Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.     

Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene

Human iris color was one of the first traits for which Mendelian segregation was established. To date, the genetics of iris color is still not fully understood and is of interest, particularly in view of forensic applications. In three independent genome-wide association (GWA) studies of a total of 1406 persons and a genome-wide linkage study of 1292 relatives, all from the Netherlands, we found that the 15q13.1 region is the predominant region involved in human iris color. There were no other regions showing consistent genome-wide evidence for association and linkage to iris color. Single nucleotide polymorphisms (SNPs) in the HERC2 gene and, to a lesser extent, in the neighboring OCA2 gene were independently associated to iris color variation. OCA2 has been implicated in iris color previously. A replication study within two populations confirmed that the HERC2 gene is a new and significant determinant of human iris color variation, in addition to OCA2. Furthermore, HERC2 rs916977 showed a clinal allele distribution across 23 European populations, which was significantly correlated to iris color variation. We suggest that genetic variants regulating expression of the OCA2 gene exist in the HERC2 gene or, alternatively, within the 11.7 kb of sequence between OCA2 and HERC2, and that most iris color variation in Europeans is explained by those two genes. Testing markers in the HERC2-OCA2 region may be useful in forensic applications to predict eye color phenotypes of unknown persons of European genetic origin.     

Technical note: quantitative measures of iris color using high resolution photographs

Our understanding of the genetic architecture of iris color is still limited. This is partly related to difficulties associated with obtaining quantitative measurements of eye color. Here we introduce a new automated method for measuring iris color using high resolution photographs. This method extracts color measurements in the CIE 1976 L*a*b* (CIELAB) color space from a 256 by 256 pixel square sampled from the 9:00 meridian of the iris. Color is defined across three dimensions: L* (the lightness coordinate), a* (the red-green coordinate), and b* (the blue-yellow coordinate). We applied this method to a sample of individuals of diverse ancestry (East Asian, European and South Asian) that was genotyped for the HERC2 rs12913832 polymorphism, which is strongly associated with blue eye color. We identified substantial variation in the CIELAB color space, not only in the European sample, but also in the East Asian and South Asian samples. As expected, rs12913832 was significantly associated with quantitative iris color measurements in subjects of European ancestry. However, this SNP was also strongly associated with iris color in the South Asian sample, although there were no participants with blue irides in this sample. The usefulness of this method is not restricted only to the study of iris pigmentation. High-resolution pictures of the iris will also make it possible to study the genetic variation involved in iris textural patterns, which show substantial heritability in human populations.     

Molecular and biochemical mechanisms of human iris color: A comprehensive review

Eye color is determined as a polymorphism and polygenic trait. Brown is the most common eye color in the world, accounting for about 79%, blue eye color for about 8–10%, hazel for 5%, and green for 2%. Rare-colored eyes include gray and red/violet. Different factors are involved in determining eye color. The two most important factors are the iris pigment and the way light is scattered from the iris. Gene expression determines the iris pigmentation and how much melanin is present in the eye, which is the number of melanin subunits that identify eye color. The genes involved in the pigmentation of single-nucleotide polymorphism (SNP) have a significant role; and even some genes are included only in the eye color through SNP. MicroRNAs also affect melanocyte synthesis, which is usually affected by the downregulation of essential genes involved in pigmentation. In this study, we assess the biochemical pathways of melanin synthesis, and the role of each gene in this pathway also has been examined in the signaling pathway that stimulates melanin synthesis.     

Characterization of the Reflective Materials and Organelles in the Bright Irides of North American Blackbirds (Icterinae)

The reflective materials in the iris stroma of bright-irised American blackbirds (Icterinae, Emberizidae) and the red-eyed vireo (Vireo olivaceus) (Vireonidae) were characterized using high-performance liquid chromatography (HPLC) and diode-array detection. Two purines, guanine and hypoxanthine, and two pteridines, leucopterin and xanthopterin, were detected in large amounts in all bright irides. The brown iris of the red-winged blackbird (Agelaius phoeniceus) by comparison contained only small amounts of these and additional unidentified compounds. The absolute and relative amounts of light-absorbing compounds in the iris varied somewhat among species of blackbirds with bright irides, and markedly within one species (brewer's blackbird, Euphagus cyanocephalus) between sexes and age classes that vary in eye color. Differences in the types, numbers, and sizes of pigment organelles in the irides appeared to underlie the differences in amounts of light-absorbing compounds. Guanine was the most abundant light-absorbing compound in all bright irides, accounting for about 90% of the total absorption at 250 nm. A wide range of concentrations of guanine, from 96 to 9 μg per iris, produced bright irides. The primary pigment organelles of pigment cells in bright irides were reflecting platelets, which typically appeared as open spaces on electron micrographs. In the red-eyed vireo there were in addition red pterinosome-like pigment organelles in the pigment cells on the anterior surface of the iris stroma. Guanine was present even in irides with no overt reflecting platelets.     

Iris pigmentation in domestic pigeons

Summary and Conclusions Analysis of the records of iris color in the University of Wisconsin colony reveals that a simple autosomal recessive factor is responsible for the pearl condition as opposed to the normal orange of wild-typeColumba livia. The symboltr for the pearl factor, as proposed byBessmertnaja (1928), will be retained.A very similar color to pearl, but faintly yellow, is shown to accompany the factor for chocolate plumage color.No evidence for linkage oftr with the factorsS, C, oro has been detected.Unlike the chicken iris, the pigeon iris contains no carotenoid pigments. According to chemical tests it also contains no flavines of flavones, and the yellow pigment is not xanthine. The pigment substances are probably melanin-like.Iris color is a poor index of breed relationships in pigeons.Paper from the Department of Genetics, Agricultural Experiment Station, University of Wisconsin, No. 243.     

Characterization of melanin in human iridal and choroidal melanocytes from eyes with various colored irides

Variance in iris color is related to the incidence of several important ocular diseases, including uveal melanoma and age-related macular degeneration. The purposes of this study were to determine the quantity and the types of melanin in cultured human uveal melanocytes in relation to the iris color. Sixty-one cell cultures of pure uveal melanocytes were isolated from donor eyes with various iris colors. The amount of eumelanin (EM) and pheomelanin (PM) of these cells was measured by chemical degradation and microanalytical high-performance liquid chromatography (HPLC) methods. The total amount of melanin was measured by both microanalytical methods and spectrophotometry. Total melanin content, measured by HPLC and spectrophotometry, correlated well with r = 0.872 (P < 0.0001). The quantity and type of melanin in iridal and choroidal melanocytes showed no significant difference (P > 0.05). When cells became senescent, the levels of EM, PM and total melanin were significantly increased. In both growing and senescent melanocytes, the quantity and type of melanin were closely correlated to the iris color. In cells from eyes with dark-colored irides (dark brown and brown), the amount of EM, the ratio of EM/PM and total melanin were significantly greater than that from eyes with light-colored irides (hazel, green, yellow-brown and blue) (P < 0.0001). The quantity of PM in uveal melanocytes from eyes with light-colored irides was slightly greater than that from dark-colored irides, although not statistically significant (P > 0.05). The present study shows that iris color is determined by both the quantity and the type of melanin in uveal melanocytes. These results suggest a possibility that uveal melanin in eyes with dark-colored irides is eumelanic at the surface and acts as an antioxidant while that in eyes with light-colored irides exposes pheomelanic core and behaves as a pro-oxidant.     

Pigment cell refugia in homeotherms--the unique evolutionary position of the iris.

Homeotherms are generally considered to lack classical active dermal pigment cells (chromatophores) in their integument, attributable to the development of an outer covering coat of hair or feathers. However, bright colored dermal pigment cells, comparable to chromatophores of lower vertebrates, are found in the irides of many birds. We propose that, because of its exposed location, the iris is an area in which color from pigment cells has sustained a selective advantage and appears to have evolved independently of the general integument. In birds, the iris appears to have retained the potential for the complete expression of all dermal chromatophore types. Differences in cell morphology and the presence of unusual pigments in birds are suggested to be the result of evolutionary changes that followed the divergence of birds from reptiles. By comparison, mammals appear to have lost the potential for producing iridophores, xanthophores, or erythrophores comparable to those of lower vertebrates, even though some species possess brightly colored irides. It is proposed that at least one species of mammal (the domestic cat) has recruited a novel iridial reflecting pigment organelle originally developed in the choroidal tapetum lucidum. The potential presence of classical chromatophores in mammals remains open, as few species with bright irides have been examined.     

Pigment Cell Refugia in Homeotherms—The Unique Evolutionary Position of the Iris

Homeotherms are generally considered to lack classical active dermal pigment cells (chromatophores) in their integument, attributable to the development of an outer covering coat of hair or feathers. However, bright colored dermal pigment cells, comparable to chromatophores of lower vertebrates, are found in the irides of many birds. We propose that, because of its exposed location, the iris is an area in which color from pigment cells has sustained a selective advantage and appears to have evolved independently of the general integument. In birds, the iris appears to have retained the potential for the complete expression of all dermal chromatophore types. Differences in cell morphology and the presence of unusual pigments in birds are suggested to be the result of evolutionary changes that followed the divergence of birds from reptiles. By comparison, mammals appear to have lost the potential for producing iridophores, xanthophores, or erythrophores comparable to those of lower vertebrates, even though some species possess brightly colored irides. It is proposed that at least one species of mammal (the domestic cat) has recruited a novel iridial reflecting pigment organelle originally developed in the choroidal tapetum lucidum. The potential presence of classical chromatophores in mammals remains open, as few species with bright irides have been examined.     

The convergent evolution of blue iris pigmentation in primates took distinct molecular paths

How many distinct molecular paths lead to the same phenotype? One approach to this question has been to examine the genetic basis of convergent traits, which likely evolved repeatedly under a shared selective pressure. We investigated the convergent phenotype of blue iris pigmentation, which has arisen independently in four primate lineages: humans, blue‐eyed black lemurs, Japanese macaques, and spider monkeys. Characterizing the phenotype across these species, we found that the variation within the blue‐eyed subsets of each species occupies strongly overlapping regions of CIE L*a*b* color space. Yet whereas Japanese macaques and humans display continuous variation, the phenotypes of blue‐eyed black lemurs and their sister species (whose irises are brown) occupy more clustered subspaces. Variation in an enhancer of OCA2 is primarily responsible for the phenotypic difference between humans with blue and brown irises. In the orthologous region, we found no variant that distinguishes the two lemur species or associates with quantitative phenotypic variation in Japanese macaques. Given the high similarity between the blue iris phenotypes in these species and that in humans, this finding implies that evolution has used different molecular paths to reach the same end. Am J Phys Anthropol 151:398–407, 2013.© 2013 Wiley Periodicals, Inc.     

Sequences associated with human iris pigmentation

To determine whether and how common polymorphisms are associated with natural distributions of iris colors, we surveyed 851 individuals of mainly European descent at 335 SNP loci in 13 pigmentation genes and 419 other SNPs distributed throughout the genome and known or thought to be informative for certain elements of population structure. We identified numerous SNPs, haplotypes, and diplotypes (diploid pairs of haplotypes) within the OCA2, MYO5A, TYRP1, AIM, DCT, and TYR genes and the CYP1A2-15q22-ter, CYP1B1-2p21, CYP2C8-10q23, CYP2C9-10q24, and MAOA-Xp11.4 regions as significantly associated with iris colors. Half of the associated SNPs were located on chromosome 15, which corresponds with results that others have previously obtained from linkage analysis. We identified 5 additional genes (ASIP, MC1R, POMC, and SILV) and one additional region (GSTT2-22q11.23) with haplotype and/or diplotypes, but not individual SNP alleles associated with iris colors. For most of the genes, multilocus gene-wise genotype sequences were more strongly associated with iris colors than were haplotypes or SNP alleles. Diplotypes for these genes explain 15% of iris color variation. Apart from representing the first comprehensive candidate gene study for variable iris pigmentation and constituting a first step toward developing a classification model for the inference of iris color from DNA, our results suggest that cryptic population structure might serve as a leverage tool for complex trait gene mapping if genomes are screened with the appropriate ancestry informative markers.     

Multilocus OCA2 genotypes specify human iris colors

Human iris color is a quantitative, multifactorial phenotype that exhibits quasi-Mendelian inheritance. Recent studies have shown that OCA2 polymorphism underlies most of the natural variability in human iris pigmentation but to date, only a few associated polymorphisms in this gene have been described. Herein, we describe an iris color score (C) for quantifying iris melanin content in-silico and undertake a more detailed survey of the OCA2 locus (n = 271 SNPs). In 1,317 subjects, we confirmed six previously described associations and identified another 27 strongly associated with C that were not explained by continental population stratification (OR 1.5–17.9, P = 0.03 to <0.001). Haplotype analysis with respect to these 33 SNPs revealed six haplotype blocks and 11 hap-tags within these blocks. To identify genetic features for best-predicting iris color, we selected sets of SNPs by parsing P values among possible combinations and identified four discontinuous and non-overlapping sets across the LD blocks (p-Selected SNP sets). In a second, partially overlapping sample of 1,072, samples with matching diplotypes comprised of these p-Selected OCA2 SNPs exhibited a rate of C concordance of 96.3% (n = 82), which was significantly greater than that obtained from randomly selected samples (62.6%, n = 246, P<0.0001). In contrast, the rate of C concordance using diplotypes comprised of the 11 identified hap-tags was only 83.7%, and that obtained using diplotypes comprised of all 33 SNPs organized as contiguous sets along the locus (defined by the LD block structure) was only 93.3%. These results confirm that OCA2 is the major human iris color gene and suggest that using an empirical database-driven system, genotypes from a modest number of SNPs within this gene can be used to accurately predict iris melanin content from DNA. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Consistent contrast between eyelid and iris brightness supports a role for vigilance signalling in ducks

Signalling self‐ability to maintain vigilance may help in securing a mate, while providing accurate information about vigilance status may result in conspecifics adjusting their own scanning rate of the environment, potentially to the individual's benefit. In birds, vigilance is often associated with head‐up postures adopted within a bout of head‐down activity, and this can be used by conspecifics to assess the vigilance of their flock mates. However, vigilance behaviour is not always obvious and other cues may then be used to assess vigilance rates of conspecifics. Here we assess whether iris/eyelid/face patterns from 43 duck species are consistent with the hypothesis that eyelid brightness has evolved so as to contrast with iris brightness, which may then help in signalling individual vigilance status. Ducks generally flock when resting during the day, and because of their wide visual fields, individuals can monitor their environment while remaining in a resting head‐down position. Ducks also show a wide variety of plumage and iris patterns, with both light‐headed and dark‐headed species. Matching our prediction, most ducks with dark irises had pale eyelids, irrespective of head colour. Furthermore, the smaller number of species with a pale iris generally have darker eyelids. A phylogenetic analysis shows a clear and significant association in the evolution of eyelid and iris brightness patterns in both males and females. These data therefore provide support for the hypothesis that eyelid brightness has evolved to act as a contrast with iris brightness. Further studies are now needed to examine the extent to which and the way this is used in vigilance information transfer between individuals.     

Substance P contracts the human iris sphincter: possible modulation by endogenous enkephalinase.

Substance P-immunoreactive neurons have been found in the irides of many species including humans. In several species, substance P has been shown to induce contraction of the sphincter muscle but this action of substance P has not been previously demonstrated in the human eye. Using an eye cup model in which the sensitivity of the iris muscle to substance P is increased compared to the isolated sphincter muscle, we have observed that nanomolar amounts of substance P induced contraction of the sphincter in the human iris. This contractile response was enhanced in eyes pretreated with thiorphan, an enkephalinase inhibitor, suggesting that endogenous enkephalinase (E.C. 3.4.24.11) may modulate the substance P contraction in the human iris. Further support for this hypothesis was the finding of enkephalinase-like immunoreactivity and enzyme activity in the human iris sphincter muscle.     

Rapid color change in fish and amphibians – function,regulation, and emerging applications

Physiological color change is important for background matching, thermoregulation as well as signaling and is in vertebrates mediated by synchronous intracellular transport of pigmented organelles in chromatophores. We describe functions of and animal situations where color change occurs. A summary of endogenous and external factors that regulate this color change in fish and amphibians is provided, with special emphasis on extracellular stimuli. We describe not only color change in skin, but also highlight studies on color change that occurs using chromatophores in other areas such as iris and on the inside of the body. In addition, we discuss the growing field that applies melanophores and skin color in toxicology and as biosensors, and point out research areas with future potential.     

A New Species of the Genus Xenophrys(Amphibia: Anura: Megophryidae) from Libo County,Guizhou, China

A new species of the genus Xenophrys is described from a karst cave environment of Libo County, Guizhou Province, Southern China. The new species, Xenophrys liboensis sp. nov., is distinguished from its congeners by a combination of the following characters: 1) tympanum distinct; 2) vomerine teeth present; 3) the length of lower arm and hand larger than the half of snout-vent; 4) heels overlapped slightly when the flexed legs are held at right angles to the body axis; 5) toe tips with rudimentary webs and without grooves; 6) dermal fringes moderate; 7) tubercles on the dorsum forming an X-shaped weak ridge; 8) horn-like tubercle at the edge of the upper eyelid distinct; 9) color of the iris in life is brown. In Bayesian phylogenetic analysis of 22 species of Xenophrys, all the individuals of X. liboensis sp. nov. clustered into a monophyletic clade with high posterior probabilities. In addition, the ranges of genetic divergences of X. liboensis sp. nov. with other species were interspecific rather than intraspecific. Based on the above evidences, we consider that X. liboensis sp. nov. is a valid species in Xenophrys.     

First report of rapid eye color change in a non-avian tetrapod

Like coloration of the integument, eye color can be a significant but understudied component of communication and reproductive behavior. Eye color can change with sexual maturation and become sexually dimorphic, but in a few birds and fish, eye color can also change rapidly in response to the environment. There are few cases of the latter, and we report here several instances of such change in eye color in the Eastern box turtle (Terrapene carolina carolina), the first non-avian tetrapod in which this capability has been reported. In male turtles, the iris changed from a pale yellow color (often characteristic of juveniles) to a bright red color (characteristic of mature males) in a period of <5 s. The nature of the color change is similar to that observed in some birds and suggests a common mechanism and/or adaptive role, which could be further explored in Eastern box turtles.