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 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
