The paper led by Brian Gill on individual-level tracking of elephant diets -- Foraging History of Individual Elephants Using DNA Metabarcoding -- was just published by Royal Society Open Science. We are very proud of this paper, which revisits a set of classic studies on seasonal diet switching by elephants using stable isotopes in hair that were led by coauthors Thure Cerling and George Wittemeyer. The work was made possible with support in the field from Save the Elephants and with the botanical expertise of coauthor Paul Musili from the National Museums of Kenya.
The paper was accompanied by a great summary by Corrie Pikul and featured on the Brown University homepage: Similar to Humans, Elephants Vary What they Eat for Dinner.
The paper also attracted attention in the media, including interviews on BBC Television and Times Radio. Some nice coverage of the study was also provided by BBC (with hilarious photos), Newsweek, ZME Science, and The Times.
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.
An exciting paper from the lab on lizard behavior, let by (former) undergraduate all-star Thomas Patti, appears today in Biological Journal of the Linnean Society. The "Bite and Seek" paper focuses on the exploratory behaviors and bite force of the Podarcis lizard colony that we had on campus. Thomas and the team tested an extensive series of hypotheses about the relationship between behaviors observed in populations of this non-native lizard species and the recency of population establishment. All else equal, propensity for exploration might be expected to facilitate the establishment of new populations -- lizards have to explore at least a little to get somewhere new -- and thus recently founded populations should comprise groups of explorers. Not so in nature, Thomas reports, and this requires us to take a more nuanced view of behavioral 'syndromes' as sets of traits and behaviors that may be associated with invasion potential and success in non-native species. Great work Thomas, Colin, Andy, and Caroline!
Congratulations to Robert Ang'ila for publishing a paper based on his Masters research in African Journal of Ecology! Robert's paper reports on spatial associations between the abundance and diversity of wildlife and understory plant communities across the massive CTFS-ForestGEO plot at Mpala Research Centre in Kenya. The work highlights how fine-scale variation in soil and topography can shape plant-herbivore interaction networks that play out over much broader scales. Great work, Robert!
A million congrats to Bianca Brown on her latest publication, which now appears typeset and formatted in Molecular Ecology! Bianca's insight, creativity, and leadership are on full display in this masterpiece of a paper that investigates patterns of phylosymbiosis in the small mammal community at Mpala Research Centre. Bianca highlights the importance of phylogenetic scale in investigations of phylosymbiosis and underscores the value of studies that investigate how local ecological context can modify our 'global' expectations about host-microbiome associations. Way to go, Bianca!
Brown BRP, Goheen JR, Newsome SD, Pringle RM, Palmer TM, Khasoha LM, Kartzinel TR. 2023. Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals. Molecular Ecology doi: 10.1111/mec.16874
There is a fascinating population of Italian Wall Lizards living in Boston's Fenway Gardens. Even during the height of the pandemic, members of the Lizard Team were able to do some fieldwork observing and tracking the lizard population at this novel site for the species. In the first of several publications the team is leading from this time, we recently published a Natural History Note in Herpetological Review describing a couple of instances of avian predation observed: a hawk and a grackle separately preyed on individuals from this population. The population has only been around for a short number of years, and there are no native lizards in this region, so this represented novel predatory behaviors on a no-analog lizard population in the region. Scroll to page 500 of this [PDF] for some interesting observation and incredible photos published -- congrats team!
Congratulations to Beth and the team for publishing a strong, thoughtful, and evidence-based reply to an earlier comment in Molecular Ecology.
The take-home: there are a lot of challenges and opportunities when it comes to using dietary DNA metabarcoding strategies to advance a variety of important research agendas; Beth is leading the way when it comes to clear-thinking about how we conduct our studies and how we can strengthen the evidence we use to support our conclusions.
The exemplary professional, Beth exposes persistent and potentially problematic misconceptions in the field in a way that is clear, constructive, and self-reflective. Whether or not our decisions about how to code dietary DNA metabarcoding data have a qualitative influence on our ecological interpretations is a question that we should all be asking. Beth and the team provide invaluable insight into when we might need to pay particular attention to this issue, and offer a blueprint to help us address the issue in a more structured way by sharing computer code that we wrote to conduct simulation studies and sensitivity analyses with real data.
Littleford-Colquhoun BL, Sackett VI, Tulloss CV, Kartzinel TR. 2022. Evidence-based strategies to navigate the complexity of dietary DNA: a reply. Molecular Ecology doi: 10.1111/mec.16712. [PDF]
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.
The lab has much to celebrate as we close out another semester, even despite the disruptions of COVID-19.