DNA barcoding leads Smithsonian scientist to discover 7 new fish species

Think we know all the fish in the sea? A Smithsonian scientist recently discovered that what we thought were three species of Caribbean fish are actually 10--thanks to modern genetic analysis and traditional physical examination.

WASHINGTON -- Think we know all the fish in the sea? A Smithsonian scientist recently discovered that what we thought were three species of Caribbean fish are actually 10—thanks to modern genetic analysis and traditional morphological examination. The findings were published in the scientific journal ZooKeys on February 3.

Dr. Carole Baldwin, a museum specialist in the National Museum of Natural History’s Department of Vertebrate Zoology, Division of Fishes, and lead author of the paper, said the discovery suggests that there may be many more cases in which DNA barcoding can lead to new species discovery and that our current understanding may be “surprisingly incomplete.”

Baldwin and her team discovered that three species of blenny in the genus Starksia (fish less than two inches long that live in shallow waters) are actually 10 distinct species. I visited Baldwin at the museum earlier this month. Excerpts of our conversation are below.

Tell me about the scientific techniques that enabled you to discover seven new species of fish.

The whole barcoding thing is patterned after barcodes in the grocery store. In 2003 the DNA Barcoding Initiative began, as a way of barcoding the world so people could identify [species] just using [tissue]. Traditionally we identify using physical features—color pattern, number of scales, the cirri (antennae). So it was an identification tool for people who are not taxonomists and don’t have the expertise, and it’s been hugely successful for that.

People have been studying blennies for more than 100 years. But this one segment of DNA we found made us take a second look. You want DNA results to correspond to a species, and what’s happening is that one species will correspond to two genetic lineages.

How could you tell this was happening?

We’d go to all these sites in the Caribbean and get up to three samples of every species. Sampling has changed drastically—it used to be we’d collect a lot of samples, put them all in a tank and ship them home. Now that we want to do DNA analysis, we handle each specimen immediately, take tissue samples and take color photos before their coloring changes. We come back with 300 to 1,000 specimens and DNA samples.

And with these specimens, the discrepancies started popping out. With blennies—three blennies turned out to be 10. One species of sea bass turned out to be two. We didn’t start out with this in mind. We were trying to identify larval stages of fish.

But it’s not automatic. We don’t know for sure, and we don’t make the species decisions just based on the DNA. We look at the color photograph [and the physical characteristics]. And just about every time, it’s remarkable what we’ve missed in the past.

Such as?

Almost exclusively patterns of pigmentations. For example, we think some of the patterns are just different on the head. With the soap fish--related to the sea bass/grouper—we thought it was one, and [the two fish] turned out to be hugely different: the number of vertebrate, the fin ray counts.

The bottom line is that the beauty of the DNA barcoding data is that it’s directing us to where we need to look further.

There’s a lot of controversy. Some people thought the DNA barcoding would put us out of business. But I think just the opposite, because it illuminated a lot of problems on the classification system.

The two photos above are the heads of Starksia specimens S. robertsoni and S. weigti. You can see subtle differences in pigment patterns on the lips with S. robertsoni (top) lacking the white spotting seen in S. weigti (bottom)

What does this teach you about the traditional classification process and how that system might change in the future?

Today we have fewer resources in terms of money and staff, so I don’t know what will happen, because the DNA revolution has shown the need for more, not less.

There’s a new term: integrated taxonomy—combining molecular genetic data with traditional organism (or morphological) examination.

For lots of groups, they thought: We’re done [classifying]. What all this has taught us is that we’re so far from being done. The current estimate is 1.7 million species described on Earth, and it’s estimated that some 10 million more remain to be described. Surprisingly, this question of "How many species?" has received relatively little systematic attention, from Darwin's time to our own. At the purely factual level, we do not know to within an order of magnitude how many species of plants and animals we share the globe with. Fewer than 2 million are currently classified, and estimates of the total number range from under 5 million to more than 50 million.

Is there controversy over identifying more species, which means that some of what was identified previously would be incorrect?

There’s not that many good examples of where DNA barcoding identifies new lineages and then researchers follow up and study it and name it. I understand that, because it’s a lot of work. We spent almost two years with this.

What’s it like to name a new species?

There’s three ways to name a new species:

  • Based on geography;
  • Based on some anatomical feature. For example, the giant tortoise is Geochelone elephantopus: geo means land; chelone means turtle, elephan means big, and topus means foot;
  • In honor of someone.

So we had seven species. There were so many people who were instrumental in making this possible. One is named after a woman here, Mary Sangrey, so the fish is Sangreyae. Another was named for a scientist.

Why is it important for us to know there is a new species because of this different color pattern on the fish’s head?

Maybe the better question is, Why is it important to the fish? What we think is a tiny pigment or cheek pattern could be a huge difference. The first thing that changes is the pigment pattern, because that’s how they’re recognizing mates.

What’s next?

These fish all live in shallow water. We’re getting ready to start deeper dives and exploration of water 200 to 1,000 feet. The average depth of our oceans is 12,000 feet.

Scientists have been exploring diversity for a long time, and we’re still in our infancy. We think these kinds of diversity studies are as important as they’ve ever been, and DNA data will be just as important in deep water as it’s been in shallow water.

These small differences—identifying organisms through DNA—it’s time-consuming and expensive. But it’s important, and it has other uses as well. The FDA is using barcoding to identify seafood, to see if it’s really what they say it is. I just read about someone selling monkfish, and it turned out to be puffer that had serious toxins in it.

Photos: The Smithsonian

This post was originally published on Smartplanet.com


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