Phylogenetic Approach to Characterize Molecular Stress Response in Wild Populations

Overview

The overall goal of our research is to understand processes of molecular adaptation in diverse populations that experience exposure to varied abiotic stressors. Specifically we are interested in chaperone protein (HSP70) expression as well as global DNA methylation in organisms experiencing both acute and chronic stress. This type of inquiry relies on appropriate determination of relevant species identification. DNA “barcoding” is a molecular-based method that allows for rapid and inexpensive classification of species. Here, we describe our attempts to apply DNA barcode methods to two separate ecological studies that sought to reach definitive conclusions regarding species identification and delineation. In the first study described here, grasses from two differently impacted estuarine sites along the north Atlantic coast were compared for their varied responses to urban stress. Based on geographical distribution and comparative morphologies, these populations were assumed to be Spartina alterniflora. In order to confirm this species identification, we collected twelve individuals from both sites. We extracted DNA from these samples and PCR amplified the universal chloroplast gene rbcL using appropriate primers. Amplicons were purified and subject to sequence analysis. Sequences were compared using BLAST tool. Results of barcoding revealed a 99-100% sequence homogeneity amongst all individuals. Due to high level of rbcL gene sequence similarity amongst all Spartina species, we were unable to finalize species identification at the molecular level. However well documented geographic distribution maps strongly suggest alterniflora at both sampling sites. Our second study set out to compare differential stress response among individual trees living near arctic tree-line and to settle a debate surrounding species identification of Picea populating this important transitional ecosystem. We determined that barcoding methods were not adequate to definitively determine the species living at tree-line. Specifically, we found that the for multiple species of Picae, the rbcL gene, as well as many other potential genetic candidates, are too highly conserved across relevant arctic species. This may be due to the occurrence of a relatively recent speciation event. Our findings in Picae represent an important pitfall in the Barcode process. Success of DNA “fingerprinting” relies on finding the “ideal” gene that can discriminate any species. However, such analyses are highly limited in genera, such as Picea, for which genome sequence information is not complete.

Competition history

• AJAS 2019 Category not listed

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