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Health

Pigmentation, phylogeny, history, and adaptation

Gene ExpressionBy Razib KhanAugust 7, 2013 11:45 AM
slc45a2.jpg

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SLC45A2 rs16891982 frequency

, Norton, Heather L., et al. "Genetic evidence for the convergent evolution of light skin in Europeans and East Asians." Molecular biology and evolution 24.3 (2007): 710-722.

slc24a5.jpg

SLC24A5 The above figure is from Norton et al.'s Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. It shows that rs16891982 on the SLC45A2 locus exhibits strong differentiation between Europe and the rest of the world. This is in contrast to SLC24A5, where the well known allele which differentiates Africans/East Asians from Europeans is found at very high frequencies across Western Eurasia (both my parents are homozygotes for the "European" variant; in fact SLC24A5's derived variantis found at fractions on the order of ~50% in eastern and southern India). The ancestral allele on SLC24A5 is very difficult to find in Europeans, it is so close to fixation for the derived variant. In contrast SLC45A2's minor allele is segregating at appreciable frequencies in places like southern Spain, and the derived allele is not fixed even in Northern Europe. I won't review the literature on the genomics and evolution of human pigmentation at this point. Rather, I'll just note that it seems most of the inter-population variation is controlled by a handful of genes. It's a polygenic trait, but just. Second, a fair amount of evidence has emerged that some of the lightening derived variants have increased in frequency only very recently (e.g., on the order of ~10,000 years). Pigmentation is then a peculiar trait where the genetic underpinnings can give historical phylogenetic information because of the varied dates of differentiation and selective sweeps. Below I've collated results from several studies on frequencies of SLC45A2. I invite readers to persue them. I will say two things. First, the frequency of the "European" variant in ~140 northern Ethiopians is 0%. This is peculiar for a population which may be on the order of ~50% West Eurasian. Second, the fraction of SLC45A2 derived variant in South Asians coincidentally tracks the "NE Euro" percentage in Zack Ajmal's results.

Country/RegionGroup/PlaceNFrequency light allele

A Decreasing Gradient of 374F Allele Frequencies in the Skin Pigmentation GeneSLC45A2, from the North of West Europe to North Africa

DenmarkCopenhagen510.98

EnglandLondon560.955

BelgiumBrussels530.934

FranceLille640.945

Rheims980.893

Rennes520.971

Marseilles3120.888

Perpignan1010.827

Corsica3280.878

GermanyMulheim590.975

SwitzerlandBasel510.96

ItalyGenoa970.85

Roma640.898

Napoli1280.859

Sicily390.833

Sardinia1000.805

SpainBarcelona590.856

Sevilla710.725

PortugalNorth790.829

South590.78

Near Fixation of 374l Allele Frequencies of the Skin Pigmentation Gene SLC45A2 in Africa

AlgeriaAlgiers1410.7

MoroccoTangier1230.69

Rabat1020.68

Berbers from Morocco750.57

LibyaTripoli380.58

EgyptAlexandria1620.65

Assouan660.14

South460.2

MauritaniaMoors650.41

SenegalWolof2090

Serrere920

Mandingue510

Diola420

Balant210

Peuls710.1

Toucouleur700.03

Soninké690.03

EthiopiaAddis Ababa1040

Falashas380

Democratic Republic of Congo1880

Distribution of the F374 Allele of the SLC45A2 (MATP) Gene and Founder-Haplotype Analysis

MunichGerman930.962

West GermanyTurk2000.615

New DelhiIndian510.147

DhakaBangladeshi1180.059

Ulaan BaatorKhalha1730.113

DashbalbarBuryat1430.115

ShenyangHan890.028

WuxiHan1190

HuizhouHan1110.005

TottoriJapanese1030

OkinawaJapanese870

SurabayaIndonesian1050.005

White S African540.89

Ghanaian500

New Guinean520

Japanese490

Polymorphisms of four pigmentation genes (SLC45A2, SLC24A5, MC1R and TYRP1) among eleven endogamous populations of India

JharkhandMunda680.03

Madhya PradeshKanyabuja Brahmin780.11

Madhya PradeshGond750.02

MaharashtraKonkanastha Brahmin710.06

MaharashtraMahadev Koli650.06

Tamil NaduIyengar Brahmin660.07

Tamil NaduKurumans670.07

TripuraTripuri650

TripuraRiang670.01

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