Sequencing ultraconserved DNA for phylogenetic research is a hot topic in evolution right now. As the name implies, Ultraconserved Elements (UCEs) are regions of the genome that are nearly identical among distantly related organisms. They can provide useful information for difficult phylogenetic questions. The list of advantages is long – among others, UCEs are:
phylogenetically informative on different timescales.
A key reason for the method’s success is the developers’ commitment to full transparency, active tutoring, and willingness to help next-gen sequencing newbies like me to get started. Help is just a github-issue post away.
Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.
Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it! Continue reading →
The study of interactions and their impacts on communities is a fundamental part of ecology. Much work has been done on measuring the interactions between species and their impacts on relative abundances of species. Progress has been made in understanding of the interactions at the ecological level, but we know that co-evolution is important in shaping the structure of communities in terms of the species that live there and their characteristics. Continue reading →
Plant-pollinator interactions are often considered to be the textbook example of co-evolution. But specialised interactions between plants and pollinators are the exception, not the rule. Plants tend to be visited by many different putative pollinator species, and pollinating insects tend to visit many plant hosts. This means that diffuse co-evolution is a much more likely driver of speciation in these communities. So, the standard phylogenetic methods for evaluating co-evolution aren’t applicable in most plant-pollinator interactions. Also, many plant-pollinator communities involve insect species for which we do not yet have fully resolved phylogenies. Continue reading →
In our recent publication (Rabosky et al. 2018) we assembled a huge phylogeny of ray-finned fishes: the most comprehensive to date! While all of our data are accessible via Dryad, we felt like we could go the extra mile to make it easy to repurpose and reuse our work. I’m pleased to report that this effort has resulted in two resources for the community: the Fish Tree of Life website, and the fishtree R package. The package is available on CRAN now, and you can install it with:
The source is on GitHub in the repository jonchang/fishtree. The manuscript describing these resources has been published in Methods in Ecology and Evolution (Chang et al. 2019).
Analyzing diversification rate heterogeneity across phylogenies allows us to explore all manner of questions, including why Australia has such an incredible diversity of lizards and snakes.
Within the tree of life there are differences in speciation and extinction rates over time and across lineages. Biologists have long been interested in how speciation rates change as a function of ecological opportunity or whether key innovations lead to increases in the rate of speciation. Exploring this rate variation and examining how clades differ in terms of their diversification dynamics can help us to understand why species diversity varies so dramatically in time and space. Learning more about the relationship between traits and diversification rates is especially important because it has the potential to reveal the causes of pervasive variation in species richness among clades and across geographic regions.
Post provided by Damien Farine, Sebastian Sosa, David Jacoby, Mathieu Lihoreau and Cédric Sueur
Social network visualization. Photo by Martin Grandjean CC-SA.
Here at Methods in Ecology & Evolution and the Journal of Animal Ecology we are excited by the new directions that the next decade of research into animal social networks will bring. We hope to encourage new advances in the study of animal social networks by calling for high-quality papers for a cross-journal Special Feature on animal social networks. Below, Damien Farine and the Special Feature Guest Editors have reviewed some areas of animal social network research that deserve particular attention.
There are a wide variety of network metrics (node-based, dyadic, and global) and the application and development of new metrics continue to evolve. It is crucial to consider how the values generated by a network metrics (new and old) are interpreted biologically and recognize their limitations. It would be useful to have manuscripts that address questions about:
How mathematical definitions of different network metrics translate to biological processes;
Which metrics provide similar, redundant, or unique information relative to other metrics.
I had the pleasure of delivering one of the plenary talks at the first (hopefully of many) Crossing the Palaeontological – Ecological Gap meeting held in the University of Leeds on August 30th and 31st. I’m a geologist and a botanist, so this is a topic that’s close to my heart and my professional interests.
As we move into an ecologically uncertain future with pressures of climate change, land-use change and resource limitations, the fossil record offers the only truly long-term record of how Earth’s ecosystems respond to major environmental upheaval driven by climate change events. The fossil record is, of course, not without its problems – there are gaps, not everything fossilises in the same way or numbers, and comparisons to today’s ecology are extremely difficult. It’s these difficulties (and other challenges) that make the uniting of palaeontology and ecology essential to fully address how plants, animals and other organisms have responded to major changes in the past. Perhaps uniting them could give us an idea of what to expect in our near-term future, as carbon dioxide levels return to those not previously experienced on Earth since the Pliocene, over 2 million years ago. Continue reading →
The latest Methods in Ecology and Evolution Virtual Issue – ‘Integrating Evolution and Ecology‘ – is in honour of the late Isabelle Olivieri (1957-2016): an international, interdisciplinary and ground-breaking biologist. It was edited by Louise Johnson and James Bullock and features papers on topics she researched, and in many cases pioneered. But it might perhaps have been more difficult to find 15 Methods papers on areas outside of Isabelle’s research interests!
Isabelle was the first Professor of Population Genetics at Montpellier, a past President of the European Society for Evolutionary Biology (2007-2009), and a member of the European Molecular Biology Organization. She spanned subject boundaries as easily as she collaborated across geographical borders. Her publications range through metapopulation and dispersal ecology, host-parasite coevolution, life history, invasive species and conservation ecology. In keeping with this breadth of interests, she also combined theory easily with experiment, and worked with a wide range of study systems from mites to Medicago. Continue reading →
Understanding how wild populations respond and adapt to environmental change is a key question in evolutionary biology. To understand this, we need to be able to separate genetic and environmental effects on phenotypic variation. Statistical ‘animal models’, which can do just this, have revolutionised the field of quantitative genetics. A lack of full knowledge of individual pedigrees can lead to severe bias in quantitative genetic parameter estimates though – particularly when genetic values for focal traits vary non-randomly in unknown parents.