Science Literature

Now that the opossum genome has been sequenced, both winners and losers have emerged. The main loser is the 'Genes-R-Us' school, who have argued that genes are the only really interesting components of the genome. This group is a loser because the "vast majority of the opossum's genes are identical to other placental mammals". Genes do not distinguish marsupials from placentals, but the non-coding elements (previously referred to as 'Junk DNA' are distinctly different. Thus, "most of the genetic difference between marsupials and placental mammals comes from non-coding sequences, not proteins."
The Evo-Devo community appears to consider itself a winner. The new research "is bound to make the [evolutionary developmental biology] community very happy, because they've been saying all along that it's the regulation of genes that is what's driving the changes that we see in the evolution of animals." Some of this confidence is, however, misplaced: it is one thing to say that gene regulation is the key to understanding the difference between placentals and marsupials, but linking this to origins is theory-laden. The data does not speak for itself but is interpreted, often through an evolutionary filter.
The ID community is also a winner. ID scholars have long been sceptical of the genetic reductionism displayed by most evolutionary biologists, and have also been quick to recognise the functionality of much of the so-called Junk DNA. These scholars have much in common with evo-devo, but see the regulation system as an extraordinarily complex system that invites design inferences when considering origins.
ID scholars will also welcome the recognition that marsupials are not primitive mammals: "The study helps to erode a common misconception that marsupials are somehow an archaic or second-rate category of mammal. One scientist comments on the discovery of a gene that encodes for a unique form of T-cell receptor not found in placental mammals: this "knocks that assumption on its head [. . .] It shows that they have a very sophisticated immune system, but one that's very different."

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen, et al.
Nature 447, 167-177 (10 May 2007) | doi:10.1038/nature05805

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

See also:

Fairless, D., The awesome opossum gets sequenced, News@nature.com, 9 May 2007; | doi:10.1038/news070508-8

Lee Phillips, M., First marsupial genome released, The Scientist, 9th May 2007.