Asher Jones and Dr. Keith A. Crandall, Integrative Biology
Pediomelum pariense, also known as Paria River Indian Breadroot, has been listed by NatureServe as an imperiled organism because of its low population numbers. However, no state or federal agency has made any effort to promote the preservation of this species. Ashley Egan, PhD, designed a study with the purpose of changing that. Through the use of methods designed to measure genetic diversity, I was able to assist Dr. Egan in discovering if the amount of genetic variation that exists among the remaining P. pariense populations should be a cause of government concern.
The subject of the study, Pediomelum pariense, is an extremely rare plant with only 12 known populations, all of which are in Kane County, Utah. It was Dr. Egan’s belief that geographical separation between populations of this species may have led to a decrease in gene flow by making cross pollination more difficult between them. Such a decrease in gene flow could cause separate populations to take on distinct evolutionary trajectories. Since a species copes with environmental changes better when genetic diversity is present within its populations, it is important to preserve genetic diversity. The study’s main purpose was to investigate whether the populations had indeed begun to differ genetically, hopefully leading to increased efforts aimed toward the conservation of the species by state and federal agencies. State and federal aid would include provisions such as more protection for any populations located in high traffic areas, the creation of new P. pariense populations, and an increase in research performed in order to find out how to best promote the growth and proliferation of the species. Both the Bureau of Land Management and the Utah Native Plant society had previously expressed interest in the outcome of this research in order to provide insight into conservation management policies and plans.
In order to accurately determine and quantify genetic variation within and among populations of Pediomelum pariense, Dr. Egan and I had to employ the use of microsatellite analysis techniques. Microsatellites, or simple sequence repeats (SSRs), are areas of DNA that are more likely to be variable in separate populations of a given organism. By studying and comparing these areas of the genetic material, one is able to make accurate conclusions about the amount of genetic variation found within a single species across several populations.
Dr. Egan had previously collected leaf samples from approximately 240 different plants from 12 different populations in Southern Utah. One of my main tasks was to first perform DNA extractions of the dry leaf material collected by Dr. Egan. I then had the job of amplifying the microsatellite regions of interest through the use of Polymerase Chain Reaction (PCR). This was done in order to have enough genetic material for any variation to be visible to us by gel electrophoresis. Using these techniques, we were able to acquire data showing the differences in SSR lengths from one population to another and, thus, reveal the extent of genetic variation among them.
I had the opportunity to perform a statistical analysis of the microsatellite data using the program STRUCTURE version 2.2 (Pritchard et al. 2000). Analysis of the genetic variance among the twelve existing populations showed the presence of a strong population structure which provides evidence that the clusters are indeed beginning to take on different evolutionary trajectories. This newly acquired evidence of increased genetic diversity in this species will hopefully lead to increased government conservation efforts.
I encountered many trials and experienced frustrations throughout my participation in this study. My tasks during this research were, at times, extremely tedious and usually involved a great deal of repetition owing to the large number of DNA samples. PCR, in particular, is an extremely temperature sensitive reaction and failed often throughout the study, costing me hours of my time. The statistical analysis also presented a challenge to me as neither I nor Dr. Egan was previously familiar with how to use the program STRUCTURE. I was able to successfully overcome these obstacles, and I feel that I learned much from my experiences.
All in all, my involvement in this study was both an intellectually enlarging and character building experience that I would not trade for anything. This mentored research opportunity allowed me to gain a greater understanding of the world around me on the molecular level, and it brought to life many of the concepts and techniques that I had learned of in previous courses of my biology major program. I was also grateful for the chance I had to sacrifice my time and energy to help to learn more about and preserve one of this Earth’s many treasures. I just graduated and plan to attend medical school this coming year. The skills and abilities I gained during my mentored research will be valuable to me during the clinical and laboratory research that I will be involved in throughout my study of medicine.