Carol Wilson, Research Botanist

Closed (1) Morphology and Biogeography of African Mistletoe Haustorial Systems in the family Loranthaceae

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Mistletoes are shrubby, aerial-branch parasites belonging to order Santalales. Most are hemiparasites that obtain water and mineral nutrients and a portion of their carbon from the xylem sap of their host plants. Although they can be forest pathogens, particularly to conifer tree species that are under stress from drought, pollution, and/or pest infestations, mistletoes are recognized as keystone species in forest landscapes worldwide. These flowering plants provide structural complexity and enhance soil nutrients in forest ecosystems and provide significant food and shelter resources for animal and insect species. With this project Dr. Wilson proposes to investigate the morphological diversity and biogeography of haustoria in the Loranthaceae across different habitats within Africa.

Hypotheses tested are:
1. Haustorial types are correlated with environmental parameters.
2. Haustoria with extensive exposed tissue will occur in lowland, mesic environments while those with extensive internal tissue will occur at both low and high elevations in dryer environments.
3. Patterns of haustorial diversity will differ with coastal regions in Africa displaying higher diversity than inland regions.

During this study, haustorial samples from Africa will be organized in specialty boxes by genus. Collection data labels will be produced from existing and newly produced excel spreadsheets.

Haustorial morphology will be compared across species and genera using the available collections and descriptions in literature.

Distribution and range data for African species will be gathered from Calvin/Wilson collections, Global Biodiversity Information Facility (GBIF), and the Mistletoes of Africa by Pohill and Wiens.

Measures of the distributions and ranges of selected species representing haustorial types will be determined by projecting distributional data on maps using 100 x 100 km grids. Ecological studies will use 19 BIOCLIM variables including annual trends in temperature and precipitation, seasonality, and extreme or limiting environmental factors.

Hypotheses of correlation among species, genera, haustorial type, and environmental parameters will be tested in the GIS framework using spatial modeling, spatial statistics, and multivariate statistical methods.

This project will begin in Spring semester.

The apprentice will be trained in:
• geo-referencing, a basic skill set for natural history studies.
• ecological mapping, a skill set used in ecological studies.
• curation of natural history collections.
• basic statistical analyses.

Qualifications: The apprenticeship for this semester does not require a specific skill set. The student is required to have good organizational skills and basic computer and mathematical skills including familiarity with Excel. A knowledge of the statistical computing environment R is desirable but not essential.

Weekly Hours: 9-11 hrs

Closed (2) Phylogeny and biogeography of Iris series Californicae based on next-generation sequencing

Applications for fall 2021 are now closed for this project.

Carol A. Wilson is conducting research that examines phylogeny, biogeography, endemism, and ecology of a lineage of Iris that mostly occur in a biodiversity hotspot (California Floristic Province). Iris comprise a highly diverse genus of perennials that provide significant food resources including nectar, pollen, arils, and underground structures, as well as showy flowers of horticultural and cultural value. There are about 11 species and seven infraspecific taxa in the series. Previous studies by Dr. Carol A. Wilson showed that the series is monophyletic. These studies used sequence data from several plastid markers to resolve relationships among Iris lineages and included single populations of all species from this series.

The study outlined here will utilize next-generation sequence (NGS) data from about 190 populations that represent all species and infraspecific taxa to fully resolve relationships.

Whole plastomes and 635 nuclear markers will be sequenced for about 90 populations representing the diversity present in the group.

One species, I. macrosiphon, will be investigated in more detail. Whole genome sequencing of one sample of I. macrosiphon from the Bay Area is currently underway. Resequencing of 99 additional populations covering the entire range of I. macrosiphon will be accomplished.

The data gathered will be used to produce hypotheses of relationships, to investigate area of origin, ecological niches of species, diversity within an exemplar species, and how this diversity is correlated with ecological parameters.

Hypotheses tested during this portion of the study are:
1. Some infraspecific taxa represent distinct species.
2. Gene flow has occurred between some species leading to populations with intermediate morphologies.
3. Widespread species have eco- and morpho-types that correlate with specialized ecological niches such as pygmy forests and serpentine soils that are present in California.

This study offers laboratory, web, and high performance computing (SAVIO-UC and XSEDE-NSF) based research apprenticeship opportunities. It is desirable that students gain knowledge in all aspects of the research although they may focus on specific portions of the study.

Apprenticeships will be flexible to assure safety and may only utilize previously gathered data if new sequence data cannot be gathered.

Laboratory: DNA will be extracted from leaf material, DNA libraries constructed, targeted nuclear markers will be captured using previously developed probes, and the resulting enriched DNA will be submitted for sequencing. Apprentices will work closely with Dr. Wilson during this laboratory-based research. Students can join this portion of the research based on the ability to safely distance.

• DNA will be extracted from 24 leaf samples.
• DNA library construction and marker enrichment will be accomplished on 45 previously extracted DNAs.
• Apprentices will master basic laboratory techniques such as accurate pipetting, gel electrophoresis, and DNA enrichment using polymerase cycling reactions (PCR).
• Apprentices are expected to read and discuss papers on methods used and Iris species studied.

Web: Apprentices and Dr. Wilson will use web-based resources to investigate species distributions and ecological niche. Statistical analyses will be used to compare distributions and ecological parameters. Primary literature on species will also be compiled.

• On-line (focusing on California Consortium of Herbaria and Pacific Northwest Consortium of Herbaria) herbaria will be utilized to gather distributional data for 18 Iris species.
• Outliers in distribution or ecology for a species will be checked on-line if images are available. If images are not online, specimens will be studied in the University and Jepson herbaria from their collections or loans if housed in other herbaria.
• Statistical methods, mostly in the R environment, will be used to summarize findings.
• Apprentices are expected to read and discuss papers on methods used and Iris species studied.

High performance computing: Apprentices and Dr. Wilson will use the Savio cluster at UC Berkeley and the XSEDE accessed through the CIPRES portal to filter, clean and organize next-generation sequence data consisting of targeted nuclear markers, high copy organellar genomes, and re-sequencing of whole genomes. Datasets will be developed using the software program Geneious and analyzed using mostly programs available through the CIPRES portal and computing resources of XSEDE.

• Apprentices will utilize pipelines developed previously and housed on the SAVIO cluster to transform raw sequence data into data ready for assembly into datasets. This may involve troubleshooting and reworking of the pipeline.
• Apprentices will utilize phylogenetic programs available on the CIPRES portal to analyze datasets developed by Dr. Wilson.
• Apprentices are expected to read and discuss papers on methods used and Iris species studied.

Qualifications: It is desirable that students have some experience in laboratory methods, statistical analyses, and/or computer languages. If experience is limited, students should be highly motivated to master skills related in at least one of the areas covered. It is necessary that students are organized and have good communication with the PI.

Weekly Hours: 9-11 hrs

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