Phylogenetics & Speciation


Diversity and evolutionary history of plasmids

Eva Top Ph.D., Celeste Brown Ph.D. and Jack Sullivan Ph.D.

Although plasmid-mediated gene transfer is now recognized as a key mechanism in the alarming rise of antibiotic resistance, little is known about the reservoirs of multi-drug resistance (MDR) plasmids, their evolutionary history and extant genetic diversity. Therefore our aim is to improve our insight in the diversity and evolutionary history of MDR plasmid through comparative genomics of plasmids isolated from various habitats (partly in collaboration with Drs. D. Cummings and R. Botts) and through phylogenetic studies.


Divergence with Gene Flow in Chipmunks (Phylogeny and Speciation)

Jack Sullivan Ph.D., Jeff Good Ph.D. and John Demboski Ph.D.

Increasing evidence has accumulated over the last two decades to support the importance of Divergence with Gene Flow (DGF) in the generation of biological diversity. We will leverage emerging genomic resources to provide a highly resolve species tree estimate for a rapid radiation of chipmunks (Tamias); 23 species have evolved in approximately 2.7 MY in western North America in spite of a complex history of hybridization between diverging lineages. We will then assess the interaction of sexual selection and ecological differentiation in driving the radiation by reconstructing niche evolution as well as differentiation in reproductive morphology (shape of the os penis, or baculum) and chip vocalizations that are used to advertise approaching estrus. This will allow us to ascertain if either ecological or reproductive differentiation preceded the other, if divergence in ecology and reproduction was linked, or if there was no consistent pattern. Furthermore, we will assess character displacement in both bacular morphology and chip vocalizations at contact zones both where hybridization has bee identified and where no introgression is occurring.


Diversification dynamics in angiosperms: large-scale analyses addressing long-standing questions

David Tank Ph.D. and Luke Harmon Ph.D. 

Using the well-sampled and highly resolved angiosperm phylogenies that were produced during the Angiosperm Tree of Life Project as a starting point, we are investigating the diversification dynamics (e.g., shifts in diversification rates and/or the rate of trait evolution) of this large and diverse clade in an attempt to answer the long standing questions of 1) why is the angiosperm lineage so diverse, and 2) what role, if any, do ancient polyploid events play in this diversity? To this end, we are using trees ranging from 640 taxa to more than 32,000, in combination with functional trait data compiled as part of a NESCent working group, to address this question with macroevolutionary analyses at unprecedented scales.


Investigating the accumulation of evidence for speciation: species delimitation in a rapid and recent radiation

Simon Uribe-Convers and David Tank Ph.D.

The unified species concept acknowledges that speciation is a gradual and constant process with no clear boundaries or thresholds for the identification of species. Although this concept is widely accepted by evolutionary biologists, to our knowledge, very few studies have empirically evaluated the accumulation of species properties across time scales or from a comparative phylogenetic perspective. Our research seeks to understand how the evidence for speciation has accumulated over time in the mostly South American plant genus Bartsia (Orobanchaceae), inferring if there is an order or a sequence for the acquisition of species criteria, and if a specific criterion is more important than other at a certain point in time, e.g. is morphological differentiation more prominent than ecological divergence in recently diverged species?


Species delimitation and the identification of the correlates of diversification in a large species complex: phylogeny and systematics of the paintbrushes (Castilleja, Orobanchaceae)

Sarah Jacobs and David Tank Ph.D.

In recently diverged groups, the identification of independently evolving lineages that have acquired unique species properties (morphological, ecological, geographic, and/or molecular characteristics) can be difficult and requires multiple lines of evidence. Our research, examines species delimitation in rapidly and recently diversifying clade of mostly western North American plants – the genus Castilleja (the paintbrushes). Castilleja comprises more than 200 species and there is a large amount of overlapping morphological, geographic, and ecological variation that makes species delimitation and phylogenetic reconstruction especially difficult. We use multiple approaches including species-level phylogenetic and network analyses of sub-genomic data, molecular methods for species delimitation, ecological niche modeling, and phylogenetic comparative analyses of morphological traits to investigate the speciation process and identify the morphological, ecological, and/or geographic correlates of speciation.


Evolution and biogeography of an Andean radiation: diversification of Lachemilla (Rosaceae)

Diego Morales-Briones and David Tank Ph.D.

The Andes are one of the world’s hotspots of plant diversity, but the origin and evolution of this diversity remains unclear. Our research focuses on the diverse genus Lachemilla (Rosaceae) that is a characteristic member of the alpine flora of Andean South America. Using DNA sequence data, cytological analyses, and comparative morphological studies, combined with extensive fieldwork, we are building a comprehensive understanding of the evolutionary history of this group that will be used to evaluate current taxonomies, determine species boundaries, and importantly, understand the patterns and processes that have driven the diversification of this clade. With this investigation of the ecological and evolutionary history of this key group of the Andean flora, we add to a growing literature aimed at a comprehensive understanding of the biogeographic history of the montane neotropical radiations.