There has been considerable interest in the publication of the platypus genome, which is good. Unfortunately, much of the reporting has been distorted, which is bad. However, rather than picking on the press, I want to focus on an example from the scientific literature where a misconception about evolutionary relationships seems to creep in and generate confusion.

In Phylogenetic Fallacies: Early Branching Must Mean Primitive I focused on the misconception that an "early branching" lineage was necessarily "primitive" (i.e., very similar to a distant ancestor). This time, I want to discuss something slightly more subtle, but nonetheless important, with regard to interpreting phylogenies. Specifically, I want to note a problem with the very concept of one lineage "branching off from" another lineage. There can be a tendency to consider evolutionary trees as reflecting a main line with a series of "side branches". This is especially true when the tree is "unbalanced" (lineages are depicted with uneven amounts of diversity) and "ladderized" (the more diverse branches are placed on the same side of each node). The following is a general unbalanced, right-ladderized tree.

Here we go again, just this morning the Florida House of Representatives passed a bill that directs teachers to engage in “critical analysis” of evolution in public schools. The bill’s chief sponsor, Republican Alan Hays of Umatilla, says that evolution “has holes in it,” and that “no one has any record -- no fossils have been found.” That will come as a big shock to the thousands of natural history museums around the world, displaying hundreds of thousands of fossils.

But of course factual truth has never been the forte of creationists. Nor has honesty. The bill is ironically called “The Evolution Academic Freedom Act,” and who would possibly want to be against academic freedom? The bill aims at protecting teachers who wish to be critical of evolution teaching in public schools, except for the minor detail that there doesn’t seem to be a record of any teacher filing a complaint on the matter (I guess they are all truly scared out of their wits by the evolution police).

The Florida Senate has already passed a similar bill, which would prohibit school officials from penalizing teachers that challenge evolution based on “scientific information.” I wonder where these teachers would get such information. Oh, right, from the Discovery Institute in Seattle, the so-called think tank that actually drafted the “model” legislation on which the bill is based.

Evolutionary trees, or "phylogenies", are a major part of modern evolutionary science. They depict hypotheses regarding the relationships among taxa, and are therefore important in reconstructions of the historical path of evolution (Gregory 2008a,b).

Various approaches can be taken to formulating phylogenetic hypotheses, including analyses based on morphological, fossil, and/or molecular data. These methods often agree well, but sometimes one or another can throw up some surprises and challenge previous hypotheses about the relationships among groups of organisms.

Reconstructing the tree of life is a difficult and complicated process, and one should expect there to be significant refinements and revisions along the way. This is especially true of the deepest branches of the tree, which are often the most difficult to resolve.

Case in point, the Tree of Life Web Project gives the following summary of deep branches among major animal lineages:

"The placenta is this amazing, complex structure and it's unique to mammals, but we've had no idea what its evolutionary origins are," says Julie Baker, PhD, assistant professor of genetics at Stanford Univeristy and senior author of a study in Genome Research which discusses its evolution.

The placenta is the mother's intricate lifeline to her unborn baby, delivering oxygen and nutrients critical to the baby's health. New evidence suggests the placenta of humans and other mammals evolved from the much simpler tissue that attached to the inside of eggshells and enabled the embryos of our distant ancestors, the birds and reptiles, to get oxygen.

In research published in Nature, researchers at Rockefeller University and the University of Tokyo state that insects have adopted a strategy to detect odors that is radically different from those of other organisms -- an unexpected and controversial finding that may dissolve a dominant ideology in the field.

They state that insects use fast-acting ion channels to smell odors, a major break with current ideology, and that this means Darwin's tree of life will need to be redrawn.

Since 1991, researchers assumed that all vertebrates and invertebrates smell odors by using a complicated biological apparatus much like a Rube Goldberg device. For instance, someone pushing a doorbell would set off a series of elaborate, somewhat wacky, steps that culminate in the rather simple task of opening the door.

Nice blog today on mutualisms by Olivia Judson who writes the Wild Side blog/column for the New York Times (I seem to be writing a lot about writers for the NY Times these days ... not sure what is going on with that). She even features one of my favorite organisms in the blog:

The clam Calyptogena magnifica, which lives on deep-sea vents, depends on a bacterium to supply it with nutrients; the bacterium is transmitted through the clam’s eggs

Last year we published a paper on the complete genome sequence of this symbiont (which I wrote about here when I was clearly in a whiny kind of mood). And Judson picks up on a part of the story on the clam that is rarely discussed - the symbionts are transmitted vertically from parent to offspring. Vertical transmission seems to be linked to multiple properties of the symbionts (see my discussion of this regarding the glassy winged sharpshooter symbionts here).

Judson's post is really worth checking out for the symbiosis fans out there. She does a good job of highlighting diversity and evolution of mutualisms in a relatively short post.

See the YouTube video below of a dissection of a baby Calyptogena

The Human Genome Project revealed that only a small fraction of the 3 billion “letter” DNA code actually instructs cells to manufacture proteins, the workhorses of most life processes. This has raised the question of what the remaining part of the human genome does. How much of the rest performs other biological functions, and how much is merely residue of prior genetic events"

Scientists from Cold Spring Harbor Laboratory (CSHL) and the University of Chicago now report that one of the steps in turning genetic information into proteins leaves genetic fingerprints, even on regions of the DNA that are not involved in coding for the final protein. They estimate that such fingerprints affect at least a third of the genome, suggesting that while most DNA does not code for proteins, much of it is nonetheless biologically important – important enough, that is, to persist during evolution.

In the first experiment of its kind conducted in nature, a University of British Columbia evolutionary biologist has come up with strong evidence for one of Charles Darwin’s cornerstone ideas – adaptation to the environment accelerates the creation of new species.

“A single adaptive trait such as color could move a population towards the process of forming a new species, but adaptation in many traits may be required to actually complete the formation of an entirely new species,” says UBC post-doctoral fellow Patrik Nosil. “The more ways a population can adapt to its unique surroundings, the more likely it will ultimately diverge into a separate species.”

Nosil studied walking-stick insects in the Santa Barbara Chaparral in southern California. Stick insects cannot fly and live and feed on their host plants. Different “eco-types” of walking-stick insects are found on different plants and exhibit different color patterns that match the features of their host plants. For example, insects of the cristinae eco-type, which feed on plants with needle-like leaves, have a white line along their green bodies.

By displacing some eco-types away from their customary host plants and protecting others from their natural predators, Nosil found that color pattern alone could initiate speciation, while natural selection on additional adaptive traits such as the ability to detoxify different host-plant chemicals are required to “seal the deal,” or complete the speciation process initiated by differences in color pattern.

Higher organisms do not have a “cost of complexity” — or slowdown in the evolution of complex traits — according to a report by researchers at Yale and Washington University in Nature.

Biologists have long puzzled over the relationship between evolution of complex traits and the randomness of mutations in genes. Some have proposed that a “cost of complexity” makes it more difficult to evolve a complicated trait by random mutations, because effects of beneficial mutations are diluted.