Workshop on Integrating Molecular Phylogenies and the Fossil Record

Last week I attended a workshop organized by Hélène Morlon, Tiago Quental, and Charles Marshall on integrating data from the fossil record into phylogenetic methods. This three-day workshop was sponsored by the the France-Berkeley Fund, a cool program that provides seed grants to build partnerships between UC Berkeley researchers and French collaborators. All of the events took place at the UCMP on the UC Berkeley campus.

Hélène, Charles, and Tiago recognized the increasing interest in methods and analyses that incorporate data from fossil taxa; and since there are several of us working in this area–particularly in methods development–the need for building a collaborative network is critical. Furthermore, as methods become more and more reliant on data from the fossil record, connections between neontologists and paleontologists must be formed. Notably, a similar working group – organized by Sam Price and Lars Schmitz – was held at NESCent this past spring and was made up of an overlapping set of researchers. One result of the NESCent catalysis meeting will be a SSE Symposium at Evolution 2014 on “Reuniting fossil and extant approaches to macroevolution”.

Overall, this was one of the most productive and intellectually stimulating working groups I have participated in. There were about 20 participants (including graduate students, postdocs, research scientists, and professors) for the whole three days – a good number of people for an exciting discussion, but not so large as to prevent people from participating. The workshop began with a symposium of talks (listed below) by 12 researchers from Europe and North America. Reading the talk titles, it’s hard to ignore the importance of activities like this. Much of the work presented had significant overlap, so this was a great opportunity to establish new collaborations. I presented a project I’m working on with Tanja Stadler and John Huelsenbeck (see my slides from a similar talk). We have developed a model that unifies fossil occurrence times and extant lineages into a single macroevolutionary process. So, Daniele Silvestro‘s work on statistical models for estimating preservation rates and other macroevolutionary parameters from the fossil record was of particular interest to me. And in our discussions, Daniele and I discovered that our complementary methods can be extended and combined in ways that could lead to the development of approaches for constructing informed priors for Bayesian divergence-time estimation. As theoreticians, it’s easy to work on a project without knowing that someone else (many time zones away or even in the same institution) is working on something similar or an idea that could nicely fit into some unified framework. This really underscores the importance of efforts like this workshop and all of the awesome working groups/catalysis meetings held at NESCent.

The following day, we all got together in the morning and started brainstorming about important directions in the field of macroevolution. This was a thoroughly enjoyable discussion that culminated in an outline of important questions in macroevolution and how fossil information can help to answer them. We then formed small, break-out groups on four important topics: (1) diversity dynamics, (2) phenotypic evolution, (3) adaptive radiations and (4) biogeography. The break-out groups developed these ideas for the rest of the workshop, discussing methodological, conceptual, and data shortfalls. We are already developing ideas for exciting review papers and new research projects, so be sure to keep an eye out for cool stuff resulting from this workshop.

FBF Fossils & Phylogenies Symposium

Sam Price & Lars Schmitz — Report from the NESCent catalysis meeting: Successes and areas requiring further effort

Charles Marshall — Some observations of the value of the fossil record in quantifying diversity dynamics, and the need for improvement in the use of fossils in calibrating molecular phylogenies

Michael Alfaro — Challenges to integrating fossils and molecular data

Daniele Silvestro — Estimation of macroevolutionary rates from fossil occurrence data

Todd Parsons — Estimating long term diversity dynamics using molecular phylogenies and limited fossil record

Tracy Heath (@trayc7) — The fossilized birth-death process: A coherent model of fossil calibration for divergence time estimation (collaborative work with Tanja Stadler and John Huelsenbeck)

Gilles Didier — Integrating the fossil record in speciation and extinction rates estimations

Nick Matzke (@NickJMatzke) — Statistical model choice for old and new biogeographical cladogenesis models: Comparing DEC, DIVA, BayArea, and measuring the importance of founder-event speciation, with and without models for imperfect detection of fossils

Thomas Ezard (@tomezard) — The meaning of birth and death in macroevolutionary birth-death models, and its consequences for models of molecular evolution

Hervé Sauquet — Proteaceae diversification through time

Joshua Schraiber — Dating the great ape phylogeny using phylogenomics and fossil tip dating

Chelsea Specht — To be or not to be (resolved): Incorporating fossils in phylogenies of Zingiberales

In addition to the presenters and organizers listed above, among the participants were also Susana Magallon, Lucy Chang, Jun Ying Lim, Gustavo Burin Ferreira, Susan Tremblay, and Jenna Judge.