Jacobs Lab
California Academy of Sciences | Institute for Biodiversity Science and Sustainability | Department of Botany
Lab Projects
Our work is generally geared towards characterizing the early stages of the speciation process. Using robust phylogenies, carefully delimited species, and datasets of species traits, we can compare and contrast across species and through time to characterize diversification in a lineage. This simplified outline of our work is deceptive, however, and Castilleja continues to be an enigmatic genus. Each of our projects tackles various elements of biology and evolution in the group, contributing to our overall understanding of Castilleja systematics.
Along with this research are opportunities to address challenging, but very important questions that apply more broadly to evolution, outside of Castilleja or other plant species. For example, how can we define species and infer evolutionary relationships in incipient lineages when various lines of evidence are incongruent? How does this affect classification and taxonomy? What are the intrinsic and extrinsic traits that drive the earliest stages of diversification? Can we detect patterns of trait acquisition associated with diversification in the genus? Does this pattern hold in other genera, other geographic regions?
Genus-wide phylogenetics
A species tree of Castilleja has been especially challenging to estimate, largely because of the age of the genus (the MRCA of Castilleja is ~4-6 myo with most of the diversity estimated to have been generated less than 1 mya), the prevalence of polyploidy in the group (varying ploidy levels within and across many species), and apparent widespread gene flow when species co-occur. We have multiple projects and collaborations that address different aspects of this complexity.
With Dave Tank and Maribeth Latvis we are building robust chloroplast and nuclear phylogenies. Unsurprisingly, preliminary work tells us that there is a good deal of cyto-nuclear discord as well as extreme phylogenetic geographic structure in the chloroplast genome, and a taxonomy (largely based on morphology) that is potentially at odds with phylogeny. As part of this work we have developed a shiny app (interact with it here) that allows us to visualize these patterns.
Species delimitation and species complexes
Robustly delimited species are an essential component of systematic work, particularly in systems like Castilleja. In each of these complexes we independently apply multiple lines of evidence to define species (genomic, phenomic, biotic and abiotic factors) and then combine evidential lines to identify and describe the types of species. There are multiple species complexes that are currently being studied and many awaiting focus and attention.
Generating genomic resources
Our lab is in the process of generating a high quality, phased and annotated reference genome that, when combined with additional molecular resources, will provide an important architecture to our efforts at understanding molecular evolution in the genus. Along these lines we are actively generating ploidy estimates across species using chromosome squashes and flow cytometry, with the ultimate aim of creating a more thorough understanding of variation in ploidy levels in the genus.