Craig Miller, Professor

Closed (1) Genetic analysis of head skeletal evolution

Applications for Fall 2017 are now closed for this project.

A fantastic diversity in organismal form is seen in nature, yet we know little about the genetic basis of evolutionary change. We are using the head skeleton of the threespine stickleback (Gasterosteus aculeatus) as a model system to study the genetic basis of development and evolution. Sticklebacks have undergone one of the most dramatic and recent adaptive radiations on earth. Ancestral marine sticklebacks colonized and rapidly adapted to new freshwater lakes and streams at the end of the last ice age about 10,000 years ago. Major changes to the head skeleton have evolved repeatedly as populations adapt to new diets found in new freshwater environments. Fish with different morphologies can be crossed in the lab, allowing genetic analysis to identify which chromosome regions control the changes to the head skeleton. In a previous detailed genetic analysis, we identified a set of chromosome regions controlling a suite of head skeletal traits. We now want to ask how predictable evolution is, and how general the use of these chromosome regions is in other populations where the same skeletal changes have evolved in parallel. Several F2 genetic crosses have been generated and will be the focus of this project. Molecular biology methods will be used to isolate DNA, and the polymerase chain reaction (PCR) used to amplify genetic markers that can be used to genotype different genomic locations of interest. The skeletons of fish from these genetic crosses will be stained with dyes that label bone, allowing the size and number of various bones to be quantified. These phenotypes will be compared to the genotypes to identify chromosome regions underlying evolutionary change. In other genetic crosses, candidate genes have been knocked out with new genome editing tools.

Please see recent 2014-2015 papers from the lab (see website for references: papers with Ellis, Erickson, Glazer, or Cleves as first authors) for more details. All of these papers have former URAP students as co-authors.

Qualifications: The apprentice should be willing to work 12+ hours/week on average (including about two hours/week meeting to plan research and discuss results, possibly up to two hours/week helping with animal husbandry, and at least eight hours/week doing independent research). No specific skills are required, but the apprentice should be familiar with basic concepts of genetics and molecular biology, and excited to learn about genetics, development and evolution. Ideally, the apprentice is highly-motivated, committed to doing research, pays attention to detail, enjoys working with their hands and looking through a microscope, and is familiar with Macs and PCs. We are especially interested in apprentices with a strong desire to potentially continue the project in future semesters.

Weekly Hours: more than 12 hrs

Related website: http://mcb.berkeley.edu/index.php?option=com_mcbfaculty&name=millerc
Related website: http://mcb.berkeley.edu/labs/miller/

Closed (2) Evolutionary genetics of local California stickleback populations

Applications for Fall 2017 are now closed for this project.

The general concept, system, methods, and qualifications are similar to Project 1, but this project will specifically focus on local Bay Area stickleback populations. We have collected fish from several local freshwater and marine populations and want to ask whether evolution is predictable in these populations: are patterns of morphological evolution seen in the Pacific Northwest and Canada also true for local Bay Area populations? Have local stickleback populations evolved using the same genomic regions previously identified in the Pacific Northwest and Canada?

Weekly Hours: more than 12 hrs

Closed (3) Developmental biology of head skeletal evolution

Applications for Fall 2017 are now closed for this project.

The general concept, system, methods, and qualifications are similar to Project 1, but this project will specifically focus on analyzing embryos and larvae from different lab-reared populations to answer the question: when, during embryonic and larval development, do different evolved morphologies appear? How is the developmental genetic circuitry altered by evolution to achieve adaptive changes in adult morphology?

Weekly Hours: more than 12 hrs