Exercise 3.1

Gene Networks and the Evolution of Complex Traits

(This exercise is based on Monteiro, A., and O. Podlaha. 2009. Wings, horns, and butterfly eyespots: How do complex traits evolve? PLoS Biology 7: 209–216.)

(Note: The reference above links directly to the article on the journal’s website. To access the full text of the article, you may need to be on your institution’s network [or logged in remotely], so that you can use your institution’s access privileges.)

INTRODUCTION

One of the arguments that gets creationists most excited is the notion that natural selection is incapable of resulting in complex structures like eyes or wings because there are no useful intermediates for selection to act on; you either have a functional eye or you don’t. This is a spurious argument for several reasons, one of which is discussed by the authors of this paper.

One of the ways that a complex structure can evolve without the need for a series of intermediate forms is by co-opting gene networks that have already evolved for other functions or structures. Co-option certainly occurs in nature, but distinguishing co-option from de novo evolution of similar gene networks (independently of each other) is not so straightforward. The authors of this paper propose a test by which the two scenarios (emergence of similar gene networks by co-option versus de novo evolution) could be distinguished by looking at the cis-regulatory elements (CREs) involved in the networks.

A CRE is a part of a gene that doesn’t code for a protein but rather acts as a promoter or enhancer that regulates the production of the protein at precise times and places in a developing organism. The cis- prefix refers to the fact that the regulatory element in question is located on the same DNA molecule as and relatively close to the protein-coding sequence that it regulates. Regulatory elements that are located more distantly or on a different DNA molecule (a different chromosome) are called trans-regulatory elements. Trans-regulatory elements are usually genes that encode proteins that bind to cis-regulatory elements of a different gene in order to activate or repress the activity of that gene. Gene networks are sets of genes that participate in such regulatory interactions over the course of development. The networks are usually represented with arrows connecting different genes (see Figure 1A).

The authors of this paper argue that if a gene network is co-opted for another function (say in a different tissue), then genes in the middle of the network will use the same CREs for two different functions (i.e., these CREs will become pleiotropic) (see Figure 1B). In other words, the same CREs will affect two phenotypes—the one in the original tissue and the one in the new tissue. On the other hand, if the gene network evolves independently in the two different tissues, the regulatory elements will not be pleiotropic, but rather each tissue will have its own CREs (see Figure 1C). Figure 2 shows some examples of pleiotropic CREs.

QUESTIONS

Figure 1 Hypothetical Illustration of Gene Network Co-Option and De Novo Network Evolution: (A) Modular gene network where gene X, at the top of a regulatory network, directs expression of gene Y, which in turn directs expression of gene Z. All these genes are expressed in the tip of an appendage (e.g., leg) depicted on the right. (B) The modular gene network is co-opted into a new tissue by the evolution of a novel CRE in gene X. The Y and Z genes, which only receive inputs from X and Y genes, respectively, are also turned on in the new tissue (e.g., eyespot centers in a butterfly larval wing). The CREs of the Y and Z genes now have a dual function in directing gene expression in two separate developmental contexts, e.g., they are pleiotropic. (C) De novo network evolution where elements of the same non-modular gene network, X, Y, and Z, each evolve a separate CRE that drives gene expression in the novel developmental context.

Question 1. Why would co-opted gene networks help in the rapid evolution of complex structures?

Question 2. When a phenotypic trait is controlled by a gene network such as that shown in Figure 1, is that trait more likely or less likely to be modified by random mutation than a trait that is controlled by a single gene? Why?

Question 3. How does the gene network responsible for insect leg development act in developing butterfly wing tissue (in other words, what are the analogous structures in each of these tissues)?

Question 4. Looking at Figure 1, what would be another term for what are called “enhancers” in the figure?

Question 5. Cis-regulatory elements (CREs) can easily be duplicated along with the genes that they control. Is this also true of trans-regulatory elements? Why or why not?

Figure 2 Examples of Pleiotropic CREs: A schematic representation of putatively pleiotropic CREs is shown for: (A) The spalt (sal and salr) gene complex; (B) spineless (ss); (C) yellow (y); (D) oddskipped (odd). Gene orientation is marked by arrows. Ovals show approximate position of CREs surrounding the protein-coding genes. Checkmarks of tissue/organs above CREs represent the multiple domains of gene expression driven by the same CRE. Modified from [24, 26–28]. The multiple CREs that drive gene expression in the same tissue or organ mostly drive gene expression in distinct cell populations. Abbreviations: CNS, central nervous system; PNS, peripheral nervous system.

Question 6. Refer to Figure 2 above. Why do the arrows that define the directions of the genes on the DNA strand point in both directions?

Question 7. Thinking about your answer to Question 6, is a gene on one DNA strand matched by a copy of itself on the complementary strand?

Question 8. How many of the CREs shown in Figure 2A (the spalt gene complex) are not pleiotropic, and which tissues do they operate in?

Question 9. Of the 5 CREs shown in Figure 2A, how many are located upstream of either the salr or the sal gene?

Question 10. In Figure 2D, is the CRE shown for the odd gene pleiotropic or not?