeding and the genetic architecture of inbreeding depression of ecologically important traits. Further, the wider application of previously discovered SNPs can be realized through highly multiplexed PCR based assays. Such studies illuminate long-standing questions regarding the genetic architecture of reproductive traits, and have direct application to the conservation of plant populations.

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12.30-13.00: Sean RogersUniversity of Calgary
Integration of ecological genomic approaches in the study of adaptation and speciation in fishes
E.B. Ford’s 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. Studies of adaptive divergence and reproductive isolation in fishes have reinforced that while genomic approaches offer tantalizing opportunities to measure genetic variation in nature, such efforts are most informative when integrative. In this talk, I will discuss the advantages and challenges currently associated with such integrative efforts and demonstrate how next-generation sequencing under this framework need not be a millstone around our necks in ecology and evolution.

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13.00-14.00: Lunch

14.00-14.30: Jessica F BrinkworthUniversity of Montreal & University of Illinois Urbana-Champaign
Evolution of Primate Early Immune Function and Disease
As the first line of defense against invading pathogens, the early or “innate” immune response is both mandatory for life and under tremendous selective pressure. Over millions of years, primate immune responses have diversified such that closely related species exhibit striking differences in susceptibility to infectious diseases marked by the dysregulation of innate immunity. Humans and chimpanzees are highly susceptible to Gram-negative bacterial sepsis, while Old World monkeys are resistant to this condition. Toxoplasma infections are largely asymptomatic in hominoids, but rapidly progress to lethal disease in some New World monkey species. The responsible molecular mechanisms have been difficult to resolve due to a lack comparative functional data from animals within the order. Next generation sequencing in combination with new bioinformatics techniques now allows us to characterize how the whole genome of any species responds to pathogens during the first hours of infection. We’ve stimulated the blood from a broad range of primate species with bacterial and viral molecules ex vivo, and measured leukocyte gene expression via RNA sequencing. Here we describe how a combination of evolutionary genomics and analysis of whole genome expression patterns during the early hours of infection provides a new understanding of primate immunity.

14.30-15.00: Sam YeamanUniversity of British Columbia
Using individual-based simulations to model the genomics of adaptation
With the massive volumes of genomic data that are available using current sequencing technologies, we face a major challenge as we seek to find patterns and interpret their meaning. Having theoretical predictions and hypotheses that are strongly grounded in evolutionary theory gives us one way to make sense of this data. Here, I will discuss how individual-based simulation platforms, such as Nemo, can be used to explore how demography and environment can shape patterns of genetic diversity. These results can then be used to formulate predictions under various scenarios and compared to empirically observed patterns from genome scans. I will also show how the parameters we use in these simulations can yield dramatic differences in the evolutionary trajectories that emerge, and discuss the prospects and pitfalls of these approaches.

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15.00-15.30: Emily Brown, McGill University
Metabarcoding: applications for biodiversity monitoring and invasive species detection.
Metabarcoding has become a popular tool for describing the composition of complex communities. However, concern has been raised over the accuracy of biodiversity estimates generated using this method. Whilst metabarcoding holds much promise, it comes with several technical considerations, including the value of singletons (sequences that occur only once within datasets) and the use of uniform divergence thresholds when generating operational taxonomic units (OTUs). Using a combination of mock and natural zooplanktons communities, we explore the potential for metabarcoding to be applied as a means to both describe native biodiversity and to detect aquatic invasive species. We highlight particular technical issues encountered and aim to provide advice to the metabarcoding community as to how these could be overcome.

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15.30-16.00: Coffee

16.00-16.30: Paul Galpern, University of Calgary
Reading the landscape: Detecting evidence of animal dispersal in spatial genomic data
Landscape genetics and landscape genomics are increasingly used to understand how features of the landscape have affected organism movement and dispersal in the recent past. Applications are many, including managing the risks of habitat fragmentation for animals of conservation concern, mitigating the spread of invasive species, and limiting the transmission of zoonotic diseases. However, subtle influences of the landscape on organism dispersal may be difficult to detect from genetic data. In particular, organisms with highly-mobile life history stages are hard to study. Here, I discuss the potential for genomics to improve a reading of the landscape for highly-mobile dispersers. Using simulations, I also explore the advantages and limitations of a new spatial analysis, applied to genomic data, for detecting cryptic influences on dispersal.

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16.30-17.00: Jana McPherson, University of Calgary
Discussion session

17.00-19.00: Poster session and wine reception

 

Enquiries

If you have any enquirires please contact coordinator@methodsinecologyandevolution.org

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