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.
***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.
Chrishen Gomez is the recipient of a prestigious 2019 Merdeka Award Grant from Malaysia, which was established “to reward citizens and organizations who have made outstanding contributions in their respective fields to the people of Malaysia.”
Chrishen joins the lab for three months as a Visiting Research Associate affiliated with EEB. During his visit, Chrishen will collaborate on DNA-based analyses of animal diets and genetics. Chrishen aims to apply these approaches and his affiliation with the Bornean Carnivore Program to establish a conservation genetics research program that focuses on the Sunda Clouded Leopard in Malaysia.
Check out Chrishen's Merdeka Award acceptance speech to learn about his amazing research and conservation efforts in Borneo!
As the fall semester gets into swing, the lab is having a lot of fun and making progress on research. Several milestones should not go unnoticed, and there are photos to boot. In no particular order:
Howard Hughes Medical Institute (HHMI) just released a “BioInteractive” lab featuring our research on the diets of savanna herbivores.
Educators and students in high school and college biology courses will go on an expedition to Mpala Research Centre in Kenya, where they can investigate niche partitioning as a mechanism that enables similar species to coexist.
This extraordinarily engaging and informative BioInteractive module is inspired by — and uses real data from — our 2015 PNAS paper: “DNA metabarcoding illuminates dietary niche partitioning by African large herbivores.” The paper is becoming a “textbook” example of niche partitioning and DNA-based approaches in ecology.
Together with Rob Pringle and our collaborators, we hope this interactive will reach thousands of students worldwide.
As we kick off the new academic year, we extend the warmest welcome to Dr. Brian Gill, inaugural IBES postdoc in the lab. Brian's doctoral research fused a cutting-edge molecular tool kit with some extremely rugged field research to test important ideas in ecology and evolution. For example, Brian used DNA barcoding to identify a huge diversity of mayflies from tropical and temperate streams, revealing that their elevational ranges are narrower in the tropics, where species may be more sensitive to the effects of climate change -- a result that may not have been so clearcut in the absence of molecular data, due to the prevalence of cryptic species. We all look forward to benefiting from Brian's leadership and skills as we study how species are respond to environmental changes in New England, in East Africa, and around the world.
Two graduate students are joining the Kartzinel Lab in Fall of 2017!
Bianca Brown is arriving from the Rand Lab, where she investigated how climate change may alter the microbiomes of barnacles and fruit flies. Bianca is developing cutting-edge research on how defaunation—the decline of African large herbivores in particular—can have cascading effects on the diets and gut microbiota of other herbivores in the community. With better understanding of these relationships, we expect to help improve wildlife conservation and reintroduction programs.
Patrick Freeman is arriving from Stanford, where he began researching the behavior and conservation of African elephants. Through his photographs and presentations, Patrick shares his experiences in ways that have brought his audiences to tears. By integrating a new repertoire of laboratory analyses with on-the-ground fieldwork, we aim to develop rigorous conservation strategies to protect for countless plants and animals in Kenya (especially the really big ones)!