Bruce Baldwin, Professor

Closed (1) Phylogenomics and cryptic diversity in parasitic Orobanche

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

Among flowering plants, parasitism is a successful life history strategy that has evolved at least 12 times. Parasitic plants usually form stem or leaf connections to access the water, nutrient, and carbon reserves of host plants. Often times this results in highly derived and reduced morphologies such as the loss of chlorophyll, stems, and leaves, which has made it difficult to assess relationships. Host specificity may play an important role in speciation of such parasites, although poor knowledge of species boundaries has made this difficult to assess.

A recent study in this lab (currently in review in the journal Annals of Botany) has found that there are numerous undescribed species, each of which correspond to a unique host. Further research is now need to describe these lineages, as well as understand trait evolution across the phylogeny. A URAP student is sought to prepare extracted DNAs for sequencing using the Illumina sequencing platform.


The URAP student will participate in one or more of the four projects listed above. (In your application, please indicate which projects are most interesting to you and/or you are most qualified for). Specific tasks may be more lab-oriented, analysis-oriented, or museum-oriented depending on interest, and there may be some opportunity to assist with fieldwork around California.

As the student becomes familiar with the project and study system, there may be opportunities for the student to develop, explore, and design their own experiments and studies, potentially including field and/or herbarium work. Students will also be encouraged to attend and present at regional botanical conferences and there is financial assistance available.

Learning outcomes include:
1. Understand and participate in the process of original scientific research
2. Apply the principles of cladistics to design a phylogenetic study
3. Evaluate a hypothesis in light of new data
4. Explain the genetic structure of plants and how this can be useful in inferring ancestry
5. Effectively communicate the results of a scientific study to a broad audience, including possible co-authorship on a scientific paper.

Day-to-day supervisor for this project: Adam Schneider, Ph.D. candidate

Qualifications: Student qualifications: 1. Reliable and responsible 2. Strong communication skills 3. Willingness to learn 4. Interest in phylogenetics 5. Interest in botany/natural history 6. Grade of B+ or better in BIO 1B Experience working with PCR and other molecular biology techniques, or familiarity with basic programing in R is desirable but not required.

Weekly Hours: to be negotiated

Closed (2) Biogeography and taxonomy of flax (Linum: Linaceae)

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

The genus Linum is best known for the economic value of L. usitatissimum (flax), for its food, fiber, and nutrition. However, the genus contains approximately 200 species and is found on every continent except Antarctica. This project will investigate how and when these plants were able to achieve such a large distribution. Is the diversity in the Americas the result of several independent colonizations, or one colonization and subsequent diversification?

A second aim of this study will be a taxonomic revision of Linum. A recent phylogenetic study showed that Linum is not monophyletic due to several small genera nested within it. Taxonomic changes are necessary to ensure genera represent monophyletic lineages.

The URAP student will participate in extensive literature searches to determine biogeographic range and nomenclatorial history of each Linum species. The student will use probabilistic modeling of geographic range evolution to infer the ancestral geographic ranges of Linaceae lineages over a fossil calibrated molecular phylogeny. Students will also be encouraged to attend and present at conferences and contribute in the writing of a manuscript.

Specific tasks include:
1. Using online and print resources to find literature pertaining to Linum and extract relevant information on morphological traits, nomenclature, and biogeographic range
2. Using the software RevBayes and/or BioGeoBEARS to perform probabilistic inference of biogeographic history of Linaceae


Learning outcomes include:
1. Understand and participate in the process of original scientific research
2. Ability to use Bayesian and likelihood frameworks to model the diversification and biogeographic expansion of a lineage
3. Evaluate hypotheses in light of new data
4. Become familiar with the International Code of Nomenclature for algae, fungi, and plants
5. Effectively communicate the results of a scientific study to a broad audience, both through oral and written communication.
6. Contribute towards and potentially share authorship on a scientific paper.

Day-to-day supervisor for this project: Adam Schneider and Will Freyman, Ph.D. candidate

Qualifications: Student qualifications 1. Reliable and responsible 2. Strong communication skills 3. Library/Research skills. 4. Interest in phylogenetics, biogeography, and taxonomy 5. Interest in botany/natural history 5. Grade of B+ or better in BIO 1B

Weekly Hours: to be negotiated

Closed (3) Computational evolutionary biology / phylogenetic modeling

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

Phylogenetic modeling is essential as evolutionary biologists reconstruct the tree of life. This project will develop novel models of evolution in a statistical framework to study macroevolutionary patterns of speciation, extinction, and phenotypic evolution. What are the evolutionary processes responsible for generating biodiversity?

The URAP student will be involved in the application of new cutting edge methods of modeling evolutionary processes. Possible projects include (1) a novel approach to modeling a phenotypic character's effect on speciation and extinction rates, (2) a correlation model that tests whether a variable is responsible for historical population size changes, (3) assessing the ability of phylogenetic birth-death models to infer diversification rates, (4) applying novel models of chromosome number evolution.

The project will require knowledge of a scripting language such as R or Python, and will rely heavily on the software RevBayes, which provides an interactive environment for modeling, simulation, and Bayesian inference in evolutionary biology. Training will be provided, but some programming experience is preferred.

Learning outcomes include:
1. Understand and participate in the process of original scientific research
2. Evaluate hypotheses in light of new data
3. Training in bioinformatics and quantitative skills
4. Ability to use a Bayesian statistical framework to model macroevolutionary dynamics
5. Effectively communicate the results of a scientific study to a broad audience, both through oral and written communication.
6. Contribute towards and potentially share authorship on a scientific paper.

Day-to-day supervisors for this project:
Will Freyman, Ph.D. candidate ( http://willfreyman.org )
Sebastian Höhna, post-doc and lead developer of RevBayes ( http://revbayes.com )

Day-to-day supervisor for this project: Will Freyman and Sebastian Höhna, Ph.D. candidate

Qualifications: Student qualifications 1. Reliable, responsible, and self-motivated 2. Strong communication skills 3. Some experience in R or Python, or enthusiasm to learn quickly 4. Interest in phylogenetic modeling 5. Interest in macroevolution, population genetics, or other areas of quantitative biology 6. Grade of B+ or better in BIO 1B

Weekly Hours: to be negotiated

Related website: http://revbayes.com

Open (4) Evolutionary ecology of the rock daisies (Peritylinae; Asteraceae).

Open. Apprentices needed for the fall semester. Please do NOT contact faculty before September 11th (the start of the 4th week of classes)! Enter your application on the web beginning August 16th. The deadline to apply is Tuesday, August 29th at 8 AM.

The aim of this project is to document and understand the diversity, evolution, and ecology of the Rock daisies (Peritylinae), a diverse tribe of arid adapted sunflowers. Since 2016, the Baldwin lab has been building a phylogeny of the rock daisies based on next generation molecular evidence. This phylogeny provides the basis for more focused molecular phylogenetic studies within this fascinating group of plants and it also provides the backbone for testing long standing hypotheses about the evolutiona and ecology of desert adapted plants.

Undergraduate research assistants will gain a variety of skills related to 1) extraction and library preparation of DNA samples from field collected plants and herbarium samples, 2) propagation of seeds from field collected material for common garden study, and 3) computational analayses of phylogenetic evidence.

Day-to-day supervisor for this project: Isaac Marck, Graduate Student

Qualifications: A desirable URAP student for this project wants experience in the following areas: 1)lab work, 2) greenhouse work, 3) field work, and 4)data analysis. sophomore and above desirable. interest in plants is desirable. appropriate majors would include: IB, ESPM, PMB, MCB, and Genetics.

Weekly Hours: to be negotiated

Related website: http://ucjeps.berkeley.edu/Baldwin-Lab.html