Genetics of Adaptation Graduate Seminar
Author: Brian Carlson
Marines know the value of making a “strategic advance to the rear,” and this begs the question: Can evolution do the same? In fact, it can and it does. The best-known examples of such so-called “reverse evolution” include the return of sexually dimorphic species to monomorphism and the loss and recovery of wings in stick insects (Nagai et al. 2010).
With nature providing such interesting examples of the apparent action of reverse evolution, what is the missing piece? Why does the investigation of this phenomenon remain relevant and interesting? The answer is actually quite simple: While many examples can be cited which suggest the action of reverse evolution, very little is known about the mechanism that drives such evolutionary backtracking.
Previously, the only published study that attempted to address this topic on a genetic level was the work of Kitano et al. (2008), in which it was demonstrated that the reoccurrence of armor plates in stickleback fish was the result of a reverse shift in allele frequencies from the derived (mutant) allele to the ancestral allele. Even this important study left questions regarding the mechanism(s) by which reverse evolution is accomplished, however, as the derived allele had never become fixed. As a result, the published body of work on the topic has failed to shed any light on how a new trait could arise, become fixed in the population and later be replaced by the fixation of a “new” mutation, restoring the ancestral phenotype… until now.
Recent work by Nagai et al. (2010) has finally provided an example of reverse evolution in which the genetic changes underpinning the re-emergence and fixation of ancestral traits can be confidently demonstrated. Their study, conducted in African cichlid species from Lake Tanganyika, reveals several substitution events and subsequent reversals of the amino acid at position 292 in the RH1 rod-opsin photopigment, together with their inferred evolutionary impacts.
Before moving any further, it is important to first understand the mechanism of such change and its functional effects. In brief, the authors compiled sequence data for the RH1 gene in 293 individuals, representing 67 cichlid species from four tribes (“tribe” being a secondary taxonomic rank, referring to a closely-related group of genera) native to Lake Tanganyika. Analysis of sequence data revealed that all fish examined possessed either an alanine (292A) or a serine (292S) amino acid residue at position 292 in the RH1 proteins for which they encode. Further, it was observed that, at this position, alanine was always coded for using the GCC codon in the inferred mRNA transcript sequence. Similarly, serine was always coded for using UCC. This is an important point: it indicates that a single nucleotide substitution in the RH1 gene can result in a change from one protein form to another. Analysis of the absorbance spectra for both forms of RH1 opsin showed a difference in the maximum absorbance (λmax), with RH1 proteins containing 292S showing maximum absorbance at shorter wavelengths (488-494 nm) than those containing 292A (497-504 nm).
So, why is this single nucleotide change important? The peptide sequence differences between the two forms of the RH1 protein found in these cichlids are significant for two main reasons: First, expression of each form of this visual photopigment is believed to be advantageous in certain habitats. In shallower waters that tend to be blue-green, maximum absorbance at a longer wavelength (i.e. expression of RH1 with 292A) is believed to confer an advantage in light-dark discrimination and, by extension, such things as feeding, mate choice, predator avoidance, etc (Nagai et al. 2010). Conversely, in the bluer waters of deeper habitats, absorbance at shorter wavelengths (i.e. expression of RH1 with 292S) is likely advantageous. Second, the data collected indicates that either one form of RH1 or the other tends to be found in each population, with only one population examined possessing both forms (Fig. 1). This suggests that natural selection is likely acting on this trait.
Figure 1. Distribution by depth (in meters) of the sampled species (numbered columns) in the Cyprichromini (A), Perissodini (B), Lamprologini (C) and Ectodini (D) tribes. Bars represent the depth ranges at which species are found and bar color indicates whether the ancestral 292A allele (gray) or the derived 292S allele (black) is fixed in that species. Maximum RH1 absorbance values are indicated for the given species, where available (Nagai et al. 2010, Fig. 3).
Alright, things are getting a little more interesting, but I promised you a compelling example of reverse evolution, which, so far, I have yet to deliver. I am not one to disappoint, so lets add a few broad strokes of phylogenetics (phylogenetics being the study of the evolutionary relationships among species) and finish the picture we’re painting here.
Using a variety of techniques, Nagai et al. (2010) inferred the evolutionary history of the RH1 gene in the species studied. The phylogeny that they generated reveals several important facts. First, the species generally clustered with other members of their tribe, suggesting genetic similarity across the region of the genome that was sequenced in this study. Second, the ancestral form of the RH1 protein likely contained 292A. Third, the derived form (292S) of the protein has been acquired at least four different times as the result of a single nucleotide substitution. Subsequently, the ancestral (292A) phenotype has been reacquired in at least three distinct lineages by reversing the original substitution (Fig. 2).
Figure 2. Neighbor-joining tree based on RH1 sequence data. Capital letters represent the allele known (for existing species) or predicted (for ancestral species) to be fixed in a species or lineage. Species with shallow (including depths <20 meters), deep (including depths >50 meters) and wide (including depths <20 and >60 meters) distributions are highlighted in orange, blue and green, respectively. Portions of the tree highlighted in yellow represent inferred shallow lineages and portions highlighted in blue represent inferred deep lineages. Maximum RH1 absorbance values are indicated for the given species, where available (Nagai et al. 2010, Fig. 4).
When data relative to the respective habitats of the species examined and the natural history of the lake is considered, the following picture of cichlid evolutionary history emerges: The common ancestor of these species carried the 292A form of the RH1 protein and likely lived in a shallow habitat. Later in evolutionary history, a single-nucleotide substitution resulted in the expression of the derived 292S form of RH1, which conferred a visual advantage in bluer water, allowing some species to colonize deeper habitats. In some lineages, subsequent reacquisition of the ancestral trait either led to, or resulted from, recolonization of shallow habitats.
There you have it! You have witnessed science take its first real steps in understanding the genetic underpinnings of reverse evolution, which represents real, forward progress in our understanding of how Earth’s myriad species came to be the way that they are. Hopefully, such exciting research will encourage us to continually sharpen and redefine our understanding of evolution and the way that we communicate the concept to others. Evolutionarily speaking, “forward” progress is made by selecting for traits that confer some advantage, whether novel or ancestral; sometimes natural selection simply orders, “About face, double time!”
Kitano J, Bolnick DI, Beauchamp DA, Mazur MM, Mori S, Nakano T, Peichel CL. 2008. Reverse evolution of armor plates in the threespine stickleback. Curr. Biol. 18: 769–774.
Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, Okada N. 2010. Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika. Mol. Biol. Evol. Advance online publication. doi:10.1093/molbev/msq344.