Rapid evolutionary innovation

Inspired by Nate's question I was looking up some research on the evolution of aerobic respiration and I found this really interesting paper in Nature from last year about a narrow window of genetic expansion between about 3.3 and 2.8 billion years ago, called the Archaean expansion, during which 27% of the largest modern gene families arose.The paper is called: Rapid evolutionary innovation during an Archaean genetic expansion and there is also a commentary on the paper: Evolution: Old genes

During the Great Oxidation Event about 2.4 billion years ago, the surface of the Earth tipped irrevocably into an oxygenated state, as free molecular oxygen began to accumulate in the oceans and atmosphere. But the first whiffs of oxygen began to appear at least 300 million years earlier, as organisms capable of producing the gas through photosynthesis evolved. As the Earth's chemistry changed, so too must have the microbes that lived on its surface. But the rock record leaves only hints of the ecosystem, primarily in the form of isotopic fractionation of the elements — including iron and sulphur — that presumably fuelled the bacteria.

To assess the evolution of these metabolisms, Lawrence David and Eric Alm of the Massachusetts Institute of Technology looked to the genetics of extant organisms. They re-examined existing gene families using a technique that accounts for both the evolution of new genes, and the transfer of genes between different species.

The paper is interesting not just because of the results but because it gives you an insight into the techniques you need to use to address these sorts of questions.