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The Guppy Color Manual: Explorations of Guppy Color Biology and Genetics

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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.

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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. . . . . . . . . . . . . . . . . . . . . . . . . . . 13

1 The Study of Guppy Color 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 . . . . . . . . . . . . . . . . . . . . . . . . . . 24

2 The Color Cells 27

Color and Water Depth. . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
The Skin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
The Color Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Two Different Embryonic Origins of Color Cells. . . . . . . . . . . . . . . . 33
Color Cell Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Color Cell Biochemistry. . . . . . . . . . . . . . . . . . . . . . . . . . 36
Pigment Color Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Melanophores (Black Color Cells) . . . . . . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . . 67

3 Color Cell Layering 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
The Interplay Between Iridophores and Red Color. . . . . . . . . . . . . . 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. . . . . . . . . . . . . . . . . 100
Winge treated the patterns as two dimensional patterns (Figure 18). . . . . 100
Winge and XX Males. . . . . . . . . . . . . . . . . . . . . . . . . . 103
The Wingean Supergene. . . . . . . . . . . . . . . . . . . . . . . . . . 104
Wild-Type Patterns Highly Homozygous Across Loci . . . . . . . . . . . . . . 108
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

5 Pattern Theory 111

Bagnara’s Review of Pattern Theory. . . . . . . . . . . . . . . . . . . . . 111
Color Pattern Formation in Zebrafish. . . . . . . . . . . . . . . . . . . 112
Hormonal Influences on the Development of Pigmentation Patterns . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . 123
The Segmented Body: Fin and Color Patterns. . . . . . . . . . . . . . . 128
Mapping the Body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
The Geography of the Body (and Patterns!) . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

6 Guppy Black: Hypomelanism 145

The Story So Far.... . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Guppy Polymorphism and Black. . . . . . . . . . . . . . . . . . . . . . . 147
Hypomelanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Moscows Are a Simple Combination of Wild-Type and the Moscow Gene(s). . 176
The Onyx Gene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
The Midnight Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
NiI and NiII in the Scientific Literature. . . . . . . . . . . . . . . . . . . 184
The “Half Half-Black” Pattern. . . . . . . . . . . . . . . . . . . . . . . 188
A Biological Basis for Color Suppression in the Guppy Anterior? . . . . . . . . . 190
Is there a genetic type-switch between melanophores and leucophores?. . . . 193

8 Red and Yellow Mutants 201

The Full Red Debate. . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Full Red Crossing Experiments . . . . . . . . . . . . . . . . . . . . . . . . 205
F1 Full Red Male to Wild-Type Female. . . . . . . . . . . . . . . . . . . 206
The Glass belly Gene and Full Red . . . . . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Asian blau Fin Development. . . . . . . . . . . . . . . . . . . . . . . 219
Asian blau As a Color Tool in Guppy Genetics. . . . . . . . . . . . . . . . . 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

9 The Striped Guppy 229

Snakeskin Cells Under the Microscope . . . . . . . . . . . . . . . . . . 231
Snakeskin as “Disorganized” Reticulation Pattern . . . . . . . . . . . . . 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Snakeskin Breeders Comments. . . . . . . . . . . . . . . . . . . . . . 257

10 Fin Shape and Color 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. . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Swallow (Berlin) Fin Shape. . . . . . . . . . . . . . . . . . . . . . . 283
Breeding the Swallows. . . . . . . . . . . . . . . . . . . . . . . . . 284

A References 287

B Guppy Dictionary 291

Other Guppy Designer Books.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
   | 9

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 sys-
tems 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 sig-
nificant 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
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 hobby-
ists 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? Search-
ing 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 Se-
lection,” 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 net-
works 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 dupli-
cates 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 infor-
mation 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 deter-
mined 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 descrip-
tion 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 in developing a guppy genetics “theory of everything”
that makes sense of all of those crosses. What began as a search for guppy genes has ended with a hypoth-
esis that makes sense of all the crosses I have conducted or have seen conducted by others.

Wikipedia: A theory of everything (ToE) or final theory is a putative theory of theoretical physics that fully explains and links
together all known physical phenomena, and predicts the outcome of any experiment that could be carried out in principle.

Perhaps it is more accurate to describe my hypothesis about guppy genetics as one of the keys to under-
standing how guppy color and pattern are expressed and inherited. I erect the hypothesis on the back of
current research into pattern formation and expression. It also came out of my struggle to solve some old
hobbyist conundrums such as the nature of full red phenotype genetics. Full Red breeders argue about
whether the Full Red gene is autosomal or sex-linked, and I say it is both because all secondary sex colors
 The Guppy Color MaNUAL  | 13

on guppies are determined by both sex-linked and autosomal genes. Similarly black color in guppies
is determined by both sex-linked genes and autosomal genes that interact with each other in the same
developmental pigment pathways. That is a conclusion I have come to after thirteen years of study and
hundreds and hundreds of crosses.
There is also much we can learn about guppy color by studying the work scientists have done with zebraf-
ish (Danio rerio). The same genetic mechanisms that determine stripes in zebrafish probably determine
the snakeskin pattern in guppies. And zebrafish scientists have gained insight into pattern and color of
zebrafish by studying the work of other scientists studying the coats of mice or chickens. That is another
very basic shift in modern genetics. We once believed that each animal had its own specific genes. But by
examining genes at the molecular level we have discovered that many of the genes involved in color pat-
tern development and differentiation are highly conserved across species, meaning the fair skin of Northern
Europeans is due to the same basic gene as that found in light colored zebrafish or blond guppies.
Far from being esoteric, my study of the scientific literature has opened my eyes to the incredible beauty of
the guppy in this tiny corner of the universe. Indeed because the guppy is indeed a full participant in the
evolutionary history of the universe, I have always felt that in doing fundamental research into the guppy,
both in the library as well as in my fish room, I was peeking into the simple beauty and elegance of the
laws of the universe. The particular method I use to explore this realm is called “forward genetics,” which
simply means altering the genotype to observe aberrant expressions of mutant genes in the phenotype.
And it is still used extensively in more animal pattern research.
This books records a thirteen year exploration of guppy color biology and genetics, ending with a hypoth-
esis about guppy secondary sex color and pattern that I find very useful because it seems have a great deal
of generality. It helps explain what happens in most of the crosses involved secondary sex color patterns
that I have examined. In many ways I feel my journey is over. Not because I think there is nothing new in
guppy genetics, but because I have accomplished what I set out to do.
I hope that this book will become a stepping stone for the work of others. I hope that the sense of wonder
and excitement I have felt as I pushed forward in my explorations comes across in my prose. I hope that
you see what I see. It is the mysterious and timeless dance of the universe...dancing to the laws we are only
beginning to understand.

Acknowledgements
Thanks to all those guppy breeders who have shared their observations about guppy color inheritance
on Guppy Designer and other guppy forums and in private discussions with me. Thanks to those have
allowed me to publish their guppy pictures in this book. Alan Bias read and commented on early drafts
of chapters of this book, suggesting better communication strategies. Bill Gill has always been a patient
sounding board for my guppy genetics rants. Oscar Inostroza has been generous in his support of my work
and in sharing his own thoughtful research. Anthony Rae has been an enthusiastic cheerleader. There are
many others, but there is one who is special. That is Rick Squire who has been a patient and generous cor-
respondent as I developed many of the ideas in this book. He read through the entire manuscript, offering
many corrections and helpful suggestions. When I started out on this journey, I would never have guessed
at the end of it I would find my very own Yoda, helping me fight my way through the political and scien-
tific morass. My deepest thanks.
14 |  The Color Cells

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