Researchers from Canada and the USA found that tree and shrub genetics can be used to produce more accurate predictions of when leaves will burst bud in the spring. Their study was published in Methods in Ecology and Evolution.
Although climate sceptics might find it hard to believe with this year’s endless snow and freezing temperatures, climate change is making warm, sunny early springs increasingly common. And that affects when trees start to leaf out. But how much?
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.
Today is the first day of the Crossing the Palaeontological-Ecological Gap (CPEG) conference. The aim of the conference is to open a dialogue between palaeontologists and ecologists who work on similar questions but across vastly different timescales. This splitting of temporal scales tends to make communication, data integration and synthesis in ecology harder. A lot of this comes from the fact that palaeontologists and ecologists tend to publish in different journals and attend different meetings.
‘babette‘ is an R package that works with the popular phylogenetic tool BEAST2. BEAST2 uses one or more alignments and a model setup to create a Bayesian posterior of jointly estimated model parameters and phylogenies.
babette lets you call BEAST2 from an R script. This makes it easier to explore models and/or alignments than using the graphical user interface programs that BEAST2 provides. It will also help you to improve the reproducibility of your work with BEAST2.
babette Tutorial Videos
If you’re new to phylogentic analyses, the video ‘babette demo‘ demonstrates the package. It has all of the information that you need to be able to start using the package
Today, everyone knows about the importance of accounting for phylogenetic effects when it comes to understanding trait evolution. How to account for phylogenetic effects is another matter though.
A couple of years ago, I was having a discussion on the R-sig-phylo blog and dared to define the Brownian Motion (BM) as kind of a null hypothesis that more realistic scenarios should be compared to. Maybe I crossed a line or made too simplistic a statement (see Adams and Collyer’s article in Systematic Biology for an explanation of why this matter is far trickier and more complicated than my reply suggested). The point is, my comment was hotly contested and a colleague ‘put the onus on me’ to do something better than the almighty (emphasis mine) BM.
The RRphylo method was my attempt to do just that. It may not be better than BM, but it is different. Often, that can be exactly what you need. Continue reading →
Today we are welcoming another two Associate Editors to the Methods in Ecology and Evolution. Just like the seven AEs who joined last week, Michael Matschiner (of the University of Basel, Switzerland) and Tiago Bosisio Quental (of the University of São Paulo, Brazil) were both invited to work with the journal following our open call earlier this year. You can find out more about both of them below.
“I am an evolutionary biologist interested in the processes that drive speciation and generate biodiversity. To learn about these processes, I use phylogenetic divergence-time estimation based on genome sequences and the fossil record. Since both of these data sources do not usually conform to expectations in standard phylogenetic workflows (no recombination, no hybridization, no sampling bias), much of my work involves method development to assess the impact of model violations, and to account for them in phylogenetic reconstruction.”
Tiago Bosisio Quental
“I am interested on understanding spatial and temporal patterns of biodiversity and the mechanisms involved in generating species diversity. I have a particular interest in mammals, but my research interests are not limited to a specific taxonomic group but are instead motivated by a range of questions and structured around them. At the moment, I am particularly interested in understanding the role of biotic interactions on biodiversity changes in deep time. The main tools used to approach those questions are molecular phylogenies, fossil record, ecological data and numerical simulation.”
We are thrilled to welcome Michael and Tiago to the Associate Editor Board and we look forward to working with them over the coming years.
The comparative methods we use to study the evolution of traits are mainly based on the idea that since species share a common evolutionary history, the traits observed on these lineages will share this same history. In the light of phylogenetics, we can always make a good bet about how a species will look if we know how closely related it is to another species or group. Comparative models aim to quantify the likelihood of our bet being right and use the same principle to estimate how fast evolutionary changes accumulate over time. Continue reading →