1. New evolutionary research disproves living missing link theories

Evolution is not a steady march towards ever more sophisticated beings and therefore the search for the living “missing links” is pointless, according to findings published by a team of researchers led by Dr. Hervé Philippe of the Université de Montréal’s Department of Biochemistry.

And according to the most basic grasp of how evolution works.

2. Primates’ Unique Gene Regulation Mechanism: Little-Understood DNA Elements Serve Important Purpose

“Previously, no one knew what Alu elements and long noncoding RNAs did, whether they were junk or if they had any purpose. Now, we’ve shown that they actually have important roles in regulating protein production,” said Maquat, the J. Lowell Orbison Chair, professor of Biochemistry and Biophysics and director of the Center for RNA Biology at the University of Rochester Medical Center.

There’s been plenty of interest in possible roles for some Alu elements. There are more than 1,000,000 of them in the human genome. Seems like overkill, no?

Anyway, it seems Coyne may have taken one small step away from absolute adaptationism in his post “Redundant parts“. (I have to admit, the question he posed about “superfluous” veins, “Maybe we can live without them, but couldn’t they have evolved as ‘backups’—in case something went wrong with a partner vessel?” is the kind of thing I would expect one of my introductory evolution students to ask at the beginning of the course).

You can’t go for a month without seeing a claim that some new discovery has rewritten evolutionary history. If headlines are to be believed, phylogeny – the business of drawing family trees between different species – is an etch-a-sketch science. No sooner are family trees drawn before they’re rearranged. It’s easy to rile against these seemingly sensationalist claims, but James Tarver from the University of Bristol has found that the reality is more complex.

Check out the full post.

• The Curious Disconnect: Introduction (March 19, 2010).
• The Mutationism Myth 1. The Monk’s Lost Code and the Great Confusion (March 29, 2010) describes how the mutationism story is told in books and articles.
• Theory₁ vs Theory₂ (April 13, 2010) explores a hidden distinction that will prove very useful later.
• The Mutationism Myth, 2. Revolution (April 30, 2010) will show you how to think about evolution the way Darwin did.
• The Mutationism Myth, 3. Foundations of Evolutionary Genetics (May 19, 2010) shows some of the synthetic thinking of the Mendelians.
• The Mutationism Myth, 4. Mendelian Heterodoxies (May 25, 2010) explains their views of mutation as a source of initiative, discontinuity, creativity and direction.
• The Mutationism Myth, 5.  The Restoration (June 14, 2010) tells how the Modern Synthesis restored “Darwinism”, at least in name.
• The Mutationism Myth, 6. Back to the Future (August 31, 2010) wrap ups the Mutationism Myth series and sets the stage for the future by locating the primary weakness of the 20th century neo-Darwinian consensus in its theory of variation.

Arlin is contemplating starting a new blog where this kind of topic could be explored and discussed, so stay tuned.

I have my agents in Zambia looking to identify and acquire a specimen for me, but does anyone happen to know the name of this plant?

The links mentioned in response to a question:

Evolver Zone

Understanding Evolution

My paper on phylogenetic trees, and one on natural selection.

Segmentation Is the Secret Behind the Extraordinary Diversification of Animals

ScienceDaily (July 27, 2010) — Segmentation, the repetition of identical anatomical units, seems to be the secret behind the diversity and longevity of the largest and most common animal groups on Earth. Researchers from CNRS and Université Paris Diderot have shown that this characteristic was inherited from a common segmented ancestor thought to have lived 600 million years ago and whose presence “changed the face of the world.”

…

[Arthropods, vertebrates, and annelids] are not closely related to one another. So, where does their segmentation come from? Is it possible that they all inherited this feature from a very distant common ancestor that lived 600 million years ago, before the Cambrian explosion, which produced most of the large animal groups that exist today? Or has segmentation occurred several times during the history of evolution? This is the question addressed by the researchers of CNRS and Université Paris Diderot at the Institut Jacques Monod, because segments seem to offer a significant advantage to the groups that have them, in terms of diversity, longevity and overall evolutionary success.

…

The researchers found that the genes controlling segment formation during embryo development are almost the same in drosophila (an arthropod) and in annelid marine worms, on which they concentrated their studies. These similarities led them to conclude that the genes had been inherited from a common ancestor, which was itself segmented. It also appears that vertebrates inherited this characteristic from an ancestor they share with the arthopods and the annelids. This is what the researchers are now seeking to confirm.

Arthropods are segmented and very diverse. Nothing newsworthy there. But wait, what’s that? The second largest phylum is molluscs, which aren’t segmented? And what else? Nematodes, which are undoubtedly hyperdiverse, aren’t segmented either? Early-branching animals like sponges, cnidarians, and ctenophores aren’t segmented either, you say? Only three phyla are segmented, two of which (Chordata and Annelida) are not as large as Mollusca and Nematoda? Hmmm.

Anyway, the story (which is bad, even by press release standards) suggests that finding a common gene involved in segmentation in three distantly related phyla implies that their common ancestor had the gene and therefore was segmented as well. We’ve been through this whole “shared regulatory gene equals homology of morphological trait” issue with the eye. The alternative interpretation is that the same genes were co-opted for similar functions independently. The authors of the original paper dismiss this possibility in one sentence:

“Because they are not known to be part of a conserved core regulatory network or “kernel” that might have been coopted en bloc, each gene would have been recruited independently, which seems unlikely.”

Let’s think about this for a minute. Yes, it seems “unlikely” that the same genes would be co-opted three times for similar functions. But the hypothesis that the ancestor was segmented requires another major assumption.

Here is a very basic phylogeny from an introductory textbook.

For the ancestor of chordates, annelids, and arthropods to have been segmented, this means that segmentation must have been lost in molluscs, nematodes, echinoderms, brachiopods, rotifers, flatworms, and various smaller phyla. Moreover, several of these phyla that lost segmentation subsequently became more diverse than chordates and annelids.

Another example of misunderstanding phylogenetics.

An example:

This is the duck-billed platypus, Ornithorhynchus anatinus. It is a mammal, but as a monotreme it also lays eggs. It has fur and produces milk, but it does not have nipples. Because of these features, it is often considered a “primitive” species and people often compare features of the platypus to those of placental mammals in order to draw conclusions about the evolution of “modern” placental mammals.

It’s true that platypuses lay eggs and lack nipples. They also have a bill, can sense electric currents in the water, and (in males) have a spur that delivers venom. Does this mean that the ancestor of platypuses and placental mammals had bills and venom? No, it doesn’t. That’s because these are derived traits that evolved in the platypus lineage after the monotreme and placental mammal lineages diverged from a common ancestor.

There is no such thing as a primitive species, only primitive or derived traits. The platypus, like every species, is a mixture of the two. As such, comparing it with other living species of mammals does not automatically tell you anything about what the ancestral mammal was like.

What about the claim that the monotremes are an “older” group of mammals? It’s possible that, as a recognizable group, monotremes appeared before placentals. However, the lineage of which the modern platypus is a representative and the lineage of which humans are a representative have been evolving for exactly the same amount of time. This is simply a result of the fact that they share a common ancestor at some point in the past. The two lineages diverged from this ancestor and then began evolving separately. Some traits found in the ancestor were maintained in the platypus lineage, others in the human lineage, and in both cases there were new features that evolved that were not found in the common ancestor.

The take-home message is this. You can’t consider one species “primitive” and another “derived” and assume that any given feature in the former was found in the ancestor of the two. You need more information before you can interpret the evolutionary history of a particular characteristic.

As part of one inquiry case, we will be exploring the issues surrounding freshwater mussels in the Great Lakes region, including the native diversity and the impacts of invasions by zebra mussels and quagga mussels.

Last week I was in Michigan with my friend and colleague Dave Zanatta of Central Michigan University filming vignettes about mussel research. Here is just a sample (note: unedited and unannotated) of the footage we shot.