Show Me The Science Month Day 4

How did we become human? You can ask the same question in a slightly different way: how did we become different from chimps?  Although the common ancestor that we shared with chimps 5-7 million years ago was not itself a chimp, it probably resembled modern-day chimps much more than it resembled us. Both humans and chimps have been changing under evolutionary pressure since our lineages split, but humans have obviously picked up traits that make us stand out from other modern apes, most notably our intelligence.

To understand how evolution has shaped our species, biologists are looking for the genes that have experienced the most evolutionary change since we diverged from chimps. Finding these fast-evolving genes isn't easy, because there are other, more random processes that can imitate the signature of natural selection in the genome. If you can't distinguish genes that are being pushed by natural selection from genes being shaped by non-adaptive effects, then you cannot get at the genetic roots of how our species evolved since we parted ways with chimps.

A group of researchers, based at Uppsala University in Sweden and at UC San Francisco in the US, scoured the human genome and found that a process called biased gene conversion is mimicking the genetic signature of natural selection.

The first step in this research was to find human-specific changes; that is, DNA changes that have occurred in the human lineage, after humans split off from chimps. To find these changes, you need the chimp genome and at least one other genome. Here's why: if humans have a 'G' at a particular DNA position, and chimps have an 'A' at that same position in their genomes, how can you tell which lineage experienced the change? Did the human-chimp common ancestor have an 'A' or a 'G'?

To answer that question, you have to examine the genome of a species that is more distantly related, such as the macaque. Humans, chimps, and macaques all shared a common ancestor a long way back. At some point, the macaque lineage and the human-chimp lineage went their separate ways. Millions of years later, the human and chimp lineages diverged. This means that by looking at the macaque genome, you can get some idea of whether a DNA change occurred in the human lineage or the chimp lineage.

If chimps and macaques are identical at one DNA position (let's say they have an 'A), but humans differ at that position (we have a 'G'), we infer that the human lineage acquired the mutation - a conversion from an 'A' to a 'G', since the most likely scenario is that macaques and chimps have an 'A' inherited directly from our common ancestor. Of course it's formally possible that the human sequence is the ancestral one, and that the chimp and macaque sequences both mutated in identical ways - a very improbable scenario in most cases.

Following this reasoning, it is possible to identify spots in the human genome that have changed since humans and chimps split off. Are these changes due to natural selection, or some other biological process driven by chance? The researchers found that the pattern of human-specific changes at many places in the genome were best explained by a largely non-adaptive process called biased gene conversion. This biased gene conversion, the authors suggest, is caused by a well-known biochemical process that occurs when maternal and paternal chromosomes swap pieces during the generation of sperm and egg cells. This means that the inherent biochemical jumpiness in the genome can be a powerful force, one other than natural selection, that shapes our genetics.

This is not to say that biased gene conversion is responsible for all differences - the authors detected the effects of this process at certain hotspots around the genome.

Biologists have long known of processes other than natural selection that cause evolutionary change. What is this particular paper shows is that one of these processes can generate genetic signatures that look like natural selection, even though this process is in most cases functionally neutral or even harmful. Biased gene conversion may not be a sign of natural selection, but its signature in our genomes is a clear indication that we have a long history, shaped by a variety of evolutionary forces.

Join me tomorrow for day five of Show Me the Science month. Evolution as a science is alive and well. Each day I will blog about a paper related to evolution published in 2009.