Pairing eDNA and visual data to understand biodiversity along Maine’s coast
By Emma Beauregard,
Even though the award period of the NSF EPSCoR Track-1 Maine-eDNA project comes to completion on December 31, 2024, the researchers involved remain as busy as ever going through data samples. One of these researchers is Yasmina Shah Esmaeili, a postdoctoral fellow bringing together previously collected data to reveal how kelp forest biodiversity has changed through space and time. Shah Esmaeili spent her undergraduate and master’s program studying in Belgium before heading to Brazil to earn her Ph.D. After completing a position at the Smithsonian Environmental Research Center in Maryland, Shah Esmaeili joined Maine-eDNA as part of Douglas Rasher’s lab at Bigelow Laboratory for Ocean Sciences.
Shah Esmaeili is developing a manuscript examining the overlap between eDNA and visual census data. The research brings together observations, eDNA data, and environmental data to reveal changes in kelp biodiversity and discover the emergence of “species on the move,” the forced movement of species due to human-caused climate change. Shah Esmaeili is also looking at how well four DNA primers helped detect species and which taxonomic groups are represented in the survey methods. These primers, or eDNA markers, are single-stranded DNA fragments used as a laboratory tool for detecting species. Each primer Maine-eDNA used is suited to detect a particular taxonomic group, a category of organisms based on shared characteristics. “Using a combination of multiple primers results in a clearer and more comprehensive picture of the overall diversity in an ecosystem,” Shah Esmaeili explained. These methods allow researchers to detect more species than traditional visual surveys. However, visual surveys are still needed to validate eDNA findings, and to identify some ecologically and economically important species that evade eDNA detection. Using multiple primers is costly, which makes Shah Esmaeili’s work more essential. She hopes her studies will validate the use of eDNA in biodiversity assessments, find what drives regional patterns in biodiversity across species, and identify which primers are essential to capture the majority of biodiversity in an area.
For eDNA to be effective, it must be matched to a species identified by taxonomists. As long as these references are publicly available on databases such as GenBank, researchers can use them. However, despite their importance, references are not always accessible to scientists, proving a challenge to finishing research, one Shah Esmaeili has faced.
“Applied research is becoming more and more important over the years since research is being used as a foundation for management decisions,” Shah Esmaeili remarked. Especially as climate change forces people and companies to change their behavior, research such as what Shah Esmaeili and Maine-eDNA are doing becomes increasingly relevant and crucial. “People commonly assume Maine’s kelp forests are species-poor, but eDNA has revealed that Maine’s kelp forests are quite speciose,” Shah Esmaeili said. However, as this diversity declines in the gulf and worldwide, the loss has serious consequences that are beginning to impact humans. Kelp are foundation species that provide food and shelter to many species, fueling the coastal food web, and as it begins to change, other species begin to drop out of the ecosystem. These changes can be seen in the data sets collected by Maine-eDNA and in previous data available through the Rasher Lab’s work.
The changes to the Gulf of Maine ecosystems are happening in real time, emphasizing the importance of Shah Esmaeili’s work with long-term data sets. “We need to understand how and why changes are occurring before we can come up with solutions,” Shah Esmaeili said. “That is the baseline of the work we are doing.” As Shah Esmaeili continues to go through the data sets, she expects to find more interesting revelations that will hopefully contribute to knowledge of, and a solution for, Gulf of Maine biodiversity.