MADELINE G. EPPLEY
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Field Stories: Chesapeake Bay, Virginia

12/6/2024

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By Madeline Eppley, Zea Segnitz, and Zoe Chapman

The Chesapeake Bay is one of the largest estuaries in the world, known for its historic, cultural, and ecological significance. Recently, we embarked on a fieldwork trip to the Virginia Institute of Marine Science to study one of the most iconic species of the Chesapeake Bay, the eastern oyster (C. virginica). Our research contributes insight towards understanding how oyster genetics impact survival and success under different environmental conditions.

​While there, our main goal was to monitor success of oysters growing in an ongoing
 experiment for the Lotterhos lab. This experiment involves raising juvenile eastern oysters with a variety of genetic backgrounds in two different sites within the Chesapeake Bay, the Lewisetta River and the York River. Our visit marked the 18-month point in the study, so we could really start to see substantial differences in survival and success across groups!  
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So, what does day-to-day field work look like for marine biologists? As it turns out, there really isn't one standard day! We're going to walk you through each of our days as marine biologists working on oyster genetics in the Chesapeake Bay. While we are in the field, we do everything from boating to sampling sites, working in the field lab, collaborating with other researchers at VIMS, and spending lots of time outside! 

8:00 am: Our first task of the day is to drive two hours north to the Lewisetta River in Maryland, where one of our study sites is! We raise the oysters in mesh bags on racks at each site, which allows us to sample them twice per year for growth and mortality. 

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​10:00 am:
Once we collected our samples, we return to the Aquaculture Genetics & Breeding Technology Center in the Acuff Center for Aquaculture at the Virginia Institute of Marine Science. Zea works on collecting samples for her own independent thesis! Madeline removes the predatory blue crabs from bags, where they have been eating the oysters. Unfortunately, this predation pressure can result in loss of study samples if the crabs are not routinely removed from the bags. 
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​12:00 pm: We enjoy the beautiful November weather in Virginia by eating some lunch outside. We are close enough to the York River on the VIMS campus that we can see it from our field lab, where we have been working on collecting data this morning!
1:00 pm: Our afternoon starts by driving the tractor to the York River, where our second group of oyster bags are located. In our study, each of the two sites has a distinct environment. For example, the Lewisetta River is a low-salinity site, and the York River is a high-salinity site! 

When we arrive at the site, Zoe pulls up metal cages that are sitting on the bottom of the river bed using a large hook. These cages are long lines, meaning they're all attached to a rope underwater. They cages are heavy, so it takes effort to pull them up! 

Inside of each metal cage, there are three mesh bags that hold the oysters in the study. We make sure to collect the samples at low tide so that the water level is low enough for us to go out in our waders!
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3:00 pm: Once we pull the oyster bags out of the water, we're under a time crunch to process data. Eastern oysters are filter feeders, meaning they need water to breathe, eat, and maintain basic function. They become stressed outside of the water, so we process them quickly and return them within 48 hours to the river. These oysters will continue to live over the next winter and we will check on them again in May 2025!

​5:00 pm: An important part of doing rigorous science is checking your work! At the end of our day, Madeline reviews all of the data that we collected. We check for errors and completeness. We also make an entry in our log, which is like a journal for our field data. This helps us to keep track of the environmental conditions at the site each day, hours worked, and any other important information.
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Curious what else we do in a day at VIMS? Check out our video to see more clips and highlights from a day in the life as a marine biologist in the Chesapeake Bay! 

Undergraduate researchers Zea Segnitz 
(zeasegnitz.bsky.social) and Zoe Chapman 
​(zoechapman.bsky.social) are continuing on in the Lotterhos lab with independent projects slated for 2025/2026, stay tuned for the results of their work!
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Field Stories: Coastal Resiliency in Georgia

8/26/2024

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On a recent trip to Georgia, I found myself unexpectedly (and directly!) in the path of Tropical Storm Debby. The rainfall, flooding, and wind prevented me from visiting Sapelo Island, but I was still able to participate in a week long workshop about science communication and bioinformatics in Savannah with some fellow marine scientists.  
While we experienced substantial rainfall in Savannah for several days, there was less flooding than initially forecasted. Given the circumstances, I was curious about the factors of coastal resiliency in Georgia that may have contributed to reducing the impact of flooding during Debby.

​Having collected wild oysters from Georgia for my dissertation, I knew that there are expansive natural oyster reef structures along the coastlines in the greater Savannah area. Specifically, I know that native oyster reefs play a role in shielding the coast from storm surge and erosion. 
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Tropical Storm Debby was forecasted to bring close to 30 inches of rain to Savannah, GA, a record rainfall. Image credit: NOAA & Savannah Morning News
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Some wild local oysters near Savannah, GA. Some oyster reefs occur deeper in the water column (subtidally) where they are fully covered by water. This reef is intertidal, where the oysters are exposed to air during low tides.
With a growing number of people living in coastal areas along the Atlantic and Gulf coasts of the US, it's imperative to better understand coastal mitigation strategies in the face of rapidly intensifying storms and climate change events. Natural oyster reefs are ecosystem engineers that provide a physical barrier which mitigates storm surges and prevents successive erosion (Chowdhury et al 2021). Beyond physical factors, filter-feeding oysters clear bacteria that enters the water through storm drainage and runoff. Oyster reefs also provide valuable structural habitat for many marine species. This habitat is the foundation for biodiverse ecosystems and healthy fisheries that remain resilient to extreme climatic events (Chowdhury et al 2021). ​
​To investigate additional factors of coastal resilience in Georgia, I visited Tybee Island, just east of Savannah, with other workshop attendees. While there, we were inundated with heavy rain and wind, but we were able to identify several features of the landscape that, in part, play a role in buffering the coastline from storms. 

​I teamed up with scientists Damián Santiago-Sosa, Paul Okrah, Darrian Talamantes, and Mai Fahmy, who shared their expertise on resilient coastal ecosystems and how marine scientists study these coastlines in the video that we created!

Check out our video on features of resilient coastlines such as sand dunes, bacteria, and biodiversity! These resilient features are similar among many coastlines in different marine environments, so next time you're on the coast, see how many of these features you can identify.
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We encountered strong winds & rain on Tybee Island from Tropical Storm Debby!
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Coastal scientists Paul Okrah and Damián Santiago-Sosa on Tybee Island with me!
Citations
1. Chowdhury, Mohammed Shah Nawaz, Megan La Peyre, Loren D. Coen, Rebecca L. Morris, Mark W. Luckenbach, Tom Ysebaert, Brenda Walles, and Aad C. Smaal. "Ecological engineering with oysters enhances coastal resilience efforts." Ecological Engineering 169 (2021): 106320​
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Protocol: ImageJ for Oyster Shell Parasites

7/18/2024

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Few studies have investigated how abiotic, biotic, and genetic conditions combined impact range-wide infestation rates of parasites on wild eastern oysters. I aim to map these spatial patterns of parasite infestation across the seascape and determine whether patterns correlate with environmental factors (temperature, salinity, co-occurring parasitic infestations) and/or population genetics. To achieve this, I am mapping the prevalence of parasitic Polydora worm blisters in eastern oyster shells.

​I've co-authored a lab protocol for using ImageJ to extract parasitic worm blister data with Lotterhos Lab summer intern Lisa Gouralnik! This protocol provides guidelines for identifying polydora worm blisters, using ImageJ to calculate total shell areas and areas of blister infection, and creating high-quality composite images. 
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The Polydora worm burrows into oyster shells, creating irritation and weakening shell integrity. Infected oysters exhibit a lower condition index, a measure of health, than uninfected oysters.
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Eastern oyster shells from the coastal Atlantic and Gulf of Mexico show parasitic worm blisters, outlined in dashed lines.
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Above: Lisa in the shell imaging lab at the Marine Science Center. Right: Excerpt from the protocol about collecting data on complex colored blisters.
Lisa collected >2000 data points on the polydora worm blisters over the past two months of their internship. It was great to mentor them on this project, and I'm excited to get to the next steps of data analysis!
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Preprint: Shark mislabeling in N.E. markets

6/24/2024

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A preprint of my manuscript, "DNA barcoding reveals mislabeling of endangered sharks sold as swordfish in New England fish markets" is now available to read on Research Square! The manuscript is currently under review at Conservation Genetics.

Access the preprint here: www.researchsquare.com/article/rs-4547946/v1. 

I conducted this market assessment study for my undergraduate senior thesis while at Bard College at Simon's Rock. I used DNA barcoding on the mitochondrial cytochrome oxidase I (COI) gene to determine unambiguous identification of 38 collected samples, which were either labeled as Shortfin Mako shark (Isurus oxyrinchus), Common Thresher shark (Alopias vulpinus), or swordfish (Xiphias gladius) in markets in New England. Barcoding and phylogenetic analysis revealed four mislabeled samples for a total substitution rate of 10.5%. As I collected samples  just before implementation of major import monitoring programs and a Mako fishing ban in the United States, my study established a temporal baseline that can be used to determine if market mislabeling has decreased as a result of these conservation initiatives. 
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Figure 1: From the preprint, showing collection locations, study timeline, and pictures of study samples.  
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Protocols for Building Academic Websites

6/18/2024

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My new website, madeline-eppley.github.io is published! This is a secondary website that will serve as a protocols repository with my digital lab notebook, coding and bioinformatics tutorials, and online resources for graduate students and academics. 

Some of the first content that I have developed is for building personal academic websites. I review options for choosing where to build and host your website, describe content to include, and provide instructions for building a free Quarto website using GitHub and RStudio. 

Why build personal academic websites? 
Traditional metrics (e.g. citations) by which scientists are evaluated are deeply biased and perpetuate exclusionary networks (Davies et al. 2021). These traditional metrics of "success" directly influence career advancement opportunities, funding, awards, distinctions, tenure, and more. Altmetrics, or alternative metrics, (e.g. social media activity, news articles, interviews, etc.) offer an alternative method for quantitative evaluation. Altmetrics aid in recognizing that valuable scientific impact takes many forms, including equitable communication and translation of science to general audiences (Davies et al 2021). Personal websites positively drive altmetrics, meaning that scientists can directly benefit from having a strong online presence in social media, websites, or press (Peoples et al. 2016). Promoting and evaluating scientific work in diverse ways dismantles perpetuating bias and reliance on traditional citation metrics (Davies et al. 2021). 

Beyond this, personal academic websites offer the most complete opportunity to tell the story of yourself and your scientific work. By maintaining a personal website, you have control over keeping URLs, publications, email addresses, and CVs up-to-date, whereas an institutional page may not do so for you. You are also able to link research results, media and press, grant funding, and pictures all together in one place to engage in scientific storytelling with your audience (Figure 1). Funding bodies are now recognizing the value of this type of communication with general audiences, communities, and stakeholders, so having a personal website displays commitment to this broadening values system in science. It's a no-brainer!
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Figure 1. Academic website content has three main categories: Research, Science Communication, and Networking
My associated GitHub repository that I used to build my Quarto website is publicly accessible here: github.com/madeline-eppley/madeline-eppley.github.io/tree/main. 
Citations 
1. Davies SW, Putnam HM, Ainsworth T, Baum JK, Bove CB, Crosby SC, et al. (2021) Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLoS Biol 19(6): e3001282. https://doi.org/10.1371/journal.pbio.3001282
​2. Peoples BK, Midway SR, Sackett D, Lynch A, Cooney PB (2016) Twitter Predicts Citation Rates of Ecological Research. PLoS ONE 11(11): e0166570. https://doi.org/10.1371/journal.pone.0166570
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Melbourne R. Carriker Research Award

4/8/2024

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Last week I was awarded the Melbourne R. Carriker Student Research Grant from the National Shellfisheries Association! The award is a competitive grant ($1250) awarded annually to recognize a student's excellence in the area of shellfish research. I am grateful to the NSA's funding and support towards my research, and I look forward to presenting my research at an upcoming NSA meeting.
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​The Melbourne R. Carriker Student Research Grant is named in honor of one of the Association's most distinguished past Presidents and the person who formalized the regular publication of the society meeting notes as the Proceedings of the National Shellfisheries Association.
My successful application materials can be accessed through the "Awards and Grants" section of my website! If you are interested in applying for the award in future cycles and would like to get in touch, please send me an email. 
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Ancient DNA Analysis at the AMNH

3/11/2024

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I'm spending the week at the American Museum of Natural History to participate in a week-long workshop learning about all things ancient DNA analysis! The workshop, jointly hosted by AMNH and the Center for Evolutionary Hologenomics, University of Copenhagen, aims to teach us about bioinformatics pipelines and genomics approaches for aDNA and highly degraded hDNA analysis. 

Day 1 - Intro to aDNA analysis

Today we learned all about aDNA, how it degrades, challenges and considerations for sequencing, and the basics of Unix and shell scripting. We also learned about how aDNA research has developed over the past ~40 years with advancements in modern sequencing technology.  I gave a lightning talk on the third chapter of my PhD research, investigating temporal evolution over a 25-year period in the eastern oyster. We're allowed to enter the museum early and stay late, so I've been spending lots of time exploring the museum!
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Day 2 - Ancient Wolf vs Dog Challenge

We undertook a fun challenge to figure out if a "mystery sample" from northern Russia is more closely related to modern dogs or ancient wolves. My group had a mystery sample that clustered much more closely with ancient wolves, and in particular the Ulakhan Sular ancient wolves (see my ADMIXTURE plot below). The frozen canine, which shared morphological characteristics with both wolves and early dogs, was presumed to be an early ancestor to all modern dogs. 
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Day 3 - Night at the Museum!

After a full day of learning about phylogenetic inference, we had some time to explore the museum after-hours.  The AMNH even re-tweeted me!

Night at the museum 2.0!! Held a giant squid arm, saw a case of inflated caterpillars, found the worlds largest known termite queen, and toured an ancient DNA lab @AMNH. Thanks @entomolrj and @palaeogal for being incredible tour guides! □□ pic.twitter.com/aZQ0Xop9zr

— Madeline Eppley (@MadelineGEppley) March 14, 2024

Day 4 - F-statistics and PCA

We dove deeper on our Ancient "wolf" sample from Day 2 and used F-stats and PCA to better understand how it relates to ancient wolves and modern dogs. See my results below!
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Day 5 - aDNA for Conservation Genomics

I was very excited that the last topic of the workshop was using aDNA for conservation, which relates to many of my research interests. We used a dataset of contemporary and historic (pre-1960s) African rhinos in order to determine if their populations were undergoing genomic erosion and loss of heterozygosity with population decline from sport hunting. Here are the results ... 
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Interestingly, the results (heterozygosity and runs of homozygosity) don't show overwhelming evidence for genomic erosion. As breeding populations become increasingly fractured, these measures may shift over time. This data is from the U. of Copenhagen, credit to Dr. Claudia Fontsere. 
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Copyright Madeline Eppley, 2025

LAND ACKNOWLEDGEMENT
We acknowledge the territory on which Northeastern University’s Marine Science Center stands, which is the land of the Mattakeeset tribe (1) of the Massachuset Nation (2,5) and which has been inhabited by the Pawtucket (3,5) and Naumkeag (4,5) people. We honor and respect these peoples' past, present, and future, their continuing presence in this region, and the enduring relationships that exist between them and these lands. We strive to be mindful of these relationships, and to integrate them into our research, teaching, decision-making, and actions, while also acknowledging that we still have much to learn.   

​Citations:  
1.      
https://www.mattakeeset.com/history   
2.      
https://accessgenealogy.com/massachusetts/massachuset-tribe.htm   
3.      
https://capeannhistory.org/index.php/chapter-5-what-native-people-were-on-cape-ann-at-the-time-of-contact-and-where-did-they-come-from/   
4.      
http://www.salemhistorical.org/massachusetts-indigenous-community-resources
​5.       https://native-land.ca/ 
  • ABOUT
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