We are generally interested in uncovering processes behind biogeographic shifts, speciation, extinction and determinants of community assembly. We are therefore interested in the processes regarding the distributions and genetic structuring of co-distributed organisms. Although we often focus on intertidal organisms, research in the lab ranges widely taxonomically and ecologically.
We are also heavily involved in “statistical phylogeographic” modeling to quantify and test for patterns in biogeographic concordance across multiple co-distributed taxa. To this end, we are developing an inferential framework based on hierarchical approximate Bayesian computation (HABC) called msBayes. The goal of msBayes is to be a toolbox for evaluating a broad range of complex historical scenarios across co-distributd taxa.
The Hicker-lab research is supported by National Science Foundation (NSF) Grant # DEB 0743648 (9/1/08 - 8/30/10). The title is "Testing biogeographic models of community assembly, colonization and vicariance with comparative phylogeographic data and hierarchical Bayesian models". Any opinions, findings or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the NSF.
Ongoing research projects:
1. Developing HABC software tools for phylogeography (msBayes). HABC bypasses the computational difficulties of using explicit likelihood functions by simulating data from a coalescent model. The added flexibility and power of HABC is that one can use it for parameter estimation and testing complex highly parameterized a priori models. To allow other phylogeographers to harness the HABC framework, a considerable effort has been made to develop a software pipeline (msBayes). Written in C, R and wrapped in Perl, msBayes will deploy HABC on a variety of comparative phylogeographic inferences. So far msBayes has been deployed to test simultaneous divergence across co-distributed taxon-pairs as well as test competing allopatric isolation models (i.e. vicariance and colonization). The collaboration and coordination with other large comparative phylogeographic research programs will guide the planned improvements and expansions of msBayes thereby allowing a wide range of idiosyncratic comparative phylogeographic hypotheses to be tested. The potential flexibility of HABC (arbitrary models of subdivision, migration, recombination, expansion, contraction, admixture and isolation) and ability to both estimate parameters and test complex demographic models is currently pushing the era of phylogeography into a new phase. Presently, N. Takebayashi and I are extending msBayes to use multi-locus data (and IM infiles).
2. Testing biogeographic models of community assembly, colonization and vicariance with “whole ecosystem” comparative phylogeographic data. Knowledge of biodiversity and the population-level genetic composition of species can provide insights into the history of how ecosystems were established and how species within those ecosystems evolved after they were established. This knowledge can then provide insight into how island species and communities respond to climate change, invasions, and the possible outcomes of combining species into communities that have no current or historic analogs. The imminent prospect of reconstructing the ecological and evolutionary history of all species within an island community from “whole ecosystem” phylogeographic data will enable testing controversial and unresolved hypotheses of community assembly including neutral and niche-based models. However, the analysis of DNA sequence data from many multiple individuals of many (i.e., 50 - 500) species presents analytical and computational challenges. The hierarchical approximate Bayesian computation (HABC) framework can handle such large scale data sets while incorporating genetic coalescent variance as well as uncertainty and variability in a suite of important demographic factors that vary in magnitude across taxa (i.e. population sizes, dispersal rates, mutation rates, and island colonization times). Currently I am using the HABC approach to test controversial community assembly models by inferring temporal patterns of community colonization and invasion.
3. Using “model ecosystem” data from the Moorea Biocode project and HABC to answer questions about community evolution and assembly The “Moorea Biocode”, a joint French-American effort, funded by the Moore Foundation, will provide a unique opportunity to accomplish these broadly interesting scientific goals by yielding DNA sequence data at the mtDNA CO1 locus from every species of “macro-biota” within the French Polynesian island of Moorea. The beginning phase of this project is focusing on all reef fishes, marine invertebrates and terrestrial arthropods. In collaboration with two Biocode project members (Chris Meyer - and Rosemary Gillespie) we will use the emerging Moorea datasets and the HABC framework to examine two contrasting paradigms of community assembly; a neutral model and Tilman’s stochastic competitive assembly model. Although these estimates will be based on many species sampled at a single mtDNA locus that is subject to variance associated with the coalescent as well as rate variation across taxa, these uncertainties can be built into a HABC model while also gaining information across species samples via “borrowing strength".
4. Integrating comparative phylogeography with environmental niche modeling (ENM) to understand biogeographic determinants of rocky intertidal communities Details forthcoming ...