The winner of the Harper Prize 2017 is Jenny Zambrano. Jenny’s paper, ‘Neighbourhood defence gene similarity effects on tree performance: a community transcriptomic approach’, takes a community functional phylogenomic approach to understand how defence genes drive tree community structure and dynamics. Jenny originates from Colombia and is currently a postdoctoral fellow at the National Socio-Environmental Synthesis Center (SESYNC) (University of Maryland) in Annapolis, Maryland, USA. You can read more about Jenny and her paper on the BES website. Jenny kindly agreed to answer few questions to explain her novel approach and interesting findings.
In your paper, you suggest an alternative to the functional traits approach, particularly to determine plant defense against pest and pathogens. Can you explain your new approach?
Here we propose a new research approach that leverages transcriptomic information for the purpose of investigating community structure and dynamics from a functional perspective. Functional traits have been used extensively over the past decade to interpret links among phenotypes, demography and community dynamics. Less easily measured functions, such as plant defense, have frequently gone unmeasured due to the difficulty to measure in the field. This is particularly problematic for testing important hypotheses in forest ecology, such as the Janzen-Connell Hypothesis where individual trees are expected to be at a disadvantage if their neighbors share the same natural enemies. Transcriptomes can be used to obtain information on functions otherwise difficult to measure in the field. Transcriptomic analyses have been increased in recent years, as demonstrated in the special feature “Transcriptomic and genomic analyses of communities”, as RNA analyses are becoming more accessible. Using this type of information, we can answer important ecological questions that have been previously difficult to access.
Practically, how did you do in the field and in the lab to determine the similarity in defense traits between species?
In this study, we used demographic and transcriptomic data for 21 species from the Wabikon Lake Forest Dynamics Plot, which is part of the Smithsonian’s ForestGEO research network to conduct a community analysis. We determined similarity in defense traits using neighborhood models, that had been previously described as a great quantitative approach to explore the drivers shaping plant communities. These models have helped to provide insights related to species co-occurrence patterns that are difficult to study in the field especially for long-lived species. Using neighborhood models, we were able to determine the influence of nearby neighbors on the survival and growth of a focal tree by using an index of neighborhood similarity. In other words, we were able to determine how similar/dissimilar a focal tree was from its neighbors in terms of defense genes and how this affected individual survival and growth.
The senior editors who selected your paper for the Harper Prize were quite impressed by the approach and the results of your study, so tell us, what did you find?
Our results suggest that strong conspecific effects were shaping the tree community at this North American forest. Negative conspecific density dependence has been previously described as an important driving force shaping tropical and temperate forests around the world. In addition, results of this study demonstrate that defense gene similarity in neighborhoods often does have negative effects on individual demographic performance, as predicted by the Janzen-Connell Hypothesis. Thus, this study provides an advance in understanding community dynamics as they imply potential genetic variation in defense among species.
How do you think the results of your study improve our knowledge in community ecology?
A grand challenge in ecology is to determine the processes driving community structure and composition that are often complex and difficult to assess. The study of these processes in systems such as tree communities has encountered many challenges due to the limitations of conducting experiments on long-lived species. The use of transcriptomes is novel in a community setting and might help better explain patterns of negative density dependence observed in temperate and tropical forests. Our results highlight the importance of genetic variation and differential expression of defense related genes structuring tree communities that future studies need to consider. Conceptually and analytically this study represents a major and novel step forward demonstrating that advances in sequencing and informatics tools can be utilized on non-model species that constitute the natural communities that most ecologists study.
Are you planning on pursuing this work with new experiments? What are your plans for the future?
We are currently developing a method to explore whether the presence/absence of transcriptome assemblies and neighborhood similarity determine individual survival and growth. The goal is to include other functions, aside from plant defense, (i.e. drought tolerance, photosynthetic activity, etc.), that likely play an important role in species co-occurrence patterns but that have not been fully explored for entire tree communities.
The winning and highly commended papers for each of the BES journals have been compiled into a freely available Virtual Issue.