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.
Congratulations to Courtney Reed on new awards! We're not even a week into the new year and Courtney has already landed two major awards for student research, including a SICB Fellowship of Graduate Student Travel and an IBES Graduate Research, Training, and Travel Award. That's another $6,000 for Courtney's amazing research on small mammals -- bridging fieldwork in Kenya, functional morphology analyses of museum specimens, and DNA-based lab work. Well done!
Congratulations to Robert Ang'ila on the successful defense of his MSc thesis. Robert has pioneered important work at the Kenya ForestGEO site located at Mpala Research Centre, where he ran camera traps and conducted vegetation surveys to understand how large mammalian herbivores interact with their physical and biotic environments. Robert's insightful thesis results will have a mark on the field and launch him forward in his career as a wildlife conservation researcher. Congratulations Robert!!
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!
Congratulations to Dr. Ezequiel Vanderhoeven for your Rufford Foundation Grant! Ezequiel plans to study infectious diseases circulating in populations of armadillo species native to the Argentinian Chaco. The goal of the study is to understand how diseases impact populations of these species for the benefit of conservation and to support local governments and communities in the adoption of environmental practices that minimize the risk of spillover. It is an extremely important and ambitious project. The Rufford award not only provides crucial financial support, but also represents a valuable endorsement of the work from a leading international authority on applied conservation biology.
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.
The lab is recruiting to fill two funded positions! This is a unique opportunity to join a highly collaborative and innovative team of researchers blending field ecology with cutting edge molecular biology to make a difference in conservation at important sites around the world and on campus at Brown University.
Please see posts specific to each position:
Providence and Brown University are wonderful places to live and work!
***Update: Corrected (and extended) submission deadline below!***
The lab is recruiting a new PhD student! This is a unique opportunity to join a collaborative partnership between our lab and Yellowstone National Park as we seek to understand relationships between diverse plant species and the migratory large herbivores that eat them (e.g., bison, elk, bighorn sheep, pronghorn antelope, deer). This NSF-funded position offers support for ample fieldwork, lab work, and training at state of the art facilities (e.g., herbaria, genomics centers, data science centers).
The project calls for a PhD student with broad interests in biology and will provide a supportive environment to learn new skills. If your interests and prior experiences intersect with any aspect of this project, you should consider applying! A botanist would have support to learn about wildlife ecology, and vice versa. A geneticist would have support to learn about field research, and vice versa. An ecologist would have support to learn about data science, and vice versa. Initial inquiries from prospective students are very welcome.
Prospective students will find it helpful to review information about joining our lab as well as information about our graduate program. If you are still interested, please send the PI an email to introduce yourself! I encourage prospective students to get in touch early in the recruiting process so that we can discuss ways to strengthen your application and the suitability of fellowship programs that could help advance your career.
Update: the advertisement for this PhD position originally listed December 1st as the application deadline; this does not match the official graduate school deadline, will not be until January 7th. All applications received by the official graduate school deadline will be given full consideration.
***Update: this position is closed***
The lab is hiring a new research assistant! This is a unique opportunity to join a sharp, friendly, and collaborative group of researchers who are making a difference in molecular ecology. The position is perfect for a college graduate seeking lab experience and publication opportunities before graduate school. A brief description is below.
The lab of Dr. Tyler Kartzinel at Brown University (www.kartzinellab.com) is seeking a Research Assistant to support research on the diets, microbiomes, and metagenomes of wildlife. The Research Assistant will devote ~80% of their time to specific research projects and the remaining ~20% time to general maintenance and lab support. The Research Assistant will be welcomed as a full lab member and be expected to attend lab meetings and to contribute to a supportive and interactive lab atmosphere. The Research Assistant will interface with varied research facilities including the Brown University Genomics Facility, Brown University Herbarium, Brown Center for Animal Resources and Education and diverse collaborators on our NSF-funded projects around the world. This is a unique opportunity to become deeply involved in exciting research at the interface of ecology, genetics, and conservation. As such, it is well-suited for a college graduate seeking additional experience before graduate school.
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 research projects happening in the lab.
Find full details in the the official job description. This be available to everyone starting July 17th, 2021 on Brown's Career Site. Search for "REQ171870" to find the posting and apply! We plan to begin reviewing positions in July and hope to fill the position early in the fall of 2021, but we will continue reviewing applications until the position is filled. Please email the PI with any inquiries about the position.
Bianca Brown was featured as one of seven "exceptional alumni" profiled by the Brown Alumni Magazine in 2021. As quoted below, the article "Emerging Victorious" features seven of the many exemplary students who thrived and graduated despite the pandemic. It's a very fitting and well deserved highlight for Bianca, who we are incredibly proud to have had as the first PhD to fledge from the lab. Congratulations, Bianca, we can't wait to see all the good you do in your life and career!