‘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
Phylogenetic trees represent the evolutionary relationships among different lineages. These trees give us two crucial pieces of information:
the relationships between lineages (which we can tell from the pattern of the branches (i.e., topology))
the point when lineages separated from a common ancestor (which we can tell from the length of the branches, when estimated from genetic sequences and fossils).
Phylogeny of insects inferred from genetic sequences showing the time of divergence between ants and bees.
As systematic biologists, we are interested in the evolutionary history of life. We use phylogenetic trees to uncover the past, understand the present, and predict the future of biodiversity on the planet. Among the tools for this thrilling job are the comparative methods, a broad set of statistical tools built to help us understand and interpret the tree of life.
Here’s a Tree, Now Tell Me Something
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 “Phylogenies, Trait Evolution and Fancy Glasses”
If you are attending Evolution, as well as attending the fabulous talks mentioned by Hélène below, do stop by booth 125 to see our BES colleague Simon Hoggart. Simon is the Assistant Editor of Journal of Animal Ecology and would be happy to answer your questions about any of our journals or any of the other work we do here at the BES.
RPANDA: a time machine for evolutionary biologists
Imagine “Doc”, Marty’s friend in Back to the Future, trying to travel back millions of years in an attempt to understand the history of life. Instead of building a time machine from a DeLorean sports car powered by plutonium, he could dig fossils, or more likely, he would use molecular phylogenies.
Molecular phylogenies are family trees of species that can be built from data collected today: the genes (molecules) of present-day species (Fig 1). They are often thought of as trees, in reference to Darwin’s tree of life. The leaves represent the present: species that can be found on Earth today. The branches represent the past: ancestral species, which from time to time split, giving rise to two independent species. The structure of the tree tells us which species descend from which ancestors, and when their divergence happened.
Fig 1: The phylogenetic tree of all birds (adapted from Jetz et al. 2012). Each bird order is represented by a single bird silloutter and a specific colour (the most abundant order of Passeriformes, for example is represented in dark orange). Each terminal leaf represents a present-day bird species, while internal branches represent the evolutionary relationships among these species.
Phylodiversity indices are increasingly used in spatial analyses of biodiversity, driven largely by the increased availability of phylogenetic trees and the tools to analyse them. Such analyses are integral to understanding evolutionary history and deciding where to allocate conservation resources.
Phylogenetic Indices: The Current Favourites
The most commonly used phylogenetic index is Faith’s Phylogenetic Diversity (PD; Faith 1992). PD is the phylogenetic analogue of taxon richness and is expressed as the number of tree units which are found in a sample.
More recently developed phylodiversity indices adapt the calculation of PD by adjusting the branch lengths of a sample using the local lineage range sizes and abundances, for example Phylogenetic Endemism (PE) and Abundance weighted Evolutionary Diversity (AEDt). In PE the length of each branch in a sample is multiplied by the fraction of its total geographic range found in that sample. The AEDt index uses the same general approach, but weights each branch by the fraction of total abundances found in the sample. The weighting process is generic, so one can scale the branch lengths by any relevant factor, for example the threat status (Faith 2015). Continue reading “Introducing Biodiverse: Phylodiversity Made Easy”
In the 4th and final installment of Barb Anderson’s INTECOL 2013 podcasts, she asks a number of delegates: What method has transformed your field the most, during your career?
The answers in this podcast are given by the following people:
Steve Hubbell, University of California, Los Angeles, USA (00.21)
Georgina Mace, University College London, UK (00.44)
Carsten Dormann, University of Freiburg, Germany (01.07)
In Methods’ latest video, Travis Ingram gives a brief introduction to the new phylogenetic comparative method SURFACE. This method uses stepwise AIC to fit a series of stabilizing selection models to a phylogenetic tree and trait data, and to quantify the extent of convergent evolution toward the same selective regimes. The tutorial explains how SURFACE works, and then shows an example analysis in R. You … Continue reading New Video – SURFACE: Detecting convergence with stepwise AIC
Method’s latest video, “Diversitree”, is now available to view on our YouTube channel. In this quirky demonstration, Mr Blueberry and Fairly-Small-Yellow-Bird disagree on how colour affects the diversification of birds. Rich FitzJohn shows them how to test their hypotheses using the comparative phylogenetic methods implemented in the R package “diversitree”, recently described in the Methods paper “Diversitree: comparative phylogenetic analyses of diversification in R“. This … Continue reading Diversitree video – starring Mr Blueberry and Fairly-Small-Yellow-Bird
It seems that from the number of submissions we receive at the journal, Methods in Ecology and Evolution has filled an important niche. As our editor-in-chief, Rob Freckleton, wrote to introduce our second volume: “those doing science need to be kept up to date on new approaches, and those developing new methods need a place to publish, as well as be supported in getting their … Continue reading Volume 3 Issue 1: Now online
Here is a round-up of interesting methods and methods-related papers published in the past few weeks. Please do pass on any interesting-looking papers / links and I will include them. In Heredity Blanya et al. review the use of Drosophila subobscura as a tool in research on the microevolutionary consequences of climate change. There are several methods-relevant papers in the latest issue of Evolution: Céline … Continue reading Methods Digest – November 2009
Here is a round-up of some interesting methods papers published in the past few weeks. If you see any more papers that you would like to see flagged up, leave a comment below or email me. In PLoS Biology Wayne Getz presents a thoughtful review of the models and modelling approaches that might be useful in predicting the consequences of multiple threats to ecosystems from … Continue reading Methods Digest, October 2009
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