fundamentals of eDNA

We covered a large range of topics this week and I have focused on Tall Bear 2013 for my submission to keep it (relatively) brief. I appreciated the assignment of this paper as I was not familiar with the discourse on the use of genetic information as a basis for tribal enrollment. Tall Bear asks a thought-provoking question: “Do we value genetic kin versus kin made through law, ceremony, or love?” (p. 526). Like the nature versus nurture question in psychology, there is no black-and-white answer. Questions of cultural identity are painted in grayscale. I understand why genetic proof of lineage is used by some tribes as a way to defend against exploitation of their resources (e.g., per capita casino payouts to members). Personally, I do not associate genetic identity alone with a cultural identity. To me (a person with no tribal affiliation) cultural identity is formed by the connections we make with those around us rather than something solely innate. There is relevance of genetic identity to cultural identity through the passage of traditions from parents over the course of generations and interactions- positive and negative- with those who live near us. The following is a much, much lower-stakes example than one of tribal enrollment, re-involvement from a culture that you were systemically prevented from engaging with, and access to tribal resources: I moved to Maine about five years ago from the Washington, D.C. area. I “fit in” here. It’s commonly said in Maine that you’re not a “true” Mainer unless you, your parents, and your grandparents grew up here. This statement is exclusive, and one may think if they’ve lived in Maine a few years they are “functionally” a Mainer. But a drive around town with someone who’s family has been there since the 1800s illuminates some absences in a transplant’s cultural knowledge- like the history of each building, which shortcuts to take across town, and the names of every person you pass on the street. So am I “functionally” a Mainer even if I am not one genetically? I’m certainly not culturally a Washingtonian. (Or maybe I’m a “species on the move?” I now wonder, how do, say, the invasive green crabs change functionally and genetically with geographic shifts?) We did not have much time to apply the paradigms in Tall Bear 2013 to eDNA paradigms in class. I have been thinking about this question this week, and it reminds me of taxonomic lumping vs. splitting and the use of functional groups in classification. I myself have always preferred classifying by functional groups rather than single-base pair differences- a base swap may not even change the protein produced! Taxonomic splitting can miss the forest for the trees. I am most interested in how organisms interact and react with their environment or other organisms rather than simply what their genetics imply; however, to ignore genetic identity completely misses valuable information about the role an organism plays in its environment. One of the algal groups I study are Pseudo-nitzschia spp. Some species have the capability to produce the neurotoxin domoic acid, but not all of them do. Currently, molecular detection of Pseudo-nitzschia spp. is with a genus-specific primer set. Stakeholders and policy makers are (generally speaking) not interested in what species of Pseudo-nitzschia are present in the water, they are interested in if they are capable of toxin production that will shut down fisheries and poison consumers. I am working on developing species-specific primer sets for some Gulf of Maine taxa known to produce domoic acid, but the “holy grail” assay for me would be one that targets not 18S or ITS, but the actual gene region that produces domoic acid. I am interested to hear how others may apply functional roles to classification and eDNA methodology, or if they prefer a more genetics-based approach to their research and why. I am very much looking forward to continuing these discussions in the future!