Phylogeny and biogeography of Iris series Californicae; are there unrecognized taxa across the diverse habitats of Oregon and California?
Carol Wilson, Research Botanist
University and Jepson Herbaria
Closed. This professor is continuing with Spring 2024 apprentices on this project; no new apprentices needed for Fall 2024.
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.
4. Some species are not monophyletic representing convergence of morphologies across unrelated taxa that may be correlated with ecology and/or pollinators.
Role: This study offers laboratory, microscopy, 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.
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.
• DNA will be extracted from leaf samples.
• DNA libraries with marker enrichment will be constructed.
• 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.
Morphometics: Apprentices and Dr. Wilson will examine herbarium specimens gathered across taxon ranges for morphological traits using a stereomicroscope for fine details. Statistical analyses will be used to compare morphological characters. Primary literature on species will also be compiled.
• Morphological characters will be noted and/or measured from representative herbarium specimens.
• Traditional measurements and shape analyses will be utilized to more fully describe Iris morphologies.
• 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.
Web: Apprentices and Dr. Wilson will use web-based resources to investigate species distributions and ecological niches. 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, ecological niches, and Iris species studied.
High performance computing: Apprentices and Dr. Wilson will use the Savio cluster at UC Berkeley to filter, clean and organize next-generation sequence data consisting of targeted nuclear markers, high copy organellar genomes, and re-sequenced 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, data analyses, and/or computer languages. The Savio Cluster (linux) and R environment are used to process large phylogenetic and ecological datasets. 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.
Hours: to be negotiated
Biological & Health Sciences