The natural world displays an incredible amount of innate beauty, from snow-covered mountain peaks to exotic tropical reefs. For scientists and non-scientists alike, one of its most mesmerizing features is the pigmentation and coloration of living organisms. Biological pigments, found in animals, plants, and even bacteria, are compounds that absorb certain wavelengths of light and reflect others. This combination of light absorption and reflection gives each pigment a distinct color, and is responsible for the broad spectrum of colors that we perceive in our surroundings [1]. Questions regarding the diversity, rapid evolution, and ecological significance of pigmentation patterns have garnered attention for centuries. How do zebras get their black and white stripes, and butterflies their bold and brightly colored wings? Why do some closely related species have different color patterns, while several distantly related species look similar? Only in the last hundred years, however, have the mechanisms behind pattern formation become more completely understood.

A Colorful History

Current studies of pigment pattern development owe a great deal to the amateur geneticists of the 19th and 20th centuries. Mice were particularly attractive as a tool to look at animal pigmentation because of their interesting coat colors – and trained scientists were not the only ones to feel this way. Abbie Lathrop, a former schoolteacher, became an accidental pioneer in genetics when she began selling multicolored mice that she bred as pets to research laboratories in the early 1900s [2]. These mice afforded scientists some of the first opportunities to study the molecular and cellular processes that generate complex pigment patterns, such as spots and stripes, and how alterations in these pathways might influence an animal’s exterior.

Fast forwarding to present day, many labs now use zebrafish as their primary model to investigate pigment patterns. First described by the British surgeon Francis Hamilton in 1922, the zebrafish (Danio rerio) is a small freshwater fish native to the Himalayan region with vibrantly colored horizontal stripes [3]. Conveniently for biologists, zebrafish have transparent, externally developing embryos, and they develop pigments within the first few days of life. Zebrafish and about 50 other closely related species are also studied for their dramatically varied appearance. Some have vertical instead of horizontal stripes while others have spots, and many are adorned with combinations of these pattern elements. The natural variation between the zebrafish and its relatives is therefore well suited for inquiries about the biological basis and purpose of pigment patterning (Figure 1).

Figure 1 ~ (A) Zebrafish life cycle from fertilization to adulthood. Pigment cells arise soon after embryos are fertilized (red asterisk), but it can take up to 45 days for the characteristic striped pattern to form. By IlluScientia, available at  Licensed under Creative Commons 3.0 Unported license.  (B) Normally pigmented zebrafish larva (top) compared to a mutant lacking melanin, a common pigment produced in the body (bottom). By Adam Amsterdam, Small Fish, Big Science. PLoS Biol 2/5/2004: e148. (C) Adult female zebrafish, Danio rerio. By Azul, available at Danio malabaricus. By Faucon, available at  Licensed under Creative Commons ShareAlike 2.5 Generic. (E) Danio lamparci. By Darkfalz, available at  Licensed under Creative Commons ShareAlike 3.0 Generic.

How The Zebrafish Gets Its Stripes

The stunning pattern of alternating blue and golden stripes on zebrafish can be attributed to three major types of pigment cells: xanthophores (yellow cells), melanophores (black cells), and iridophores (reflective silvery cells) [4](Figure 2). Exactly how these distinct cells emerge in the juvenile fish and then arrange in the skin to create stripes has been extensively studied over the past two decades. A few of the most eye-opening discoveries, however, have only been made within the last couple months. Two recent publications by Nobel laureate Christiane Nüsslein-Volhard and her colleagues in Germany suggest that the three cell types travel to the skin by completely different routes, and can change their position and shape to help stripes form  [5, 6].

Figure 2 ~ (A) Iridophores (silvery cells) emerge first along the horizontal axis in the center of the body. (B) Melanophores (black cells) and xanthophores (yellow cells) then begin to appear. (C) Golden stripes form in areas where iridophores and xanthophores compact and densely cover the darker melanophores. Blue stripes form in other areas where iridophores and xanthophores spread out and become thin, allowing the darker melanophores to peak through. An alternating pattern of 4-5 light and dark stripes forms over the course of three to six weeks after the zebrafish embryo is fertilized.

Thanks to the transparency of zebrafish embryos and the help of a very powerful microscope, these scientists were able to trace the movement of pigment cells in living, growing zebrafish. Silvery cells were found to emerge first along the horizontal axis in the center of the body. Black and yellow cells then begin to appear, with the black cells forming a thin, solid layer across the skin’s surface. In some areas, yellow and silvery cells compact and densely cover this layer of black cells, giving rise to a golden stripe. In other areas, the yellow and silvery cells spread out and become thin, allowing the black cells to peak through and make a blue stripe. For three to six weeks after fertilization of the zebrafish embryo, the repetition of this process results in an alternating series of light and dark skin stripes [4].

How and Why Other Organisms Create Color

Figure 3 ~ Nature is full of animals with notable pigment patterns, as well as different ways and reasons to create these colors. (A) Flamingos rely on a diet of shrimp for their vividly pink and orange feathers. By Aaron Logan, (B) Colors on the heads of certain turtles can indicate how healthy they are, and serve as a signal to potential mates. By Jmalik, available at Licensed under Creative Commons ShareAlike 2.0 Generic (C) Zebras may have evolved stripes in order to ward off biting flies. By Benh Lieu Song,  Licensed under Creative Commons ShareAlike 2.0 Generic. (D) The blue tones of bluebirds are due to light scattering off of small air sacs in their feathers. By Dehaan, available at  Licensed under Creative Commons ShareAlike 3.0 Generic.

Besides helping us to better understand pattern formation in the zebrafish, studies such as those conducted by Nüsslein-Volhard’s lab generate interest and provide insight about how other animals, including mammals, birds, and insects, produce their distinguishing colors (Figure 3). Melanin is the main biological pigment found in mammals, and is responsible for most of the color (or lack of color) in their hair and fur. Naturally red, brown, or black in color, melanin is also one of the only pigments that can be made by the body. Other animals owe their color to the food chain. For instance, algae that produce red and yellow pigments comprise the majority of the brine shrimp’s diet. Flamingos then eat brine shrimp, and with them consume the pigments necessary to color their pink and orange plumage. A third method of creating color, especially blues and greens, relies on physical structures. Bluebirds would look black if it were not for tiny air sacs in their feathers that scatter light [1].

The function and adaptive significance of pigment patterns in animals remains another key question for scientists today. Patterns are generally considered a means of avoiding predators and attracting mates, though the reasoning behind precise colorations is likely unique to each species. Biting flies may be the primary evolutionary driver behind zebra stripes, since several fly species avoid landing on black and white striped surfaces [7]. In contrast, ornamental colors on the head of a turtle might correspond to its overall health and signal this information to potential sexual partners [8].

Understanding why and how pigment patterns form in the living environment informs us about evolution, ecosystems, and even human disease. The most fatal form of skin cancer (melanoma), for example, arises when melanin-containing skin cells begin to grow and multiply out of control. Pigment formation and pattern development will therefore continue to be an exciting subject in the field of biology and, thanks to the vast diversity of organisms that inhabit our planet, is one that can be studied from a near infinite number of perspectives.

Laura Smith is a PhD student in the Biological and Biomedical Sciences at Harvard Medical School.


[1] Causes of Color: “Biological Pigments” []

[2] Steensma DP, Kyle RA, Shampo MA. (2010) Abbie Lathrop, the “Mouse Woman of Granby”: Rodent Fancier and Accidental Genetics Pioneer. Mayo Clin Proc, 85(11): e83. []

[3] Quigley IK, Parichy DM. (2002) Pigment Pattern Formation in Zebrafish: A Model for Developmental Genetics and the Evolution of Form. Microsc Res Tech, 58: 442-455.

[4] Max Planck Institute for Developmental Biology: “How The Zebrafish Gets Its Stripes” []

[5] Pratap Singh A, Schach U, Nüsslein-Volhard C. (2014) Proliferation, dispersal and patterned aggregation of iridophores in the skin prefigure striped colouration of zebrafish. Nat Cell Biol, 16(6): 604-612.

[6] Mahalwar P, Walderich B, Pratap Singh A, Nüsslein-Volhard C. (2014) Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish. Science, 345(6202): 1362-1364.

[7] Caro T, Izzo A, Reiner, Jr. RC, Walker H, Stankowich T. (2014) The function of zebra stripes. Nat Commun, 5(3535): 1-10.

[8] Ibáñez A, Polo-Cavia N, López P. (2014) Honest sexual signaling in turtles: experimental evidence of a trade-off between immune response and coloration in red-eared sliders Trachemys scripta elegans. Naturwissenschaften, 101: 803-811.

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