91̽»¨ scientists are looking at the burgeoning field of coral genetics to better predict, and maybe even prepare for, coral’s future threats. Their new study uses modern genetic-sequencing tools to reveal the relatedness of three similar-looking corals.

“This coral appears to be three different species, but it’s been debated whether it’s really three separate species or whether it’s one that’s really variable in its appearance,” said first author , a 91̽»¨doctoral student in aquatic and fishery sciences.

Defining a species matters for conservation, because you can’t monitor and protect a species if you don’t know it exists.

“In the past we’ve relied on physical characteristics, like the coral skeleton, to determine what constitutes a coral species,” Dimond said. “But the problem with that is that corals can vary their skeletal architecture. So disentangling whether you have two different species or just a single species that’s varying itself due to environmental conditions can be really tricky.”

Biologists had originally assumed that the widespread Atlantic corals were three species. Then a 2014 genetic study found that they were the same.

The new , to appear in an upcoming issue of , finds new genetic evidence that they may, in fact, be three species. It also provides a glimpse into the epigenetics, a more mysterious form of genetic expression.

“It’s the most in-depth analysis of coral epigenetics to date,” said co-author , a 91̽»¨associate professor of aquatic and fishery sciences. “It may also prompt a thorough re-evaluation of these corals’ family trees.”

The study examined , one of the more common types of corals. It is not among the roughly two dozen coral species listed as endangered. If it were to be listed in the future, biologists would need to know what constitutes a species.

The study used new tools to look at more than 1,000 single-letter changes in the genetic code, a marker of genetic diversity. The previous genetic study had looked at just 10 or 11 of these markers and found them to be the same in all three forms of coral.

“It appears to be a matter of looking more deeply into the genome, which is something we’ve only been able to do for the last couple of years,” Dimond said. “Molecular biology technology is changing so rapidly, and this is just an example of that.”

To definitively conclude that the three forms are, in fact, different species would mean using the same sequencing technique on more samples from across these corals’ range, which includes the Gulf of Mexico, the Caribbean, the western Atlantic Ocean and off the coast of West Africa.

The authors also looked at , which is any process that affects how the genetic code plays out in real life. Dimond’s research focuses on the epigenetic process of DNA methylation, in which a carbon-based methyl molecule can bind to the DNA strand and thus affect how it gets translated into a protein that acts in the body.

The study’s epigenetic analysis didn’t show any consistent pattern among the different coral branch sizes, so was inconclusive. But the authors believe it provides a step forward in understanding this process in corals.

“It just gives a glimpse of the epigenetic variation within this group,” Dimond said.

Scientists are interested in coral genetics and epigenetics because it could help them predict how corals will adapt to continued changes in the ocean environment.

Coral genetics and epigenetics could also aid in the process of selective breeding, a topic of current interest that could help corals deal with potentially rapid changes in the ocean environment.

“Selective breeding involves finding individuals that are more tolerant of high temperatures and, in some cases, finding specific genes that confer resistance to higher temperatures,” Dimond said. “Once you’re identified those genes and identified individuals that have those genes, then you can breed them, and seed reefs with those organisms.”

The new study, he said, is part of the fundamental research that could help toward achieving those goals.

The research was funded by a Hall Conservation Genetics Research Award from the 91̽»¨College of the Environment, the ARCS Foundation Seattle Chapter, the John E. Halver Fellowship to the 91̽»¨School of Aquatic & Fishery Sciences and the National Science Foundation. The other co-author is Sanoosh Gamblewood at Western Washington University in Bellingham.

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For more information, contact Dimond at jldimond@uw.edu and 360-650-7400 x253 or Roberts at sr320@uw.edu or 206-866-5141.

NSF Grant: OCE-1559940

Last year, researchers identified a type of pathogen known as a , but they still can’t explain the or why a common ocean virus can wreak havoc on so many starfish species from Alaska to Southern California.

Now, a from around the country has contributed key information about the sea stars’ immune response when infected with this virus.

The students, while taking a at the 91̽»¨’s , looked specifically at how genes expressed themselves in both healthy and sick sea stars. It’s the first time researchers have tracked how the genes behave when encountering this naturally occurring pathogen, which could help explain how sea stars attempt to fight the virus and why they develop lesions and appear to melt.

The researchers in the journal PLOS ONE in July.

“Doing this study isn’t going to save the sea stars, but from an ecological perspective, it provides new information,” said , a 91̽»¨associate professor of aquatic and fishery sciences. “This could be a building block for future studies on the evolution of immune repertoires.”

Roberts co-taught the five-week course in summer 2014 with the UW’s , an associate professor of aquatic and fishery sciences, and , a professor at Cornell University, with a focus on publishing results, methods and observations online using the .

Students tracked their progress and discoveries through , and all of their code and analyses are available for anyone to see and reproduce. This transparency, combined with the rigorous, all-consuming five weeks at Friday Harbor Labs, made it a useful and memorable experience, students said.

“I learned so much about open science and the idea of having open lab notebooks, where everything is available. That has had the biggest impact on how I do my science,” said co-author , a doctoral student at Northeastern University. “Open science was really integral to us being able to work on this paper together.”

Sharing their results in a paper published in open-access journal PLOS ONE was an added bonus for this particularly driven group of students, Roberts said. The paper-writing and submission process all happened after class ended for the summer.

“This was clearly the most experienced, ambitious group we’ve had in this course,” Roberts said. “All of them certainly were dedicated to get it done.”

The eight students who share lead authorship on the paper met for hours on video conference calls, talking through specific details of the paper. The students — from the University of Texas at Arlington, Pennsylvania State University, University of California, Santa Cruz and others — all contributed equally to writing and editing the manuscript, housed as a shared Google document, which is a rare approach in today’s academic publishing world.

“I work in smaller groups or with researchers from only one or two institutions for most of my projects,” said co-author , a doctoral student at Cornell. “This was really interesting because we were able to collaborate across so many different backgrounds and institutions.”

Before the students arrived at Friday Harbor Labs, the course instructors and research assistants collected sea stars from four sites in Washington, then infected some with the virus. They sent the samples away to get RNA data for each group of sea stars, then the students analyzed those data during class.

The students started by looking at 30,000 genes from healthy and sick sea stars. They found that sick sea stars expressed genes differently than healthy ones, and they saw strong evidence of an immune response at the genetic level among infected sea stars. They also found that some of the genes involved in the nervous system and tissue-building were expressed differently in sick and healthy sea stars, which could help scientists better understand how the disease wreaks havoc on the sea stars’ bodies.

Researchers now suspect certain environmental conditions or perhaps water temperature contribute to the rate of disease or how effectively the sea stars can fight it off. As scientists around the country as well as studying the genetic code of the densovirus, they hopefully can use this initial characterization of how sea stars respond to disease, Roberts said.

“This gives us a bit of insight into what’s going on,” Roberts said. “One could argue that in the long term, this information could be used to build upon.”

Other co-authors are Lauren Fuess of the University of Texas at Arlington; Morgan Eisenlord, Reyn Yoshioka, Colleen Burge, Ian Hewson and Harvell of Cornell; Collin Closek of Penn State; Ruth Mauntz of San Diego State University; Monica Moritsch of UC Santa Cruz; Paul Hershberger of the U.S. Geological Survey Western Fisheries Research Center; and Friedman and Roberts of the UW.

This research was funded by the National Science Foundation’s Ecology of Infectious Marine Diseases Research Coordination Network Workshop.

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For more information, contact Roberts at sr320@uw.edu or 206-866-5141.

Grant number: OCE #1215977