About the author
Shelby Tisinai is a PhD Candidate in the Busch Lab at Washington State University. She is currently using molecular techniques to explore environmental and genomic drivers of local adaptation in plant populations endemic to steep elevational gradients.
“It’s called research because you always have to redo it.”
A cynical statement formed from a cynical outlook from a seasoned and ready-to-graduate Ph.D. Candidate. He related it to me, then a fresh and dewy-eyed Ph.D. student, who had just sympathized with him after he had found out one of his final experiments needed to be redone. Eventually, that seasoned Ph.D. Candidate found success in his experiments, and he graduated. Soon after, I, too, learned that research is often peppered with hiccoughs, if not outright failures that require a change in methods and some patience with oneself.
Last year in late May, after I had been awarded the EECG grant, a virus swept through the greenhouse where my plants were supposed to be happily growing. My plants survived, but I couldn’t very well use the plants to continue my AGA-funded research. My aim was to study gene expression differences along an elevational gradient and relate them back to environmental differences that covary with elevation. For gene expression studies in particular, maternal effects must be normalized among individuals and among populations for at least one generation to minimize noise in the dataset. This greenhouse-grown generation was supposed to serve as the parental generation, from which I would collect seeds to generate an F1 generation. Cardamine cordifolia (Figure 1), a wetland crucifer endemic to a steep elevational gradient in the Southern Rocky Mountains, is slow-growing. As it takes around 4 months for this plant to flower and another month or so for them to set seed, losing this generation to a virus was quite the setback. While I was not enthusiastic about switching to a different study system, a change seemed prudent. The only thing I needed to do was to humble myself and ask for help. Determination and persistence are well and good, but at some point, you’ve got to recognize when it’s time to let go and move on.
Dr. Jill Anderson and her lab at University of Georgia, studies a different crucifer — Boechera stricta (Figure 2). B. stricta grows along the same elevational gradient in the same region — though different habitat types — and grows a little bit faster. As diploid organism, it has also been deemed a sort of “non-model model system” for ecological evolution (eco-evo) studies in natural settings. Past work has found that populations are predominantly inbreeding (FIS = 0.89; Song et al., 2009) with low among-population differentiation (Fst ~ 0.07; Rushworth et al., 2011) Dr. Anderson and other collaborators have used populations of B. stricta in the Southern Rocky Mountains, near the Rocky Mountain Biological Laboratory (RMBL) for many studies — both organismal and molecular — on local adaptation (e.g., Anderson et al., 2012; Wadgymar et al., 2018; Bemmels and Anderson, 2019; Anderson and Wadgymar, 2020). Using B. stricta would allow me to ask the same questions that I wanted to ask using C. cordifolia using very similar methods. I reached out to see if she’d be willing to share some of her seeds collected from greenhouse-grown plants that originated from wild populations. Thankfully, she was. And, thankfully, the setback to my timeline would be minimal.
As of now, RNA has been successfully extracted, RNA samples have been sent off for sequencing, and I’m set to receive the data within the next week or two. I’m looking forward to spending the next couple of months eyeball-deep in data analysis and writing, working out the intricacies of gene expression and its importance to local adaptation. Fall semester should commence with the analysis complete and a manuscript nearly ready for submission.
I suppose, in addition to learning how to properly conduct research, graduate school is a place where you learn how to overcome setbacks, to reassess your strategies, gain resilience, and perhaps more importantly, learn to be patient and kind to yourself. Maybe, rather than thinking that “it’s called research because you always have to redo it”, we can instead think of it as “it’s called research because you get to redo it (how cool is that?)”.
References:
Anderson, J. T., D. W. Inouye, A. M. McKinney, R. I. Colautti, and T. Mitchell-Olds. 2012. Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change. Proceedings of the Royal Society B: Biological Sciences 279: 3843–3852. https://doi.org/10.1098/rspb.2012.1051
Anderson, J. T., and S. M. Wadgymar. 2020. Climate change disrupts local adaptation and favours upslope migration A. Angert [ed.],. Ecology Letters 23: 181–192. https://doi.org/10.1111/ele.13427
Bemmels, J. B., and J. T. Anderson. 2019. Climate change shifts natural selection and the adaptive potential of the perennial forb Boechera stricta in the Rocky Mountains. Evolution 73: 2247–2262. https://doi.org/10.1111/evo.13854
Rushworth, C. A., B.-H. Song, C.-R. Lee, and T. Mitchell-Olds. 2011. Boechera, a model system for ecological genomics: ECOLOGICAL GENOMICS IN BOECHERA. Molecular Ecology 20: 4843–4857. https://doi.org/10.1111/j.1365-294X.2011.05340.x
Song, B.-H., A. J. Windsor, K. J. Schmid, S. Ramos-Onsins, M. E. Schranz, A. J. Heidel, and T. Mitchell-Olds. 2009. Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta , a Wild Relative of Arabidopsis. Genetics 181: 1021–1033. https://doi.org/10.1534/genetics.108.095364
Wadgymar, S. M., R. M. Mactavish, and J. T. Anderson. 2018. Transgenerational and Within-Generation Plasticity in Response to Climate Change: Insights from a Manipulative Field Experiment across an Elevational Gradient. The American Naturalist 192: 698–714. https://doi.org/10.1086/700097