Lisa Busby and Dr. Leigh Johnson, Life Science
The plant genus Collomia shows great morphological and genetic diversity, however, its current classification is based on a morphological study done in 1940. This year I was able to assemble a great deal of DNA sequence information and compare the variation in these sequences with previous classifications to begin reevaluating the genus and further define relationships between Collomia species. I have also made a great deal of progress in sharing this data with the general public by helping to construct internet web pages for the Tree of Life Web Project.
To begin this research, several samples of each of the fifteen species of Collomia were obtained by the lab I worked in. We obtained DNA sequences from several regions from the chloroplast and the nuclear genomes. These genomes are inherited differently, and therefore, by sequencing genes from both genomes, we gain a greater picture of the genetic histories of these plants. The sequences were assembled into data sets that were analyzed by phylogenetic software. This software uses shared similarities and differences between sequences to show how the DNA regions (and by inference, the species) are related to each other. We analyzed the chloroplast and nuclear data sets separately and applied different statistical analyses to assess how similar or different the phylogenetic trees from the different genomes were. There are still additional analyses to run, but we are well on our way in writing a manuscript that will report these results and what we have learned about relationships among these species in a scientific journal. As we studied the results of our analyses, we have found that the present methods for presenting these phylogenetic relationships into trees is insufficient for our needs. We have been developing a new system of drawing trees to be able to include the incongruent information that is being shown from the chloroplast DNA and the nuclear DNA.
Beyond the analysis work described above, a portion of my time was devoted to working with the Tree of Life website, which is an online encyclopedia of accurate information for species written for a general audience. Phylogenetics research is something that most people do not come across very often, but which is an important area of scientific research. One of the goals of this project was to educate the public about the research we have done, and we have made great progress in this area. Since beginning this project we have added a genus page for Collomia to its family, Polemoniaceae. This page includes general information about Collomia, evolutionary history and phylogenetics, and ethnobotany. We have also added individual species pages for each of the fifteen species in the genus that currently contain the several synonyms for each of the species as each have been named and renamed several times since the genus’ beginnings. These pages will be assessable by selecting “Collomia” from the Polemoniaceae tree at: http://www.tolweb.org/Polemoniaceae/20812. The primary page for Collomia is completed and we expect the TOL administrators to make the link to this page active at any time.
I began working in the Johnson lab helping to generate DNA sequence data. Through this project, I have gained a greater understanding of phylogenetic research and the kinds of questions DNA sequence data can answer about relationships among organisms. I have been able to go through each step of the process required to assemble phylogenetic data and complete many of the analyses myself. Being able to complete the analyses of the data has been particularly helpful to me in that I have been able to put all the principles I have learned through the entire process together to obtain an outcome that has helped me better understand the relationships among these species. I summarize this understanding as follows, using the information developed through my experience that is part of the Tree of Life page for Collomia.
The first hypothesis of phylogenetic relationships in Collomia was proposed by Wherry (1944) who suggested the perennial species were ancestral and the linear leaved annuals the most advanced. Wherry grouped species into three sections that have been accepted by latter authors (e.g., Grant 1959; Chuang et al. 1978; Hsiao and Chuang 1981). Section Collomiastrum contained the four perennial species, section Courtoisa contained the two species that have more than three seeds per fruit, and the remaining species were placed in section Collomia.
Grant (1959) accepted Wherry’s views of relationships and suggested several progenitor/derivative species pairs. In this view, new species have arisen most likely from allopatric speciation. Hybridization, which has been shown to be important in other Polemoniaceae genera such as Gilia and Phlox, has never been considered important in the history of Collomia.
Comparative DNA sequencing provides strong evidence that two Collomia species, C. biflora and C. wilkenii, are allotetraploids (Johnson and Johnson, 2006). Collomia mazama has most likely obtained its chloroplast from an annual species and C. diversifolia has also likely experienced hybridization in its past.
Collomia diversifolia and C. heterophylla are strongly supported as sister by chloroplast DNA, but not with nuclear rDNA ITS or low copy nuclear genes. C. diversifolia’s pollen morphology matches the linear leaved annuals such as C. linearis (Chuang et al. 1978), but it is otherwise similar to C. heterophylla in habit and in its number of seeds per fruit.
Collomia tracyi and C. tinctoria are naturally considered sister taxa morphologically and are strongly supported as such with DNA sequence data. They have a unique pollen type in the genus and do not belong phylogenetically with the other species of section Collomia.
The perennial species are well-supported as monophyletic with nuclear DNA sequences and morphology (e.g., Chuang et al., 1978; Hsaio and Chuang, 1981), but C. mazama possesses a chloroplast genome that appears sister to the large group of linear leaved annuals.
The linear leaved annuals excluding Collomia grandiflora form a group, with C. grandiflora either sister or unresolved in its relationship in the genus. Chuang et al. (1978) suggested the pollen of C. grandiflora was somewhat intermediate between the other linear leaved species and the perennial species, which parallels the placement of this taxon on the phylogenetic trees.