First Edition The Guppy Color Manual Exp PDF

Preview

Summary

For Guppy breeders and those interested in guppy genetics...

Description

The Guppy Color Manual Explorations of Guppy Color Biology and Genetics

First Edition June 2012

The Guppy Color Manual: Explorations in Guppy Color Biology and Genetics © 2012 Philip Shaddock This book is copyrighted and may not be reproduced in whole or in part. If you wish to quote more than a few lines from the book or use any of its figures, graphics or images, please contact Philip Shaddock through the Guppy Designer website: www.guppydesigner.com. If you find inaccuracies or mistakes in the book, please contact Philip Shaddock through the Guppy Designer site. Your help would be very much appreciated. www.guppydesigner.com Support for this book is provided on the Guppy Designer facebook page Discuss the papers with the author and other members of the site. 10 9 8 7 6 5 4 3 2 1

Contents Foreword

9

Preface

11 Acknowledgements

1 The Study of Guppy Color

13 15

The Birth of Guppy Genetics

15

Mining the Data

15

The First Guppy Color Cell Paper

16

Developmental Biology

18

The Discovery of Gene Regulation

18

Guppy Color Layering

19

The Fourth Dimension

22

The Multipotent Color Cell

22

Puppets on A Stage

23

Evo-Devo: A New Synthesis 2 The Color Cells

24 27

Color and Water Depth

27

The Skin

30

The Color Cells Two Different Embryonic Origins of Color Cells

32 33

Color Cell Types Color Cell Biochemistry

36 36

Pigment Color Cells Melanophores (Black Color Cells)

38 38

Dermal Melanophores

41

Types of Melanophores

42

Melanosomes

44

Pigment Color Cells: Red and Yellow

44

Carotenoids and Pteridines

46

Guppy Orange

47

Pteridine Biosynthesis

47

Pigment Blues Versus Reflective Blues

48

Guppy Sun Tan Lotion

49

The Structural Color Cells of the Guppy

49

Common Types of Iridophores

52

Comparing Leucophores and Iridophores

53

Reflecting Platelets of the Iridophores

56

Mosaic Color Cells

58

Color Cell Motility (Chameleon Effect)

59

Hormonal and Nervous Control

60

Chameleon Color

60

Hormonal Factors in Color Change

61

Color Change

61

Color Cells Result From Biological Pathways

63

Color Cell Development and Differentiation

65

Other Factors

66

Pigmentation Anomalies 3 Color Cell Layering

67 69

The Bagnara Dermal Chromatophore Unit

70

Filtering Layer

71

Reflecting Layer

72

Absorbing Layer

73

Altering the Saturation or Intensity of a Color

74

Color Cells Interact to Produce Novel Color

74

Pastel Colors

75

Structural Colors

76

Blue and Silver Iridophores

76

Blue Iridophores The Interplay Between Iridophores and Red Color

79 83

Tyndall Blue

84

Melanistic Guppies

85

4 The Wild-Type Guppy Patterns

89

Guppy Reticulation Pattern

89

Melanophores and the Reticulation Pattern

91

The Reticulation Pattern and the Fins

96

Male Polymorphic Color Pattern

99

The Wingean Pattern is Strictly Y-Linked Winge treated the patterns as two dimensional patterns (Figure 18)

100 100

Winge and XX Males

103

The Wingean Supergene

104

Wild-Type Patterns Highly Homozygous Across Loci

108

Summary 5 Pattern Theory

109 111

Bagnara’s Review of Pattern Theory

111

Color Pattern Formation in Zebrafish Hormonal Influences on the Development of Pigmentation Patterns

112 113

Fujii on Patterns

113

Kelsh on Patterns

114

Other Factors

115

What Other Animal Studies Teach Us About Patterns

115

Fundamental Design

116

Variations in Number and Kind

117

Symmetry and Polarity

118

Spemann Organizer

118

Master Building Genes: Hox Genes

120

The Guppy Segmented Body The Segmented Body: Fin and Color Patterns

123 128

Mapping the Body The Geography of the Body (and Patterns!)

128 128

Lateral Inhibitions

132

Patterns and Genetic Switches

133

Combinatorial Logic of Switches

138

Patterns Are the Whole of a Sum of Parts

140

Conclusion 6 Guppy Black: Hypomelanism

142 145

The Story So Far Guppy Polymorphism and Black Hypomelanism

145 147 150

Melanosynthesis Fault: Albinism

150

WREA Guppies

152

Melanophore Migration Faults

153

The Blond and Golden Mutations

158

The Golden Mutation

158

The Blond Mutation

163

Bleach Blonds

165

The NII Gene

165

The Cream Double Recessive

167

7 Guppy Black: Melanism

169

Moscow Blue Moscows Are a Simple Combination of Wild-Type and the Moscow Gene(s)

175 176

The Onyx Gene

178

The Midnight Gene

180

NiI and NiII in the Scientific Literature

184

The “Half Half-Black” Pattern A Biological Basis for Color Suppression in the Guppy Anterior? Is there a genetic type-switch between melanophores and leucophores? 8 Red and Yellow Mutants

188 190 193 201

The Full Red Debate

204

Full Red Crossing Experiments F1 Full Red Male to Wild-Type Female The Glass belly Gene and Full Red

205 206 208

The Blaus

210

European blau

210

European versus Asian Blau

211

Asian blau

212

The Effect of the Blau Mutations on Guppy Patterns

214

Blau Removes Red, Does Not Substitute Blue

214

Black and Blau

215

Dosage Effects Asian blau Fin Development Asian blau As a Color Tool in Guppy Genetics

218 219 219

Heterozygous Blau Moscow

219

Asian blau Genetic Notation

222

The Magenta Mutation

222

Magenta Description

222

The Magenta genetic Switch

224

Fin Shape

227

Magenta Notation 9 The Striped Guppy Snakeskin Cells Under the Microscope Snakeskin as “Disorganized” Reticulation Pattern

227 229 231 233

Colors and the Snakeskin Pattern

236

Snakeskin Caudal fin Patterns

239

Research Information on Patterns

241

Lace Genetics

245

Half-Black Snake Hybrids

246

Dorsal Length in Snakeskins

246

Peduncle Vertical Bar Pattern

247

The Zebrinus Gene

250

The Tigrinus Gene

251

Is There a Bar, Zebrinus or Tigrinus Gene?

252

Other Spots in Snakeskin Patterns

252

Grass Guppy

253

Grass Genetics Snakeskin Breeders Comments 10 Fin Shape and Color

257 257 259

Wild Type

260

Fin Anatomy

262

Wild Type Fin Shapes

264

Caudal Fin

264

Dorsal Fin

265

Pectoral Fins

265

Pelvic Fins

265

Anal Fin

265

Basic Fin Genetics

265

Speculating About Fin Shape Factors

267

Testosterone and Fin Extensions

269

Fin Extensions and Color

270

The Fin Shapes

270

The Swords

270

Sex-Reversed Swordtail Female

275

Pintail

276

Elongated Dorsal (Hi-Fin)

276

Fantail Fin Shape

277

Merah Fin Shape

277

Ribbon or Giessen Fin Shape

278

Roundtail Fin Shape

280

Spadetail (Coffertail) Fin Shape

280

Speartail Fin Shape

A

281

Swallow (Berlin) Fin Shape

283

Breeding the Swallows

284

References

B Guppy Dictionary

287 291

Other Guppy Designer Books 301

|

Foreword Philip Shaddock decided to systematically document how guppy color genes interact with each other. This fundamentally important topic was not adequately treated by any scientific text or hobbyist reference book. To be sure, many individual interactions had been reported, but no systematic study could be found. Years later, the results of these studies, often done and analyzed by the author himself with frequently added information, results and interpretations gleaned from others, is now in print. This monograph is an authoritative textbook on guppy color biology. It assumes a knowledge of basic guppy genetics, which is very well covered in the author’s earlier books “Guppy Genetics Simplified” and “The Theory and Practice of Guppy Breeding”. This book develops the more complex concepts needed to really understand the biology of guppy pigmentation. A vast range of different color genes and their interactions is described and explained. This book is a handy reference to both the guppy hobbyist and professional guppy breeder. In fact, I believe that no serious guppy hobbyist or breeder can afford to miss this book! It is also the only reference I know of that will be equally valuable to the scientist who is interested in guppy pigment biology. Every researcher interested in fish pigment systems will want a copy of this book as well. The author refers to earlier work showing that many Y-linked genes are maintained together within “Wingean super genes” on the Y chromosome. This led him to construct his own significant hypothesis regarding guppy color genetics. He has suggested that most of the color genes that code for structural proteins are located on the autosomes (non-sex chromosomes) rather than on the sex chromosomes themselves. His unique suggestion is that the sex chromosomes (and the Y-chromosome in particular) contain genes that regulate these actual color genes that are found on the autosomes. This is a significant shift in the scientific concept of which genes are sex-linked as opposed to being autosomally linked. I am confident that this hypothesis will be investigated by molecular biologists in the years to come. This book contains a wealth of information for the reader regardless of their level of expertise. Basic concepts and hard-to-find journal articles are described so that any one can understand them. Philip’s training as an English major makes itself evident. This well written book will be enjoyed by hobbyist and scientist alike. I learned a lot reading the manuscripts, and enjoyed every minute! Richard Squire, Ph.D. (Genetics) Retired Full Professor of Biology University of Puerto Rico – Mayaguez Campus

9

10 | Foreword

| 11

Preface

Thirteen years ago I began my journey with guppies at the place where most people start: in the petstore. I bought red guppies with a pretty pattern and placed them in my tanks at home. They dropped fry and then died. I raised the fry. They dropped and died. Their offspring looked nothing like their parents. I wandered why. Why were they so fragile? Why did they not breed true? The first question took me a long time to answer. And in retrospect I can put my finger on the problem. I was just ignorant of proper guppy husbandry. The path of knowledge turned out to be full of twists and turns. I received a lot of advice from longtime guppy breeders on guppy forums. But the advice did not boil down to fundamental principles. Often the discussion about best practices is distorted by guppy hobbyist politics. The rules of thumb of many expert breeders are somewhat idiosyncratic and lack generality. So I went to sources I could trust, the scientists working in aquaculture and at university labs. I applied their fundamental research to practices in my own guppy room. Eventually I got my fish room to the point where I had few guppy deaths and invested comparatively little labor in maintenance. I decided to share this experience. The outcome was my book “Guppy Care Simplified.” The journey was over. Solving the problem of color and pattern inheritance proved to be a lot more intractable. Among hobbyists there was a handful of genes identified as pattern genes, like the half-black gene. And to some extent it was useful to know that a guppy with a half-black gene will produce fry with the potential to show the half-black pattern. But this was not always the case. Sometimes the half-black pattern disappeared, as in crosses with guppies with the Platinum and Mg (Metallic Gold) genes. I was left wondering why? Searching for genes did not seem to be the answer if the expression of those genes when combined with others just pushed a new mystery out. Where was the fundamental knowledge in the hobby? What breeding practices were durable? So I did what I learned to do in educating myself about guppy care. I went back to sources of information I could trust, the science. But there was a problem, something I recognized only after years of study. My view of guppy genetics was heavily distorted by an outdated science education. And the experts in the hobby were operating with this same handicap: the hobbyist paradigm that sees color patterns as due to pattern genes is wrong. What my initial research uncovered is that the basic groundwork for guppy genetics had been laid down as early as the 1920s with the publication of the Ö. Winge’s “The location of eighteen genes in Lebistes reticulatus.” (Winge, 1927) (The citation for this and other sources I quote in the book can be found in the References appendix, listed according to the author’s name and the year of publication.) I remember one hobbyist telling me that if we could identify all the guppy genes on guppy DNA we would be able to predict the outcome of any cross. (This proved to be wrong.) The old guppy genetics paradigm survived as late as 1981, with the publication of a Russian aquaculture scientist’s book, “The Genetic Bases of Fish Selection,” which lists a compendium of guppy pattern genes (Kirpichnikov, 1981). The prevailing view was that somehow genes for patterns like the Zebrinus vertical bars on guppies were stored in DNA as little

12 | The Color Cells

prepatterns. Even some more contemporary papers, like those of the Singapore scientist Violet Phang, seemed to support this paradigm, at least could be misinterpreted that way. My university education in genetics was seriously holding me back. It was not until years later that I began to ask the right questions. How can a simple DNA base pair or series of base pairs store patterns? I would learn later that there is actually no such thing as a pattern gene. Patterns on guppies form in the same way as patterns in almost any other biological system...indeed in art or science. They are emergent, a term in systems theory used to describe how complex systems emerge from the simple interactions of constituent parts. As this book will show the idea that complex color patterns on guppies can be reduced to single genes is the wrong paradigm for the exploration of guppy genetics. Guppy color genes participate in gene networks and never express themselves in isolation, although some faulty genes can affect whole patterns, like the removal of black color in the guppy albino. Indeed how genes participate in regulatory networks or build tissues or color cells in biological pathways is something you can discover for yourself if you pick up and read a current college level introduction to genetics. The books I have written over the years are records of my own difficult transition from the hobbyist paradigm to a more current paradigm found in the scientific community. My book Guppy Genetics Simplified is an introduction to classical genetics and how it is applied to guppies, along with a review of what I consider the classical papers on guppy color and patterns. It is written from a more current paradigm, preserving what is useful in the old papers. My book Theory and Practice of Guppy Breeding picks up where the Simplified leaves off, first reviewing classical genetics and then introducing modern molecular genetics and showing you how to apply this research to your breeding programs. The third and final book completes the journey I made through the science, learning its precise language and adopting a more current paradigm. It is somewhat amazing to me that nothing in this book duplicates the other two books in the series. The first chapter of this book is the same as the first chapter of the Guppy Genetics Simplified book, and the second chapter is a much more detailed and advanced chapter on guppy color biology than that found in the Theory and Practice book. But most of the book is new information on the color cells of the guppy, how they interact in the Bagnara chromatophore unit to produce the illusion of thousands of colors and how their development, differentiation and interaction are determined by genes. I was going to subtitle this book “The Missing Guppy Breeding Manual” but backed away from promising that it was a complete guide to the genetic manipulation of the color of your guppies. I opted instead to subtitle the book “Explorations in Guppy Color Biology and Genetics.” I think that is a better description of what I have tried to do in the book, indeed of what I tried to do in my fish room. I have recorded a thirteen year exploration of the color and pattern genetics of my guppies that resulted from that very first question that arose after the death and failed resurrection of the red pattern petstore guppies. While I have read widely in the scientific literature and paid attention to what hobby breeders have to say, ultimately I applied what I learned to breeding experiments with a cross section of guppies with the major known phenotypes. As the questions arose or as I gained insights, I conducted crosses with these inbred or pure strains to further my understanding and to test hypotheses, my own theories and those of others. While it may appear to others that my experiments are random, without clear goals, or so specific to have no generality, in fact I have always been interested...