evolgen

Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the host, but there are also transposable elements (TEs), sequences from mitochondria (numts), and endogenous retroviruses (ERVs). In addition to those examples, other symbionts also infect eukaryotes and leave traces of their presence in the genomes of the hosts. One such parasite of many invertebrates is Wolbachia, a bacteria that invades the germ cells of its host and inflicts odd behaviors such as male killing, feminization of males, and reproductive isolation of infected males and uninfected females. Each of these strategies is intended to produce the same result: maximal transmission of the symbiont from one generation to the next.

Because symbionts live in such close quarters with (or within) their hosts, they often exchange genetic material with each other. We can search for evidence of these lateral gene transfers (LGT) by examining eukaryotic genomes for sequences that resemble those of a particular symbiont. These searches are often not possible with the off the shelf assemblies of genomes because bacterial sequences are usually excluded from those assemblies. A paper in the pipeline in Science presents the results of a search for Wolbachia sequences in various invertebrate genomes. The authors searched these genomes for sequences with good matches to the Wolbachia genome, but they had to start from the raw data rather than any available assemblies.

They started with Drosophila genomes, and found a lot of evidence for LGT between Wolbachia and the flies. In fact, they found one example of the entire Wolbachia genome inserted into the genome of D. ananassae. On top of that, 2% of the genes from the Wolbachia genome are transcribed from the host genome. The authors are careful to point out that transcription of these genes does not necessarily mean they're functional, but future experiments to determine if they are would be pretty cool.

In some of the press surrounding this article, adaptationist undertones are emerging. Take, for example, this news item from Nature:

The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

Are these insertions under selection? Thankfully, I don't have to debunk this claim, as Jonathan Eisen has done a good job responding to the adaptationists. Essentially, assuming that there's some functional role for these sequences (especially the entire genome insertion) just because they're there is absurd. Conversely, I'd also be careful before invoking any nearly neutral explanations for these LGT events.

The authors also searched the genomes of some wasps and roundworms for evidence of LGT between Wolbachia and the hosts. Many of the Wolbachia insertions are species specific with high identity to the relevant reference Wolbachia genome. That suggests that these insertions are fairly recent. Additionally, they don't present any evidence for ancient insertion events that have not degenerated. That sends up a red flag that these sequences are deleterious and cannot persist very long in the face of purifying selection.

Despite the adaptationist press surrounding this article, the science is very good. None of the crazy claims of selection favoring the LGT events are presented in the actual article, thankfully. But, sadly, the media need to spin this in such a manner to obfuscate the actual science.

Jonathan Badger and John Timmer have also written about this article.

Hotopp et al. 2007. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science In press doi:10.1126/science.1142490