"The emerging principles of regulatory evolution"

[rwatts]

Conclusion

The scientists state that a growing body of evidence points to CRE changes as an important mechanism underpinning morphological evolution. From the examples they described, they think they have elucidated three general principles associated with CRE evolution:-

1) The coopting of existing genetic components and changing these. It’s far easier to use what is already there to generate novelty, than to have to re-evolve something from scratch.



2) The link between transcription factors and their DNA binding sites (the CREs) being anywhere within a gene regulatory network, not just between adjacent rungs on the regulatory hierarchy.

3) The existence of CREs “modularises” gene expression and so by evolution happening at this level, changes can be made within the context of one module, without invoking fitness penalties by doing harm to gene expression in other modules.

These rules they argue:-





...offer a rationale explaining why regulatory changes are more commonly favored over other kinds of genetic changes in the process of morphological evolution, from the simplest traits diverging within or among species to body-plan differences at higher taxonomic levels.





That is, they claim that this kind of evolution extends microevolution through to macroevolution, and in their paper they argue that macroevolution really is the accumulation of lots of microevolution.



However, they note that a lot of work remains to be done. Thus, while a reasonably clear picture has emerged concerning the evolution of CREs for a single gene, two areas are largely unexplored. The first is that a dynamic picture of CRE evolution within populations is required. At the moment, their understanding really is based on a few examples that have been relatively easy to study such as the abdomen stripes on flies, the spots on wings of butterflies, and the halteres of two winged true flies. But this is not the same as getting a trait and quantifying its variation among individuals within a population, quantifying its variation between species and from there learning how the various mechanisms such as mutation and recombination contribute to these variations, and how selection and genetic drift ensure that certain DNA variants become fixed within a population.



Secondly, as opposed to focusing on single genes and their associated CREs, scientists need to obtain a specific trait and focus on the complete sets of genes that are “involved in the formation, variation, and evolutionary divergence of the traits.”



In short an awful lot of work remains to be done, and this work is on a much larger scale that that which has been done to date (as of 2007).






The end.



[rwatts]

Connecting the Dots from Pigmentation Patterns to Body Plan Diver- sification: The Compounding of Regulatory Changes Over Eons

There has been a longstanding discussion, if not debate within evolutionary biology concerning the mechanism behind macroevolution. Certainly it’s common descent with modification. The evidence shows that conclusively. 



But what are the nuts and bolts of that mechanism. 



Most consider that microevolution (perhaps with the occasional whole genome duplication) over the eons is what brings about macroevolution. But this has never really been demonstrated in a satisfactorily conclusive manner. Might there be something more?



The authors “submit that an expanding body of evidence, including the examples described in the previous sections, is affirming that macroevolution is a matter of the very same genetic and molecular changes ongoing in populations, compounded over longer periods of time and large numbers of cladogenetic events.”



That is, they think that microevolution occurring over long periods produces macroevolution. And they think that most of this microevolution is due to the mechanisms described in their paper, namely changes to gene regulation.

The kinds of things they have been describing, namely re-patterning of spots and stripes on closely related species, are brought about by ordinary mutational changes to CREs. If these kinds of mutations can bring on such drastic changes in patterns between species, then why not even more drastic changes between organisms at higher levels of taxonomic classification?



The research that points in this direction concerns itself with the evolution of hox genes and how they regulate other genes, particularly with respect to the “evolution of the two-winged dipteran [fly] body plan from four-winged ancestors by reduction of the hindwings.” 



Many insects have two pairs of wings, one pair on their second (T2) thoracic segment and the other pair on the third (T3) segment. And this was so with the more primitive insects from the very deep past. However, with the true flies, the Diptera, the pair of hind-wings have been modified to become halteres, small balancing organs.



The scientists briefly discuss research which has shown that the loss of the hind-wings and gain of the halteres in the Diptera can be pinned down to changes in the regulatory connections between the hox gene Ubx and downstream target genes, via changes to the target gene CREs.


(Interestingly the hox proteins don’t seem to bind to DNA with much strength, leading researchers to wonder just how the hox genes themselves could be so influential in laying out body plans and directing so much of an organism’s developmental morphology. Two early ideas were - 1) that target genes had many hox protein binding sites, allowing numbers of hox proteins to influence the target gene, or 2) hox proteins interacted with the target gene via cofactors, other proteins that bound to regulatory regions, thereby strengthening hox protein binding stability. Early research favoured 2) but later research showed that 1) also played a role. It seems that there is a lot of flexibility in how hox genes can influence other genes.)



Thus, with respect to the three principles the authors write:-

Importantly, the evolutionary mechanisms of hindwing reduction comply with the regulatory principles we have described. The repression of wing-patterning genes in halteres exploits available CREs and transcription factors (Ubx). Because Ubx is involved in many developmental processes other than wing development, evolution of downstream wing-specific CREs en- abled the selective changes in gene expression in the haltere while preserving other functions. Finally, multiple genes, at different levels of the wing genetic regulatory hierarchy, evolved Ubx regulation (61, 68), suggesting that any gene of the wing developmental program can fall under the regulation of Ubx.





It seems then that this is an example of a relatively major morphological change (loss of hind-wings and gain of halteres) being driven by the same underlying mechanism that guides changes to insect wing and abdomen patterning. Possibly macroevolution really is driven by an accumulation of these kinds of regulatory changes across time.



So what of mutational changes to the structural genes (as opposed to regulatory genes) themselves, and what of gene duplications? They note that there is abundant evidence for the reality of these evolutionary mechanisms and the effects they have caused. Hence the question is to the relative importance of those evolutionary mechanisms versus the mechanism described in this paper.



They think that the conventional kind of mechanisms are relatively rare in comparison to regulatory evolution which is “pervasive and constitutes the primary fuel of the continuous morphological diversification of lineages and traits in the ‘far between.’”



However, the issue of relative importance of mechanisms is, I think, far from settled. 







To be continued ....

[rwatts]

Losses are easier, gains harder

Having discussed their three principles of regulatory evolution, the scientists explore another factor noted from the research, and its a fairly intuitive one - it’s easier for regulatory evolution to come about via losses than it is by gains.

This happens for a couple of reasons. If the common ancestor to several descendant species gains a trait or simply has a trait, then each descendant species represents a potential means of losing that trait. And given that the expression of a trait often involves several successive steps (e.g. a transcription factor regulates a gene which expresses another transcription factor which regulates the structural gene), then mutating any one step represents a possible means of losing the trait. They note that the male wing spot and abdominal markings described earlier have been lost independently five and three times respectively in D. melanogaster and closely related species. And in the case of the abdominal markings, three different mutational pathways causing the loss have been discovered. They write - “ For these reasons, losses of morphological traits are expected to be frequent and relatively “easy,” i.e., they have a simple genetic basis and may even occur in a single step.”



Gains however, are different, requiring the deployment of several gene products and/or or regulatory regions and doing so in a coordinated manner. This is unlikely to happen in a single step because it probably requires numerous changes at multiple places in the genome. In the case of CRE gains, it most likely requires the acquisition of multiple transcription factor binding sites.


With CRE evolution, observations to date where a new regulatory activity had evolved by the cooption of an existing CRE, the two existing CRE activities were widely separated on the genome, suggesting to the researchers that subfunctionalisation of an ancestral CRE had occurred. In other words, a fine tuning of a complex CRE activity had occurred via a duplication whereby the functions of the ancestral CRE were now shared between the two descendant CREs.






To be continued ...





[rwatts]

Interaction May Evolve Between Any Transcription Factor and Downstream CRE.

The third principle the authors think underlies regulatory evolution is that interaction may evolve between any transcription factor and downstream CRE.



What allowed them to derive this principle was the following question - to what extent do constraints exist between transcription factors and CREs. Can any transcription factor be coopted into regulating any CRE or are there limits? 



The reason for asking this kind of question is that embryonic development begins with a small group of cells expressing a particular combination of transcription factors. These proteins then go on to regulate downstream genes which most often code for additional transcription factors in an ever expanding level of gene expression. Ultimately these cascading hierarchies of transcription factors regulate cells that code for structural proteins that build parts of the organism. 


So there are hierarchical tiers of transcription factors and perhaps the logical thought is that during evolution, modifications to interactions between transcription factors and CREs would affect only consecutive levels as opposed to evolution in a transcription factor at one level in affecting the expression of a gene several levels away. 



Studies in pigmentation pattern evolution in flies showed again that expectations were wrong.



The authors describe research into pigmentation patterns on the abdomen of the fruit fly D. melanogaster and its close relatives.



It had been shown that the up-regulation of the expression of the yellow gene which gave some fruit flies a dark rear end, was tied to the expression of the Hox gene Abdominal-B (Abd-B). However, because the Hox genes like Abd-B sit high in the gene expression hierarchy and yellow sits very low in the hierarchy, it had been though that Abd-B would affect yellow via at least one other transcription factor. Much to their surprise however, researchers found that Abd-B affects yellow directly. The gain or loss of pigmentation stripes in the abdomen of D. melanogaster and its close relatives was pinned down to the direct association between Abd-B and the gain or loss of yellow CREs.



The same thing was found with respect to wing spots. As described earlier, the transcription factor Engrailed, a wing building protein, was found to have been coopted to control the regulation of the seemingly unrelated yellow pigmentation gene.


These transcription factors were shown to be, unlike the yellow gene, deeply conserved. That is, they could be found in a wide variety of disparate organisms sharing common ancestors in deep time, and in all cases were body plan marking and body part building transcription factors which were expressed early in embryonic development. Yet here they were being coopted to control the expression of structural genes like yellow which lay well down in the hierarchy of gene expression, with yellow only being up regulated late in embryonic development.



And so, these kinds of studies lead the authors to propose the third principle of regulatory evolution:-



association between any transcription factor and a down- stream CRE may evolve, irrespective of positions of these components in genetic hierarchies.



They think that this opportunistic nature of regulatory interactions “contributes to the vast evolutionary potential of CREs.”



They argue that their three principles explain the "the mechanisms through and circumstances in which regulatory changes are more likely to contribute to morphological evolution."

However, this is not the end of the story. Their rules have implications for understanding overall patterns of morphological evolution. In the next sections they expand further and discuss issues concerning the ease of change in direction (i.e. gain or loss of function) and the magnitude of trait evolution over long periods of evolutionary time.





To be continued ...


[rwatts]

Cis-Regulatory Evolution Minimizes Fitness Penalties

They begin this brief section by noting the importance of selection in all of this. “Selection pressures ... constraint the scope of genetic changes permitted under natural selection.”



The reasoning here is that two processes shape the course of evolution. One is mechanisms that generate variations between individuals in a population, regardless of their outcome as far as the individual is concerned. These variation creating mechanisms could produce an individual that is not good at collecting food, or an individual that is superior at collecting food, or one that is a superior runner and hence better at collecting food and escaping predators. These variation generating processes pay no regard to the potential outcomes. The second is a mechanism that actually sorts these variations out either by simple random drift in a population as time goes by, or more importantly, by ensuring that some variants in the context of the associated environment, have greater reproductive success, that is, the variants are fitter. And of course other variants are less fit and have less reproductive success, while most maintain the average fitness. This average moves over time, as the variant genes of the fitter individuals spread through the population.

The point is, selection constrains evolution in how the variant individuals succeed (or otherwise) in the context of the environment.



Now morphological evolution can affect protein function through mutations in gene coding sequences or through mutations in gene regulatory sequences (particularly changes to CREs). So the question is, which of these types of changes is more likely to be tolerated by natural selection? What are the circumstances which allow this greater toleration? The researchers write:-

The study of pigmentation pattern evolution has also proven insightful to address this question. During the course of Drosophila evolution, discrete pigmentation patterns have been gained by the ancestors of identified groups of flies, preserved in many descendant species, and occasionally lost in others.



The loss of a pigmentation pattern could come about because of the failure of a pigmentation gene to be expressed (that is, a regulatory switch failed, either to act where it should act, or it failed to act altogether), or because of the failure of the gene itself, due to genetic mutations producing a dud protein or a protein that no longer had a specific pigmentation function.



The problem with the latter kind of mutation is that a gene is often expressed in several different contexts. That is, it generates proteins at different times, at different places, in different tissues during embryonic development. And so collateral effects cannot be avoided when the gene varies. They write:-


Many fly pigmentation proteins are also involved in cuticle formation and the metabolism of dopamine, an essential neurotransmitter, and D. melanogaster yellow mutants are notorious for their poor mating success (37, 40–42).



So it should be easy to see that disruptions to the gene itself causing it to produce defective proteins, will be unlikely to be tolerated by natural selection. A fly may be at a selective advantage to lose a particular wing patterning, but will be at a massive disadvantage to have a dud neurotransmitter.



Against this, the researchers point to three cases of loss of pigmentation patterns that have involved “the selective functional inactivation a CRE of the yellow locus.” That is, these losses have been pinpointed to one of the several regulatory regions lying outside of the yellow gene. They direct the reader to their Figure 4 and they cite this paper:-



Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

- and this paper:-


Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution..

In the first paper, loss of wing spots was shown to be related to the loss of a specific CRE. In the second paper the loss of the dark abdomen was shown to be related to the loss of another CRE, a5/a6, which is controlled by the Hox gene ABD-B (I think :) ).



As the authors note:-

In each case, mutations altered the spatial distribution of the gene product in only one domain of the body, leaving the rest of the expression pattern and the protein activity intact.



They continue and point out that:-



These examples illustrate that disruption of a dedicated CRE minimizes the fitness penalties by affecting only one specific aspect of a gene’s function while leaving the other functions undisturbed.





They write of additional examples where loss of gene expression is inferred to be associated with CRE evolution - loss of larval hairs in Drosophila and pelvic reduction and bony armor loss in stickleback fish. 

In all cases they note, the common denominator has been a pleiotropic gene, a gene with multiple functions. And the changes bringing on the morphological evolution has been to the CREs affecting the gene as opposed to the gene itself. 

They reinforce the point that pleiotropy imposes a genetic constraint on just what can actually evolve when changes are made to the gene itself as opposed to the elements that control the gene. And they argue that “[h]ighly pleiotropic genes (including most developmentally regulated genes) are more likely to contribute to morphological evolution through cis-regulatory changes than through coding sequence alterations.” 



When changes to the protein coding sequences are involved in pigmentation evolution, it’s then that researchers find that the genes are involved in a single process only. Overall fish, mammal and bird body colour genes appear to be examples, and they cite several references (see below) illustrating this point. In effect “[c]oding sequence changes appear to be better tolerated in minimally pleiotropic genes.”



Because fitness penalties are too great and much more likely with genes coding for proteins which have several different functions at different times and different places in a growing embryo, then there is a real limit to the kinds of changes that can be tolerated by natural selection in such circumstances, meaning that morphological evolution is much more likely to be due to changes in the CREs that are associated with such genes.






To be continued ....





Those references re changes to developmental genes that have only a single effect.



Ritland K, Newton C, Marshall HD (2001) Curr Biol 11:1468–1472.


Theron E, Hawkins K, Bermingham E, Ricklefs RE, Mundy NI (2001) Curr 
Biol 11:550–557.


Eizirik E, Yuhki N, Johnson WE, Menotti-Raymond M, Hannah SS, O’Brien 
SJ (2003) Curr Biol 13:448–453. 


Nachman MW, Hoekstra HE, D’Agostino SL (2003) Proc Natl Acad Sci USA 
100:5268 –5273.


Mundy NI, Badcock NS, Hart T, Scribner K, Janssen K, Nadeau NJ (2004) 
Science 303:1870–1873. 


Protas ME, Hersey C, Kochanek D, Zhou Y, Wilkens H, Jeffery WR, Zon LI, 
Borowsky R, Tabin CJ (2006) Nat Genet 38:107–111. 


Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP (2006) 
Science 313:101–104. 


[rwatts]

Thank you rwatts for your efforts. Personally I only follow and read your posts and check references.

Thank you shunyadragon. They are hard work, but I do learn a lot from them. Hopefully I don't mess up too much and get things wrong.

[shunyadragon]

Thank you rwatts for your efforts. Personally I only follow and read your posts and check references.

[rwatts]

So the authors expand on what they had just been discussing and generalize it:-



The development of the wing or any body part or organ is a sequential process controlled by an array of regulatory proteins (9). As development proceeds, the expression of these proteins progressively delineates the wing layout, position of the veins, sensory organs, and so on. Collectively, the expression profiles of all wing-building transcription factors compose a complex mosaic of superimposed patterns or ‘‘trans-regulatory landscape’’ (Fig. 3). If and when combinations of binding sites for members of the trans-regulatory landscape evolve in the CRE of a pigmentation gene, then the expression profile of this gene may change. Because the formation of pigmentation patterns requires the coincident deployment of multiple pigmentation genes, it can be anticipated that these genes will fall under the control of a common suite of trans-acting factors.

Changing the switching patterns of regulatory genes and evolving different combinations of CREs and their interactions with transcription factors can bring on markedly different pigmentation patterns. Accumulating regulatory links between these factors and CREs can bring on more complex patterning. In Figure 1 of the paper, the top three wings on the right hand column illustrate this point.



They think this kind of evolution in wing patterning illustrates an even more general principle when they write:-



More generally, the evolution of wing patterns illustrates a fundamental principle of regulatory evolution: novel patterns arise more readily from the recruitment of available components, CREs, and transcription factors into new regulatory interactions rather than from the de novo creation of genes or CREs. Indeed, all of the diversity of wing pigmentation patterns illustrated in Fig. 1 may be accounted for by regulatory changes and would not require, in principle, any coding sequence changes among species.



Next, the researchers discuss how cis-regulatory evolution minimises fitness penalties.


 That is, by evolution operating outside the gene itself, and operating on these cis-regulatory elements and/or their associated transcription factors, morphological change can occur without a major risk of large fitness penalties due to the fact that a specific gene is required to express in different locations and/or at different times in the developing organism.



To be continued ...





[rwatts]

Using Available Genetic Components To Generate Novelty

Under the above title, the authors describe the first of the three principles of regulatory evolution that were mentioned in a previous post.

Using existing components to generate novelty is also known as “cooption”.

Their description relies on the fact that within the Drosophila melanogaster “species group”, (I presume they are referring to D. melanogaster and very closely related species), some males bear a dark spot on the far (anterior) end of their wings, while most other species do not.

Given that the wings are similar in all other respects, e.g. shape and venation, scientists are presented with a question that allows them to focus on a simple question - what has changed between the spotted and unspotted species?

Differences in the expression of pigmentation genes drive the different pigmentation patterns, particularly in this case, a pigmentation gene called yellow. yellow is critical in the formation of black pigment. :) In both the spotted and unspotted species it is expressed in very low levels across the developing wing, but where the spot occurs, its expression levels rise drastically.



So the question is, how did the yellow expression evolve?



Two papers cited, reveal how this came to be understood. Thus, in:-



Evolution in black and white: genetic control of pigment patterns in Drosophila


- the reader learns how the CRE which drove the uniform expression of the yellow gene was tracked down. This is the wing CRE.

 And in:-



Chance caught on the wing: cis-regulatory evolution and the origin
of pigment patterns in Drosophila

- the reader learns how the same CRE region has changed to drive the up regulated expression in the anterior portion of the wing where the spot forms.



They write:-

“Therefore, in this instance, an ancestral CRE has been coopted and functionally modified to become a wing + spot CRE and to generate a novel pattern.”



The authors note that a specific spot forming CRE system with a full complement of its own transcription factors could have evolved anywhere near the yellow locus. But this is not what happened. What happened was that an existing system was modified, as if it is easier to go down the route of coopting existing systems and modifying them. 

Why is it easier to co-opt existing CREs - presuming this is in fact the case?

The researchers note that a functional CRE usually requires a substantial number of inputs to generate a pattern on a fly’s wing. Therefore “[i]f a functional CRE were to evolve from natıve DNA, the evolutionary path to acquire all of the necessary transcription factor-binding sites, in a functional arrangement, would be relatively long, and it is difficult to see how selection might favor the intermediates.” On the other hand, with a CRE (controlling the expression of yellow) already active in a certain tissue (say the wing) at a certain time (when the wing has nearly formed it’s overall shape), then it already contains some sites necessary to direct gene activity in that tissue. So it’s a relatively short pathway (as opposed to evolving everything from scratch), to co-opt some of the elements of the CRE to do something different. In this case, the different thing was to up regulate the expression of yellow in the wing tip only.

Therefore they argue, “it seems more probable that a novel gene expression pattern in a tissue will arise from random mutations creating binding sites in the vicinity of an existing CRE driving expression in that tissue than from mutations in nonfunctional DNA.”

But specifically which transcription factor binding sites evolved in the wing CRE to create the wing + spot CRE? Again, they note that sites for a specific transcription factor could have changed. However, the formation of the yellow spot pattern involved both activators and repressors that are used in building the wing, and one particular transcription factor named Engrailed is active throughout wing development as well as during pigmentation formation. In the case of pigmentation, it’s active in the area of the wing closest to the body, repressing expression of yellow, therefore confining enhanced expression to the anterior part of the wing.



Now engrailed is a key factor involved in the identity and formation of arthropod body parts (segments and appendages) and it can be traced back in time to well before it was ever used in pigmentation of a spot on a fly wing. That is, it’s not a transcription factor specifically dedicated to wing pigmentation.



Yet evolution took advantage of the presence of Engrailed and “established a direct regulatory connection between Engrailed and a pigmentation gene, thus sculpting the contour of the pigmentation spot. In this instance, Engrailed has been recruited for a new function, without any change occurring in its activity, protein sequence, or expression.”


To be continued ...





[rwatts]

Morphological evolution is the outcome of changes to patterns in gene expression, and therefore to understand morphological evolution, scientists need to understand how changes in gene expression patterns occur.



Perhaps a good way of thinking about this is to understand that a whale (a mammal) is just a rearranged hippo (a mammal) like animal. They more or less have the same bits and pieces. So, to rearrange the hippo like mammal into the whale, one needs to rearrange the way the hippo like mammal genes are expressed.

To gain the required understanding scientists have been studying pigmentation expression patterns in insects. A couple of reasons for these types of studies have already been given, but there are another two reasons for this choice. The pigmentation genes in insects are fairly well known and characterised, and the pigmentation patterns in some closely related insects species are highly variable, even though the underlying wing structure - its shape and venation - are quite stable across the species. Thus the researchers can study pigmentation patterns on a system that is stable with respect to other potential morphological changes.

A classic case is that of the higher Diptera (flies), and the authors provide an example of the large difference in patterning and colour on stable wing structures between closely related species in Figure 1 of their article.

Pigment patterns are formed by several enzymes acting locally on depositions of metabolites (small molecules that are the partial products of metabolism processes) to produce the colouring. This occurs late in the life of the embryo when the growing organism has more or less reached it’s adult size and shape. The metabolites have a relatively uniform distribution but the enzymes are laid down in the pattern that will shortly produce the pigmentation pattern itself.



So to understand the laying down of the enzyme blue print, scientists need to understand how the genes that create the enzymes are orchestrated.



(How the patterns are laid down can be read about in this later article:-



Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation)




Knowing this, scientists can then probe the means by which these expression patterns change, even between closely related species of fly or butterfly.



There are two possible ways of manipulating these expression patterns:-



1) changing the activity or spatial deployment of the transcription factors that regulate the enzyme creating genes and/or

2) changing the CREs of the pigmentation genes.



The second option provides two additional paths:-



a) alter existing CREs, or



b) denovo evolution of CREs.

The authors note 6 cases of gain or loss of pigment gene expression that can be directly traced to the evolution of pigment gene CREs. (The associated papers cited had their abstracts quoted in my last post).



Papers like these, and additional studies of changes to transcription factors associated with pigmentation, as well as other studies on the morphological evolution of closely related species illustrate what the authors think are the general principles behind the “process of evolution by gene regulation”. A couple of those additional studies cited are:-



Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element

Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene







To be continued …

[rwatts]

By using closely related species and concentrating on patterns in pigmentation, researchers were able to provide direct evidence for the role of changes to CREs in morphological evolution. For example:-


Nicolas Gompel, Benjamin Prud'homme, Patricia J. Wittkopp, Victoria A. Kassner & Sean B. Carroll, Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila, Nature 433, 481-487 (3 February 2005)



The gain, loss or modification of morphological traits is generally associated with changes in gene regulation during development. However, the molecular bases underlying these evolutionary changes have remained elusive. Here we identify one of the molecular mechanisms that contributes to the evolutionary gain of a male-specific wing pigmentation spot in Drosophila biarmipes, a species closely related to Drosophila melanogaster. We show that the evolution of this spot involved modifications of an ancestral cis-regulatory element of the yellow pigmentation gene. This element has gained multiple binding sites for transcription factors that are deeply conserved components of the regulatory landscape controlling wing development, including the selector protein Engrailed. The evolutionary stability of components of regulatory landscapes, which can be co-opted by chance mutations in cis-regulatory elements, might explain the repeated evolution of similar morphological patterns, such as wing pigmentation patterns in flies.

Jeong S, Rokas A, Carroll SB., Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution, Cell. 2006 Jun 30;125(7):1387-99.

Hox genes have been implicated in the evolution of many animal body patterns, but the molecular events underlying trait modification have not been elucidated. Pigmentation of the posterior male abdomen is a recently acquired trait in the Drosophila melanogaster lineage. Here, we show that the Abdominal-B (ABD-B) Hox protein directly activates expression of the yellow pigmentation gene in posterior segments. ABD-B regulation of pigmentation evolved through the gain of ABD-B binding sites in a specific cis-regulatory element of the yellow gene of a common ancestor of sexually dimorphic species. Within the melanogaster species group, male-specific pigmentation has subsequently been lost by at least three different mechanisms, including the mutational inactivation of a key ABD-B binding site in one lineage. These results demonstrate how Hox regulation of traits and target genes is gained and lost at the species level and have general implications for the evolution of body form at higher taxonomic levels.

and:-

Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh SD, True JR, Carroll SB., Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene., Nature. 2006 Apr 20;440(7087):1050-3.




The independent evolution of morphological similarities is widespread. For simple traits, such as overall body colour, repeated transitions by means of mutations in the same gene may be common. However, for more complex traits, the possible genetic paths may be more numerous; the molecular mechanisms underlying their independent origins and the extent to which they are constrained to follow certain genetic paths are largely unknown. Here we show that a male wing pigmentation pattern involved in courtship display has been gained and lost multiple times in a Drosophila clade. Each of the cases we have analysed (two gains and two losses) involved regulatory changes at the pleiotropic pigmentation gene yellow. Losses involved the parallel inactivation of the same cis-regulatory element (CRE), with changes at a few nucleotides sufficient to account for the functional divergence of one element between two sibling species. Surprisingly, two independent gains of wing spots resulted from the co-option of distinct ancestral CREs. These results demonstrate how the functional diversification of the modular CREs of pleiotropic genes contributes to evolutionary novelty and the independent evolution of morphological similarities.






Based on the above kinds of studies, researchers began to see some principles operating behind the evolution of gene regulation, principles which they felt applied generally and the aim of this article was to explain those principles. Gene regulation evolution or cis regulatory evolution in this case:-



(i) “proceeds using available preexisting genetic components” - it’s easier for evolution to re-use already existing components than to evolve new ones.



(ii) “introduces discrete changes in gene expression thus minimizing deleterious effects and fitness penalties” - that is, given that a gene is generally expressed in many different places at different times, then by evolution tampering with individual cis-regulatory units, a change to one location and one time can be made, without affecting the gene expression at other times and other locations, and 



(iii) “allows the association between any transcription factor and any downstream gene and thereby provides immense potential for evolutionary novelty.” Not much need be said here. It’s a no-brainer.



These principles the authors argue, explain how and why regulatory sequence evolution is so powerful and widespread, even though its not the exclusive means by which organisms evolve over time.





To be continued ….

[rwatts]

In my last post I wrote that the authors of this paper claimed that acceptance of the importance of gene regulation to evolution was somewhat gradual and that it still may not be universally appreciated today (as of 2007).



They offer several reasons for this:-

1) Ever since the discovery of the gene, population genetics and evolutionary studies have focussed on protein coding sequences (as opposed to the sequences of DNA that regulate the genes). People’s heads were, and perhaps still are in some cases, buried in this research, unaware of what was happening elsewhere. The problem of scientific specialisation.


2) Gene duplication had long been shown to be important to evolution and the origin of new genes. People’s attentions focussed on this, diverting them from other important findings. Besides, as the authors noted “the recognition of the complexity and evolutionary potential of CREs is more recent and has emerged primarily from molecular developmental genetics, outside of the primary literature of evolutionary genetics.” Using somewhat loose language, researchers can, like people in any other culture, have their fads, which distract them from what is happening outside the area of immediate and interesting concern.


3) Until the time of writing of the article, there had been few studies of CRE evolution. Most earlier studies had concentrated on the reasons for CRE conservation across time. There had been very few studies linking changes to CREs to morphological evolution.


So why the fascination with mere fly stripes and butterfly wing patterns?


To be able to address the problem of the general lack of knowledge (and acceptance) of the importance of CRE regulation, scientists needed appropriate systems to study.



At first sight it would appear sensible to do what had been done with respect to genes, namely examine CREs across a range of taxonomic classifications, including very distantly related organisms. People examining the evolution of genes could often track homologous genes right across the animal kingdom at all levels of taxonomic classification. So why not with respect to CREs?

But when it came to CREs, there was a snag.



Relatively speaking, genes mutate slowly whereas the “junk” DNA regions between the genes, in which the CREs reside, mutate much more rapidly, destroying any signals that might unite CREs between different organisms in widely separated taxa. It's not that mutations happen in these regions more frequently. They happen just as frequently to genes. However, given the nature of genes, more mutations are likely to be harmful there than outside the gene and so gene mutations tend to be removed from the population (via the death of the hosting organism, or because its inability to reproduce relatively successfully). The non coding regions have fewer functional constraints than do the coding regions and hence the higher mutation rates which destroy any homology signals.

To get around this problem, scientists have relied on rapidly evolving traits among closely related species or populations. Hence the focus on fly stripes or butterfly wing patterns.



Doing this offered researchers two advantages:-



1) Given that the organisms were closely related species then recent divergence is likely and hence “the number of genetic changes responsible for morphological divergence will be relatively modest and more readily distinguished from other changes not involved in morphological divergence.”



2) In some cases, the relevant genetic changes have been investigated in the context of the native habitat of the associated organisms allowing researchers to probe the link between DNA mutation and the possible adaptive role of such mutations on morphological evolution.



By using closely related species, and rapidly evolving traits, researchers began to understand the link between changes to CREs and morphological evolution.






To be continued ….

[rwatts]

i take it then, my replies annoy you.

ok, i leave you alone.

It does not annoy me.

You seem to be joyed about something, and it's something due to epigenetics. But this paper has nothing to do with that topic, other than in a very round about way.

Hence I am wanting you to justify your assertion, as opposed to saying that you will leave things alone because, so you say, your prodding is annoying me.

All I want you to do is justify your assertion.

[jordanriver]

before you try jumping up and down.

i take it then, my replies annoy you.

ok, i leave you alone.

[rwatts]

ok, Roland, you seem to be interested in Hox genes.

Are you on the verge of concluding that Hox genes are doing all their work on their own?

in your POST 2 you reported the paradox:
"The paradox


As the authors of the article put it - “if all animals are built by using similar genetic tools, how did their seemingly endless morphological diversity arise?”

For example, if the families of hox genes between man, mouse and camel are so darn similar, then how come we look so different? Why don’t all humans have two humps on their backs, and why aren’t camels walking upright?""

then you cited 'Homeotic genes and the evolution of arthropods and chordates' by Sean Carroll
where on page 484:
"We now know that Hox genes are regulated by many upstream factors, and that Hox proteins act as sculptors that modify the basic arthropod or chordate metamere by modulating the expression of potentially dozens of interactive genes, the products of which determine the cellular events of morphogenesis"

Roland, what do you think are some of those "upstream factors"

If the Hox genes are just "sculptors" then that would possibly explain the paradox ,
if by "sculptor", the writer is referring to the tool, the same wood chisel 'morphs' a variety of sculptures.

its just the tool.

Or do you think the Hox gene is a "sculptor" in the sense of being 'the craftsman' who uses the tool, and is not regulated by some other director?









JR, you asserted that:-

"Its about dna methylation (by epigenetic control) whether they acknowledge it or not."

I'm asking you how you managed to work that out (based on their paper)?

Or do you think the Hox gene is a "sculptor" in the sense of being 'the craftsman' who uses the tool, and is not regulated by some other director?

?

Hox genes have to be triggered by something else. And they can be regulated by other things (read my last post to find out what kind of things they can interact with). What's the biggie about that? If you are thinking of papers such as this:-

DNA methylation and differentiation: HOX genes in muscle cells

-then read the conclusion, before you try jumping up and down. And as Klaus asked, what on earth does this have to do with ToE being wrong, and a 6 day creation 6,000 years ago being correct?