By Lillian Pavord

I had never heard of the concept of genetically monitoring a species’ through environmental DNA (eDNA) assays until I became a teaching assistant for a genetics lab taught by Dr. Sard. I was immediately intrigued. I started learning and reading about population genetics and genetic ‘tools’ used for conservation efforts. I have always wanted to work in conservation and management but had no idea that the field actually was so expansive. 

I decided that I wanted to work on a research project associated with eDNA assay development and it’s associated application, which is the process of screening soil and/or water samples for DNA that organisms leave behind (Barnes et al., 2014) using species-specific polymerase chain reaction assays. eDNA can be nuclear or mitochondrial (Nielson et al., 2007). Mitochondrial is preferred for assays because it is more stable in water and soil due to it being circular and the fact that it is shielded from cytoplasmic nucleases so it doesn’t degrade as quickly (Nielson et al., 2007). Species detections resulting from eDNA assays can be used to determine the distribution and relative abundance for a wide range of species (Yates et al., 2019). Using genetic-based methods of detection is more efficient especially for smaller, more evasive critters. Ideally, full mitochondrial genomes (mitomes) for the target species and its close relatives are used to develop eDNA assays because the sequencing data itself is high quality (i.e., high sequencing coverage) and many loci can be evaluated in silico at the same time.

Dr. Sard explained that eDNA assays can be applied to any species I wanted to study. I started looking into various endangered and invasive species. Having never felt drawn to one species or another, I did feel that I wanted to focus on the conservation of critically endangered species. 

Dr. Sard also shared that he had been talking to Dr. Peter Rosenbaum about his collection of bog turtle (Glyptemys muhlenbergii) blood samples, a species that has been critically endangered since 1997 (US Fish and Wildlife Service, 2001). He proposed that with previously collected samples we could extract DNA from the blood and create a genomic resource to be used for conservation efforts associated with the bog turtle. Initially, the project only entailed working with the bog turtle blood samples but after compiling a database of every blood sample Dr. Rosenbaum collected (over 1000 samples!), the scope of the project expanded dramatically to include six additional turtle species. We are now planning on extracting the DNA from samples of bog, wood (Glyptemys insculpta), box (Terrapene carolina), painted (Chrysemys picta), musk (Sternotherus odoratus), spotted (Clemmys guttata), and Blanding’s (Emydoidea blandingii) turtles. I’ve been trained to perform the extractions on my own using a Qiagen DNEasy extraction kit. Its repetitive protocol made it easy to learn basic laboratory practices and techniques. 

My goal was to complete all extractions prior to the summer semester, which is when we intended to prepare extracted DNAs for sequencing. However, COVID-19 has impacted all of us in ways we could never imagine. While I am personally disappointed that the campus closed, as did my research, I realize this pandemic is impacting people’s lives and livelihoods. I’ve gained a new appreciation for the importance of research in light of what people in the research field are risking to help the greater good. Maybe I sound like a broken record, but as a budding animal conservation researcher, I pledge to stay home, wash my hands frequently, and wait and watch until given the green light to get back into the lab. I hope my fellow budding researchers do the same so we can all get back to work.

Citations

Barnes, M. A., Turner, C. R., Jerde, C. L., Renshaw, M. A., Chadderton, W. L., & Lodge, D. M. (2014). Environmental conditions influence eDNA persistence in aquatic systems. Environmental science & technology, 48(3), 1819-1827.

Nielsen, K. M., Johnsen, P. J., Bensasson, D., & Daffonchio, D. (2007). Release and persistence of extracellular DNA in the environment. Environmental biosafety research, 6(1-2), 37-53.

US Fish and Wildlife Service. (2001). Bog Turtle (Clemmys muhlenbergii), Northern Population Recovery Plan. Bog Turtle (Clemmys muhlenbergii), Northern Population Recovery Plan.

Yates, M. C., Fraser, D. J., & Derry, A. M. (2019). Meta‐analysis supports further refinement of eDNA for monitoring aquatic species‐specific abundance in nature. Environmental DNA, 1(1), 5-13.

By Caroline Sheldon

Due to excessive trapping in the early 1900s, Martes pennanti (Fisher) populations experienced a significant decline in New York State, but thanks to trapping regulations and reintroduction efforts, populations are now thriving (Baginski et al., 2015). However, in the Northwest United States, Fisher populations are declining due to habitat destruction and fragmentation because Fishers reside in a specific range of habitat conditions (Baginski et al., 2015).

Currently, Fisher populations are monitored using camera traps and reports from the public, but these methods are not always a reliable source. The use of environmental DNA (eDNA) is a relatively new method of detection that uses trace DNA released from organisms into soil or water in the surrounding environment (Bohmann et al., 2014). We are working on the development of an eDNA assay for Fishers as a way to non-invasively detect the elusive species. By using eDNA as a detection method we will be able to gather information about the occupancy and changes in relative abundance of  Fishers, however, there are some challenges that come from using eDNA extracted from water samples when trying to detect a terrestrial mammal. Since Fishers are a terrestrial animal they spend little time in, or around water which lowers the chances of finding eDNA, and any eDNA that is found may be old and degraded. Once the eDNA assay is developed, we will be analyzing water samples from primary streams and vernal pools around the SUNY Oswego Rice Creek Field Station in order to test for the presence of  Fishers, as well as study the environmental conditions (e.g., sampling timing) under which the detection rates are highest. The ultimate goal of this project is to successfully create an eDNA assay for the Fisher that can be used as another source of detection, particularly when the species is rare (i.e., on the edge of its range expansion or in the Pacific Northwest where it is threatened).

Citations:

New York State Department of Environmental Conservation (NYSDEC). 2015. New York State     Fisher Management Plan. Albany, NY.

Kristine Bohmann, Alice Evans, M. Thomas P. Gilbert, Gary R. Carvalho, Simon Creer, Michael Knapp, Douglas w. Yu, & Mark de Bruyn. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29(6), 358–365.

By Sydney Waloven

Most people are probably familiar with the cute, small, furry mammals known as otters because captive sea otter populations often serve to educate the public about local coastal habitats and greater conservation issues surrounding these species (Brennan and Houck 1996). For instance, if you’re from California you are probably more familiar with the sea otter since it is The Monterey Bay Aquarium’s most widely known furry friend. Unfortunately, the sea otter has been marked with the “Endangered” status on IUCN’s Red List, with a decreasing population. The IUCN’s Red List is used by many wildlife departments, conservation organizations, and government agencies to monitor and propel protection and conservation action for our biodiversity and natural resources. Like the endangered sea otters, the North American river otters are also placed on IUCN’s Red List with a “vulnerable” status. In contrast to the otter’s lovable nature, they face many anthropogenic threats. Some threats include habitat destruction, pesticide pollution from agricultural development, and overexploitation (IUCN Otter Specialist Group). 

Species of conservation concern, like those on the IUCN’s Red List, are challenging to manage due to the difficulty associated with sampling individuals from small populations or populations of low-density. This lack of information creates uncertainty associated with providing protective measures and conservation plans for threatened and endangered species (Elith et al. 2006). To enable more effective protection of the habitats that these species reside in, we must improve our ability to detect certain species to better assess their distributions (Wilcox et al. 2013).

Environmental DNA (eDNA) sampling is an emerging tool in the fields of ecology and conservation used to infer the presence of a species during the recent past. eDNA is any DNA that can be sampled from the environment typically from water, sediment, or soil (Rees et al. 2014). Therefore, eDNA sampling does not need to be directly sampled from the target organism. eDNA sampling can be more efficient and sensitive at detecting low abundance species compared to traditional trapping and netting methods (e.g., Jerde et al. 2011). However, the knowledge surrounding the ‘ecology’ of eDNA (i.e. the origin, state, fate, and transport) is still poorly understood (Barnes and Turner 2016). 

Due to the similarities to the sea otter’s habitat and lifestyle, the North American river otter can serve as a model species to study the ecology of eDNA of aquatic mammals; then apply it to conservation management. This aims to improve detection rates and sampling methodology. In a study by Port et al. (2016), eDNA was used to characterize the spatial trends in sea otters in Monterey, who are a keynote species vital to the health of the kelp forest ecosystems. My research aims to expand on these and determine whether the state at which eDNA is collected, the method of detection, and/or the season of collection plays a role in the detection rate of an organism. Applying this information from my research may improve detection rates for rare species and more generally help to contribute critical knowledge used in innovative new conservation efforts to protect our endangered and threatened biodiversity.

Citations:

Barnes, M. and Turner, C. (2016) The ecology of environmental DNA and implications for conservation genetics. Conserv Genet 17(1): 1-17.

Brennan, J. and Houck, J. (1996) Sea otters in captivity: the need for coordinated management as a conservation strategy. Endangered Species Update 13(12): 61-66.

Elith, J. et al. (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29(2). https://doi.org/10.1111/j.2006.0906-7590.04596.x 

Jerde, C. et al. (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4(2): 150-157.

Port, J. et al . (2016) Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol Ecol 25(2): 527 541. 

Rees, H. et al. (2014) Review: the detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology. J Appl Ecol 51(5). https://doi.org/10.1111/1365-2664.12306 

Silva, P. (2020) IUCN Otter Specialist Group: North American river otter. http://www.otterspecialistgroup.org/newweb/otters/north-american-river-otter#sthash.6AG09f1c.MIAV7K9L.dpbs Accessed on April 7, 2020.
Wilcox, T. et al. (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. Plos One 8(3). https://doi.org/10.1371/journal.pone.0059520