Pigmentation, phylogeny, history, and adaptation

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 variant is 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/Region Group/Place N Frequency light allele





A Decreasing Gradient of 374F Allele Frequencies in the Skin Pigmentation GeneSLC45A2, from the North of West Europe to North Africa
Denmark Copenhagen 51 0.98


England London 56 0.955


Belgium Brussels 53 0.934


France Lille 64 0.945


  Rheims 98 0.893


  Rennes 52 0.971


  Marseilles 312 0.888


  Perpignan 101 0.827


  Corsica 328 0.878


Germany Mulheim 59 0.975


Switzerland Basel 51 0.96


Italy Genoa 97 0.85


  Roma 64 0.898


  Napoli 128 0.859


  Sicily 39 0.833


  Sardinia 100 0.805


Spain Barcelona 59 0.856


  Sevilla 71 0.725


Portugal North 79 0.829


  South 59 0.78


Near Fixation of 374l Allele Frequencies of the Skin Pigmentation Gene SLC45A2 in Africa
Algeria Algiers 141 0.7


Morocco Tangier 123 0.69


Rabat 102 0.68


Berbers from Morocco 75 0.57


Libya Tripoli 38 0.58


Egypt Alexandria 162 0.65


Assouan 66 0.14


South 46 0.2


Mauritania Moors 65 0.41


Senegal Wolof 209 0


Serrere 92 0


Mandingue 51 0


Diola 42 0


Balant 21 0


Peuls 71 0.1


Toucouleur 70 0.03


Soninké 69 0.03


Ethiopia Addis Ababa 104 0


Falashas 38 0


Democratic Republic of Congo
188 0
Distribution of the F374 Allele of the SLC45A2 (MATP) Gene and Founder-Haplotype Analysis
Munich German 93 0.962


West Germany Turk 200 0.615


New Delhi Indian 51 0.147


Dhaka Bangladeshi 118 0.059


Ulaan Baator Khalha 173 0.113


Dashbalbar Buryat 143 0.115


Shenyang Han 89 0.028


Wuxi Han 119 0


Huizhou Han 111 0.005


Tottori Japanese 103 0


Okinawa Japanese 87 0


Surabaya Indonesian 105 0.005


  White S African 54 0.89


  Ghanaian 50 0


  New Guinean 52 0


  Japanese 49 0


Polymorphisms of four pigmentation genes (SLC45A2, SLC24A5, MC1R and TYRP1) among eleven endogamous populations of India
Jharkhand Munda 68 0.03


Madhya Pradesh Kanyabuja Brahmin 78 0.11


Madhya Pradesh Gond 75 0.02


Maharashtra Konkanastha Brahmin 71 0.06


Maharashtra Mahadev Koli 65 0.06


Tamil Nadu Iyengar Brahmin 66 0.07


Tamil Nadu Kurumans 67 0.07


Tripura Tripuri 65 0


Tripura Riang 67 0.01


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Source: Discover Magazine – Gene Expression