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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.
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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 Eastern oyster shells from the coastal Atlantic and Gulf of Mexico show parasitic worm blisters, outlined in dashed lines.
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.  Figure 1: From the preprint, showing collection locations, study timeline, and pictures of study samples.
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!  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 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.  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.
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
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.
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!
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!
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 ...
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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