There are no Guppy Genes

Throughout the last century most people believed that each organism had its own genes, that each animal was cut from a different cloth. Beginning about twenty years ago, scientists discovered that all species share common genes. Did you know that humans have 70% of the same genes as guppies, that we share not only the same number of chromosomes (23 pairs) but roughly the same number of genes (about 25,000 or so)?

You may not see much similarity between a guppy's body and your body when you look into the mirror, but we share the same body building genes. Where are the arms and legs? The paired guppy fins (pelvic and pectoral) contain the same basic genetic toolkit genes as arms and legs.

There are no guppy-specific genes. There is a guppy specific way of using common genes found in other animals to create its body architecture and of course its colorful patterns.

I think it will be found that it is not the genes in guppies that will be found to be unique, it will be how the guppy uses them. It has the same genes as other fish. The real mystery is why guppies are so good at changing its appearance. And that mystery is slowly being solved, not by guppy scientists but by scientists studying genes in general and the way related species to the guppies use their genes.

In his book "Endless Forms Most Beautiful," Sean B. Carroll writes about the mechanisms that generate variety in body patterns. And those mechanisms lie outside of the gene in the "dark matter" of the guppy DNA molecule. Genes in the guppy, like all other animals, are under the control of genetic switches that determine how, where and when they are expressed. These genetic switches are like the software that runs the computer that is reading this blog. They literally program the guppy color genes to express themselves in the hundreds of hues and patterns we see. So there are no special guppy genes that give this little fish its ability to change its patterns like the costumes of performers in a play or circus.

See a segment of a 60 Minutes interview with Sean B. Carroll online for a succinct statement of the idea of switches: http://www.cbsnews.com/video/watch/?id=5658057n .

I read "Endless Forms Most Beautiful" several years ago, but it is not until recently that I truly appreciated how much Sean B. Carroll's book has to teach us about genetics and development, and by extension guppy color genetics and pattern development. Carroll describes the ability of genetic switches to create the myriad patterns we see on a zebra, a butterfly or a guppy.

Imagine the possibilities of combining bands, stripes, lines, spots, dots, and patches of activators and repressors and the ability to draw these in any place, in any tissue, and in any combination. (Endless, p. 126).

You do not have to imagine the possibilities, all you have to do is walk out to your fish room and spend a few minutes looking at your guppies. The guppy in the picture below is the latest generation of a two year undertaking to discover the genetics of the Galaxy guppy.

The title of the Carroll book, "Endless Forms Most Beautiful," which he adopted from the last line in Charles Darwin's "Origin of Species," seems to apply most aptly to this guppy. Carroll has a detail from a butterfly wing on the paperback edition of his book, but I think this guppy would make a great cover subject.

Here is a test. What do you see when you look at this guppy? (No peeking.)

First of all I see that the body is divided into distinct zones of expression. I have tracked this cross now through three generations, so I have the founding lines (Lace snakeskin and Schimmelpfennig Platinum) to reference it to. The caudal fin is divided into two zones, a middle zone of finely detailed pattern suffused with yellow, and an outer zone of larger more widely spaced dots. The Schimmelpfennig Platinum yellow is expressed in the front of the body and in the caudal fin, where it may after the pattern of the snakeskin there. The peduncle is divided into two zones, and upper and lower. There is white color along the bottom of the guppy. There is a dark blue area above the belly in the front, which may be the bandit marking of the Galaxy prototype. These are all observations that are guided by my study of guppy pattern and color.

The deeper I go into an understanding of Carroll's Endless book, the more I realize how it holds the fundamental keys to unlocking guppy color diversity. In my last post I said that the guppy body naturally falls into zones of gene expression, probably because that is how hox genes divide up the body to give the different parts specific roles to play. In the picture above you can see that the different zones I diagrammed have different patterns. Look at the top and bottom halves of the peduncle. In the top half you see four stripes. In the bottom half you see 12 stripes. A lot of people would say, "So what?", and walk away. Carroll's discussion of hox zones of expressions teaches you to look at such a guppy with a more educated eye. You begin to see things that escaped notice before.

An example. He teaches us that it is not common that patterns are due to a single factor. This is a fact that was recently confirmed in the zebrafish, which has a striped body. Researchers discovered that each stripe is under different genetic control. You would expect that this adds incredible complexity to fish stripe formation. But it turns out that the stripes all use the same basic genes, but each stripe is "programmed" differently by genetic switches. This is a very useful principle to have in mind when examining guppies. The fact that the upper and lower parts of the Galaxy peduncle have a different number of stripes now seems more plausible. The majority of guppy genetics pundits will tell you that the vertical pattern in the peduncle is due to the Wingean Zebrinus gene. But there is no single monolithic gene controlling stripe formation in the peduncle. There are a number of genes each controlled by genetic switches, responding to local conditions or requirements in the different zones of the body. I think that that the snakeskin trait is expressed primarily in the bottom of the body and the Schimmelpfennig Platinum trait in the top half and that might explain why the number of stripes differ between the top and bottom of the peduncle. Further research and experimentation required.

I know it is hard work to extract these kinds of meanings from a picture of a fish. And most people would counter that their hobby is supposed to be an escape from complexity not an embrace of it. If they wanted to study they would go back to school. What they want is practical information. But there is no more practical information than that found in books like Carroll's. I am going to use it to form the basis for my next major thrust into the research, reading and studying the research done specifically in fish color and pattern molecular genetics. To what benefit? So that I can get more relaxation and enjoyment from contemplating the patterns on my guppies. And so that I have the information and educated eye I need to design new and interesting guppy varieties, like the See-Thru guppy, the Silverado or the newest, the Double Yellow.

The Double Yellow shown above is a combination of the Metallic Gold (Mg) gene and the Schimmelpfennig Platinum gene (Sc). At first glance it might appear to be a Full Platinum or Full Gold guppy. As a matter of fact, one well known breeder told me he had invented just such a guppy some months before. But what is genetically unique about the Double Yellow is that it combines two different yellow platinum genes, one that colors the front of the body (Schimmelpfennig Platinum) and the other that colors the peduncle (Metallic gold). It is also a swordtail, although I have some work to do to bring it up to show quality standards. What makes it different from a Full Platinum is that it does not have the half-black gene, which is found in both the Full Platinum and Full Gold strains. It cannot have the half-black gene because it is a swordtail and there has never been a half-black swordtail. I know all of this is true of this new strain because I deliberately designed the strain from established strains and fully documented it.

I am always having to explain the value of doing the background research necessary for guppy design. Whether or not you agree with me that the Double Yellow is an interesting design, the fact is that it is a part of a deliberate design. Isn't that what brought you to guppies in the first place? Maybe you thought it was just a matter of throwing two guppies together and was disappointed that the result did not meet expectations. Sorry, some homework is required.

I have tried to lessen the burden of that homework by writing accessible books that put the research into guppy terms (just as I have done above). And I am working on a book with a major chapter on Carroll's insights. It will try to apply the principles he outlines to examples drawn from my own experiments. But how simple can I  make it? Is it not more important to learn the basic principles and then try to apply them yourself? Crossing a half-black yellow guppy with a half-black blue guppy does not create a green guppy. This has been known for a long time. But why? I provide the reason in a previous blog. I wish guppy genetics were simple.

No I don't. That would take all the fun and relaxation out of it.

I really do recommend that you buy and read, and re-read, Carroll's Endless book, even though it contains no information on "guppy genetics." He will not teach you specifically how to build a better show quality guppy. But you will learn to think about genetics in an entirely different way and your guppies will start yielding up their secrets to your hungry eye.

There is a PBS program based on Carroll's book called "What Darwin Never Knew," showing how the field of Evo-Devo has helped solved mysteries Darwin would surely have thrilled over. It showcases many of the basic ideas found in the book. For those in the U.S. you can see the program at this web address: http://www.pbs.org/wgbh/nova/beta/evolution/darwin-never-knew.html . For my friends outside the U.S. drop me a line, or get your hands on his book.

Addendum

After briefly reading the blog, Dr. Squire points out that there may be some structural genes that do have a few different bases in the guppy and it is entirely possible these genes will be found to account for the differences between guppies and most other species of fish. He predicts there will be found a low number of unique genes (derived from more widely found genes) unique to the guppy.

So my title "No Guppy Genes" in the sense of no guppy structural genes specific to guppies, may prove to be wrong.

Thanks Rick!

Genes: You are Richer Than You Think

I have been so busy on my books this summer that I have been neglecting the documentation of my crosses, like the above beauty that came out of an experimental cross between a Kaden Snakeskin male and a Silverado (Magenta) female. I wanted to see the effect of the magenta gene on the snakeskin pattern. I got a wide variety of phenotypes, including a version with a solid blue body and red spotted fins. and the above Peacock version with its expression of the snakeskin pattern in the belly and fins. In fact, what really surprised me about this phenotype is that it has the same pattern of expressions as the Schimmelpfennig Platinum sword X Kaden snakeskin cross I did some time ago. I called the result of the cross a "Medusa."

You can see why I call this phenotype a "Peacock" can't you?

I have created a graphic for a new book I am writing that attempts to divide the guppy body into the zones you see in crosses like these.

The graphic is based on a photo of the Medusa. As you can see the Peacock's pattern of expression fits these zones.

The new book I am writing surveys the scientific literature of guppy genetics and color biology, and wanders into related fields and even goes as far afield as the work of Sean B. Carroll, the Evo-Devo proselytizer. I have found his book "Endless Forms Most Beautiful" to be a treasure trove of information on the biological and genetic basis for patterns, from zebrafish to zebras.

You do not normally think of guppy bodies as being segmented, but it is, and it is well established that color cells migrate to positions on the body probably using a world coordinate system (longitude and latitude plus height and depth) as well as local cues like the segmentation of the body. Reading Carroll's account of how hox genes pattern the body leads me to believe that the half-black pattern is coincident with a major division of the body. I develop a case for this in the new book.

Actually Carroll's book is not that far afield from guppy studies as you might think. Carroll is presenting fundamental research into how vertebrate bodies are patterned. The patterns on animals like butterflies, zebras and zebrafish are the expression of the same basic processes that create arms or fins, hair or scales. So the key to reading Carroll is to relate his fundamental principles of pattern formation back to guppies. That is exactly what I am doing in the new book. Of course this is only one chapter in the book. In another chapter I survey the work of Fujii and Bagnara, whose study of pigmentation systems is key to understanding guppy color and pattern. And I plan to do a chapter on the current research being done on zebrafish patterns.

In the past couple of months I have also been working diligently on a project that I set for myself a couple of years ago, which was to collect and incorporate into crosses all the known mutant genes of the guppy. The snakeskin X magenta and snakeskin X platinum crosses are part of that program. I have a grid on the wall in my fish room that lists all the genes I have collected and the combinations I have done, or are in the process of doing. I am documenting those crosses and using the results to update my existing books and as fodder for new books. For example, I have discovered that the Micariff guppy is not the result of a simple cross of a snakeskin and a Stoerzbach guppy. So the prevailing wisdom about the genotype of a Micariff is probably wrong. I will probably have to go the other way and take apart a Micariff to see what genes it really does have. I have tentatively called it the "solid" gene, using the name given to it by some Asian sources.

One of the crosses I have done is a reciprocal cross between a Moscow and Full Red. I wrote about this in a previous blog. The update is that I succeeded in creating a Full Red Moscow in the very first generation. All you need to do is use a heterozygous or homozygous blond Moscow and a blond x-linked Full Red. At first I was incredulous. But fortunately Rick Squire (the retired genetics professor) was riding shotgun on this foray into the unknown. He helped me analyze my results and came up with many astute theories for the anomalies I found. This is going to be a chapter in one of the books I have planned. Here is a picture of a Red Moscow male taken at four months of age.

You see a lot of blue and purple metallic in the body...but this is typical of a Full Red at this age. Here it is five weeks since that picture was taken, and the male in the picture is just as red as his Full Red cousins at the same age. And the Red Moscows have something their cousins do not have: there is red color developing on their heads. The other trait that betrays their Moscow heritage is the spotting you see in the caudal fin. It will be interesting to see how they turn out in a couple of more months. Meanwhile I have them set up with Full Red females. I already have a drop from siblings. It will be interesting to see how they color up, as they have the Midnight black gene...

I titled this blog, "Genes: You are Richer Than You Think." The phrase is actually an echo of a advertising slogan used by a Canadian bank. What it means in the context of guppy breeding is that you can create new guppy strains from the genes you already have in your fish room, like the Peacock from snakeskin and magenta strains, or the Red Moscow from Moscow and Full Red strains. But there is another meaning. I have been missing an important gene in my grid of crosses. That is the golden gene, which is called Bronze by Americans, Tiger by Asians, and Gold by Europeans. But last week a Midnight Black Moscow female dropped what I first took to be a blond fry. Then it developed some black color. I was puzzled until Rick pointed out that it may in fact be a Golden. I think that must be it. So I have had the golden gene all along, hidden in my Midnights. In terms of guppy color genes, I am richer than I think.