We deploy a diversity of approaches to contribute to our understanding of plant evolution, and evolution in general. Here are the main approaches being utilized.
Systematics/Phylogenetics: The lab has used molecular phylogenetics to address a diversity of problems: morphological evolution, the evolution of plant-pollinator interactions, biogeography, rates of evolution, key innovations, hybridization, ring species, and species limits. Current projects include using a targeted sequence capture platform to address the origins of polyploidy, reticulate evolution, and species delimitation in Adansonia (and other bombacoids). This work is being lead by Nisa Karimi, and is a collaboration with Corrinne Grover and Jonathan Wendel at Iowa State University. Alison Scott is using a similar methodology to reconstruct the evolutionary history of redwoods. Noah Stenz is doing bioinformatic computer program for this project.
As part of this work we have ongoing collaborations with statisticians Cécile Ané and Bret Larget to develop new methods related to low-level phylogenetics. The aim is to use multilocus sequence data to estimate the distribution of gene genealogies that coexist within a set of genomes. We can then extract insights into the evolutionary forces (incomplete lineage sorting, introgression, etc.) that have shaped that distribution. One prominent product of this collaboration is the program BUCKy, which conducts Bayesian concordance analysis. We are improving the underlying model to better distinguish discordance due to incomplete lineage sorting along the branches of a strictly divergent population tree from other causes of discordance, such as introgression. We recently developed a statistical test that can be used to evaluate whether patterns of gene-to-gene discordance can be explained by incomplete lineage or if other factors, most notably introgression, need to be invoked.
Biopoiesis (Origin of life): In collaboration with several colleagues in the Department of Chemistry, Geosciences, and the Wisconsin Institute for Discovery, we are working on a project that explores the potential for deploying selection in a lab setting to drive the de novo appearance of life-like chemical consortia. The experiment involves selecting random chemical consortia for an ability to colonize mineral surfaces and then evaluates whether there has been a response to this selection. If we see a response to selection, this will indicate that we have generated new, life-like chemical processes in the laboratory, which would open up many fascinating research questions. This work is being spearheaded by Michael Berg. More details are available in our Benefunder profile.
Origin of eukaryotic cells. In collaboration with Buzz Baum (University College, London) we recently published a novel theory for the origin of eukaryotic cell structure. This “inside-out” theory suggests that an an ancestral prokaryotic cell extruded membrane blebs through its cell wall and that these ultimately fused to give rise to the cytoplasmic compartment. A paper describing this new theory in detail was published in BMC Biology, with a follow-up article in New Scientist.
Previous Research Contributions
Conceptual issues and philosophy of biology: Understanding evolutionary phenomena can be aided by thinking clearly about terms and the concepts they are intended to capture. A number of publications have dealt with the thorny problem of the nature of species. A more recent focus has been on developing a new concept of homology based on developmental causation and a formalism for representing the relationship between genotype and phenotype. More information on this approach is described in this publication.
Candidate gene Evolutionary Developmental Genetics (Evo-Devo): A long-standing interest in the lab is developing methods for identifying genes underlying species differences. We have used developmental genetic knowledge from model species to guide studies of several different traits in different plant groups. In many cases, projects started in my lab are still being pursued by former graduate students or post-docs in their own independent labs. Examples of phenotypes studied are: inflorescence architecture, trichome shape, flower color, petal spot position, dioecy, and stamen number. The approaches used have included electron micrography, in situ hybridization, immunolocalization, qPCR, analyses of molecular evolution, and plant transformation.
Transgenomics: The dependence on candidate gene hypotheses has long limited evo-devo research in cases where species cannot be crossed. We have pioneered an approach called transgenomics which entails making a genomic library from a donor species and introducing this into a recipient species’ genome by high-throughput transformation. Transgenic plants are then screened to identify genes from the donor genome that have a trans-dominant effect on plant phenotype. A proof-of-concept screen was published in New Phytologist. Possible extensions include reciprocal transgenomics and library enrichment for genes expressed in a certain tissues.