Sodium/potassium/calcium exchanger 5 (NCKX5), also known as solute carrier family 24 member 5 (SLC24A5), is a protein that in humans is encoded by the SLC24A5 gene that has a major influence on natural skin colour variation. [5] The NCKX5 protein is a member of the potassium-dependent sodium/calcium exchanger family. Sequence variation in the SLC24A5 gene, particularly a non-synonymous SNP changing the amino acid at position 111 in NCKX5 from alanine to threonine, has been associated with differences in skin pigmentation. [6]
The SLC24A5 gene's derived threonine or Ala111Thr allele (rs1426654 [7] ) has been shown to be a major factor in the light skin tone of Europeans compared to Sub-Saharan Africans, and is believed to represent as much as 25–40% of the average skin tone difference between Europeans and West Africans. [5] [8] Possibly originating as long as 19,000 years ago, it has been the subject of selection in the ancestors of Europeans as recently as within the last 5,000 years, [9] and is fixed in modern European populations. [10] [11] [12] It was introduced into Khoisan people via "back-to-Africa" migration around 2,000 years ago is partly responsible for their differing skin tone to most other African populations. [13]
The SLC24A5 gene, in humans, is located on the long (q) arm of chromosome 15 on position 21.1, from base pair 46,200,461 to base pair 46,221,881. [5]
NCKX5 is 43 kDa protein that is partially localized to the trans-Golgi network in melanocytes. Removal of the NCKX5 protein disrupts melanogenesis in human and mouse melanocytes, causing a significant reduction in melanin pigment production. Site-directed mutagenesis corresponding to a non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue in NCKX5 (A111T) that is important for NCKX5 sodium-calcium exchanger activity. [6]
SLC24A5 appears to have played a key role in the evolution of light skin in humans of European ancestry. The gene's function in pigmentation was discovered in zebrafish as a result of the positional cloning of the gene responsible for the "golden" variety of this common pet store fish. Evidence in the International HapMap Project database of genetic variation in human populations showed that Europeans, represented by the "CEU" population, had two primary alleles differing by only one nucleotide, changing the 111th amino acid from alanine to threonine, abbreviated "A111T". [5] [14] [15]
The derived threonine allele (Ala111Thr; also known as A111T or Thr111) represented 98.7 to 100% of the alleles in European samples, while the ancestral or alanine form was found in 93 to 100% of samples of Sub-Saharan Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. This single change in SLC24A5 explains between 25 and 38% of the difference in skin melanin index between peoples of sub-Saharan African and European ancestry. [5]
The SNP rs2470102 independently affects skin pigmentation variation among the South Asian population. [16]
Furthermore, the European mutation is associated with the largest region of diminished genetic variation in the CEU HapMap population, suggesting the possibility that the A111T mutation may be the subject of the single largest degree of selection in human populations of European ancestry. [5] It is hypothesized that selection for the derived allele is based on the need for sunlight to produce the essential nutrient vitamin D. In northerly latitudes, where there is less sun, greater requirement for body coverage due to colder climate, and frequently, diets poor in vitamin D, making lighter skin more suitable for survival. [17]
The earliest known sample of the threonine allele is 13,000 years old from Satsurblia Cave in Georgia. [18] The allele was widespread from Anatolia to Ukraine and Iran at the beginning of the Neolithic. [19] [20] [21]
This allele forms part of the HIrisplex DNA test system used to estimate pigmentation in forensic investigations. [22] [23]
Human skin color ranges from the darkest brown to the lightest hues. Differences in skin color among individuals is caused by variation in pigmentation, which is the result of genetics, exposure to the sun, disorders, or all of these. Differences across populations evolved through natural selection or sexual selection, because of social norms and differences in environment, as well as regulations of the biochemical effects of ultraviolet radiation penetrating the skin.
Melanin consist of oligomers or polymers arranged in a disordered manner which among other functions provide the pigments of many organisms. Melanin pigments are produced in a specialized group of cells known as melanocytes. They have been described as "among the last remaining biological frontiers with the unknown".
Melanocytes are melanin-producing neural crest-derived cells located in the bottom layer of the skin's epidermis, the middle layer of the eye, the inner ear, vaginal epithelium, meninges, bones, and heart. Melanin is a dark pigment primarily responsible for skin color. Once synthesized, melanin is contained in special organelles called melanosomes which can be transported to nearby keratinocytes to induce pigmentation. Thus darker skin tones have more melanosomes present than lighter skin tones. Functionally, melanin serves as protection against UV radiation. Melanocytes also have a role in the immune system.
Tiger eye or goat eye is a gene causing diluted eye color in horses. There are two variants, Tiger-eye 1 (TE1) and Tiger-eye 2 (TE2), which are both recessive. Horses displaying tiger eye typically have a yellow, orange, or amber iris. Tiger eye has only been found in Puerto Rican Paso Fino horses. Horses of related breeds were tested, and none were found to have either tiger eye allele. No obvious link between eye shade and coat color was seen, making this the first studied gene in horses to affect eye color but not coat color. Tiger eye does not appear to affect vision, and there were no signs of reduced pigment on the retina or retinal pigment epithelium.
In genetics and bioinformatics, a single-nucleotide polymorphism is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population.
Human genetic variation is the genetic differences in and among populations. There may be multiple variants of any given gene in the human population (alleles), a situation called polymorphism.
A white horse is born predominantly white and stays white throughout its life. A white horse has mostly pink skin under its hair coat, and may have brown, blue, or hazel eyes. "True white" horses, especially those that carry one of the dominant white (W) genes, are rare. Most horses that are commonly referred to as "white" are actually "gray" horses whose hair coats are completely white. Gray horses may be born of any color and their hairs gradually turn white as time goes by and take on a white appearance. Nearly all gray horses have dark skin, except under any white markings present at birth. Skin color is the most common method for an observer to distinguish between mature white and gray horses.
In genomics, a genome-wide association study, is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
The genetic basis of coat colour in the Labrador Retriever has been found to depend on several distinct genes. The interplay among these genes is used as an example of epistasis.
Tyrosinase-related protein 1, also known as TYRP1, is an intermembrane enzyme which in humans is encoded by the TYRP1 gene.
P protein, also known as melanocyte-specific transporter protein or pink-eyed dilution protein homolog, is a protein that in humans is encoded by the oculocutaneous albinism II (OCA2) gene. The P protein is believed to be an integral membrane protein involved in small molecule transport, specifically of tyrosine—a precursor of melanin. Certain mutations in OCA2 result in type 2 oculocutaneous albinism. OCA2 encodes the human homologue of the mouse p gene.
ATP-binding cassette transporter sub-family C member 11, also MRP8, is a membrane transporter that exports certain molecules from inside a cell. It is a protein that in humans is encoded by gene ABCC11.
Membrane-associated transporter protein (MATP), also known as solute carrier family 45 member 2 (SLC45A2) or melanoma antigen AIM1, is a protein that in humans is encoded by the SLC45A2 gene.
Light skin is a human skin color that has a base level of eumelanin pigmentation that has adapted to environments of low UV radiation. Light skin is most commonly found amongst the native populations of Europe, Central Asia, and Northeast Asia as measured through skin reflectance. People with light skin pigmentation are often referred to as "white" although these usages can be ambiguous in some countries where they are used to refer specifically to certain ethnic groups or populations.
The melanocortin 1 receptor (MC1R), also known as melanocyte-stimulating hormone receptor (MSHR), melanin-activating peptide receptor, or melanotropin receptor, is a G protein–coupled receptor that binds to a class of pituitary peptide hormones known as the melanocortins, which include adrenocorticotropic hormone (ACTH) and the different forms of melanocyte-stimulating hormone (MSH). It is coupled to Gαs and upregulates levels of cAMP by activating adenylyl cyclase in cells expressing this receptor. It is normally expressed in skin and melanocytes, and to a lesser degree in periaqueductal gray matter, astrocytes and leukocytes. In skin cancer, MC1R is highly expressed in melanomas but not carcinomas.
Dark skin is a type of human skin color that is rich in melanin pigments. People with very dark skin are often referred to as "black people", although this usage can be ambiguous in some countries where it is also used to specifically refer to different ethnic groups or populations.
Recent human evolution refers to evolutionary adaptation, sexual and natural selection, and genetic drift within Homo sapiens populations, since their separation and dispersal in the Middle Paleolithic about 50,000 years ago. Contrary to popular belief, not only are humans still evolving, their evolution since the dawn of agriculture is faster than ever before. It has been proposed that human culture acts as a selective force in human evolution and has accelerated it; however, this is disputed. With a sufficiently large data set and modern research methods, scientists can study the changes in the frequency of an allele occurring in a tiny subset of the population over a single lifetime, the shortest meaningful time scale in evolution. Comparing a given gene with that of other species enables geneticists to determine whether it is rapidly evolving in humans alone. For example, while human DNA is on average 98% identical to chimp DNA, the so-called Human Accelerated Region 1 (HAR1), involved in the development of the brain, is only 85% similar.
In archaeogenetics, the term Western Hunter-Gatherer (WHG), West European Hunter-Gatherer, Western European Hunter-Gatherer, Villabruna cluster, or Oberkassel cluster is the name given to a distinct ancestral component of modern Europeans, representing descent from a population of Mesolithic hunter-gatherers who scattered over Western, Southern and Central Europe, from the British Isles in the west to the Carpathians in the east, following the retreat of the ice sheet of the Last Glacial Maximum.
In archaeogenetics, the term Eastern Hunter-Gatherer (EHG), sometimes East European Hunter-Gatherer, or Eastern European Hunter-Gatherer is the name given to a distinct ancestral component that represents Mesolithic hunter-gatherers of Eastern Europe.
In archaeogenetics, the term Scandinavian Hunter-Gatherer (SHG) is the name given to a distinct ancestral component that represents descent from Mesolithic hunter-gatherers of Scandinavia. Genetic studies suggest that the SHGs were a mix of Western Hunter-Gatherers (WHGs) initially populating Scandinavia from the south during the Holocene, and Eastern Hunter-Gatherers (EHGs), who later entered Scandinavia from the north along the Norwegian coast. During the Neolithic, they admixed further with Early European Farmers (EEFs) and Western Steppe Herders (WSHs). Genetic continuity has been detected between the SHGs and members of the Pitted Ware culture (PWC), and to a certain degree, between SHGs and modern northern Europeans. The Sámi, on the other hand, have been found to be completely unrelated to the PWC.