EEB 122. Principles of Evolution, Ecology and Behavior ?

Lecture 07.?The Importance of Development in Evolution

https://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-7

We are?going to introduce the role of development in evolution.?I want you to think of yourself as inside a single-celled bacterium and the complexity of the?gene networks and the biochemical networks.?Development doesn't arise until we get to multi-cellular organisms. It's just as complex as the whole picture down inside that one single-celled bacterium with?all the signaling pathways, all the way that information is transferred and integrated in a multi-cellular organism.

So there are two huge kinds of orders of magnitude, levels of hierarchical complexity of information integration that happen in a multi-cellular organism. We call the way that the information in the genes maps into the structure of the genotype the genotype-phenotype map. Another name for the genotype-phenotype map is development.?

What's involved in development? It isn't really just the production of the adult?from an egg. It is the living of the entire lifecycle, from the formation of the gamete, through the adult, through all the changes the adult goes through until it dies and produces the next generation. So development refers to the entire lifecycle, and evolution shapes the entire lifecycle.?

Life is all built out of cells, and that means that the problem of development is a problem of communicating between cells. And cells are all set up as information signalers and receivers. They have cell adhesion molecules on their surfaces. They produce information molecules, hormones, and other signaling molecules for export.?

Now every cell in your body has all the information in it that's needed to build you, and that is true of virtually every organism. The only exception in us is our red blood cells because they don't have any nuclei, so they don't have any DNA in them. That means that development is a matter of editing, determining?which information gets turned on in the right place at the right time. Development?has a strong role in the course of the production of individual organisms in shaping the kind of variation or?pattern?that is presented to selection.?This is why we actually see, morphologically, the Tree of Life. It's because they share developmental pathways that have been inherited from ancestors and that have constrained the range of phenotypes that can be presented to selection.?

You might think that you could conceive of the body as produced by an engineer, but it's not really constructed that way in evolution. What goes on is that genes can only build organisms out of the materials that are available at a certain time, and then there is an evolutionary memory, of which materials are selected, and of the control systems that are used to shape the phenotype with them.?

• The cell membrane is a lipid bilayer and?has all sorts of special channels in it, things that are filters to let particular stuff in and keep other stuff out. It's been heavily modified by evolution. But there is no way that you can take simply the DNA sequence in the genome and get a reaction system that's going to construct cell membranes. All known cell membranes are actually constructed biologically by using pre-existing cell membranes as templates. In other words, the cell membrane itself is an information transfer molecule.

• The?bones are made out of a material called hydroxyapatite, which is a calcium phosphate material. And hydroxyapatite has the following extremely convenient feature. If you take hydroxyapatite and you put it under stress, it will strengthen itself in the direction of the stress. That means that the genes don't have to have sensor systems to detect stress. In fact, there are modifier genes that then take this and use it to their own advantage, by building in protein molecules that strengthen the bone in the direction of the stress.?But the initial signal, which direction is the stress coming from, is a freebie. It's given by the biochemical properties of a hydroxyapatite.

• And then?gastrulation. When vertebrate embryos, and many other embryos, grow, they grow up as a ball of cells which then becomes a hollow sphere of cells, and that hollow sphere of cells, which by the time it gastrulates has thousands of cells in it. You can think of it as a little pulsing basketball,?a little sphere that's pulsing. And if you simply let this thing grow to a certain size, the tension in the actin tubules in the cells will cause it to spontaneously invaginate. So it'll get a dimple in it, like you pushed your thumbs into it. This happens spontaneously.?

So these are some of the properties of the biological materials that organisms are constructed out of, and it means that on the one hand the genes don't have complete control over the phenotype, but on the other hand they are given certain things by the materials that don't have to be specified in the DNA sequence.?

So where does development fit??The biological disciplines that we call Ecology and Behavior study the mechanics of natural selection and?deal with the processes that reduce the cohort of newborn organisms to the ones that survive to reproduce.

Genetics takes the genotypes of the parents and it transforms the genotypes of the parents and maps them?into the genotypes of the offspring?through Hardy-Weinberg equations or?the selection that's operating on them.?Development as being a big transduction mechanism that takes information and turns it into material. In the process, Development?places limits on what the phenotypes can look like, so that only a certain range of?conceivable phenotypes are?going to arise out of the DNA sequence in a genome.

• In animal kindom,?Humans are?chordates.?A bryozoan is a moss animalcule. Bryozoans produce beautiful exoskeletons and they live on?tropical reefs. A priapulid is a deep-sea worm that forages with a tentacle and when you pull it out of its hole, it looks like a penis; which is why it's called a priapulid.?Tardigrades are tiny?water bears that?look a little bit like insects or crustaceans.?Insects, crustaceans,?spiders?and their relativesare are?arthropods.?Arthropods are anything with jointed legs.?Pogonophorans are a?tiny phylum of worms that live in the sand and are living fossils and haven't really changed their morphology for about 400 million years.

• If you look at what happened when multi-cellular organisms formed and one branch of them went off to become animals, this is what development was able to produce. It could produce body axes--front and back, left/right; produce a skeleton, organ system, symmetry and cell layers. And figuring out the shared general mechanisms by which development can produce those things, and then how evolution can tweak them to make them different in these different groups, is evolutionary developmental biology, or evo-devo.

• There are some big and striking differences among these groups. For example, this group up here has an exoskeleton, and this group down here has an endoskeleton; and that places very fundamental constraints on growth, size, all kinds of things.

• What can it do in plants? Basically what this does is it takes you from ferns and their relatives through cycads, ginkgoes, pine trees and fir trees; the gnetophyta, which have some really cool plants that live in Namibia; Wellitschia and other things like that are gnetophytes. And then the magnoliophyta are all flowering plants, going out here. So this is a huge group down here. These guys are all variations on the same?themes: a meristem-root axis; where xylem and phloem appear; where wood appears; the kinds of branching patterns they have; whether they have naked or covered seeds; whether they have leaves; and whether they have flowers.?

So you can see that the image that I'm trying to create here, in both plants and in animals, is that there's certain shared general features, and that what evolution has done is that it has made many, many different combinations of those features, to create the diversity that we see, and that this is done through the evolution of development.?

Mechanistically a lot of this is going on at the level of gene regulation; and this is a recap of the structure of the eukaryotic gene. And the parts that I want you to focus on right now are the promoters and the enhancers. So these are parts of the DNA molecule that receive a signal, which says turn this gene on or turn it off.?

• You can think of there being regulators and?then they?feed into a signaling cascade where a signal goes out, there's a receiver and?transducer that turn?that signal into a transcription factor. A transcription factor then is going to go out and it's going to bind to the enhancer region of a gene, or a promoter region of a gene.

• In an average gene in Drosophila there are about ten to twenty binding sites in its control region. That means that ten to twenty different transcription factors can sit down on a single gene, and one transcription factor can bind to the control regions of anywhere from one gene to several hundred genes. There are about 13,000 genes in a drosophila genome.?That is a huge array of possibilities?of turning all those things on or off.?Evolution might have had to use a lot of them, in order to turn something like a worm into something like a fruit fly or?an?onychophoran?into a Drosophila.

• Or?think about the control region of a gene as the keys on a piano, and think about the transcription factors as the fingers on the hand of the person who's playing the piano, and think about evolution as the composer who wrote the score.

In the control of development, the chemical gradient?sets?up gene expression, and the transcription factors?appropriate?to that position get turned on.?

• At the beginning of development, when the first cell is getting set up to divide, and in the formation of the very early multi-cellular stages, there are concentration gradients that are produced. So before the first cell divides, there will be like a front end and a back end of the cell, and chemistry will get set up to produce molecules that then form a concentration gradient across the cell, and the concentration of those molecules is positional information on what's the front and what's the back. And as the cell divides, it retains that information on where it is in the front or the back.

• That's how the Drosophila embryo is set up. And we will also see that this kind of concentration gradient is used in the construction of the vertebrate limb. By the way, the signaling center on the vertebrate limb, when it's just a little paddle of cells, is basically in the armpit.

• What then happens is that transcription factors are used to define specific areas where only a precise subset of genes is expressed. All the info in the whole genome is in every cell and you only want a certain subset for this part of the organism that you're making.?

Genes are regulated by combinations of activators and repressors, and this combinatorial control is what gives you the huge diversity of cell specific gene expressions. When I say combinatorial control, think of composers writing notes and people playing pianos. All the music that's ever been written, that can be played on a piano, is simply a variation on all the combinations of those keys in space and time.?

• The control can get complex. It can be a cascade of information, and genes that produce transcription factors can be regulated by genes that produce transcription factors. And this sets up situations where genes can switch their roles. It is not correct to think that there are?early development genes, and then there are other adult genes.?

• Genes are used flexibly, in many different contexts, depending upon the information that's coming in to regulate them. Certainly there are some genes that are quite important in the embryo, but it turns out they also play a role in the adult.?

• It's the genes that determine the general pattern that switch on first, and the ones that are controlling detail switch on later. So when I say 'general pattern' I mean--for example, in the vertebrate embryo, the front and the back, the top and the bottom, the left and the right: that gets laid down first.

• Then the embryo gets chopped up into a sequence of segments. Some of them turn into the head, some of them turn into leg segments; some of them have extremities, some of them don't.?So this sequence of how the early general pattern gets set up, and then how the details are developed, that's all developmental genetics.

You're going to hear about homeoboxes?and MADS boxes.I want to tell you what boxes are. They are very highly conserved sequence motifs, and they are found in the DNA that codes for a particular family of transcription factors.?

• These boxes are not too long. They're conserved because they have a very important function, and that is to bind to the DNA. So they have a helix twist/structure, and that means that if the DNA molecule is here, this part of that protein, this part of that transcription factor, is going to fit right into it.

• And it's because they are transcription factors--the boxes are found in transcription factors--that this is a very conserved interaction. Because DNA hasn't changed its structure in three billion years. So if they're going to bind to it, they have to have that structure, and so selection has made sure that that sequence is preserved.

• They're called boxes simply because if you lay these DNA sequences out and?sequence a lot of DNA,?what you find is that wherever there's a transcription factor, there is a stereotypic sequence. And the people who were analyzing this, first on computer printouts, or now with imaging on computer screens, drew boxes around them, to locate them. That's why the word 'box'.

Here's the homeobox family. There are thirteen homeobox genes that have been identified. And this is from a number of years ago; this has probably been filled out now. And they have two--well there's more than two striking things about them.?

• The first thing that's striking about them is that they're deeply conserved. That means that they have retained so much of their sequence identity that you can recognize homeobox gene 1 in a human, and you can see that the same gene is there in flatworms and in earthworms, in priapulids and so forth, and conserved?all the way through the animal kingdom.

• How did there get to be thirteen in this family? Here you can see a gene duplication event right here. Homeobox gene 1 in the jellyfish and corals was duplicated right here--this was the expansion of the central HOX genes--and it happened here as well, so that now there were two copies. And that meant that this developmental control switch, which was an extremely clever piece of machinery to have around, now existed in two copies. You could use the first one to do whatever it used to be doing, and you can now evolve a new function for the second one.

• This went on up until the time that the vertebrates started to evolve. And in our closest relatives there's one copy of the HOX gene, and it was duplicated twice. It was duplicated at the level of the Agnatha; so the ancestors of the sharks. And that means that all of the vertebrates, the higher vertebrates, have four sets of developmental control genes. Interestingly, the first set is still used to lay down the major body axis, and the fourth set is used to make a limb; that's the new function.

• Now they have deeply conserved sequences, but they are also collinear.?The parts that are on one end control the head area, the parts on the other end control the tail area, and the parts in the middle control the stuff in the middle of the body. It's probably simply that when animals, prior to vertebrates, first started to get formed as multi-cellular things, this happened to be one convenient way to control development. But logically speaking, giving the signaling apparatus that's available in the genes, there's no reason logically that the genes have to be collinear.

• You can take homeobox genes and look at their DNA sequences.?If?they have similar DNA sequences, and then look at what parts of the bodies they control and see that a homeobox gene in a fly, that is homologous to a homeobox gene in a mouse, is controlling a similar part of the body.?So the things that are controlling the tail end, the green genes here, are expressed in this part of the fly and in this part of the mouse, and the things that are controlling the head end, that are expressed here in the fly, are actually expressed here in the mouse.?

Here's the vertebrate limb. The ones that are on one end of the gene are controlling the shoulder, and the ones that are on the other end of the gene are controlling the fingers.?So it's still collinear. It's the like the body axis, it's just been translated into a limb.?How simple, how logical. Remember when I said at the beginning we have these orders of magnitude of complexity within cells and?between cells. Out of all of that complexity, this simple pattern emerges.?

In flowers, the MADS genes also have a sequence in them which shows that they're a transcription factor; there's a MADS box. M-A-D-S is an acronym for the original names that these genes had. Okay? Some of them started with an m, some with an a, some with a d, some with an s. Then after all that had happened, it was noticed that they were related. So people started calling them MADS genes.?

They're scattered throughout the genome and are?not collinear. In Arabidopsis, they're on all five chromosomes.?They fall into three groups: the A group, the B group and the C group.?And within each of these groups the genes are sharing phylogenetic relationship. That means that the members of the A group are probably all duplicates of an ancestral gene; the members of the B group are probably duplicates of an ancestral gene for the B group.

Now the neat thing about the MADS genes is the way they control flowers. And we're going to see that evolutionary developmental biology has a lot to do with the production of beauty, such as?flowers and butterfly wings.

• The ABC model of flower development goes like this. If only a gene from Group A is turned on, make a sepal; if only A and B are turned on, make a petal; if only B and C are turned on, make an anther; if only C is turned on make a pistol and an ovary. So the regulation of B and C is controlling male and female organ development. This is combinatorial?,?the same general logical principle.

• However, it's with a completely different set of genes, and plants evolved multi-cellularity independently of animals, which means that plants invented development in evolution independently of animals. They both hit upon combinatorial control as a simple, logical way to control development. That probably means it's a very good idea.?It's a very simple and economical way of expressing information.

• Every gene has a history, and these MADS genes were doing something before they made flowers.?It's not as though these genes were invented in order to make flowers. They were pre-existing, and they were co-opted by evolution at the point where flowers started to evolve; and gene duplications probably helped in that process.?

If we go back to the Burgess Shale and?Cambrian, we find lots of onychophorans running around.?500 million years of evolution hasn't changed onychophorans. Onychophorans are these neat, velvet worms that?are?viviparous. If you pick them up they squirt glue on you.?They are the ancestors of the arthropods. So what evolution basically did was it took an onychophoran and, among other things, it turned them into fruit flies, and butterflies, and horseshoe crabs and king crabs and lobsters and shrimp.?

• It was done basically by changing the range of segments in which particular things were expressed. If we go back here, you can see that the onychophoran has a lot of segments. It's got one leg on each segment.?The fruit fly has many fewer segments and only six legs; the onychophoran has fifty legs or so.

• The way this initially happened--and you can find fossils that replicate some of these stages--you first make a generalized segment that?got both legs and wings on it.?You make it many times. So you've got both legs and wings on lots of segments. Then you restrict the range of expression so that only certain segments have wings, only certain segments have legs.

• Of course, this goes on in seconds; evolution took hundreds of millions of years. So it's not the same process. Some of these HOX genes have retained incredibly conserved functions. In a famous experiment that was done in the 1990s, Walter Gehring's group in Switzerland, took Pax6, which is a gene that's shared by all bilateral organisms, and they genetically engineered fruit flies with an extra copy of Pax6--it is a gene that induces the development of eyes--and by turning this gene on, they were able to make that fruit fly grow eyes in unexpected places. So it could grow one on its--this is the regular eye; this is an eye growing on an antenna; this is an eye growing on a haltier; and so forth.?The interesting thing was that they could do this with Pax6 from a human or a mouse; in other words, the DNA sequence in the gene was so similar that it could be used to control the developmental pathway in an organism in which that gene had not been sitting for 600 million years.?

Development is not easy to evolve, and I think this gets across one of the reasons that it's not easy to evolve changes in development.?

• Every organism has to function and reproduce in order for a gene to get transmitted, and you can't tweak its development around too much or you'll make it fall apart. So?that causes constraints; there's only certain things that you can do while you're moving down the road.

• These developmental constraints are not permanent. The genetic control of development does change more slowly than many other things, but?if we wiped out everything on the planet--let's first duplicate earth ten million times, and then let's go through and wipe out everything on all of those ten million planets, except for one species, and we leave it some food.?It's the only thing that's there.

• But on some planets all you've got is fruit flies or?redwood trees or?butterflies or?albatrosses; but they have a food supply, they can live. Every one of those planets is going to have highly diverse life on it, and you will see many of the things that we see on this planet.

• They will contain a signature, probably a very interesting signature, of this huge disturbance that has been created on them. But I think that it's possible for redwood trees to evolve into squid. I just think it takes them a very long time.

The things that change slowly constrain things that change rapidly, and genes don't cause development by themselves. They're steering the dynamics of gene products that interact with environmental inputs. So the genes actually are a fair distance away, biochemically, physiologically, from the things they're controlling. They are working through complicated interaction systems.?

So, a few take-home points.?

• Development maps the information in genotypes into the material of phenotypes.?

• Developmental control genes use combinatorial logic. When you compare plants and animals, that they both hit upon this method of controlling gene regulation.

• The ancestors of currently existing organisms often had an awful lot of the genes that are now involved in controlling development. A?lot of what has gone on in evolution is changing the specificity of expression in time and space, and the specificity of receptors in time and space. Rather than necessarily evolving new genes that make new kinds of proteins, a lot of evolution has been concerned with making combinations of existing genes.?