Interview with the authors: Parent and offspring genotypes influence gene expression in early life

Early life stress can often have long-term fitness effects on organisms, and the molecular mechanisms behind this have long been of interest to biologists. While much work has demonstrated that changes in DNA methylation patterns are involved, the transcriptional effects of early life stress are less well-understood, particularly at a genome-wide level. In a recent Molecular Ecology paper, Daniel J. Newhouse and colleagues investigate the transcriptional effects of different parental care strategies in white-throated sparrows. In white-throated sparrows, there are two morphs, and two associated mating pair types: tan male x white female (TxW) pairs, and white female x tan male (WxT) pairs. While TxW pairs provide biparental care, WxT pairs provide female-biased parental care. Newhouse and colleagues use RNA sequencing to assess the transcriptional effects of these differences in parental care strategies. They find evidence of an elevated stress response in offspring of WxT pairs, which provide female-biased parental care. For more information, read the full article, and see the in-depth interview with the authors below.

 A white morph female white-throated sparrow feeding her nestlings. Photo credit: Tiffany Deater.

What led to your interest in this topic / what was the motivation for this study? 
Early in graduate school, I participated in the white-throated sparrow genome sequencing project. That project was my crash course in white-throated sparrow biology, and the unique genetics and associated behaviors of the sparrows fascinated me. Most work on white-throated sparrows focuses on the adults, but nestlings are relatively understudied.  Depending on the adult pair type of the nest, nestlings will either receive biparental care (parents=tan morph male & white morph female) or female-biased parental care (parents=white morph male & tan morph female). Essentially, I wanted to see how this parental care variation impacted the nestlings.

What difficulties did you run into along the way? 
Finding white-throated sparrow nests was much harder than I ever imagined. Hiking through bogs while fighting off swarms of biting insects made it even more difficult. Thankfully, I have wonderful collaborators who are amazing at finding nests.
Also, when we designed this study, there weren’t many examples of RNA-seq from bird blood. White-throated sparrow nestlings are very small, so the amount of blood we can collect is quite small. RNA extractions proved more difficult than expected, but we managed to sequence a sufficient amount for the study.

What is the biggest or most surprising finding from this study? 
It was surprising to see a solid signature of morph-specific gene expression. As adults, there are many differences in the transcriptome between morphs and these correlate strongly with their behavior. White-morph and tan-morph nestlings look the same and do not exhibit any morph-specific behaviors like we see in adults. Despite this, we found that a large number of genes found within the chromosomal inversion are differentially regulated. Some of these genes have also been previously identified in the brain of adult white-throated sparrows. It was cool to see the same genes appear very early in life and in a much different tissue (blood).

Moving forward, what are the next steps for this research? 
From a genomics perspective, it would be great to identify the regulatory mechanisms underlying the gene expression signatures we identified here. Additionally, within a single nest, there are both white morph and tan morph nestlings. This allows us to look at nestling morph specific responses to variation in parental care. We identified some differences between the morphs within a nest, but were ultimately limited by sample size to discuss this in depth. I think this will be a really interesting topic to explore further.

What would your message be for students about to start their first research projects in this topic? 
I suggest pursuing integrative projects, like much of the work published in Molecular Ecology. Associated with that, I suggest networking and establishing collaborations early. We can’t all be experts in everything, so collaborating with research groups that complement your interests can be beneficial.
More generally, keep up with the literature as much as you can. The more you know about your system and anything related to it, the better. Don’t forget to read up on methods papers, too. Data analysis is very important so having a grasp on analytical concepts will really help.

What have you learned about science over the course of this project? 
There’s no universal way to analyze data. There are so many tools to process genomic data, so it can be overwhelming at times to keep track of everything. I also learned that data analysis takes much longer than you plan. Inevitably something won’t work, so keeping a positive attitude throughout is crucial.

Describe the significance of this research for the general scientific community in one sentence.
Parental genotype is correlated with a transcriptomic stress response in their offspring.

Describe the significance of this research for your scientific community in one sentence.
Half of all adult white-throated sparrow pairs provide female-biased parental care and this stable parental care strategy induces a transcriptomic stress response in their offspring.

Newhouse DJ, Barcelo‐Serra M, Tuttle EM, Gonser RA, Balakrishnan CN. Parent and offspring genotypes influence gene expression in early life. Mol Ecol. 2019;28:4166–4180. https://doi.org/10.1111/mec.15205.

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