Pigmentation, phylogeny, history, and adaptation

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