Origin story: Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish

Dong, Y., T.S. Blanchard, A. Noll, P. Vasquez, J. Schmitz, S.P. Kelly, P.A. Wright, and A. Whitehead (2021). Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fishJournal of Experimental Biology.

Here is the origin story underlying the events and the science that led to this manuscript, which was a truly collaborative effort between multiple research labs including senior and junior scientists that spanned four nations. This all started with two co-incident serendipitous events. First, I (Andrew Whitehead) was invited to give a seminar talk at McMaster University (Ontario, Canada) by Graham Scott. Learning that I was going to be in the area, Pat Wright at the nearby University of Guelph (my alma mater) graciously invited me to give a seminar talk there too, and to meet with her research group. It was while meeting with Pat’s group that I learned of the mangrove rivulus and it’s extraordinary physiology: the only vertebrate self-fertilizing hermaphrodite (can create isogenic lines), amphibious, can live out of water for months, etc… I’ve always admired Pat’s research and had been keen to work with her; her group is world-renown for their experimental animal physiology work. And she was keen to see what our genomics tools could reveal about the inner workings of this extraordinary creature. So a tentative plan was hatched: Tessa Blanchard, a Masters student in Pat’s lab at the time, was doing some air-exposure experiments, and she would save us some tissues for transcriptomics. Serendipitous event number two: my colleague and my scientific hero George Somero had dropped me a line: A former postdoc of his, Yun-Wei Dong, now a professor in China, was seeking a home for his sabbatical, where he sought to build some skills and experience in transcriptomics. I had never met Yun-Wei, but a recommendation from George was good enough for me. Yun-Wei arrived in Davis about the same time that Tessa was sending us tissue samples – the team was shaping up. Yun-Wei dove head-first into making RNA-seq libraries under the guidance of lab manager Jen Roach, and we soon had a data set which provided the foundation for Yun-Wei’s quick mastery of bioinformatics skills; skills he eventually returned to China with, and embedded them within his own exciting research program, passing them on to his own students and colleagues. The data also provided a training opportunity for Picasso Vasquez, a talented undergraduate student in my lab, who ended up constructing the detailed GitHub repository that supports the transparency and reproducibility of this work. The RNA-seq data, coupled with Tessa’s physiology data, were lifting the hood on the amazing amphibious abilities of these fish, and we wanted to know more, particularly at the level of skin structure. Pat recommended her colleague Scott Kelly at nearby York University – like Pat, a core member of Canada’s cabal of famous comparative animal physiologists, and an expert in electron microscopy specializing in epithelial transport. After hearing about the experiment, and seeing some data, he was hooked. The team was growing. Tessa sent him tissues. Scott’s images were beautiful, and the discoveries were expanding. Of course more answers lead to more questions, so the team was to grow yet again. We wanted to get a sense of which proteins may have evolved in the ancestors of mangrove rivulus to support their unusual physiological abilities. The first person who came to mind was Wes Warren, an expert in comparative genomics – he and I had worked together on a study of comparative protein evolution including our Fundulus killifish. Wes was keen but too busy at the time, so recommended his close colleague Juergen Schmitz in Germany. I had never met Juergen, but a quick look at his outstanding record of research and a recommendation from Wes was all that was needed for me to try to convince Juergen to join our team. After a quick look at the data, Juergen and his student Angela Noll were on board – I was thrilled. What had started as a chance visit with Pat’s group and a tip from George Somero had grown into a collaborative integrative interdisciplinary research endeavor that wrapped around the world (though conference calls between California, Ontario, Germany, and China were challenging). I feel very fortunate to work with this outstanding group of individuals: they are all wonderful human beings, and badass scientists. It has solidified research collaborations and friendships that wrap around the globe. And it has been a stepping stone for several junior folks: Tessa is now a Ph.D. student in Trish Schulte’s lab a UBC, Picasso is a programmer in Titus Brown’s lab at UC Davis and is destined for graduate school, and Angela is a postdoctoral researcher at the German Primate Center. I am reminded that science is a product of teams of people, and serendipity plays a large role in how those teams come to be. The science that emerges is a product of good will, enthusiasm, creativity, hard work, and good communication. You never know when a chance event leads to a whole new research direction, which leads to a whole new group of friends and colleagues spread across the globe. And I am reminded that the work is nucleated by this extraordinary creature mangrove rivulus: ““There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” (Charles Darwin)

About whiteheadresearch

Andrew Whitehead is a Professor in the Environmental Toxicology Department at UC Davis, and a member of the Coastal and Marine Sciences Institute, the Center for Population Biology, the Graduate Group in Ecology, the Integrative Genetics and Genomics Graduate Group, and the Pharmacology and Toxicology Graduate Group.
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