evolution of human skin pigmentation. genetic ... - seaf lopez 33.pdfintroduction skin color is one...

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Evolution of human skin pigmentation. Genetic factors underlying variability and association with eye and hair color LÓPEZ S. 1 , SMITH-ZUBIAGA I. 2 , IZAGIRRE N. 1 Y ALONSO S. 1 1 Dpto. Genética, Antropología Física y Fisiología Animal. UPV/EHU 2 Dpto. Zoología y Biología Celular Animal. UPV/EHU Corresponding Author: Saioa López Dpto. Genética, Antropología Física y Fisiología Animal Universidad del País Vasco / Euskal Herriko Unibertsitatea Barrio Sarriena s/n 48940. Leioa (Vizcaya) [email protected] +34 946015430 Rev. Esp. Antrop. Fís. (2012) Vol. 33: 7-19 ISSN: 2253-9921 © 2012 Sociedad Española de Antropología Física Keywords: Skin Pigmentation Genetics Evolution Melanogenesis ABSTRACT In this review we present an updated overview of the main current hypotheses for the evolution of skin color and the genetic factors underlying its variability, as well as a brief remark of the relationship of skin pigmentation with other pigmentary phenotypes, such as eye and hair color. Pigmentation has also important biomedical implications, for instance as regards skin cancer development. The continuous nature of skin color in humans seems likely to be the result of adaptive evolution; however, it is currently unknown how selection has affected the genetic ar- chitecture of pigmentation loci in different populations. Many hypotheses have been proposed to explain this issue: protection from skin cancer and sunburn, protection against folate deficiency, protection against DNA damage and oxidative stress, permeability barrier or sexual selection. Human pigmentation is presumed to be under the control of an undetermined number of genes, which may act at different stages of melanogenesis. To date, however, only a few genes have been shown to have effects on normal variation in pigmentation; the strongest evidences are found in the melanogenic genes MC1R, ASIP, SLC24A5, MATP, TYR, TYRP1, DCT, OCA2 and KITLG. There are also other non-melanogenic genes with a putative role in skin pigmentation, such as VDR or beta defensins. RESUMEN En esta revisión presentamos una visión general actualizada de las principales hipótesis sobre la evolución del color de la piel y los factores genéticos responsables de la variabilidad, así como una breve descripción de la relación de la pigmentación de la piel con otros fenotipos pigmenta- rios, como el color de los ojos o del pelo. El estudio de la pigmentación tiene también importan- tes implicaciones biomédicas, como en lo que respecta al desarrollo de cáncer de piel. La natura- leza continua del color de la piel en humanos parece ser el resultado de una evolución adaptati- va; sin embargo, actualmente se desconoce cómo la selección ha afectado a la estructura genética de los loci pigmentarios en las diferentes poblaciones. Se han propuesto varias hipótesis para explicar esto: la protección frente a cáncer de piel y quemadura solar, protección contra la defi- ciencia de folato, protección contra daño del DNA y estrés oxidativo, una barrera de permeabili- dad o la selección sexual. La pigmentación en humanos está controlada por la acción de numero- sos genes, que actúan en diferentes etapas de la melanogénesis. No obstante, hasta hoy, solo se han identificado unos pocos genes que tengan efectos en la variabilidad normal de la pigmenta- ción; las mayores evidencias se encuentran en los genes melanogénicos MC1R, ASIP, SLC24A5, MATP, TYR, TYRP1, DCT, OCA2 y KITLG. También existen otros genes no-melanogénicos con un posible papel en la pigmentación, como VDR o las beta defensinas. Palabras clave: Pigmentación de la piel Genética Evolución Melanogénesis Recibido: 28-10-2012 Aceptado: 12-12-2012

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Page 1: Evolution of human skin pigmentation. Genetic ... - SEAF lopez 33.pdfIntroduction Skin color is one of the most conspicuous mor-phological traits in humans and its continuous nature

Evolution of human skin pigmentation. Genetic factors underlying variability and association with eye and hair color

LÓPEZ S.1, SMITH-ZUBIAGA I.2, IZAGIRRE N.1 Y ALONSO S.1

1 Dpto. Genética, Antropología Física y Fisiología Animal. UPV/EHU 2 Dpto. Zoología y Biología Celular Animal. UPV/EHU

Corresponding Author: Saioa López Dpto. Genética, Antropología Física y Fisiología Animal Universidad del País Vasco / Euskal Herriko Unibertsitatea Barrio Sarriena s/n 48940. Leioa (Vizcaya) [email protected] +34 946015430

Rev. Esp. Antrop. Fís. (2012) Vol. 33: 7-19

ISSN: 2253-9921 © 2012 Sociedad Española de Antropología Física

Keywords:

Skin PigmentationGeneticsEvolutionMelanogenesis

ABSTRACT

In this review we present an updated overview of the main current hypotheses for the evolution of skin color and the genetic factors underlying its variability, as well as a brief remark of the relationship of skin pigmentation with other pigmentary phenotypes, such as eye and hair color. Pigmentation has also important biomedical implications, for instance as regards skin cancer development. The continuous nature of skin color in humans seems likely to be the result of adaptive evolution; however, it is currently unknown how selection has affected the genetic ar-chitecture of pigmentation loci in different populations. Many hypotheses have been proposed to explain this issue: protection from skin cancer and sunburn, protection against folate deficiency, protection against DNA damage and oxidative stress, permeability barrier or sexual selection. Human pigmentation is presumed to be under the control of an undetermined number of genes, which may act at different stages of melanogenesis. To date, however, only a few genes have been shown to have effects on normal variation in pigmentation; the strongest evidences are found in the melanogenic genes MC1R, ASIP, SLC24A5, MATP, TYR, TYRP1, DCT, OCA2 and KITLG. There are also other non-melanogenic genes with a putative role in skin pigmentation, such as VDR or beta defensins.

RESUMEN

En esta revisión presentamos una visión general actualizada de las principales hipótesis sobre la evolución del color de la piel y los factores genéticos responsables de la variabilidad, así como una breve descripción de la relación de la pigmentación de la piel con otros fenotipos pigmenta-rios, como el color de los ojos o del pelo. El estudio de la pigmentación tiene también importan-tes implicaciones biomédicas, como en lo que respecta al desarrollo de cáncer de piel. La natura-leza continua del color de la piel en humanos parece ser el resultado de una evolución adaptati-va; sin embargo, actualmente se desconoce cómo la selección ha afectado a la estructura genética de los loci pigmentarios en las diferentes poblaciones. Se han propuesto varias hipótesis para explicar esto: la protección frente a cáncer de piel y quemadura solar, protección contra la defi-ciencia de folato, protección contra daño del DNA y estrés oxidativo, una barrera de permeabili-dad o la selección sexual. La pigmentación en humanos está controlada por la acción de numero-sos genes, que actúan en diferentes etapas de la melanogénesis. No obstante, hasta hoy, solo se han identificado unos pocos genes que tengan efectos en la variabilidad normal de la pigmenta-ción; las mayores evidencias se encuentran en los genes melanogénicos MC1R, ASIP, SLC24A5, MATP, TYR, TYRP1, DCT, OCA2 y KITLG. También existen otros genes no-melanogénicos con un posible papel en la pigmentación, como VDR o las beta defensinas.

Palabras clave:

Pigmentación de la pielGenéticaEvoluciónMelanogénesis

Recibido: 28-10-2012

Aceptado: 12-12-2012

Page 2: Evolution of human skin pigmentation. Genetic ... - SEAF lopez 33.pdfIntroduction Skin color is one of the most conspicuous mor-phological traits in humans and its continuous nature

Introduction

Skin color is one of the most conspicuous mor-phological traits in humans and its continuous nature seems likely to be the result of adaptive evolution. The association of this human trait with the environment roots in the mid-18th century when naturalists such as John Mitchell first related human skin pigmentation with latitude and solar radiation (Mitchell & Collinson, 1744). Further support for the adaptive nature of pig-mentation comes from Relethford et al. (2002) who observed that, contrary to other neutral genetic mar-kers and DNA polymorphisms (which show most of their diversity within local populations), in skin color 88% of total variation is due to differences among ma-jor geographic groups.

The study of pigmentation is not only a major anthropological issue, but it also has important biome-dical implications. For instance, exposure to UVB ra-diation from the sun increases the risk of developing skin cancer (Ravanat et al. 2001), so, individuals with more pigmented or darker skin are very much less li-kely to suffer damage in their DNA by UV radiation than those with pale skin. Therefore, the study of the genetic patterns that shape the distribution of pigmen-tation among humans can shed some light on the evo-lutionary forces that have molded human genetic di-versity protecting against pigmentation and ultraviolet radiation related diseases in populations such as cuta-neous malignant melanoma. An insufficient UVB ex-posure is also related to other diseases due to the diffi-culty to maintain adequate vitamin D levels, including rickets or multiple sclerosis (Jablonski & Chaplin, 2012). Our understanding of the genes involved in these processes can be of the highest relevance as re-gards prevention and development of targeted treat-ments for specific populations. Here, we aim to review the main current hypothesis for the evolution of skin color and the genetic factors underlying its variability, as well as to summarize the relationship of skin pig-mentation with other pigmentary phenotypes, such as eye and hair color.

Biology of skin pigmentation

The skin is the largest organ of the body, consti-tuting 16% of body weight. It functions as a dynamic

protective barrier to the environment, regulating the passage of water and electrolytes while simultaneously providing protection against damaging agents, such as microorganisms, ultraviolet radiation or toxic agents. It seems also to be involved in thermoregulation and in the immune system (Menon & Kligman, 2009; Ban-gert et al. 2011) constituting thus a further layer of protection against disease. The skin is made up of three main layers: epidermis, dermis and subcutaneous tissue. The epidermis is the outer layer, serving as the physical and chemical barrier between the interior bo-dy and environment; the dermis is the deeper layer, providing the structural support of the skin. Below the dermis lies the subcutaneous tissue, an important depot of fat (Menon, 2002). As regards pigmentation, the epidermis is the most important layer, as it is where melanin, the pigmentary polymer, is synthesized and distributed. Nevertheless, skin pigmentation is also influenced, although to a minor extent, by other pig-ments such as carotene, reduced hemoglobin and oxyhemoglobin.

Melanin is a complex mixture of biopolymers, exclusively synthesized by melanocytes of the skin and the retinal pigment epithelium. Melanocytes depo-sit granules of melanin into cellular organelles called melanosomes. Then melanosomes are transferred to keratinocytes, the cells that constitute most of the epi-dermis, through a process that has not been definiti-vely unraveled yet. Recent works suggest that this may occur via the shedding vesicle system -packaging, re-lease, uptake, and dispersion- (Ando et al. 2012; Scott, 2012). Melanosomes can be of two basic types depen-ding on their shape and the melanin they contain: eu-melanosomes, ellipsoid and with black-brown eumela-nin, and pheomelanosomes, spherical, with yellow-reddish-brown melanin (pheomelanin). These two ba-sic types of melanosomes can be produced by the me-lanocyte at different times, switching from one to the other (Marks & Seabra, 2001). Rather than the number of melanocytes in the skin, it is the number and size of melanosomes, the amount, type, internal arrangement of melanin and the efficiency and characteristics of melanosome transfer to keratinocytes, which seems to determine the high degree of variation in skin colour between individuals, within and among geographical groups. Thus, within skin keratinocytes, dark Africans and native Australians show large and singly dispersed

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melanosomes, whereas in Caucasians melanosomes are smaller and aggregated into membrane-bound me-lanosome compelexes. Interestingly, keratinocytes of all geographical groups exist in the single form in hair bulb keratinocytes (Robins, 1991).

The process by which melanin is synthesized in melanosomes is called melanogenesis (reviewed by Lin & Fisher, 2007; Simon et al. 2009; Park et al. 2009). Briefly, in the absence of alpha-melanocortin (α-MSH), pheomelanin is synthesized by default. ACTH and α-MSH, subproducts of the pro-opiomela-nocortin gene (POMC), act as ligands of MC1R. The union of α-MSH and ACTH to MC1R leads to an in-crease in cellular cAMP, which in its turn, leads to an activation of protein kinase A (PKA). This leads to increased levels of microphtalmia transcription factor (MITF) expression, which upregulates the transcrip-tion of tyrosinase (TYR) and tyrosine related proteins (TYRP1 and DCT/TYRP2). Synthesis of melanin be-gins with the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine (DOPA), a step catalyzed by the enzymes TYR and TYRP1. DOPA is then oxidized to DOPAquinone. In the presence of cysteine, DOPA-quinone is reduced to cysteinylDOPA, to form phaeo-melanin. In the absence of cysteine, DOPAquinone is converted to DOPAchrome and then to eumelanin by DCT. Basal pigmentation seems to be mostly genetica-lly determined, but skin melanocytes can also adapt their melanogenic abilities to extracellular stimuli, either generated by the organism as paracrine and en-docrine factors, or by the external environment, like ultraviolet radiation (Schiaffino, 2010).

Hypotheses for the evolution of skin colour

It is speculated that first hominids that appeared in Africa probably had a lightly pigmented skin cove-red with hair (Jablonski & Chaplin, 2000). Hot envi-ronmental conditions and higher activity levels asso-ciated with the limb proportions and bipedalism made the loss of hair necessary for the thermoregulation of the body, leading to an unpigmented skin, unprotected against high intensity solar radiation (Montagna, 1981; Chaplin et al. 1994). Others suggest that the main rea-son for the evolution of dark pigmentation was to pro-tect against folate deficiency caused by elevated de-mands for folate in cell division, DNA repair, and me-

lanogenesis stimulated by UVR (see Jablonsky, 2012 and references therein). Thus, the subsequent evolution of dark skin was likely an adaptive process that occu-rred parallel to or immediately after the loss of hair, in order to provide protection against the noxious effects of UV radiation. Afterwards, as modern humans mi-grated out of Africa towards northern latitudes where solar radiation was less intense, it is speculated that they suffered again an adaptive skin depigmentation process, whose nature has been associated to the need to synthesize vitamin D (Murray, 1934; Loomis, 1967; see also Robins, 1991 or Jablonsky, 2012 and referen-ces therein). This process has been suggested to occur independently in Asia and Europe (Norton et al. 2007) prompting to the existence of a convergent evolutio-nary force.

In this regard, although it is strongly assumed that the evolution of skin pigmentation has been adap-tive, it is currently unknown how selection has affec-ted the genetic architecture of pigmentation loci in different populations. Many hypotheses have been proposed to explain this issue; most of them however are non-exclusive.

Protection from skin cancer and sunburn

UV radiation that reaches the Earth surface is composed of a mixture of UVA (320-400 nm), which can penetrate deeply into the dermis of skin as well as UVB (280-320 nm), which is more energetic and da-maging, but is absorbed and scattered in the atmosphe-re and generally does not penetrate the dermis. The third type of UV radiation, UVC (100-280 nm), is al-most completely absorbed by the ozone layer and the-refore, it does not affect the skin. Levels of UVA are considerable higher than UVB, being the tropical and subtropical areas those that receive the highest intensi-ties. Levels of UVB are also highest in the tropics, near the equator and in high altitude areas (Jablonski & Chaplin, 2010). It has been proposed that darker skins would have been favored in regions of high ul-traviolet radiation, where heavily pigmented mela-nocytes would minimize the damaging effects of UV radiation, hence protecting against skin cancer (Ro-bins, 1991) and sunburn (Thomson, 1951). Povey et al. (2007) discovered that XPD, ERCC1 and XPF, which play an important role in the nucleotide excision repair

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(NER) pathway that deals with UV-induced damage, show polymorphisms related to the susceptibility to cutaneous melanoma. From an evolutionary point of view this hypothesis has been prone to some objec-tions, as skin cancers generally do not develop in deve-loped societies until late in the third decade, and there-fore it is expected that it should have a minimal effect on reproductive success or fitness (Johnson et al. 1998). However, there is evidence that supports the idea of protection. For instance, squamous cell carci-noma in African albinos has been reported to be the commonest skin malignancy, which usually appears in young adults by the age of 20 (Okoro, 1975; Opara & Jiburum, 2010). Furthermore, the incidence of mela-noma in the USA is nowadays around ten times higher in Caucasians compared to African Americans (Ameri-can Cancer Society, 2012). It also seems that death rates from melanoma are not negligible in the age group in reproductive age. Thus death rates in young people (aged 25-49) are increased 2-3% per year in some north and west European countries and up to 8% in Spain (de Vries & Coebergh, 2005). Also, Robins (1991) points out that studies done in 1975 and 1985 indicated that in Nigeria and Tanzania all the “Ne-groid” albinos studied exhibited skin cancers or pre-malignant lesions by the age of 20. Only a 6% of Nige-rian albinos were in the age-range of 31-60 years com-pared to 20% of the non-albinos. In any case, it is im-portant to consider the selective relevance in evolutio-nary terms, not in present-day terms only (i.e. from a clinical perspective). We, in fact, ignore what was the effect of prolonged sun exposure, say, 20,000 year ago, in prehistoric human hunter-gatherer societies.

Protection against folate deficiency

Folate is an essential vitamin to fetal deve-lopment and male fertility. It has been shown that defi-ciency of this vitamin during pregnancy can result in congenital neural tube anomalies and reduced sperma-togenesis (Jablonski & Chaplin, 2000). The levels of folate are influenced both by dietary intake and by destructive factors such as UVB radiation; therefore, the high concentration of melanin in dark skins would provide protection against folate photolysis due to UV radiation. Given that there seems to be an obvious rela-tionship between maintaining adequate folate levels and fitness (or reproductive success) this hypothesis is

biologically meaningful from an evolutionary pers-pective, but to our knowledge, it has not been tested so far.

Protection against low vitamin D levels

Vitamin D is essential to promote a good mine-ralization of the bones by stimulating the absorption of calcium. Precursors of vitamin D are synthesized in the skin from 7-dehydrocholesterol in a process ca-talyzed by UVB. These precursors are taken up by the liver and converted into 25-hydroxyvitamin D (25-OHD), which is carried to the kidney and metabolized into 1,25-hydroxivitamin D (1,25-(OH)2D), the active form of vitamin D. Thus, it is speculated that a dark skin would have been disadvantageous at high latitu-des because it would prevent the synthesis of enough vitamin D. Instead, the lighter tones would have resul-ted beneficial in the less radiation-intensive regions situated at high latitudes, as low amounts of eumelanin would allow UV radiation to penetrate the skin and catalyze the synthesis of the right levels of vitamin D (Holick, 2003). It was also speculated that dark skins could have evolved in order to avoid intoxication cau-sed by an excess of vitamin D synthesis. However, it has already been demonstrated that high UVB irradia-tion does not lead to vitamin D over-synthesis. Instead, when previtamin D reaches a critical level, it is con-verted into two inert compounds avoiding the synthe-sis of more vitamin D (Holick et al. 1981).

Protection against oxidative stress

It has also been suggested that the higher sus-ceptibility to skin cancer in fair-skinned Caucasians could be due to a reduced ability to detoxify the oxygen radicals that are produced in the cell after UV exposure. It has been shown that mutations in glu-tathione S-transferases, such as GSTT1, that contribute to the defense against oxidative stress, are associated with increased sunburn sensitivity and predisposition to non-melanoma skin cancer (Kerb et al. 2002).

Permeability barrier

Other authors suggest that the development of epidermal pigmentation in UV-enriched environments could have provided a superior permeability barrier,

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not only to prevent desiccation of the organism, but also to defend against microbial pathogens or allergens (Elias et al. 2010).

Sexual selection

It was Darwin who first linked variation in skin pigmentation with sexual selection. More recently, some authors still maintain the existence of a unidirec-tional sexual selection in women’s skin color favoring lighter pigmentation (Aoki, 2002). However, the role of sexual selection might have been secondary, having women’s lighter skin first evolved for other reasons. For instance, van der Berghe and Frost (1986) specula-ted that differences in skin tones between males and females would have arisen as a hormonal consequence, and then males would have preferred lighter colors as a measure of hormonal status and reproductive poten-tial. Others suggested that a fairer skin color was acquired by women as a childlike trait that reduced aggressiveness in men (Guthrie, 1970). And thirdly, it was proposed that the acquisition of a lighter skin by women would facilitate vitamin D synthesis in order to obtain adequate quantities of calcium for pregnancy and lactation (Jablonski & Chaplin, 2000).

In summary, many hypotheses have been pro-posed to explain differences in pigmentation between populations, but none has been fully tested yet. In this regard, analyzing the diversity patterns of pigmenta-tion genes can offer some insights into the evolution of skin pigmentation.

Genetics of skin pigmentation variability

Initially, studies carried out in mice allowed the identification of at least 150 loci that regulate eye, skin and hair colour, and that follow a Mendelian pattern of inheritance (Silvers, 1979). It is clear that constitutive pigmentation, that is, the pigmentation that is genetica-lly determined and is not influenced by environmental conditions, is a complex phenomenon that follows a polygenic model with a few major genes (Sturm et al. 2001) and that varies in its heritability between diffe-rent populations (Byard, 1981). It is obvious too that pigmentation is not influenced only by genes, but also by other factors such as age, sex, social habits or the effect of environment (Robins, 1991).

Initial candidate genes for skin pigmentation have been identified from mutations that lead to pig-mentation disorders, such as oculocutaneous albinism, linked to OCA2 (Lee et al. 1994), Xeroderma pigmen-tosum, caused by a mutation in XPA gene that encodes a protein involved in DNA excision repair (Tanaka et al. 1990) or Waardenburg Syndrome type 2, associated with mutations in the MITF gene (Tassabehji et al. 1994). To date, however, only a few genes have been shown to have effects on normal variation in pigmen-tation (Table 1). The strongest evidences are found in the melanogenic genes MC1R, ASIP, SLC24A5, MATP, TYR, TYRP1, DCT, OCA2 and KITLG. Due to the pro-ved relevance of these genes in pigmentation variation, we are going to review them in more detail; however it must be taken into consideration that there are other genes that have also been reported to play a role in pigmentation, like PMEL, which encodes a melanoso-mal matrix protein, SHROOM2 and GPR143, impor-tant in melanosomal biogenesis or ATRN, implicated in the eumelanin/pheomelanin switch. For further infor-mation (Oetting & Bennett, 2012), a database contai-ning all coat color genes described so far in mice and t h e i r h u m a n h o m o l o g u e s i s a v a i l a b l e a t www.espcr.org/micemut.

MC1R

MC1R is a single-exon gene that codes for a seven pass transmembrane G protein coupled receptor located in the cell membrane of the melanocytes. This gene is highly polymorphic in European populations and most of the polymorphisms correspond to non-synonym nucleotidic positions. Interestingly, non-synonymous variants are nearly absent in the African samples analyzed so far (Rana et al. 1999; Harding et al. 2000). Many of these variants have been correlated to a fair skin and red-hair phenotype, as well as to a low tanning ability and a higher skin cancer risk (Val-verde et al. 1995; Box et al. 1997). The alleles associa-ted to the reddish-hair phenotype have been classified into two groups, depending on their penetrance: high-penetrance “R” alleles (Asp84Glu, Arg151Cys, Arg160Trp and Asp294His) and low-penetrance “r” alleles (Val60Leu, Val92Met and Arg163Gln). The functionality of these mutations has been studied in vitro, showing that many of them lead to a reduced ability to bind either α-MSH or activate adenylyl cy-clase, which results in an increased production of

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pheomelanin, instead of eumelanin, in melanocytes that confers a red hair and light skin phenotype (Schiöth et al. 1999; Ringholm et al. 2004).

Interestingly, MC1R is also located in the brain, where it acts as a receptor of the endorphins, or pain relieving hormones. Thus, a mutation in MC1R would lead to the production of the reddish pheomelanin in melanocytes, and also to a different tolerance or res-ponse to pain in the brain. This is why it has been hypothesized that red-haired individuals have a diffe-rent sensitivity to pain compared to individuals with other hair phenotype (Liem et al. 2004; Liem et al. 2005, Mogil et al. 2005).

ASIP

ASIP is a homologue of the mouse agouti signa-ling protein gene (ASP), which has an essential role in determining coat color in mice. In humans, the protein codified by ASIP (Agouti signaling peptide) is an in-verse agonist of α-MSH that hampers its union with MC1R, promoting the synthesis of pheomelanin. A SNP in the 3’ untranslated region of this gene (g.8818A→G) has been strongly associated with dark hair, brown eyes and dark skin in African Americans (Kanetsky et al. 2002; Bonilla et al. 2005). It has been suggested that the G allele could lead to mRNA insta-bility and premature degradation of the protein, thus favoring the union of MC1R to its antagonist α-MSH,

leading to the production of eumelanin instead of pheomelanin (Kanetsky et al. 2002).

SLC24A5

SLC24A5 (Solute carrier family 24, member 5), encodes the NCKX5 protein. NCKX5 is a member of the potassium-dependent sodium calcium exchanger protein family that locates in normal human epidermal melanocytes. SLC24A5 seems to be one of the major human pigmentation genes, as it appears to be crucial for melanin synthesis. In particular, Lamason et al. (2005) showed a polymorphism in SLC24A5, rs1426654 (Ala111Thr), which accounts for a high percentage of normal variation in pigmentation among individuals. This SNP is located in the third exon of SLC24A5. Whereas alanine form is found in 93 to 100% of samples of Africans, East Asians and Indige-nous Americans, the threonine variant is nearly fixed in Europeans. It has been estimated that around 25-38% variation in skin pigmentation can be explained by this mutation.

MATP

Mutations in MATP (human membrane associa-ted transporter gene), also known as SLC45A2, can cause oculocutaneous albinism type 4 (Newton et al, 2001) and are also associated with pigmentary phe-notypes. Two polymorphisms in this gene, Leu374Phe

Evolution of human skin pigmentation

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Table 1: SNPs known to have an effect on normal pigmentation variation

SNP Aminoacidic change Gene Pigmentary phenotype

rs1805006 Asp84Glu MC1R fair skin and red hair (R variant) rs1805007 Arg151Cys MC1R fair skin and red hair (R variant) rs1805008 Arg160Trp MC1R fair skin and red hair (R variant) rs1805009 Asp294His MC1R fair skin and red hair (R variant) rs1805006 Val60Leu MC1R fair skin and red hair (r variant) rs2228479 Val92Met MC1R fair skin and red hair (r variant) rs885479 Arg163Gln MC1R fair skin and red hair (r variant) rs6058017 g.8818A>G ASIP brown eyes and dark hair and skin rs1426654 Ala111Thr SLC24A5 light skin in Europeans rs16891982 Leu374Phe MATP dark hair and skin in Europeans rs1042602 Ser192Tyr TYR light skin in Europeans rs1800414 His615Arg OCA2 light skin in East Asia

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and Glu272Lys have been strongly associated with dark hair, skin and eye pigmentation and shown to be distinctively distributed among the different popula-tion groups (Graf et al. 2005). These non-synonymous SNPs lead to aminoacidic substitutions that could affect the gene’s function. It has been proposed that 374Leu allele contributes to a melanosomal environ-ment favoring optimal eumelanin production, while 374Phe allele would originate an acidic environment, due to an alteration in the transport of protons that negatively affects tyrosinase activity.

TYR, TYRP1 and DCT

Tyrosinase (TYR) and tyrosinase-related pro-teins 1 and 2 (TYRP1 and DCT) coordinate the produc-tion of melanin from tyrosine. The rate-limiting enzy-me in melanogenesis is tyrosinase, which catalyses the conversion of tyrosine into dopaquinone (Cooksey, 1997). This activity is required for the synthesis of the two types of melanins: pheomelanins or the more pho-toprotective eumelanins. Mutations in these genes re-sult in different types of oculocutaneous albinism, but nonpathologic polymorphisms have been also shown to result in skin pigmentation variation. For instance, two nonsynonymous SNPs in TYR, rs1042602 (Ser192Tyr) (Shriver et al. 2003; Stokowski et al. 2007) and rs1126809 (Arg402Gln) (Nan et al. 2009) have been significantly associated with skin color and tanning ability.

OCA2

This gene encodes the human protein P, an in-tegral membrane protein involved in the transport of tyrosine. Mutations in OCA2 result in type II oculocu-taneous albinism, but polymorphisms in this gene have also been associated with skin and eye pigment varia-tion. A missense mutation (rs1800414) is a candidate variant for light skin pigmentation in East Asia, where it is found at high frequencies but absent in European and West African populations (Yuasa et al. 2007; Ed-wards et al. 2010; Donnelly et al. 2012). It has been estimated that each copy of the derived G allele de-creases skin pigmentation by 0.85–1.3 melanin units (Edwards et al. 2010), contrary to polymorphisms in other genes that have an effect of more than 3 melanin units per allele copy (Lamason et al. 2005; Norton et

al. 2007), thus suggesting that rs1800414 in OCA2 fits a codominant model of inheritance.

KITLG

This gene encodes the ligand of the tyrosine-ki-nase receptor encoded by the KIT locus. It plays an important role in the localization of melanocytes, and in the regulation of survival and proliferation of fully differentiated melanocytes in adults (Wehrle-Haller, 2003). Genetic variations in KITLG are associated with variation in skin, hair and eye pigmentation. Recent DNA sequence-based evidence has revealed a signifi-cant departure from neutrality for this gene in the Eu-ropean population (de Gruijter, 2011).

Other non-melanogenic genes with a role in skinpigmentation

The vitamin D receptor gene, VDR

Given the major role of UV radiation in vitamin D synthesis, it has been speculated that polymorphisms in VDR could also interact epistatically with skin co-lor-determining genes (Hochberg & Templeton, 2010). The VDR gene has four major polymorphic SNPs in humans and several other rare ones. Li et al. (2008) showed that polymorphisms in this gene do affect me-lanoma risk, although there are not strong evidences that correlate directly these polymorphisms with skin color.

Beta defensins

Defensins are short cationic and cysteine rich peptides that play an essential role in innate immune system, the first line of host defense against many common microorganisms. They are classified into three main classes, α-, β- and θ-defensins, (Yang et al. 2002). It has been demonstrated that antimicrobial activities of defensins protect the host against bacteria, fungi, viruses and parasites. However, they have in-creasingly been observed to exhibit numerous other activities, both in vitro and in vivo, that do not always relate directly to host defense. Beta defensins are highly polymorphic in sequence and copy number (Hollox et al. 2003). It has been demonstrated that

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higher copy numbers of beta defensin genes are signi-ficantly associated with the risk of psoriasis (Hollox et al. 2008), while lower copy numbers are correlated with predisposition to Crohn’s disease (Fellerman et al. 2006). Interestingly, polymorphisms in these genes have also recently been associated with pigmentation. In fact, Candille et al. (2007) identified a mutation in a β-defensin, CBD103, which correlates with black coat color in dogs by acting as an alternative ligand for MC1R. They suggest that its ability to modulate mela-nocortin receptor signaling (MC1R and others) may have been selected during vertebrate evolution to pro-vide camouflage and adaptive visual cues. Soon after-wards, Anderson et al. (2009) demonstrated the exis-tence of this mutation in the grey wolf, which exhibits a molecular signature of positive selection, and in the coyote. Following this thread, researchers are now focusing on studying the role of β-defensins in human pigmentation (Gläser et al. 2009; Beaumont et al. 2012).

High-throughput sequencing methods have suggested many other candidate genes with a role in pigmentation variability, such as SLC24A4, TPCN2 or IRF4. SLC24A4 encodes a member of the potassium-dependent sodium/calcium exchanger protein family and has been reported to contain three SNPs in linkage disequilibrium associated with blond hair color (Sulem et al. 2007). For TPCN2, two identified coding va-riants have also been associated with hair color (Sulem et al. 2007). The protein encoded by IRF4 is a member of the interferon regulatory factor family of transcrip-tion factors that has been proposed as specific marker for melanoma and benign melanocytic nevi. A SNP in intron 4 of IRF4 has been proposed to be associated with hair color and tanning ability (Han et al. 2008).

A brief remark on hair and eye colour

Skin color is correlated with other pigmentary phenotypes, such as eye and hair color. However, it should be highlighted that apart from some alleles for fair skin, red hair and blue eyes (described for instance in MC1R) skin color is weakly influenced by the diffe-rent alleles for hair or eye color. We have to bear in mind that although hair and skin melanocytes arise from the same embryonic source, the genes affecting

colour can be expressed independently with different combinations in humans (Sturm et al. 2001).

Genetics of eye color variation

Eye color is determined by two different fac-tors: the pigmentation if the iris (Prota, 1998) and the scattering of light in the stroma of the iris (Fox, 1979). It is categorized into blue, grey, green, yellow, hazel, light brown and dark brown, while the shades of hair color range from light blond, blond, dark blond, red, red blond to brown and dark brown/black. Eye colour is determined by the distribution and content of the melanocyte cells in the uveal tract of the eye. It has been suggested that the number of melanocytes does not differ between eye colours, being the melanin (in the form of eumelanin or pheomelanin) quantity, packaging and quality responsible for the range of eye shades (Prota, 1998). Although many genes responsi-ble for eye color have been so far identified, it is mostly attributed to two adjacent genes located on chromosome 15: OCA2 and HERC2, which explain 74% of the variability (Lehman et al. 1998; Eiberg et al. 2008; Rebbeck, 2002). Nevertheless, polymor-phisms in other genes such as TYR, TYRP1, DCT, SLC45A2, ASIP, MYO5A, IRF4, SLC24A4 and SILV are also of relative importance in determining eye co-lor (Reviewed in Sturm & Larsson, 2009).

Genetics of hair color variation

Red hair colour (RHC) phenotype, characteri-zed by high pheomelanin content, is caused by polymorphisms in MC1R which also lead to light skin, as explained above. This phenotype has been widely studied due to its relationship with propensity to sun-burn and risk of skin cancer. SNPs in other pigmentary genes have also been signaled as candidates leading to red hair (SLC45A2, SLC24A5, OCA2, HERC2 and ASIP) (Valenzuela et al. 2010). Quite surprisingly, blond hair contains mostly eumelanin, being the con-tribution of pheomelanin less than 20% (Ito & Waka-matsu, 2011a). Although the genetic basis of blonde hair are not as clear as in the red hair colour, this phe-notype is known to be in association with SNPs in pigmentary genes ASIP, TPCN2, SLC24A4, MC1R and

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TYRP1 (Valenzuela et al. 2010; Sulem et al. 2008). A genome-wide association study has recently revealed a SNP in TYRP1, rs13289810, which causes an arginine-to-cysteine mutation that is strongly associated to blond hair in a population from the Solomon Islands (Kenny et al. 2012) which proves that blond hair is not an exclusive trait from nor-European populations and that it can be adquired by different mutations. Finally, brown or black hair, which contains mostly eumelanin, has been shown to be associated with SNPs in SLC45A2, HERC2 and SLC24A5. Other pigmentary genes are also likely related to this phenotype, such as DCT, TYR, TYRP1, MC1R, OCA2, TPCN2 or CTNS (Ito & Wakamatsu, 2011b).

Hair and eye color variability

While variation in skin pigmentation is notable between populations, hair and eye colour variation is most notable within European populations, being dark brown eyes and hair dominant in African and Asian populations. Many hypotheses have been proposed to explain the variability of eye and hair color among Europeans: relaxation of selection, admixture with Neanderthals, and natural or sexual selection. It has been rejected that these high levels of diversity are due to relaxation of selection, as it has been estimated that it would have taken more than 850,000 years to deve-lop, and humans have just been in Europe for 35,000 years (Harding et al. 2000; Templeton, 2002). It has also been speculated that this diversity could be due to admixture with Neanderthals, an older European popu-lation. Although first mtDNA comparative studies showed lack of inbreeding with Neanderthals (Currat & Excoffier, 2004; Serre et al. 2004), comparisons of the Neanderthal genome with the complete genomes of humans from different parts of the world showed that Europeans and Asians share 1% to 4% of their nuclear DNA with Neanderthals, contrary to Africans that do not share any genetic variants with them (Green et al. 2010). However, a study by Lalueza-Fox (2007) revea-led a Neanderthal-specific MC1R sequence that led to light skin color and/or red hair, supporting the hypo-thesis of convergent evolution between humans and Neanderthals, at least with regard to this pigmentary gene. It is more likely that some selective force might be responsible for high levels of diversity in eye and hair color among Europeans. It could be a side effect

of natural selection for fairer skins. However, in con-trast to skin pigmentation where selective advantages for lighter tones have been described (protection against low vitamin D levels), the adaptive significan-ce of a loss of eye or hair colour pigmentation is less certain.

Conclusions

Some SNPs in pigmentary genes have already been identified as an important source of variability; nevertheless, a high percentage of this variation cannot still be explained. Being a polygenic trait it becomes a difficult task to associate a particular polymorphism with a concrete phenotype, thus, it can generally only be regarded as a predisposition or susceptibility that might be interacting at the same time with other polymorphisms in other genes. Epistasis, that is, the phenomenon by which the effects of one gene are mo-dified by one or several other genes, is also of the upmost importance in pigmentation. Albinism, which affects hair, skin, and eye color in humans, is an example of epistasis. In its recessive form it has the ability to mask a substantial amount of genotypic in-formation, thus drastically altering the human's phe-notypes (Brilliant, 2001). Red hair is another example of epistasis, in which an individual that is homozygous for red hair alleles has the expression of other brown/blonde hair loci overridden, and therefore resulting in red hair phenotype (Valverde, 1995).

Furthermore, the study of diverse populations is essential to unraveling the genetic basis of pigmenta-tion, as it can vary among ethnic groups. A good example of convergent evolution, that is, groups that independently evolve similar traits, is the recent paper by Kenny et al. (2012). Here, they described a new mutation that is responsible for blond hair in Melane-sians, but that is not seen in other human groups worldwide.

Finally, the identification in beta defensins of a mutation responsible for pigmentation, first in dogs, and now also in humans is a rather promising new direction for future research. It is a good example that our efforts to understand the phenomenon of skin color

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cannot be focused only on candidate pigmentary genes and pathways; rather, we must investigate alternative hypotheses that complement current knowledge.

Acknowledgements

This work was partly supported by grants CGL-2008-040666/BOS from the former Spanish Ministry of Science and Innovation, grant GIC 10/46 IT542–10 from the Basque Government to Research Groups of the Basque University System and UFI 11/09 from the University of the Basque Country (UPV/EHU). S. L. has a predoctoral fellowship from the Basque Go-vernment (BFI09.258).

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