The lab has been awarded a Life and Medical Sciences Seed Award from Brown's OVPR for 2024!

This $50,000 award will support improvements in our ability to use DNA barcoding to characterize gastrointestinal nematodes that infect tropical wildlife species. Our own Dr. Ezequiel Vanderhoeven is a world expert in the parasitology of tropical wildlife and the seed award will help us extend our funding base for OneHealth research at the nexus of animal health and ecology.

Leveraging expert-verified data to bring wildlife parasitology into the genomics ageWe are on the cusp of a genomics revolution to usher in an era of precision wildlife parasitology—but achieving it requires reforming long-standing traditions in the field. Biologists and health practitioners need to monitor wildlife to ensure effective conservation and identify emerging infectious diseases that may threaten humans and livestock. But we may often misunderstand host-parasite interactions because we rely on overly simplistic methods to study parasite diversity in nature. Fortunately, emerging molecular and bioinformatic techniques can help overcome traditional limitations. We plan to establish genomic workflows to more precisely characterize the diversity and distribution of gastrointestinal parasites that infect wildlife in tropical hotspots. We will accomplish this by constructing and utilizing one of the largest expert-verified databases of helminth DNA in the world. This database will bridge the gap between today’s ‘gold-standard’ practice of using microscopes to painstakingly identify parasites in the field and tomorrow’s need for ‘field-ready’ methods that provide more cost-effective, accurate, and timely parasite identifications—especially for the practitioners who need these data at the right times and places to take action. We will initially use these emerging tools to map hard-to-identify parasites onto wildlife hosts in tropical forests—sloths, monkeys, and tapirs among others—in ways that are more robust than standard techniques could provide. This exciting venture features interdisciplinary collaboration among veterinarians, parasitologists, molecular biologists, and ecologists. It will provide world-class opportunities for students and researchers at Brown to engage with non-profit organizations that focus on wildlife conservation, health, and human livelihoods.
PI: Tyler Kartzinel, Peggy and Henry D. Sharpe Assistant Professor of Environmental Studies, Assistant Professor of Ecology, Evolution, and Organismal Biology and the Institute at Brown for Environment and Society

I am extremely excited to share a new job opportunity as a core member of our group: Lab Manager in Ecological Genomics at Brown. 

​This is such a unique career opportunity in our field. The position will be salaried, starting around $60,000, and it is expected to provide job security, stability, and community over the long term. There will also be opportunities for career growth as we work together to establish a new Ecological Genomics center via Brown’s Genomics Core Facility. You will be able to help shape the future of your own position.

From an insider's perspective, we very rarely see opportunities as good as this one. The formal job ad is pasted below.

Please feel free to distribute via your networks or social media to help ensure any potential candidates you know may apply.

Congratulations to Beth for having her CRISPR-based barcoding paper published at Molecular Ecology Resources! The paper is available ahead of print on the publisher's website and we will post a PDF to our lab's publications page. Our original summary based on her preprint in June is still available in the text that follows.

Beth just posted a much-anticipated BioRxiv preprint describing our new efforts to repurpose CRISPR technology in ways that might help overcome persistent drawbacks to PCR and other targeted enrichment strategies in molecular ecology (doi: 10.1101/2023.06.30.547247v1). We show that we can obtain highly accurate plant DNA barcodes and assemble entire chloroplast genomes. These advances could help with species identification, discovery, and the construction of DNA reference libraries for use in a variety of applications. Moreover, we show incredible accuracy when it comes to estimating the relative abundance of DNA from a mixture of species compared to typical PCR-based methods for DNA metabarcoding.

We hope the experimental methods will be of interest and that folks working in the field will see the great potential. Once scalable, these advantages could really transform the quality and completeness of many projects that we do in the lab -- and the kinds of project we know a lot of folks are out there trying to do around the world as well!

The approach was noted to be a potentially 'high risk / high reward' of the NSF CAREER award that supported our work. We'll update once it is peer-reviewed and published.

The individual who fills the position will have opportunities to collaborate on important partnerships around the world. Please see our Research Page for examples of funded projects that are relevant to the position. Please see our People Page to get a sense for the diversity of collaborative efforts happening in the lab.

Find full details in the the official job description Brown's Career Site (REQ177255). I plan to review applications on a rolling basis and hope to fill the position in summer of 2022. I will continue reviewing applications until the position is filled. Please email the PI with any inquiries about the position.

Congratulations to Beth on publishing an important Open Access review in Molecular Ecology!

The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation.

This paper means a lot to me, and to the group, for a number of reasons.

First and foremost, it spotlights a hugely important and often downplayed issue for folks doing dietary DNA metabarcoding work -- and similar amplicon sequencing applications with microbiomes, environmental DNA, ancient DNA, pathogens, etc. It documents a long history of reliance on abundance-filtering strategies in our bioinformatic pipelines that may inadvertently introduce more ecologically relevant errors than they eliminate. Folks tend to be well aware of the errors that our pipelines target (trace contamination, sequence errors), and they tend to be aware that abundance filtering is an imperfect solution. But at the end of the day we are trying to learn something new about ecology and the environment, and that means we need to be more attuned to how these filters impact our downstream biological interpretations. Over the years, I have worked with countless researchers to grapple with this issue in particular -- including authors, reviewers, and editors on both sides of peer review -- and I have tried to help alleviate the strain that this imbalance between the need to filter contaminants vs. the need to preserve signal in the data can cause. Researchers in the field have long needed a thoughtful review like this one to help guide the way. I hope it will inspire discussions, debates, thoughtful introspection... and ultimately progress toward more robust applications in the field.

Second and equally important, all of the molecular data presented in this paper were generated by students in my Conservation in the Genomics Age course at Brown (BIOL 1515/2015) in 2018 and 2020. Under the leadership of Patrick (TA in 2018) and Beth (co-instructor in 2020), the students received a shipment of fecal samples from Yellowstone National Park, extracted DNA, did PCR and sequencing, ran bioinformatics, and helped us come to grips with the results. I am so proud of everything we accomplished together with students in both of these classes, and I want to highlight the roles of coauthors Violet Sackett and Camille Tulloss who both stuck with the project and completed independent studies that contributed to this outcome. 

Third, we have all benefited from Beth's steady leadership on this project and in the lab. The pandemic has been hard on everyone. Beth took the reins on this work remotely and under trying circumstances. I have been blown away by her intellect, ambition, insight, knowledge, skill, and resourcefulness. This review spotlights a pervasive issue that I have felt researchers in the field needed to have for years, and all credit to Beth for making it successful. It sets a very strong foundation for the most exciting work that Beth has in the pipeline... :)

Fourth, finally, and not at all least, this paper is rooted in our long-term collaboration with Park Scientists from Yellowstone National Park, including coauthors McGarvey and Geremia. It highlights both the need to gain new understanding of wildlife diets -- not to simply rest on preconceived notions about what animals eat -- and the critical importance of ensuring the data will be both useful and robust for downstream decision-making. When the outcome of an analysis really matters, researchers will benefit from approaching their work using the types of thoughtful and thorough approaches we illustrate in this paper.

Congrats Beth and colleagues! This is an important contribution to the field. 

Littleford-Colquhoun BL, Freeman PT, Sackett VI, Tulloss CV, McGarvey LM, Geremia C, Kartzinel TR. 2022. The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation. Molecular Ecology 10.1111/mec.16352.

Under the leadership of Colin Donihue and a team of outstanding undergraduate researchers -- including Caroline Dressler, Andy Luo, Fabiola Meyer-Garza, and Thomas Patti -- our first colony of Italian Wall Lizards has arrived at Brown! Representing populations from Pennsylvania, New York, and Boston, these non-native lizards will help us understand how their populations are evolving and fitting into our local (and much colder!) environments. Super excited to see what this dream team discovers in the year ahead!

A very warm (belated) welcome to Ian Maywar, who has joined us as a laboratory research assistant. Ian has the coolest job in the country and we are unbelievably welcome to have him join us. Ian hails from Skidmore College, where he pursued both biology and mathematics; he excels in both. Ian's undergraduate thesis focused on the molecular ecology of avian malaria. In our lab, Ian is already leading some crucial molecular analyses of plant genetics, wildlife diets, and microbiomes that will directly inform NSF funded research projects and conservation.