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Nature Article Finds MicroRNAs are “Tearing Apart Traditional Ideas about the Animal Family Tree”

Casey Luskin

A striking new piece in Nature, “Rewriting Evolution,” recounts some of the severe problems that molecular data keep creating for the tree of life. The problem, as we’ve discussed many times here before, is that the molecular data often conflict with other data used to construct evolutionary trees, called phylogenies. One gene gives you one version of the tree of life, but another gene gives you a different, conflicting version of the tree.

But now that biology is discovering and understanding more and more different types of noncoding DNA elements, like microRNAs, we’re finding that they too challenge conventional wisdom about evolutionary relationships.

MicroRNAs are short RNA molecules found in eukaryotes that bind to messenger RNA to regulate gene expression. Still not completely understood, it’s thought they can have a major influence on organismal development. But consider some passages from the article, telling how microRNAs are causing problems for the tree of life:

  • “Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree”
  • “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree”
  • “What we know at this stage is that we do have a very serious incongruence”
  • “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.”

The main example according to the article has to do with problems in the phylogeny of placental mammals. Under the standard phylogeny of placentals, the line leading to elephants “branched away from the rest of the placentals around 90 million years ago. Then came dogs, followed by primates (including humans) and finally rodents.” However, new phylogenies based upon microRNAs suggest “the tree is all wrong.”

A leading researcher in this field, Kevin Peterson has “sketched out a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents.” The article continues:

When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn’t cooperate. If the traditional tree was correct, then an unprecedented number of microRNA genes would have to have been lost, and Peterson considers that highly unlikely. “The microRNAs are totally unambiguous,” he says, “but they give a totally different tree from what everyone else wants.”

What is clear from the article is that many researchers don’t “want” to have to confront this data. Some assume that the microRNA data must be wrong because it conflicts with the orthodox phylogeny of placental mammals. Some researchers appear to be in danger of throwing out data simply because it conflicts with the perceived evolutionary wisdom.

Debates will continue about the best way to reconstruct evolutionary trees. But perhaps there’s a more fundamental problem.

Maybe the reason that different genes yield different evolutionary trees is because there isn’t a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong.


Casey Luskin

Associate Director, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



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