Interview with the authors: Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

Much research in community genetics attempts to understand how genetic variation influences community composition, but the majority of studies have been done at the level of the genotype. In their new Molecular Ecology paper, Barker and colleagues use genome-wide association mapping in aspen (Populus tremuloides) to identify specific genes that may influence variation in tree traits or in insect communities. They uncover 49 SNPs that are significantly associated with tree traits or insect community composition. Notably, insects with closer associations with host plants have more genetic correlations than less closely associated insects. Barker and colleagues find a SNP associated with insect community diversity and the abundance of interacting species, providing a link between genetic variation in aspen and insect community composition. Finally, they find that tree traits explain some of the significant relationships between SNPs and insect community composition, suggesting a mechanism by which these genes may influence community composition. Read the full article here, and get a behind-the-scenes interview with lead author Hilary Barker below.

What led to your interest in this topic / what was the motivation for this study? 
For some time, we have been interested in extended phenotypes – the idea that the genes of an organism not only shape the immediate traits of that organism, but also extensions of these traits, such as the community of insects living on a tree. Yet, until our study, most of the previous research had been largely focused on differences across genotypes of ‘host’ organisms (e.g., aspen, cottonwoods, evening primrose), rather the underlying genes. Thus, there were a lot of unknowns yet to be discovered. For instance, would the genetic effects be large enough to detect and identify? Would more underlying tree genes be found for insects that are more closely associated with the tree (i.e., leaf gallers) rather than free feeding insects? Would there be an overlap between genes associated with insect communities and genes associated with particular tree traits? 

What difficulties did you run into along the way? 
I think the largest challenge of conducting a Genome-Wide Association study on a common garden of trees is the planting and maintenance of this small forest. We had 1824 trees that needed planting, phenotyping, and care. This work was most intense in the first four years of the study to ensure that each tree survived a summer drought and multiple harsh winters. The next most challenging hurdle was conducting the insect surveys. These surveys involved a large team effort and happened during some of the hottest days of the summer. 

What is the biggest or most surprising finding from this study? 
The most exciting finding from this study was the identification of an aspen gene (early nodulin-like [ENODL] transmembrane protein, Potra001060g09097) that underlies insect community composition; both diversity and the abundance of key insect species (aphids and ants). While we do not yet know the mechanism by which this gene influences insect communities, we do know that this protein is involved in the transportation of carbohydrates. Thus, it’s possible that this gene directly influences aphids and ants via their interactions with carbohydrate-rich honeydew, and/or indirectly influence insects via numerous tree traits, including both growth (size) and defense. To our knowledge, this is the first identification of allelic variation in a plant gene that is associated with a complex insect community trait (i.e., insect community composition).

Moving forward, what are the next steps for this research? 
The next step of this research is to explore how the genetic underpinnings of these aspen traits and associated insect communities may vary across different environmental gradients and with tree ontogeny. Previous research has shown that aspen growth and defense traits vary with tree age, and these traits play a significant role in determining which insects will feed upon the foliage. Thus, the genetic contributions of insect community composition may vary substantially for more mature trees. The Lindroth lab is currently working on an expanded version of this study with more detailed traits and mature (reproductive) trees. In addition, gene expression will vary with different environmental conditions, which will likely also modify which genes are most important in shaping insect communities.

What would your message be for students about to start their first research projects in this topic? 
To complete a large community genomics study such as this, you will need a few key things. First, you will need a lot of help. Start recruiting anyone and everyone in sight. Mentoring undergraduates will be essential and ensuring that you can effectively asses the learning of your mentees and volunteers is critical (e.g., can they correctly identify X insect? Can they successfully complete X protocol in the lab?). Second, get organized. Project management platforms can be really helpful (e.g., Asana, MS Teams, etc.) to keep track of tasks. Third, refine your R markdown scripts. You will generate more data than you know what to do with, and thus creating R scripts to clean up, organize, and analyze your data will be a top priority. Also, if you can get a digital microscope (e.g., Dino Lite), then the tedious task of keying out insect specimens will be much easier and less cumbersome! I highly recommend it.

What have you learned about science over the course of this project? 
In terms of a genome-wide association study, it is best to have as large a sample size as possible (more genotypes and genetic variation). You do not want to invest a lot of resources into a study that has low statistical power for association testing. Also, phenotype as many traits as you can. At the onset, it is impossible to know which genes, if any, will be associated with which traits. Thus, you could end up with a lot of investment while identifying a small number of associated genes, or potentially no genes at all. 

Describe the significance of this research for the general scientific community in one sentence.
Our findings show that specific genes in a host organism can shape the composition of associated communities.

Describe the significance of this research for your scientific community in one sentence.
Complex extended phenotypes such as community composition have an identifiable genetic basis, and thus we can use this information to test and study the extent and limitations of community evolution.

Full article: Barker HL, Riehl JF, Bernhardsson C, et al. Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition. Mol Ecol. 2019;28:4404–4421.

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