Charles Marshall, Professor

Closed (1) Biogeography and paleoecology of epeiric seaways

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

Throughout the Phanerozoic, times of rising sea level were often accompanied by the development of shallow seas on the continents. These epeiric seaways formed relatively rapidly and departed from open oceans in several aspects of the physical environment. The contrast between epeiric and open ocean habitats provides a large-scale natural experiment in which to test the ecological and phylogenetic effects of exposing an established fauna to a novel, vacant habitat in geologic time. Current projects focus on ecological and evolutionary trends and dispersal patterns in ammonites, an extinct clade of pelagic cephalopods, of the Western Interior Seaway in North America during the Cretaceous Period around 120-65 million years ago.

The URAP student will assist in collecting and analyzing data for the project described above. Duties of the successful applicant may include but are not limited to: digitizing published faunal lists for geological units associated with the early Western Interior Seaway; resolving synonymy issues that may result from older publications; collecting morphological data for Cretaceous ammonites from existing literature; analyzing spatial and temporal diversity dynamics using collected data. The student's interests will determine the exact focus of their work. Students are encouraged to develop independent projects as research progresses.

Day-to-day supervisor for this project: Lucy Chang

Qualifications: Applicants should be organized and enthusiastic and should possess an interest in paleontology and biogeography. Further interest in marine ecosystems and invertebrate biology would be welcome but not expected. Some background in geology, paleontology, and programming is ideal but not required. Applicants should be comfortable learning new computer skills as the needs arise. Up to two positions may be offered, depending on applicant qualifications and scheduling.

Weekly Hours: to be negotiated

Closed (2) The evolutionary and ecological origins of the Hawaiian flora

Applications for Fall 2017 are now closed for this project.

The Hawaiian archipelago represents an ideal model system to study the interplay of evolution and ecological processes. The isolation of the archipelago (nearly 4,000 km from the nearest continent) has lead to the prominent role of in-situ diversification in shaping the unique flora of the islands. This has resulted in the many documented extraordinary adaptive radiations of various plant lineages, and the extraordinarily high uniqueness of the local flora; over 90% of flowering plant species on Hawaii are found nowhere else on Earth!

The project is a molecular phylogenetic study of the Hawaiian peppers, which are among one of the largest radiations of vascular plants on the archipelago, as well as an investigation into their patterns of dispersal across the Pacific and the drivers of their evolutionary success!


The main project will be to help optimize and design a primer set for phylogenomic purposes. This will provide an introduction and training in the most basic and essential of molecular techniques such as PCR and DNA extractions from leaf tissue. Nevertheless, there will also be some scope for working with plant specimens (e.g., mounting plants onto herbarium sheets, looking after the living Hawaiian pepper collection in the greenhouses, georefering and databasing).

1) Molecular work and sequencing (basic molecular techniques – DNA extraction, PCR etc)
2) Georeferencing and databasing of Peperomia specimens at the UC and Jepson Herbarium

Depending on the specific aspect of the project, students will learn the basic molecular techniques, as well as downstream skills such as collection curation and databasing.


Day-to-day supervisor for this project: Jun Ying Lim, Ph.D. candidate

Qualifications: Applicants should be organized, proactive and possess an interest in phylogenetics and/or biogeography. Some background and interest in botany and/or plant ecology would be recommended but not required (the ideal candidate will have taken at least one or all of the following courses IB 200a, IB200b, IB 154). Prior background in molecular techniques would be highly desirable but training will be provided!

Weekly Hours: to be negotiated

Closed (3) Explaining the bizarre biogeography of cycads

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

The geographic distribution of cycads is most unusual – the vast majority of species are only to be found in a limited geographic area, and each species has typically has no overlap with any other cycad species. This implies that cycads have an extraordinarily low capacity for dispersal. Recent molecular work (Nagalingum et al., Science 2011) has shown that the divergences between 199 of the ~300 living species occurred in a narrow temporal window, from ~12 to 2 million years ago. This implies that the current geographic distribution was generated relatively recently. Several questions emerge (beyond the question of why the cycads’ distribution is so patchy, and why each patch has typically just one species): prior to the recent radiation of the living species did the cycads have a broad geographic range that has since become highly fragmented? That is, did the dramatic increase in species number result from the massive fragmentation of just a few broadly distributed ancestral species? Or did cycads greatly increase their geographic range as they radiated? That is, prior to their recent radiation were cycads more geographically restricted, and is the current distribution the result of a large number of dispersal events?

To use the recently published molecular phylogeny of cycad species (Nagalingum et al., Science 2011) to evaluate the possible explanations for the current distribution of cycads – fragmentation of a large ancestral geographic ranges, or expansion via dispersal from a more limited ancestral geographic range.

Qualifications: General familiarity with phylogenetic thinking, and a general interest in evolutionary biology and biogeography. The ideal candidate will have taken IB 200a and or IB 200b, but other candidates will be seriously considered.

Weekly Hours: to be negotiated

Closed (4) The footprint of extinction on phylogenies

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

The advent of easily accessible molecular techniques has led to the rapidly growing number of molecular phylogenies. Molecular phylogenies have not only shed light on the evolutionary relationships of many species, but also advanced our understanding of large-scale evolutionary dynamics. Extinction dynamics, however, are not captured in molecular phylogenies as they only contain extant species.

This project will focus on simulating lineages under various models of speciation and extinction, and examining the conditions under which extinction can severely bias our ability to interpret from phylogenetic information of only extant species.

Day-to-day supervisor for this project: Jun Ying Lim, Graduate Student

Qualifications: Background and interest in macroevolution is would be recommended (the ideal candidate will have taken either one or both IB 200a, IB200b). Some knowledge in computer programming is ideal but not required.

Weekly Hours: to be negotiated