Noah Whiteman, Professor

Closed (1) Maintenance of Genetic Variation Through Species Interactions

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

This research project centers on the origin and maintenance of biodiversity, across many levels of biological organization through species interactions. One of these projects involves the broad-tailed hummingbird (Selasphorus platycercus) and the Anna’s hummingbird (Calypte anna). We are using these systems to identify the genomic architecture underlying variation in foraging traits, and to understand the evolutionary history of those loci. This is a collaborative project with Professor Mary (Cassie) Stoddard at Princeton University and Professor David Inouye at the RMBL. Ph.D. student Tim O'Connor has developed his own model system, involving creosote plant and its community of herbivores.

The URAP apprentice should expect to perform the following tasks:

1. Use of ImageJ or other image processing software to measure quantitative traits
2. Data entry and simple statistical analyses
3. Training in safety and relevant protocols to work in a laboratory and/or museum collection.

Other tasks may include molecular lab work and some introductory bioinformatics, conducting museum specimen preparation, DNA Extraction, gel electrophoresis, PCR, Qubit, and Library Preparation.

Day-to-day supervisor for this project: Nicolas Alexandre, Ph.D. candidate

Qualifications: Benefits: The apprentice will gain extensive experience in data collection and project design, which will be of broad use in the field of evolutionary genetics. Data generation is a crucial step in conducting scientific research. This experience will serve as an excellent foundation for any student interested in evolutionary biology.

 Day-to-day supervisor: Tim O’ Connor, graduate student; Nicolas Alexandre, graduate student

 Weekly hours: 6-9 hours

 Related website:

 Qualifications: Detail-oriented, responsible, mature individuals who are capable of careful and meticulous data collection.

Weekly Hours: 6-8 hrs

Related website:

Closed (2) Multimodal chemosensory reception in herbivorous insects

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

During the evolutionary transition from one feeding guild to another, such as microbe- to plant-feeding, it is hypothesized that behavioral adaptations are among the first to evolve. In insects, changes to the chemosensory systems that determine host preference are necessary, not only for finding an appropriate host, but in deciding at a fine spatial scale within an individual host where to feed and lay eggs. Understanding the functional genetic changes that underlie these complex behavioral shifts is a long-term goal in evolutionary biology. Scaptomyza flava, a small leaf-mining fly lends itself to be an ideal study system because (1) they evolved herbivory within the last 20 million years (relatively recent compared to other well-studied herbivores), (2) they can be collected on the UC Berkeley campus and are easily grown in culture on the model plant Arabidopsis thaliana, and (3) we can leverage the genetic tools of the model organism Drosophila melanogaster, its close relative.

S. flava has a number of body parts involved in chemoreception, which include the proboscis, maxillary palps, antennae, tarsi, wings, and ovipositor, the organ used for depositing eggs. This project aims to characterize the chemosensory receptors and other necessary proteins located in some of these regions, particularly the ovipositor, which is highly modified in S. flava and its other herbivorous relatives.

The URAP student will:
1. Perform fine skilled dissections on flies
2. Maintain fly colonies
3. Learn RNase-free techniques, RNA extractions, and cDNA library preparation

Day-to-day supervisor for this project: Julianne Pelaez, Graduate Student

Qualifications: We are looking for a curious, highly motivated, and detail oriented student, who can operate independently but seek guidance when necessary. Steady hands and a positive attitude are a must.

Weekly Hours: 6-8 hrs

Related website:

Closed (3) Development of the CRISPR/Cas9 genome editing technique in a Drosophila that attacks plants

Applications for Spring 2019 are now closed for this project.

In this project, we aim to develop the CRISPR-Cas9 genome editing technique in our main lab model system, the herbivorous drosophilid Scaptomyza flava that attacks Arabidopsis thaliana plants. The establishment of this novel technique will allow us study the role of candidate genes in the evolution of herbivory. In particular, we plan to knock out candidate olfactory receptors of S. flava that may be involved in its host-finding behavior.

The URAP student will:

1. Help in the maintenance of fly colonies
2. Learn basic techniques in molecular biology, eg DNA extraction, PCR reaction, gel electrophoresis, sequencing
3. Learn about CRISPR/Cas9 genome editing

Day-to-day supervisor for this project: Marianna Karageorgi, Post-Doc

Qualifications: The student should be curious, highly motivated and have a responsible attitude in the lab. The student is also expected to be interested in reading research articles, maintain a well-organized research notebook and write down protocols. Our lab is a welcoming and friendly environment and the student should also bring a positive attitude.

Weekly Hours: 9-11 hrs

Related website:

Closed (4) The role of gut bacteria in the evolution of herbivory

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

How evolution generates novelty is a fundamental question in evolutionary biology. While innovation arises in evolution by many different mechanisms, one of the least explored (but with great potential to drive profound change) is the role of bacteria that live in and on multicellular organisms. This project seeks to understand the role of gut bacteria in an evolutionary shift from a microbe-based diet to a plant-based diet in the emerging model fly, Scaptomyza flava. The project is currently exploring the contributions of S. flava gut bacteria to breaking down host plant toxins and the effects of gut bacteria on fly fitness in the presence/absence of host plant toxins. We have also identified bacterial strains that can break down host plant toxins using a gene called SaxA. We aim to knock out SaxA and introduce the mutant strain to the microbiome of S. flava to test the role of bacterial metabolism in the fitness of host flies feeding on host plant toxins.

The URAP student will:

1) Make media for growing S. flava gut bacteria
2) Isolate gut bacteria from S. flava
4) Learn basic microbiology techniques for enumerating and describing properties of bacterial communities from S. flava guts
3) Learn basic molecular and computational techniques (e.g. PCR, gel electrophoresis, OTU sorting) to identify bacteria found in S. flava guts
4) Make a construct to knock out SaxA
5) Help set up toxicology experiments and help collect and analyze data from toxicology experiments

Day-to-day supervisor for this project: Rebecca Duncan, Post-Doc

Qualifications: Qualifications: We are looking for a student who is curious, detail-oriented, punctual, and can collect/record data in an organized fashion. The student will gain hands on experience being a scientist in a lab. Previous experience working in the Whiteman lab is required.

Weekly Hours: 6-8 hrs