Rauri Bowie, Professor

Closed (1) Determining what factors influence the microbiome of wild populations of birds

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

My lab is involved with a large collaborative project to study disease transmission within and among species of wild birds. As part of this project, swabs of a variety of bird species are being collected to study their microbial communities (i.e. their microbiome). Lab studies suggest that microbial diversity can be linked with health, so we will be testing whether the microbiome in wild birds is affected by disease status and if microbial diversity is correlated with indicators of health (e.g. body size, plumage variation). In addition, we will be using data on the microbiome to model the spread of diseases within and among bird species. We are also interested in testing what general factors affect the microbiomes of birds.

The main role for the student would be to assist with the extraction of microbial DNA from field collected samples from birds. The student would need to learn basic molecular genetics techniques, such as how to extract, quantify, and visualize DNA. They would also need to adopt sterile techniques for lab work, because contamination of the samples from outside sources is a large concern. Students who show a strong interest in the project will be invited to become involved in the analyses of the microbial data.

Day-to-day supervisor for this project: Ammon Corl, Post-Doc

Qualifications: This project would be good for students with a strong interest in learning laboratory skills and techniques for assessing microbial diversity. Good organizational skills and high levels of attention to detail in the lab is a must. Previous laboratory experience is not required, but students with prior experience are encouraged to apply, as they will be able to make more rapid progress in the lab. The DNA extraction protocol requires being in the lab for 6-8 hours. Thus, students need to have sufficient time open in their schedules to permit an extended stretch of lab work. Students will primarily be mentored by Ammon Corl, a postdoctoral researcher in the lab.

Weekly Hours: 9-11 hrs

Closed (2) Molecular and Morphology Adaptation of Savanna Sparrows to Tidal Marshes

Applications for Spring 2019 are now closed for this project.

Tidal marsh habitats have been dramatically transformed along the California coast over the past 150 years. The development of ports and shipping channels, salt pond evaporation systems, and major metropolitan areas resulted in up to 90% loss of tidal marsh habitat. Moreover, in conjunction with human development, tidal marshes over the past century have witnessed increasing salinity levels and rising temperatures that may exacerbate the physiological challenges associated with living in high salinity environments. A number of bird and mammal taxa specialize on these habitats. This project will characterize how certain human activities over the past century influenced adaptation and population demography in this community of specialized and threatened taxa with a focus on tidal marsh Savannah Sparrows (Passerculus sandwichensis). Savannah Sparrows are one of the most widespread North American songbirds and their broad range encompasses several salt marsh systems that vary in salinity and temperature. Importantly, hundreds of Savannah Sparrows specimens have been collected along the coast of California since the 1860s allowing for a robust historical comparison of genomic and phenotypic data to understand the influence of coastal development on tidal marsh populations. This project aims to take advantage of this broad temporal and spatial sampling within the species to document population responses to coastal development.

We seek an URAP student who will be supervised by an NSF postdoctoral fellow at the Museum of Vertebrate Zoology. The primary duties will include making morphological and plumage measurements of museum specimens. There will also be the potential to assist with extracting and sequencing DNA associated with historic and modern specimens. The student will gain experience in collection and analysis of morphological data, museum-based research with direct exposure to museum specimens, and instruction in the fields of evolutionary biology, avian natural history, and ecological physiology.

Day-to-day supervisor for this project: Phred Benham, Post-Doc

Qualifications: Qualifications: Looking for a disciplined, enthusiastic student who is able to pay close attention to detail, and possesses a strong interest in the fields of ornithology, natural history, and or museum-based research. Students that have taken either the Natural History of the Vertebrates (IB104) or Ornithology (IB174) courses will be considered stronger candidates.

Weekly Hours: 6-8 hrs

Closed (3) DNA sequencing to investigate bird diversification and the role of pathogens in modulating biodiversity

Applications for Spring 2019 are now closed for this project.

Students can assist with several ongoing research projects that investigate geographic variation and species limits in birds and integrate these data with quantification of prevalence of disease vectors such as bird malaria and trypanosome infections.

Day-to-day supervisor for this project: Cynthia Wang-Claypool, Graduate Student

Qualifications: Students can assist with several ongoing research projects that investigate geographic variation and species limits in birds and integrate these data with quantification of prevalence of disease vectors such as bird malaria and trypanosome infections. This project would be good for students with a strong interest in learning laboratory skills. Good organizational skills and high levels of attention to detail in the lab is a must. Previous laboratory experience is not required, but students with prior experience are encouraged to apply, as they will be able to make more rapid progress in the lab. The DNA extraction protocol requires being in the lab for 6-8 hours. Thus, students need to have sufficient time open in their schedules to permit an extended stretch of lab work.

Weekly Hours: 9-11 hrs

Closed (4) Architectural Innovation and Evolution of Weaverbird Nests

Applications for Spring 2019 are now closed for this project.

Nest structures are widespread across animals including insects, fish, amphibians, and most conspicuously, birds. Despite their ubiquity, nests remain one of the most understudied components of avian life history. Some of the most remarkable examples of elaborate nest design are within the passerine weaverbirds (family Ploceidae). Weaverbirds are an Old World radiation of sparrow-like birds primarily distributed throughout sub-Saharan Africa, with several species occurring in tropical Southeast Asia and on several islands in the Indian Ocean. The family is comprised of 116 species in 15–17 genera and as their name implies, are perhaps best known for their elaborately designed nests which some species construct by intricately “weaving” together nesting materials using specialized knots, making them exceptionally strong and pliant. Our research primarily focuses on studying the extensive nest diversity exhibited by the family, by taking morphological measurements directly from nest specimens in museum collections. Data from hundreds of nests have already been collected from representative species across the family and will be used to look at variation in nest design between them. These results will ultimately be placed within a broader evolutionary context in order to identify the potential forces of selection that have influenced avian nest design.

We seek a URAP student (or two) that will be supervised by an IB graduate student and will assist in 1.) processing and organizing images of individual nests taken from museum specimens; 2.) assisting in proper species identification of nests using online resources and published field guides; 3.) collecting morphological data from nest images using analytical software such as ImageJ. Through working on this project the URAP student will gain experience in morphological data analysis, museum-based research with direct exposure to museum specimens, and instruction in the fields of evolutionary biology, avian natural history and ecology.

Day-to-day supervisor for this project: Jackie Childers, Graduate Student

Qualifications: Qualifications: Looking for a disciplined, enthusiastic student who is able to pay close attention to detail, and possesses a strong interest in the fields of ornithology, natural history, and or museum-based research. Students that have taken either the Natural History of the Vertebrates (IB104) or Ornithology (IB174) courses will be considered stronger candidates.

Weekly Hours: 6-8 hrs