Brent Mishler, Professor

Closed (1) A taxonomic revision of a diverse clade Syntrichia from South America

Applications for Spring 2019 are now closed for this project.

Syntrichia is a diverse genus of mosses containing around 100 named species occurring worldwide in dryland habitats, and demonstrating an unusual amount of ecological variation among close relatives. It occurs in habitats ranging from mesic alpine meadows, to tree trunks and boulders in mid-elevation forests, and to late-successional desert biocrusts.

The genus is one of the most ecologically dominant groups of mosses across western and northern North America. However, almost 40% of species occur in the Neotropics and Southern South America. New reports and species have been published for the Neotropics lately, which have altered the nomenclature and number of recognized species for the group. However, no studies have been done for Southern South America, including species from the Andes, Mediterranean area and the Patagonian steppe of Chile, where Syntrichia is one of the most abundant species.

As part of a broader collaborative project we are reexamining the phylogenetic systematics of the group. Molecular phylogenetic studies are underway, but this project will focus on understanding the main taxa from South America using new morphological characters developed in this lab.

A taxonomic revision of the genus would not only contribute to know the main clades for Syntrichia, and how to recognize them in the field, but also would be the basis for further research in biogeography and trait evolution.


This project is designated for students who want to learn taxonomy and biology of mosses in general.

Specific role for the undergraduate (tasks and learning outcomes):
(1) Preparation of microscopic slides for each taxon of Syntrichia
(2) Identification of the taxa with dichotomous keys for the group
(3) Photography and description of each taxon using useful morphological characters
(4) Contribute to the preparation of a scientific paper.



Day-to-day supervisor for this project: Javier Jáuregui-Lazo, Graduate Student

Qualifications: 1: Reliable, responsible, and self-motivated 2: Background in botany, 3: Interest in identification of mosses.

Weekly Hours: to be negotiated

Closed (2) Spatial phylogenetic diversity in the Mojave National Preserve

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Identifying areas of high biodiversity and understanding the processes and conditions that support them is essential for conservation of natural ecosystems. To understand the controls on biodiversity, we will analyze vascular plant distribution and evolutionary relationships within a hydrogeologically complex 1 km² section of the Cane Spring area of Mojave National Preserve and compare them to the site’s geologic spatial patterns. Recognizing the important role that species' evolutionary histories play in their ecology and conservation, we use spatial phylogenetics methods to quantify and map patterns of biodiversity in our site. You can learn more about our methods through the URL provided in the website field for this project.

The research apprentice will have the opportunity to gain experience in most, if not all, of the following research skills:
- Aggregate relevant DNA sequences from GenBank and other databases and compare to plant occurrence data to assess level of dataset completion.
- Prepare datasets for and perform phylogenetic analyses.
- Combine spatial and phylogenetic data using specialized software to gain an understanding about evolutionary relationships in the study site.
- Compare spatial phylodiversity with other environmental spatial data and perform initial statistical analyses.

The apprentice will be expected to assist in related laboratory support tasks as needed, including but not limited to tending to laboratory plant cultures, microscopy and image analysis.

The apprentice will gain or improve upon some or all of the following research skills: bioinformatics methods to aggregate and compare DNA sequences for hundreds of species, comparative phylogenetic methods, and spatial statistical analyses.

Day-to-day supervisor for this project: Jenna Baughman, Graduate Student

Qualifications: A desirable URAP student for this project has sufficient experience with command-line computing (terminal, cygwin, or other linux-like environment), GIS, and is familiar with the concepts of evolution, OR is willing and able to teach themselves these skills at the beginning of the project through tutorials and/or workshops. Additionally, an ideal candidate wants experience in the following areas: 1) computational biology, 2) plant evolutionary biology, 3) ecological conservation, and 4) spatial data analysis. Qualified juniors and seniors from any major are welcome to apply. Applicants for this position must be self-driven and comfortable with independent work and problem-solving. Apprentices will still be working in the laboratory but it will be largely independent computational tasks.

Weekly Hours: 3-5 hrs

Related website: http://ucjeps.berkeley.edu/bryolab/CPPP/

Closed (3) Uncovering the genetic sex of clonal Syntrichia desert mosses

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In mosses that have separate male and female individuals, genetic sex is determined during meiosis by a UV chromosomal system; a spore carrying the female sex-determining locus (U) will produce a female plant while spores with the male sex-determining locus (V) develop into a male plant. As a consequence of meiosis, therefore, we expect the genetic sex ratio of moss populations to be 1:1. However, many moss species are sex-biased, most of them with more females than males, based on counting sexually mature plants in a population. Yet, in desert moss species, most of the plants in a given moss population are sterile and never reach sexual maturity. The result is that we cannot tell the sex of the plants, or the true sex ratio of the population, without performing genetic analyses. In this project, we will use a newly developed sex-identifying marker to find the genetic sex of sterile desert and dryland Syntrichia mosses and uncover sex ratios at different scales from populations in California, Nevada, and Utah.

The research apprentice will have the opportunity to gain experience in most, if not all, of the following research skills:
- Perform microscopy work to identify and prepare moss samples for DNA extraction
- Extract and isolate DNA from moss samples
- Perform and troubleshoot wet lab techniques, including PCR, restriction enzyme digestion, and gel electrophoresis, to test and validate procedure and identify genetic sex of samples
- Perform statistical analyses to compare population sex ratios

The apprentice will be expected to assist in related laboratory support tasks as needed, including but not limited to tending to laboratory plant cultures, microscopy and image analysis.

The apprentice will gain or improve upon some or all of the following research skills: botanical microscopy procedures, classic wet lab techniques including PCR and gel electrophoresis, statistical analyses., Graduate Student

Qualifications: A desirable apprentice has some experience with lab bench work (pipetting, sterile techniques), and is familiar with the concepts of meiosis, DNA replication, and PCR. Additionally, an ideal candidate wants experience in the following areas: 1) classic molecular biology techniques, 2) plant reproductive ecology, 3) desert mosses, and 4) data analysis. Students from any level in any major are welcome to apply.

Weekly Hours: 3-5 hrs

Closed (4) Presentation of Scientific Findings

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Even though sound and sufficiently robust data is the essence of a good scientific paper, the presentation of the findings is of equally great importance in communicating discoveries to the scientific community and advancing the overall knowledge in a field. Presenting data in a clear and accurate manner and putting them into context require skills that are best learned by exposure and experience. We will provide an opportunity for exceptional apprentices to be introduced to how we communicate our findings to the scientific community by preparing our work for submission to peer-reviewed scientific journals.

Using the studies already completed in the Mishler Lab, we aim to educate apprentices by involving them in as many of the following steps as possible:

a) organizing, double-checking, preparing and structuring all material used and information obtained in different phases of each project (includes specimen annotation, organization of DNA extractions for long term storage, etc.).
b) manuscript development, including a thorough search for and review of scientific and historical references
c) manuscript preparation according to the specific requirements of each journal (including illustrations, figures and tables)
d) Deposit of all data in corresponding public databases (we strongly believe in sharing all data as a good scientific practice)
e) organization and backup of all files related to each phase of each study for easy future access by anyone who may need to verify or use our work stored on the lab computers
f) other support tasks as assigned

Through this experience, the students will learn how similar or different “real” research papers are from the typical lab reports that they are required to prepare for science classes, and, in addition, will receive training in ethics of reporting the findings. We aim to help the students develop a clear understanding of the process of data preparation for a manuscript and the boundaries in scientific research and publishing, lack of which can, knowingly or unknowingly, result in scientific misconduct such as plagiarism or falsification of data.

Our overall goal is to help our apprentices develop a sense for the breadth and depth of standards that we believe result in high quality scientific publications, and provide them with a better vision for the kind of writing they are expected to produce in their upper division science courses at our university, and in their future graduate or professional careers.

All majors are welcome to apply. The students will earn URAP units upon satisfactory performance and will be mentioned in the acknowledgment section of the resulting papers.

Day-to-day supervisor for this project: Sonia Nosratinia, Staff Researcher

Qualifications: - Strong interest in science - Excellent organizational skills - Excellent attention to detail - Ability to follow instructions fully and exactly - Ability to formulate and ask questions - Excellent ability to maintain focus while doing repetitive tasks and catch mistakes. Preference for candidates with: - Interest in evolutionary biology/ phylogenetics/ bryophytes - Interest in photography, image processing or illustration - Working knowledge of Adobe CS6 (Photoshop, Illustrator, InDesign) - Prior experience in the R language and environment, or other relevant computer science training/ background/ interest.

Weekly Hours: to be negotiated