Phylogenetic Tip Rates: How Well Can We Estimate Diversification?

Post provided by Pascal Title and Dan Rabosky

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.

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.

Several different classes of methods are available for studying the effects of species traits on lineage diversification rates. These include state-dependent diversification models (e.g., BiSSE, QuaSSE, HiSSE) and several non-model-based approaches. In our article – ‘Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?’ – we assessed the accuracy of a number of model-free metrics (the DR statistic, node density metric, inverse of terminal branch lengths) and model-based approaches (Bayesian Analysis of Macroevolutionary Mixtures, BAMM) to determine how they perform under a variety of different types of rate heterogeneity. The “tip rates” using these approaches have become widely used for a few reasons, including ease of computation and how easy it is to pair them with other types of data. Continue reading

More New Associate Editors

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.

Michael Matschiner

“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.

Methods Digest – December 2009

A round-up of methods papers published in the last month. If there are any papers that you think should be featured, email me or leave a comment and I will add them.

Liam Revell has a paper in Evolution on size correction and principal components analysis of phylogenetic comparative data. Olivier Gimenez and colleagues also have a paper in the same issue on generating fitness landscapes using mark-recapture data.

Systematic Biology has a number of papers with interesting methods: Campbell & Lapointe have a paper on the use and validity of composite taxa in phylogenetic analysis; Fitzjohn et al. have a nice paper on estimating trait-dependent speciation and extinction rates in phylogenies that are not complete; Bui Quang Minh and colleages present an algorithm for efficiently estimating phylogenetic diversity; Michael D. Pirie, Aelys M. Humphreys, Nigel P. Barker, and H. Peter Linder present an approach for dealing with implications of conflicting gene trees on inferences of evolutionary history above the species level.

In Conservation Biology, Angelia Vanderlaan and Christopher Tagaart describe how a voluntary scheme for ships to avoid cetain areas has worked in preventing lethal strikes on right whales.

In Ecological Applications, Cang Hui and colleagues compare approaches for extrapolating population sizes from abundance-occupancy relationships. Matthew Etterson et al. look at the problem of estimating population trends when there is detection heterogeneity and overdipsersion in the data. Paul Beier and co-workers use a case study to examine the use of least-cost modelling to design wildlife corridors.

Oscar Puebla and colleagues describe in Ecology a study that estimates dispersal using genetic distances in a coral reef fish. Sean Connolly et al. have a new bootstrap approach for testing species abudance models in the same issue. Andy Royle et al. present Bayesian method for estimating population sizes using camera trap data. David G. Angeler, Olga Viedma, and JoséM. Moreno present a critique of time lag analysis in time series modelling. David Carslake et al. have a paper presenting useful review of constraints and rules for elasticity analysis in matrix modelling. Finally in that same issue Paul Stapp and Daniel J. Salkeld look at the use of stable isotopes in studying host-parasite interactions.

Finally for this month in Animal Conservation, Heidy Kikillus et al. look at minimising false negatives in predicting distributions of invasive species. (Thanks to Andrew Tyre for pointing this one out).