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.

I often tell undergraduates about the importance of conducting research projects in their senior year if they intend to pursue graduate studies in science. There are two main reasons for this. The first is that the labs that they have experienced up to that point in undergraduate courses, though useful for introducing specific concepts, are a poor reflection of what real science is like. As such, it is important for them to experience original lab work, rather than simply following a pre-defined, "cook book" protocol with an expected result. Novel studies have no pre-defined sequence, no a priori expectation of the outcome, and in many cases no established methods in place for generating data. The second is that there are some important lessons that they need to learn about research, perhaps most importantly that whatever they try to do in the lab will not work the first time. The sooner they hit that wall -- and get around it -- the better. Nature does not give up her secrets easily, I sometimes say.

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.

The term "genome" is oft-heard but seldom defined, and indeed has more than one meaning. Little wonder, then, that discussions about genome sequences and comparisons thereof can leave otherwise interested audiences more frustrated than enlightened. "What is a genome?" and "whose genome was sequenced?" are legitimate questions, and what follows is an attempt at clarification that is, by necessity, as much philosophical as scientific.

Definition #1: In a broad sense, a genome can be considered as the collective set of genes, non-coding DNA sequences, and all their variants that are located within the chromosomes of members of a given species. This definition does not consider variation among individuals within a species, and instead relates to distinctions between species.

Believe it or not, scientists do not always take themselves too seriously. We can laugh at ourselves and the sometimes rigid conventions of our profession. Take, for example, this guide to translating the formal language of scientific articles into plain English. (Note: This has circulated on email among scientists a number of times over at least a 10 year period; I remember taping it on the door when I was a grad student.  An astute reader pointed out that it is originally from Graham, CD. 1957. A glossary for research reports.  Metal Progress 71: 75, though it has mutated somewhat in the interim).

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:

Each copy of the human genome consists of about 3,200,000,000 base pairs, and includes about 500,000 repeats of the LINE-1 transposable element (a LINE) and twice as many copies of Alu (a SINE), as compared to around 20,000 protein-coding genes.

Whereas protein-coding regions represent about 1.5% of the genome, about half is made up LINE-1, Alu, and other transposable element sequences. These begin as parasites, and some continue to behave as detrimental mutagens implicated in disease. However, most of those in the human genome are no longer mobile, and it is possible that many of these persist as commensal freeloaders. Finally, it has long been expected that a significant subset of non-coding elements would be co-opted by the host and take on functional roles at the organism level, and there is increasing evidence to support this.

A notable fraction of the non-genic portion of human DNA is undoubtedly involved in regulation, chromosomal function, and other important processes, but based on what we know about non-coding DNA sequences, it remains a reasonable default assumption -- though one that should continue to be tested empirically -- that much or perhaps most of it is not functional at the organism level. This does not mean that a search for the functional segments is futile or irrelevant -- far from it, as many non-genic regions are critical for normal genomic operation and some have played an important role in many evolutionary transitions. It simply means that one must not extrapolate without warrant from discoveries involving a small fraction of sequences to the genome as a whole.