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Auburn and Florida State work together in "search for the Holy Grail"

 

Jon Armbruster with a Labeo collected in 2010 from the Democratic Republic of Congo. Photo by Keith Ray.

Jon Armbruster with a Labeo collected in 2010 from the Democratic Republic of Congo. Photo by Keith Ray.

Auburn University scientists have teamed up with researchers from Florida State University in an attempt to reconstruct the evolutionary relationships of minnows and their relatives, a group of fishes that represents approximately 4,000 species worldwide. According to Jonathan Armbruster, professor of biological sciences and curator of fishes for the Auburn University Museum of Natural History, constructing the phylogenetic tree, or evolutionary tree, of minnows presents a huge challenge, and it wasn't until recently, with the advent of advanced genomic sequencing techniques, that researchers were able to begin scratching the surface of such a daunting task.

"The relationship between various species of minnows has been in a state of flux because studies have shown many different and conflicting relationships between minnows," said Armbruster. "But, that was the best scientists could do at the time because they could only collect around six genes at a time. Now, thanks to a new method called ‘anchored phylogenomics,' we can look at hundreds of genes relatively rapidly and relatively cheaply."

Armbruster first became aware of anchored phylogenomics at the Evolution 2012 Conference, an event that brought together scientists from all over the world who are dedicated to the study of ecology and evolutionary biology. Two faculty members at Florida State University, Emily and Alan Lemmon, a husband-and-wife team, gave a presentation at the conference on how they developed the anchored phylogenomic technique. Emily, an assistant professor in the Department of Biological Sciences, enlisted the help of her computer-savvy husband, Alan, an assistant professor in the Department of Scientific Computing, to create the method which extracts genes at a much faster and efficient rate.

"Anchored phylogenomics is a more pointed technique. It targets specific genes and it's a more efficient way of looking at evolutionary relationships," said Armbruster.

Over the course of the past several years, Armbruster and his graduate students have travelled the world collecting minnows from places as far away as Africa and Thailand. The specimens, which are housed in Auburn's Museum of Natural History, provided the DNA for the research.

Minnows collected during a Guinea expedition in 2013. Photos by Jon Armbruster.

Minnow collected during a Guinea expedition in 2013. Photo by Jon Armbruster.

"Auburn extracted the DNA then shared it with Florida State, and after they run the sequencing, we will analyze the results," said Armbruster.

Two Auburn graduate students, Milton Tan and Carla Stout, are assisting with the project as part of their doctoral research.

"Anchored phylogenomics has changed how we do things in phylogenetic research, at least for now, and there is a lot you can do once you know the evolutionary relationship of groups," said Tan. "I am looking at minnows that do not mature to adulthood. They are paedomorphic and look like baby fishes as adults – transparent, really small, and a lot of their bones remain as cartilage. There is more than one genus of these fishes, and the question is, are they each other's closest relatives or not. If they are, this characteristic would have evolved one time. If they are not, they would have evolved this several times."

Tan said Auburn has received the initial results for about 100 genes and he has begun analyzing the data.

"The science looks good," said Tan, "but what we are seeing is also different from past results."

Armbruster likes to compare the search for a phylogenetic tree to the search for the Holy Grail.

"There is only one correct phylogenetic tree and it's probably imaginary because we are taking this complex process and simplifying it, and, in the end, you don't really know if you have found the true tree," he said. "But the research is important because it helps us make sense out of life. And many disciplines, such as ecology and morphology, do not make sense at all without knowledge of evolutionary relationships, not to mention we need a stable taxonomy."

Minnows collected during a Guinea expedition in 2013. Photos by Jon Armbruster.

Minnow collected during a Guinea expedition in 2013. Photo by Jon Armbruster.

The research is supported by a multi-institutional, four-year National Science Foundation grant in the amount of approximately $3 million titled, "All Cypriniformes Species Inventory," for which Armbruster is one of the principal investigators. Research is also supported by the Fish Collection in the Auburn University Museum of Natural History, which provides access to specimens that are integral to studying and understanding the biodiversity of minnows.

The Fish Collection in Auburn's museum contains more than 800,000 preserved specimens in more than 60,000 lots, or jars, and the collection is growing rapidly with approximately 1,800 lots added annually. Particularly strong are collections from all over Alabama and Georgia, including some of the few major collections from the southeastern U.S. made prior to 1950. Also included are specimens of most fish species of the U.S., and a significant collection of marine fishes from the Gulf of Mexico.

"In the last 15 years, we have taken a collection with mainly local interest and made it a very important global collection," said Armbruster. "We have specimens from every continent, and we have traveled to some of the most remote places on the earth to discover new species."

Also included is a Neotropical fish collection featuring species from Bolivia, Brazil, Colombia, Ecuador, Guatemala, Guyana, Panama, Peru, Suriname and Venezuela. There are also significant collections from Africa and Southeast Asia. Scientists from all over the world have used the wealth of data contained within Auburn's Fishes Collection to learn about species diversity, morphology, anatomy, genetics and distributions.

The Auburn University Museum of Natural History is sponsored by the College of Sciences and Mathematics. For more information on the Fish Collection, watch the behind-the-scenes tour here or visit the Auburn University Museum of Natural History's website. For more information on Armbruster, click here.

By Candis Birchfield, College of Sciences and Mathematics

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Last Updated: Dec. 28, 2013

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