Tan is the new black

There's a really interesting paper by Sean Carroll's group in Cell ( Jeong et al. ) on pigmentation differences between two closely related species of Drosophila (D. santomea and D yakuba). D santomea has a small range and is restricted high altitudes on the island of São Tomé, while Yakuba is more widespread and lives at lower altitudes on São Tomé. The species can hybridize, and form a natural hybrid zone, in fact the mtDNA has introgressed between species (Bachtrog et al. Llopart A et al). D. santomea unlike the rest of the Melanogaster clade lacks abdominal pigmentation. Carroll's group looks at one of the genes involved in this change in detail.

A couple of previous QTLs studies looking at abdominal pigmentation differences between these two species had identified a QTL close to a candidate gene tan on the X chromosome. While another small QTL maps near the Yellow gene also on the X chromosome. The authors show that Tan in combination with the Yellow gene produces the abdominal pigmentation in D. melanogaster. No coding differences are found between the tan gene of D santomea and D yakuba, suggesting that changes in the regulation are prime candidates for the difference in pigmentation. They then show that Yellow and Tan expression is present in the abdominal region of D Yakuba but absent in D Santomea. Replacing the X chromosome of D yakuba with that of D santomea removes the Tan expression pattern but not the yellow pattern, suggesting that the difference in Tan expression is controlled in cis (and yellow is controlled in trans). The authors identify a cis regulatory module for tan that controls the abdominal expression in D. melanogaster. They then show that this D. melanogater cis regulatory module can create the pigmentation pattern in male D. Santomea. A couple of changes have occured in the D. Santomea sequence in the regulatory module at otherwise conserved sites. The authors show that these sites are responsible for the reduced abdominal expression of tan.

At this point the authors decided to look at polymorphism and divergence data in D. santomea in this module. This is when the story gets really interesting. The authors I guess hoped to find the signal of a sweep in D. santomea around this region, and that all individuals would be fixed for the mutations that inactivated the cis module. What they found however was that the changes were not fixed in the population, but that there appear to be three distinct inactivation mutations at the cis module. They confirmed that the two newly discovered mutations (both deletions) removed the abdominal expression of tan, and so are likely to remove the pigmentation as well. Thus D. santomea has three different mutations at the same locus resulting in the same phenotype, which is pretty incredible case of parallel mutation. The authors argue that this is likely the result of selection rather than simply neutrality following relaxed constraint, and I find that pretty convincing. There is no observed polymorphism for pigmentation in D. santomea suggesting that the combined effect of these three mutations combined have removed pigmentation. It seems unlikely that this small mutational target (the module) experienced three neutral mutations that have essentially removed pigmentation.

I wonder if one of the mating choice QTLs (between D Santomea and D Yakuba) maps to the same location as the QTL that lead to the indentification of tan (I've not checked the co-ordinates of the QTLs in Moehring et al ). Interestingly, the yellow gene (the other pigmentation gene with reduced expression) seems to show a signal of introgression between D Santomea and D Yakuba (Llopart et al. ), I wonder if the
introgression at yellow gene has prevented the accumulation of strong cis mutations at yellow, meaning that its expression had to be reduced by a trans effect.

My only minor quibble with this otherwise great paper was the stridency about cis regulatory evolution. This paper is another really pretty example of cis regulatory evolution, but to my mind it in no way seals the debate about protein versus cis regulatory evolution ( Hoekstra and Coyne ). This case is another loss of function mutation, I would like to see more gain of function mutations in cis before making up my mind that cis regulatory evolution predominants. I also feel that the follow up of these cases is somewhat biased towards following up cis regulatory changes. The authors do not follow up the reduction in yellow expression which operates in trans, thus the paper has ignored a trans effect (which admittedly may be a cis effect at another upstream gene). Also the authors do not seem to show that the cis regulatory module of tan (a pleiotropic gene) is itself free of pleiotropic effects (a prerequisite for freeing up cis regulatory evolution).

References
Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell. 2008 Mar 7;132(5):783-93.

Moehring AJ, Llopart A, Elwyn S, Coyne JA, Mackay TF. The genetic basis of prezygotic reproductive isolation between Drosophila santomea and D. yakuba due to mating preference.Genetics. 2006 May;173(1):215-23.

Llopart A, Lachaise D, Coyne JA.Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea. Genetics. 2005 Sep;171(1):197-210.

Bachtrog D, Thornton K, Clark A, Andolfatto P.
Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.
Evolution Int J Org Evolution. 2006 Feb;60(2)