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Q&A: Dartmouth's Kevin Peterson Discusses miRNAs and Annelid Phylogenetics


Kevin Peterson

Associate professor, biological sciences, Dartmouth College

• Postdoc, California Institute of Technology — 1996-2000
• PhD, geology, University of California, Los Angeles — 1996
• BA, biology, Carroll College — 1989

Continuing his efforts to use microRNAs as a guide to solving a variety of evolutionary questions (see RNAi News, 2/28/2008), Dartmouth College's Kevin Peterson and colleagues this month published data showing how they used the small, non-coding RNAs to resolve conflicting theories on the evolution of annelids.

Writing in the Proceedings of the Royal Society B, Peterson and researchers from Yale University, North Carolina State University, and the Institut de Génomique Fonctionnelle in France, reported how miRNAs have the potential to "reveal the broad pattern not only
of the annelid evolutionary tree, but also that of other metazoan groups."

Last week, RNAi News spoke with Peterson about the findings and other questions to which miRNAs may hold the answer.

Let's begin with the annelid phylogenetic problem that you were looking to answer.

Morphologists have classically recognized all the segmented worms as a natural assemblage of organisms broadly split into two groups: the terrestrial forms and the marine forms. But when people started looking at their molecular sequences starting in the early 90s, they found that, first off, the terrestrial forms were nested inside the marine forms … [but it] really isn't all that surprising that the terrestrial one evolved from a marine forbearer; that's typically what we see with basically all instances of terrestrialization.

The big surprise was the non-segmented worms were often nested inside the segmented worms, suggesting that they had a segmented annelid worm ancestry. One of the groups of worms that typically falls inside the annelids is a group called peanut worms or sipunculans, but many other groups of animals, [such as] mollusks, even snails, often fall within the annelid [grouping]. It got to the point where when you say "annelids," you don't even know what that means anymore. Almost all of what we call lophotrochozoan — if you're not a vertebrate, or a C. elegans, or a Drosophila, chances are you're a lophotrochozoan — fall within the annelids [category].

The problem with that is the fossil record suggests that these groups of animals, like sipunculans, evolved before the last common ancestor of all living annelids. So there is the problem that the molecules are suggesting one view of annelid evolution, while the fossil record was suggesting something more in line with what traditional morphologists have recognized, with the caveat that the annelids were in the ocean, not on land.

So a lot of annelid [researchers] have sequenced a lot of genes, but have not been able to resolve the problem for reasons we don't understand. There is something funny about annelid sequences that make them exceedingly difficult to analyze using traditional methods.

So it was your suspicion that microRNAs might be used to address the issue?

Exactly. What I liked about [tackling this problem] was that no one had actually highlighted the fact that the fossil record was in conflict with the molecular phylogenies, and this was a perfect test case for microRNAs because they don't suffer from any of the problems that genes used for molecular phylogenies can suffer from, things like long-branch attraction.

Once you decided to look at microRNAs, how did you specifically approach the problem?

We made 454 libraries from four key taxa: two [marine] polychaete worms, a [terrestrial form of the] earthworm, and a sipunculan worm. Then, we characterized the expressed microRNA complement of one of the ones, called Capitella, because it has a sequenced genome, and found in the neighborhood of 70 to 80 microRNAs.

Then we simply asked, "Who shares what complement of these microRNAs?" We found that the sipunculan shares some but not all of the microRNAs that are conserved in the other three annelid groups. What that says is that sipunculans are more closely related to annelids than any other organism that we looked at, but they are not nested inside of the annelids, as molecular phylogeny has purported to show. In other words, [our findings] are entirely consistent with the fossil record.

Further, we showed that the earthworm is more closely related to Capitella than Capitella is to the other polychaetes — again consistent with the fossil record [indicating] that the terrestrial forms evolved from the marine forms.

Having had success here, are there other questions or organisms to which this approach can be applied?

Yeah. [In fact,] we [have studied phylogeny of jawless fishes] … and we used microRNAs to attack that problem, which is important in terms of thinking of the origins of vertebrates and the vertebrate body plan. [But with a paper being prepared publication] we can't talk about [the data].

We're also using [miRNAs] to address turtle relations because with turtles, there is a conflict between morphology and molecules, and it's another place where microRNAs might be useful. Arthropod interrelationships, like how spiders and millipedes are related to crustaceans and insects, is another area.

We also have a paper submitted right now in which we think we have solved a problem in sponge systematics.

Have you ever thought about looking at other types of small, non-coding RNAs in your research?

Well, we do know from analyses of many animals that the only conserved small RNAs are microRNAs. [Piwi-interacting RNAs], for example, evolved very quickly and they might be used for really shallow [investigation], but even there it appears unlikely [they would be of use]. It looks like for deeper time questions with respect to small RNAs, microRNAs are the only player.

Have you encountered any limitations with using microRNAs? Are there technological hurdles that still need to be overcome?

I think [miRNAs] are pretty amazing, having evolved in such an unusual way. It [happened] in the perfect way that you'd want genes to evolve for phylogeny. But as a biological system, there is always going to be some inherent noise. We're working on a problem where the microRNAs are not resolvent [with] the phylogeny, and we're trying to figure out why.

There will be places on the tree where they won't be useful, but I think that might actually be telling us something about animal evolution at that time, as opposed to being [a situation where] the experiments didn't work. Also, if you have a genome that has been secondarily reduced, then you're going to lose a lot of the microRNAs, but there is nothing you can do about that.

[It's not unlike] when people discovered that retrotransposons could be used as phylogenic markers, which was a really neat discovery because they are so rare. But the problem is that that signal degrades over time because they are not functional. But microRNAs, because they remain functional, their signal remains intact for hundreds of millions of years. So we think it's pretty cool.

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