Dissecting Fish Taxonomy

Published in the Auburn University Graduate School Magazine, as Jessica Nelson

Cataloguing the world around us is not a new occupation (or preoccupation) for humans, but the science of taxonomy still seems like murky water to many of us. Why is it important?

Milton Tan, a graduate student in biological sciences, says that even some scientists question the modern day relevance of the painstaking work that taxonomists do to catalogue new species and assign them scientific names. Perhaps in a technology-driven age, just the idea of a process devised in the 18th century seems out of place. Tan, however, believes that taxonomy is a sort of building block for the rest of biological research.

“If you don’t know what you’re studying, you can’t talk about it correctly and infer how this differs from this,” he says. “It presents the language that they use to talk about the species.” He continues in a conservationist vein: “People talk about what a shame it would be if the elephants were extinct. But there are millions of species we don’t even know about; how are we supposed to protect them?”

In other words, aside from the joy of knowledge, Tan sees it as a race to catalogue nature’s wonders before the human footprint presses them into a fossil record. In this light, taxonomy suddenly seems urgent.

The table in front of Tan is cluttered with vials containing fish immersed in dingy liquid, all members of a quirky group of fish called armored suckermouth catfishes. This lab has earned a reputation for expertise with these fish in particular, led by professor Jon Armbruster. Popular in the aquarium trade, these fish are what brought Tan to Auburn.

After several years of keeping aquarium fish, Tan says, “I kind of focused in on how I think these fish are the coolest things to keep.” He was intrigued by the breadth of diversity – over 800 species – and their bizarre appearance. They have wild color patterns, armored plates on most of their bodies, and that odd sucker mouth.

He was an undergraduate student at the University of Delaware when he noticed an article about the discovery of four new species in the genus Hypancistrus – the genus he was already fascinated by. It was Armbruster’s lab that had described these fish, and Tan was immediately interested in both the lab and taxonomy.

He was already leaning toward biological research, probably with fish. But the news that he could have a career that included working with and describing his favorite fish was exciting.

“I was like ‘This is awesome! You can do this? Like as a living?’” Tan’s own turn for making fish news came in 2012, when he was contacted by National Geographic magazine about a new species of armored suckermouth catfish that he described. For him, it was another day in the lab. “It’s kind of funny, because Jon, my advisor, has described 30 or 40 of these species, and none of them have gotten a feature. It seems kind of random, but I’m not going to turn down National Geographic,” he says.

Tan had recently published his description and name for Cordylancistrus santarosensis, which was collected in Ecuador and sent to the lab by a collaborator. The description appeared in the journal Zootaxa, a “megajournal” for publishing new species descriptions, and Tan thinks perhaps their decision to make the paper open access helped attract notice. He is bemused but glad for the unexpected notice.

When a scientist talks about “describing” a species, something very specific is meant. Every single physical detail must be noted, and this description serves as the final word in defining the characteristics of a new species and how it differs from close relatives. The taxonomist also has the responsibility of assigning a scientific name.

Scientists can get a little proprietary over the naming rights to new species, which is one of the reasons the journal Zootaxa is useful in getting descriptions on the public record in a speedy manner. The first description published is the one that sticks – and no one wants to do the work of description and then get edged out by a few weeks. Although he laughs about the scenario, Tan admits that sometimes people get a little combative over naming rights.

“You obviously don’t want to be duplicating someone else’s work, but it’s also something that’s special to you,” he says. “This group of fish that I’m working on, for example, I want to be the person that puts the name on these.”

Although he had assumed that his dissertation would stay with the armored suckermouth catfishes, his other interest in evolutionary questions has led him in another direction. Students in this lab also study systematics, which tries to reconstruct evolutionary relationships.

Although studying physical specimens is one way to tackle systematics, Tan explains that they can now use DNA sequences to look at relationships between fish in a group. He points to a poster he and his lab mates put together.

“So these are all members of the same species of Hemiancistrus, and these are another species, and they all group together in a single genus. That may change as we add more species, but it’s a start.” He says that they can use this kind of genetic data to interpret not only relationships, but “biogeography,” or how the fish migrate.

In contrast to the archaic-seeming process of describing new species, DNA sequencing brings biotechnology to the science of taxonomy. It is this technology that makes possible the kind of research that Tan intends to pursue for his dissertation.

He will be studying an entirely different group of fish called cyprinids – or minnows. One fish in this group, the zebrafish, is what is considered a model organism in that it is heavily studied and figures prominently in developmental research for fish. One reason for this is that they have transparent larvae.

These baby minnows are transparent and also external to the mother (as opposed to mammals, which gestate internally), so they provide loads of data. Because of their popularity in developmental research, their entire genome has been sequenced. “You’ve got this huge genomic database, and you’ve got all the developmental data,” Tan says. “What I’d like to look at are some of its relatives that have variation in their adult appearance.”

In particular, there are members of two groups that essentially never mature. Multiple species of the genera Paedocypris and Danionella retain juvenile characteristics into adulthood, and remain tiny, transparent fish for their entire lifespan. Because of this oddity, they have been studied some, but what Tan wants to do is entirely novel – in part because technology has only recently made it practical to attempt.

“So not only are they small, but they don’t develop completely in other ways as well – for example, in their bone development. They are missing approximately 40 bones that normally develop in zebrafish.” Here is where it gets exciting. Because there is such a wealth of data on zebrafish, a close relative of both of these species, it begins to look possible to actually try to match genetics with appearance.

Imagine reading DNA like a blueprint.

This is not possible yet, but the series of unique circumstances surrounding these three tiny fish species make Tan think that he might be making a few steps in that direction.

These Paedocypris and Danionella both have a paedomorphic (juvenile) appearance, but they are not each other’s closest relatives, evolutionarily speaking. This means that they evolved this characteristic independently – like birds and bats both have wings.

“The idea,” Tan says, “is that gives us two replicates in this experiment, allowing us to compare both of these miniature guys and normal guys like the zebrafish.”

He is enthusiastic about this new direction, but isn’t forgetting his strange catfish. “I’m still going to work on all these fish,” he says, and gestures to some of the vials, “and describe all these.”

Although this line of research could keep him busy for many years, he still hopes in the future he can bring what he learns about minnow genetics back around to take an even closer look at the armored suckermouth catfish.


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