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Genetics of Drosophila have been studied widely in the last century, trying to elucidate the molecular causes of variation among the different species of the taxa. It is currently known that differences of protein expression are commonly driven by modifications of non-coding sequences and can be due to changes in trans or cis-regulation factors; furthermore, these differences are the responsible for either inter of intra-specific variation. In this field, three important papers have highlighted the importance of evo-devo genetics and have explained different mechanisms that may underlie this variation, such as novelty by co-option. All these discoveries have been made focusing on the differences in pigmentation patterns present between or within species of Drosophila, in which yellow, tan and ebony genes play a major role.
Different pigmentation patterns: the spot on the wing and its consequences
Pigmentation patterns vary enormously between species of Drosophilids, and can underlie diverse roles, such as mate choice, thermoregulation or mimicry; which can be itself the cause of speciation. Pigmentation can differ not only between different species, but also within the species and between male and female; and affect differentially the body and the wings. General intensity of the body colour has been used to determine the role of ebony and tan genes in pigmentation (EXPLICA!!!) in Wittkopp, PJ., et al. (2009), using Drosophila americana and D. novamexicana, two sister species which show a very distinct body colour, having the first dark brown body and the later light yellow body (figure 1 - FIG 1 OF WITTKOPP 2009). Their recent divergence makes possible their mating in the laboratory and therefore this is the primary method used in this research.
Another common pattern of pigmentation is the anterior distal spot in the wings, present in males of some species of the fly. It is closely related with courtship and due, at least partially, to the differential expression of the gene yellow, enhanced in the spot. Nicolas Gompel and collaborators (2005) used D. biarmipes to determine which changes in yellow gave rise to the spot in the wing (figure 2 FIGURE 1 OF GOMPEL 2005). Similar studies were carried by Benjamin Prud'homme and collaborators (2006) who used D. elegans and D. gunungcola, being the former spotted unlike the later. They concluded that the spot formation shares a common genetic basis in D. elegans and D. biarmipes, whereas the spot present in the wings of D. tristis appears to be caused by different non-coding sequences, thus their gains were independent. In addition, checking the phylogeny of the different spotted and unspotted species of Drosophila, they discovered that it had been two independent gains and five losses in spot pigmentation (Figure 3, FIGURE 1 OF PROUD'HOMME 2006).
Discovering cis-regulatory evolution
Changes on the expression of proteins are usually due to variations on the non-coding sequences of the genes, and they can be caused by cis- or trans-regulation. Cis-regulation means that the change has been made in the locus itself, causing, for example, the loss of affinity for some transcriptional factors or the change in the number of binding sites for them. On the other hand, changes in trans-regulation address to variations in other loci, therefore, in elements that affect in trans to the gene; for example, variations in the transcriptional factors themselves.
In order to study the regulation of the expression of yellow, ebony and tan, research must address firstly this simple question: are the changes caused by trans or cis-regulation? The general approach used in the studies with spot pigmentation (Gompel et al., 2005; Prud'homme et al., 2006) consisted in making different transformations of several species of Drosophila, inserting the yellow gene along with its regulatory sequences into the genome of an unspotted Drosophila. If the transformed flies showed the spot it meant that the change was within the inserted DNA, thus it was cis-regulation, whereas non-spotted flies showed a trans-regulatory change or further changes, not related with the genome, such as cells expressing the protein differentially or different number of cells expressing it (Wittkopp et al., 2009). The spotted flies studied in Gompel et al. (2005) and Prud'homme et al. (2006) showed cis-regulatory evolution, those were D. biarmipes, D. elegans and D. tristis; and other flies with spotted ancestor appeared to lose their spot due to changes in cis too (see again figure 1, FIGURE 1 OF PRUD'HOMME 2006).
However, cis-regulation cannot be taken as a general mechanism of divergence, as it is shown by Patricia Wittkopp et al. (2009), where genes ebony and tan appear to diverge between D. americana and D. novamexicana by different means, as changes in trans or changes in the number of cells expressing the protein.
Co-option as a likely mechanism for morphological trait evolution
It is sometimes difficult to think how a few steps in evolution can lead to such huge phenotypic differences. Typically we would expect several evolutionary changes in order to explain the formation of a defined spot in the wing, however, a simpler explanation has been found. In this field, novelty by co-option refers to the gain of binding sites in regulatory sequences for proteins or transcription factors that are already present, and are important, in the organism. Therefore, they are present throughout the taxa, can be used as an explanation for the diversity of wing pigmentation patterns -because of the multiple combinations of transcription factors-, and also as an explanation for phenotypic convergence between species (Gompel et al., 2005).
It has been postulated as the evolutionary mechanism for spot formation in Gompel et al. (2005) and Prud'homme et al. (2006). The former explains that mutations in yellow regulatory sequences gave rise to binding sites for Engrailed, a transcription factor implicated in the formation of the anterior-posterior axis and proved to repress the expression of yellow gene in the posterior compartment. They also concluded that there are more factors implicated and more loci must be involved, since only yellow expression does not induce spot creation (see figure 4, FIGURE 6 OF GOMPEL). Co-option is also the proposed evolutionary mechanism in the later, although this article (Prud'homme et al., 2006) focuses more on the mechanisms of loss and gain, rather than in the specific molecular causes of every evolutionary event.
Intraspecific polymorphism explained along with interspecific variation:
Even though cis-regulation has been proved to be a general evolutionary mechanism, other mechanisms play a major role in shaping the effect of tan and ebony genes and, therefore, the body colour differences between D. americana and D. novamexicana (Wittkopp et al., 2009). This group showed that it was because of changes in non-coding sequences in these genes the differences in pigmentation patterns in both species, as well as some unidentified linked genes.
In addition, they showed that polymorphism in those genes was the cause of pigmentation differences within D. americana, which show a geographical cline in the United States going from darker to lighter body colour. Finally they stated that this alleles was present in the ancestor of D. americana and D. novamexicana and they were responsible for pigmentation differences between species but also continue to segregate within D. americana, contributing to the geographical cline.
Consequences and perspectives
Several conclusions can arise from these articles. One of the most important ones is the postulation of an evolutionary model for morphological trait evolution, in which co-option takes the major role for the appearance of completely new patterns, giving the initial variation necessary for the posterior evolutionary forces to act. Linked to this model two important ideas arise in Gompel et al. (2005): the reason why similar wing pigmentation patterns are observed in independently evolved species (phenotypic convergence) and why there are many different patterns.
On the other hand, Wittkopp et al. (2009) also postulated that variation in body colour was due to change in non-coding sequences, but they appeared to be trans-regulatory factors rather than cis. Her conclusions address both intra and inter-specific variation, concluding that they can be made by the same alleles (light-pigmentation ones in her research).
These conclusions set inevitably the bases for further research, where other traits and other model organisms should be taken in order to investigate the generality of these statements. In addition, one interesting point these articles have neglected is the spot appearance only in males, either because of being sex-linked genes or because different trans-factors implicated. Effort in making a research in females could enlighten more easily the different trans-regulatory factors that could be implicated in the morphological traits.
Furthermore, spot formation is proved to be caused by more than one cis-regulatory factor -creation of Engrailed binding sites in yellow gene, explained by Gompel et al. (2005) - so additional candidates should be studied in order to picture the whole process underlying the spot pigmentation patterns. For the same reason, identification of the alleles linked to ebony and tan genes should be made, in order to understand better the research made by Wittkopp et al. (2009).