LET’S SUPPOSE that we are interested in studying the evolution of the squamates, the snakes and lizards. We know that if we track down the evolutionary tree of the squamates we find that they are lepidosauromorphs, and a sister group to the archosauromorphs. Ah-hah! The archosauromorphs diverged before the evolution of the lizards, so living archosauromorphs must preserve ancestral traits, we think. So we go forth and find an archosauromorph and sequence its genome. There are multiple species from which to choose, but we grab the closest one—the European starling. Since this is an archosauromorph and early diverging compared to the snakes and lizards that must mean that it is “primitive”.

Does this seem odd to you?

I hope so! But this exact kind of thinking has led to some very muddled ideas related to the sequencing of the platypus genome, reported this week in Nature. The train of thought goes something like this:

  1. Jurassic mammals diverged into a lineage leading to the monotremes and a lineage leading to the therians (marsupials and placental mammals) about 166 million years ago.
  2. Since marsupials and placental mammals diverged from each other about 145 million years ago, that means monotremes are older.
  3. Since monotremes are older, they must be more primitive than marsupials and placental mammals.

The problem is that the therians are exactly as old as the monotremes since we share a common ancestor some 166 million years ago. We seem to recognize easily that the therians have evolved significantly since they first appeared, but have a bias towards thinking that monotremes did not do the same during this same time period. In actuality when the monotremes and therians diverged both groups had the same set of ancestral traits. In each lineage some ancestral traits were replaced with new, derived traits, while other ancestral traits were retained. We have a tendency to emphasize the derived traits of placental mammals while overlooking ancestral traits. Then when we come across a different set of ancestral traits in a mammal on a different evolutionary branch, we find the set of ancestral traits that they happened to retain surprising and “primitive”. Add in a mix of novel derived features and you get, well, journalists saying silly things.

The Associated Press says:

The platypus is classed as a mammal because it has fur and feeds its young with milk. But it also has bird and reptile features—it lays eggs, has a duck-like bill and webbed feet, it and lives mostly underwater. Males also have spurs on their heels that inject pain-causing venom to ward off mating rivals.

Scientists believe the platypus and humans shared an evolutionary path until about 165 million years ago when the platypus branched off. Unlike other evolving mammals, the platypus retained characteristics of snakes and lizards, Graves said.

Meanwhile, Science News gets it completely wrong.

Though it’s a true mammal with fur, milk and sweat, the waddling duck-billed platypus also retains reptilian features, like venom production and egg-laying. . . . Take the venom genes—common in reptiles, but not in mammals. Spurs on platypus males’ hind legs inject venom like snake fangs do—venom that evolved as snake venom did, from tweaks in extra copies of the same types of ordinary nontoxic genes, the genome analysis shows.

Platypus venom genes, the study shows, are similar to reptilian venom genes but aren’t exactly the same. The genes are like skinny, blond, spoiled party-girls who grew up on different continents. Although they look alike, the genes became toxic independently.

ScienceDaily adds to the confusion, although partly redeeming themselves later in the article.

The duck-billed platypus: part bird, part reptile, part mammal—and the genome to prove it.

T. Ryan Gregory at Genomicron has written about misunderstandings of phylogenetic trees and the evolutionary process even among scientists, and thinks that these misunderstandings are responsible for some of the weird quotations showing up in the news. I think that it’s at the very least misleading when scientists are saying things like this:

The research showed the animal’s multifaceted features are reflected in its DNA with a mix of genes that crosses different classifications of animals, said Jenny Graves, an Australian National University genomics expert who co-wrote the paper.

“What we found was the genome, just like the animal, is an amazing amalgam of reptilian and mammal characteristics with quite a few unique platypus characteristics as well,” she told the Australian Broadcasting Corp.

So what’s wrong with saying that a monotreme has reptilian or avian traits? It makes zero sense evolutionarily. If we say marsupials have reptilian traits, then they must have descended from reptiles. As I have mentioned before, mammals are vehemently not descended from reptiles. Reptiles (and birds, who often get left out) and mammals share a common ancestor long ago that was neither a reptile nor a mammal, but an amniote. This amniote ancestor had many traits that got passed on to the sauropsid lineage and the synapsid lineage equally. Many of these traits were lost in the synapsid lineage, and others were acquired. Different traits were lost in the sauropsid lineage, and different other traits were acquired.

Platypuses do not have “reptilian” traits, they have ancestral amniote traits. The most obvious one is egg-laying. Platypuses retain a variety of amniote genes related to egg development that have been lost in the therians. In addition to retaining some ancestral amniote traits, platypuses have acquired new traits. One such trait is venom production—contrary to the Science News article above, platypus venom is not “reptilian” but an independently acquired trait and merely convergent upon reptile venom. Additionally, platypuses have an electrosensory system that allows them to detect prey based on electrical fields. Possessing these traits, a platypus might look at us and ask, “Who are you calling ‘primitive’?” since we preserve the ancestral (“primitive”) state by lacking both features.

I do not mean to diminish the significance of this paper. By studying the genomes of all extant synapsids and comparing these to extant sauropsids, we can learn more about our amniote common ancestor, and better understand when various traits evolved. But it is important to recognize that platypuses and echidnas are creatures with evolutionary histories as long as those of the therians. They do not represent basal monotremes, and have a variety of derived traits. Additionally, the amniote traits that are retained by monotremes do not make them “primitive” any more than the amniote traits retained by therians make that group “primitive”. As sister groups, the monotremes and therians both have ancestral amniote traits plus additional derived traits. We just overlook our “primitive” traits due to their familiarity.

I initially meant to address the information in the paper itself today, but this entry has become rather long. Now that I’ve gotten the ranting out of the way I will post on the paper itself in the next few days. I will try to get the bulk of that entry done today, but since I am going out of town this weekend I may be delayed.