Jimmy McGuire, Professor

Closed (1) Reconstructing the evolutionary history of scincid lizards on Sulawesi

Applications for fall 2021 are now closed for this project.

The island of Sulawesi in Indonesia is a hotspot of biodiversity and model system for studying the evolution of organisms. Our lab has conducted numerous expeditions to the island to document its biodiversity and collect samples for genetic analysis. This project focuses on three different groups of scincid lizards that have diversified into a number of species on Sulawesi, many of which remain undescribed. We seek to reconstruct the evolutionary history of these lizards in order to understand how the unique geography of the region has impacted their evolution. We are particularly interested in how these lineages have evolved on several mountains we have surveyed on the island, as species have diverged across elevational gradients on several of the mountains we have surveyed. To accomplish this, we will first sequence the DNA of hundreds of lizards we have collected across the island using a newly developed sequencing method to sequence the entire mitochondrial genome of each specimen. This data will then be analyzed to reconstruct the evolutionary and biogeographic histories of these groups.

URAP students will assist in DNA sequencing research in the Evolutionary Genetics Laboratory at the Museum of Vertebrate Zoology at UC Berkeley. This work includes lab protocols such as DNA extraction, polymerase chain reaction, gel electrophoresis, DNA quantification, magnetic bead purification, and preparation of samples for sequencing. Students will learn useful laboratory skills as well as gain an understanding of molecular genetic methods. Interested students may also have the opportunity to conduct morphological analysis of preserved museum specimens.

Day-to-day supervisor for this project: Benjamin Karin, Graduate Student

Qualifications: Applicants should have an interest in genetics and lab-work and be well-organized. Previous experience with DNA sequencing desired but not necessary.

Weekly Hours: to be negotiated

Related website: https://mcguire.berkeley.edu/

Closed (2) AmphibiaWeb: Cataloging amphibian species, traits, and taxonomy for conservation biology

Applications for fall 2021 are now closed for this project.

Amphibians are the world’s most imperiled vertebrate group. Confounding efforts to combat amphibian declines is that we have little knowledge concerning most of the species and much of it not easily accessible. Since 2000, we have been developing an informatics platform to create a web page for every species of the amphibians in the world (over 8000 species) where we collate information on biology, natural history, taxonomy, biogeography, known occurrences and conservation. AmphibiaWeb is an authoritative, scientifically responsible, and up-to-date system, which is solidly based on real specimens and data that includes links to authority files (for the legal scientific names of the taxa) and many sources of information on the web. To do this, we need YOUR help.

This apprenticeship is an excellent opportunity to learn amphibian biology and conservation, contribute to a public resource with acknowledgments and credit, and communicate with the public in person and online about science while safely social-distancing. We train in all aspects of the apprenticeship. The primary duties for Fall Semester will include literature research, and account writing. Motivated students may also be trained in mapping and creating range maps. URAPs who stay with us into the Spring Semester will help create education resources to be presented at Cal Day (either in person, if the event is allowed to happen or with online options).

This apprenticeship can be performed remotely.


Apprentices work directly on a bioinformatics project in a major natural history museum that combines amphibian biology and biodiversity conservation with a worldwide user base. Most students will use the literature and internet research to produce accounts for species around the world. They will receive close supervision, but will be given considerable independence in producing accounts and in working on other aspects of systems development depending on interests (for example, georeferencing specimens, creating maps or new data visualizations, creating videos or other new content etc.). Their accounts will be edited for format and content by a central editing group before being published online. Student apprentices are given full credit as authors and/or editors when published to the website, a tangible product of your work.

Students are expected to work at least 5-6 hours per week during the regular semester (5 hours for one credit, or 6 or more hours for two credits). Because of the amount of training required for this URAP, we seek individuals who can commit to a full academic year to this URAP. Come join our new team this year!


Day-to-day supervisor for this project: AmphibiaWeb Coordinator Ann Chang (anntchang@berkeley.edu), and Assoc. Director Michelle Koo (mkoo@berkeley.edu)

Day-to-day supervisor for this project: Michelle Koo, Staff Researcher

Qualifications: Qualifications: Basic computer literacy required. Strong written or graphic design skills desired. Ideal applicants have a passion for amphibians, conservation biology, or biodiversity informatics. A love for learning and motivation to improve are what really count. Preference will be given to students with some biological background or a strong passion for natural history and conservation; however, all majors are welcomed. Students who can read and/or write in Spanish, Portuguese, French, German or Chinese are desired. Please visit AmphibiaWeb.org to learn more.

Weekly Hours: 3-5 hrs

Related website: https://amphibiaweb.org