Cited by 161melanin and skin pigmentationForensic and Genetic ResearchGenetic Associations and Epidemiology

The DOI matches its Crossref record; 54 of the 55 references it cites were found in a registry or an index; none of the 39 sources its claims cite is checked for support yet.

Genetic Architecture of Skin and Eye Color in an African-European Admixed Population

Open access

Beleza, Sandra, Johnson, Nicholas A., Candille, Sophie I., Absher, Devin M., Coram, Marc A., Lopes, Jailson, Campos, Joana, Araújo, Isabel Inês, Anderson, Tovi M., Vilhjálmsson, Bjarni J., Nordborg, Magnus, Correia e Silva, António, Shriver, Mark D., Rocha, Jorge, Barsh, Gregory S., Tang, Hua·2013·PLoS Genetics

DOI 10.1371/journal.pgen.1003372PMC PMC3605137

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Abstract

Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62), SLC24A5 P = 9.6 × 10(-9)) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27), TYR P = 1.1 × 10(-9), APBA2[OCA2] P = 1.5 × 10(-8), SLC45A2 P = 6 × 10(-9)) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

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Written from the paper’s full text.

TL;DR

This study maps skin and eye color in 699 Cape Verdeans, an African-European admixed population, using genotype- and ancestry-based association approaches. It finds distinct genetic architectures: a few major loci plus average genomic ancestry explain much of skin color variation, while eye color is dominated by HERC2[OCA2] with a secondary SLC24A5 signal.

Key findings

Two major eye-color loci were identified: HERC2[OCA2] rs12913832 (P = 2.3×10−62) and SLC24A5 (P = 9.6×10−9 in the abstract; Table 1 reports rs2470102 genotype P = 4.8×10−10), affecting both blue versus brown eyes and shades of brown.
Four major skin-color loci were identified: SLC24A5 (P = 5.4×10−27), TYR/GRM5 (P = 1.1×10−9), APBA2[OCA2] (P = 1.5×10−8), and SLC45A2 (P = 6×10−9); together they account for 35% of total skin-color variance, while average genomic ancestry accounts for ∼44%.
Skin and eye color have different architectures: skin color correlates with African genomic ancestry at R² = 0.44, whereas eye color correlates weakly with ancestry (R² = 0.08) and with skin color (R² = 0.14).
At 15q13.1, the eye-color signal in HERC2[OCA2] and the skin-color signal in APBA2[OCA2] are genetically separable, with weak linkage disequilibrium between peaks (R² = 0.112), suggesting adjacent cis-regulatory effects on OCA2.

Methods

Studied 699 Cape Verdeans from six islands; final analyses used 685 individuals with skin reflectance and 625 with high-quality eye photographs. Genotyping used Illumina 1M, yielding 903,837 autosomal SNPs after QC.
Skin color was measured as a modified melanin (MM) index by reflectance spectroscopy on the upper inner arm; eye color was measured as a new quantitative “T index” derived from digital photographs and a principal curve.
Association analyses used additive linear regression adjusted for sex and first three principal components, plus ancestry-based mapping with SABER+, EMMAX mixed models, imputation with MaCH, CMS selection scores, and power simulations.

Limitations

The paper states that CEU and YRI are imperfect proxies for the true ancestral populations of Cape Verde, which likely include multiple Southern European and West African groups, and cautions that “European” and “African” should not imply homogeneity.
The authors note that GCTA-style heritability estimation was not used because the genetic relationship matrix is inflated by population structure and pilot studies showed large sampling variability in this moderate-sized sample.
The paper states that failure to replicate some previously reported loci (e.g., ASIP, KITLG, MC1R) could reflect limited ancestral allelic variation, incomplete ancestry correction in earlier studies, or effects too small to detect; the APBA2[OCA2] regulatory mechanism remains a hypothesis requiring functional validation.

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Integrity signals

Registry

Crossref · 10.1371/journal.pgen.1003372

Cites

54 of 54 references verified0 citation errors · 0 not checkable

Statistics

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Claims the paper makes

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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The correlation between skin color and African genomic ancestry (R∧2 = 0.44) is apparent both across and within (Table S1) islands clusters”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Quantitative assessment of pigmentary phenotypes
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Overall, African genomic ancestry in Cape Verdeans ranges from 23.5% to 87.9%, with a median of 58%.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic admixture in Cape Verdeans
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.

Show all 75 claims

It may state two separate claims as one. 58
The quote only partly states this claim. 1
Probably not a substantial claim. 23

In the paper
“in a randomly sampled African-American cohort from the Family Blood Pressure Study (FBPP) [21], African genomic ancestry ranges from 40.6% to 99.3%, with a median of 89.5%”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic admixture in Cape Verdeans
What the sources say
- Not checked yetcites [21] H Tang, 2006, Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans, Hum Genet source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
The quote only partly states this claim.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Across different islands, the distributions of African genomic ancestry exhibit substantial overlap in range but vary in their median values, from 50.5% in Fogo to 74.4% in the capital island of Santiago”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic admixture in Cape Verdeans
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Ancestry-based association yields broader peaks than genotype-based association, but the distribution of significant regions is strikingly consistent for the two approaches, uncovering the identical set of six loci”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Mapping loci associated with skin and eye color
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The derived APBA2 (OCA2) allele is present at low frequencies in most populations of African ancestry, and at high frequencies in most populations of Asian and European ancestry.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic and evolutionary relationships of eye and skin color genes at 15q13.1
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By contrast, the derived HERC2 (OCA2) allele is absent from African and East Asian populations, and appears at high frequency only in Western and Northern Europe”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic and evolutionary relationships of eye and skin color genes at 15q13.1
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
In the paper
“By comparison, MM in individuals of European ancestry is smaller and much more narrowly distributed, with a mean of 5.38 and standard deviation of 0.27 [23].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Quantitative assessment of pigmentary phenotypes
What the sources say
- Not checked yetcites [23] SI Candille, 2012, Genome-wide association studies of quantitatively measured skin, eye, and hair pigmentation in four European populations, PLoS ONE source
Strength:plain· not yet calibrated
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The genome-wide association results described below are based on a linear regression adjusting for the first three principal components (PC) but the same model adjusting for up to 10 PCs does not qualitatively alter our results.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic admixture in Cape Verdeans
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
In the paper
“thought to encode membrane transport proteins that promote melanogenesis [13], [25]–[27].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Refinement of pigmentation loci by imputation and conditional analysis
What the sources say
- Not checked yetcites [13], [25]–[27]
Load-bearingStrength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim.
In the paper
“expression of both genes is pigment cell-specific, and null mutations dramatically impair melanin synthesis in model organisms [13], [28], [29].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Refinement of pigmentation loci by imputation and conditional analysis
What the sources say
- Not checked yetcites [13], [28], [29]
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions.”
- Also stated in: § Introduction · plain
  “In this population, extensive genetic admixture between the African and European ancestral populations during the last several centuries [16], [17] has facilitated assortment of pigmentary alleles.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Abstract
What the sources say
- Not checked yetcites [16], [17]
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibratedn = 699
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“has been well recognized to account for Mendelian-like inheritance of blue vs. brown eye color in populations of European ancestry [7], [8], [10].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Refinement of pigmentation loci by imputation and conditional analysis
What the sources say
- Not checked yetcites [7], [8], [10]
Strength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“two well-known pigmentary genes for which a complete loss-of-function causes albinism in humans and in other animals [30]–[32].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Refinement of pigmentation loci by imputation and conditional analysis
What the sources say
- Not checked yetcites [30]–[32]
Strength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“If skin color in Cape Verde is 80% heritable, the four major loci and individual ancestry explain most of that variation, with only a small amount of “missing heritability””
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Results > Genetic architecture of pigmentary variation in Cape Verde
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- The authors state this as an assumption: Skin color in Cape Verde is 80% heritable.
None of the sources cited for this claim have been checked yet.
In the paper
“OCA2 was originally considered a strong candidate gene for Afro-European pigmentary variation based on allele distribution patterns of closely linked SNPs [11], [14], [34], [35], and because of a strong association with blue vs. brown eye color in populations of European ancestry [4], [41].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [11] MD Shriver, 2003, Skin pigmentation, biogeographical ancestry and admixture mapping, Hum Genet source
- Not checked yetcites [14] HL Norton, 2007, Genetic evidence for the convergent evolution of light skin in Europeans and East Asians, Mol Biol Evol source
- Not checked yetcites [34], [35]
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
In the paper
“Previous genome-wide studies of human skin and eye color have focused on populations of European ancestry and have been based primarily on categorical and subjective assessment of pigmentary phenotype [4]–[7].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [4]–[7]
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“compared to 4.8 melanin units estimated by Lamason et al. [13] in an African-American sample.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [13] RL Lamason, 2005, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans, Science source
Load-bearingStrength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim.
In the paper
“Identity-by-states (IBS), estimated using all autosomal SNPs in PLINK [47], revealed 12 pairs of cryptic relationships (IBS>0.8). One individual from each pair was excluded.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Study population and genotyping QC
What the sources say
- Not checked yetcites [47] S Purcell, 2007, PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“SLC24A5 and KITLG have been reported to have effect sizes that correspond to 25%–38% and 20%–25% of the European-West African difference in skin color, respectively [13], [15].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [13] RL Lamason, 2005, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans, Science source
- Not checked yetcites [15] CT Miller, 2007, cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans, Cell source
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may state two separate claims as one.
In the paper
“Very recently, Visser et al. [33] showed that the critical SNP in this region, rs12913832, is part of an enhancer that forms a chromatin loop with the OCA2 promoter, and that the derivative allele causes reduced recruitment of the chromatin remodeler HLTF, leading to reduced binding of additional transcription factors and impairment of loop formation and OCA2 expression in cultured human melanocyt”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [33] M Visser, 2012, HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter, Genome Res
Strength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
In the paper
“Hypopigmentation associated with these conditions is thought to be caused by hemizygosity for OCA2 [46] and is therefore independent of any potential cis-acting regulatory region in APBA2.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [46] RA Spritz, 1997, Hypopigmentation in the Prader-Willi syndrome correlates with P gene deletion but not with haplotype of the hemizygous P allele, Am J Med Genet source
Strength:hedged· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
In the paper
“the ∼1 Mb interval between HERC2 and APBA2 contains a cluster of segmental duplications that serves as a frequent deletion breakpoint (BP3) involved in Prader-Willi and Angelman syndromes [45].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Discussion
What the sources say
- Not checked yetcites [45] AJ Makoff, 2007, Detailed analysis of 15q11–q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes, Genome Biol source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Effect sizes shown in Figure 5 for KITLG (0.19 MM–0.26 MM) are estimated from Miller et al. [15] in which the beta value for rs642742 is reported as 3.8 melanin units based on a linear regression model, and 2.8 melanin units based on ADMIXMAP.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Power calculations and estimates of effect size
What the sources say
- Not checked yetcites [15] CT Miller, 2007, cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans, Cell source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
In the paper
“We also carried out an association analysis with the program EMMAX [22], which adjusts for population stratification by including a relationship matrix as a random effect; the results (Figure S1) were similar to those obtained using conventional association analysis (Figure 3).”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Association and admixture mapping
What the sources say
- Not checked yetcites [22] HM Kang, 2010, Variance component model to account for sample structure in genome-wide association studies, Nat Genet source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“To exclude the possibility that the association between skin color and genome-wide ancestry is due to geographic confounding between islands, we examined this correlation within each island (Table S1).”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Genetic architecture
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim.
- The authors state this as an assumption: The Cape Verdean population has two ancestral populations (European and West African).
In the paper
“Similarly, the effect size shown in Figure 5 for ASIP (0.24 MM) is estimated from 3.5 melanin units based on data in Bonilla et al. [12].”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Power calculations and estimates of effect size
What the sources say
- Not checked yetcites [12] C Bonilla, 2005, The 8818G allele of the agouti signaling protein (ASIP) gene is ancestral and is associated with darker skin color in African Americans, Hum Genet source
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, while the CEU and YRI are imperfect ancestral populations, they do not cause a large bias in either genome-wide or local ancestry estimates.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Characterization of genetic admixture
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- The authors state this as an assumption: The Cape Verdean population has two ancestral populations (European and West African).
In the paper
“However, the genetic relationship matrix based on allele sharing is inflated by population structure [55]; in addition, in pilot studies we observed a large sampling variability of GCTA-estimated heritability due to the moderate size of the Cape Verde sample.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Genetic architecture
What the sources say
- Not checked yetcites [55] SR Browning, 2011, Population structure can inflate SNP-based heritability estimates, Am J Hum Genet source
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Assessment and control for population stratification is described in Results; the P values reported in Table 1 and are derived from linear regressions using PLINK in which the first 3 principle components and sex are included as covariates.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Association and admixture mapping
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may state two separate claims as one.
- The authors state this as an assumption: The Cape Verdean population has two ancestral populations (European and West African).
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This approach preserves a realistic level of correlation structure between phenotype, genome-wide ancestry proportions and genotypes, and also takes into account the two strongest predictors of phenotype: genome-wide ancestry and genotype at SLC24A5.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Power calculations and estimates of effect size
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
- The authors state this as an assumption: Residual non-genetic variance is independent of any genotype or ancestry.
- The authors state this as an assumption: The simulated phenotype has a genetic architecture with three major loci, each with the same effect as SLC24A5 and perfectly ancestrally informative.
In the paper
“Imputed genotypes were inferred with the MaCH 1.0.16 package [52] using combined CEU and YRI haplotypes as reference; we report SNPs whose predicted R∧2 between true and imputed genotypes >0.80.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Imputation, selection signature, and haplotype analysis
What the sources say
- Not checked yetcites [52] Y Li, 2010, MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes, Genet Epidemiol source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may state two separate claims as one.
In the paper
“In simulation studies, the ARHMM achieves comparable accuracy as HapMix [49], but is more flexible and does not require information about the recombination rate.”
§ Genetic Architecture of Skin and Eye Color in an African-European Admixed Population > Materials and Methods > Characterization of genetic admixture
What the sources say
- Not checked yetcites [49] AL Price, 2009, Sensitive detection of chromosomal segments of distinct ancestry in admixed populations, PLoS Genet source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.

72 of 72

The paper relies on this without support.
The true ancestral populations for Cape Verde likely include contributions from several areas of Southern Europe and several areas of West Africa.
“We also note that the true ancestral populations for Cape Verde are likely to include contributions from several areas of Southern Europe, and several areas of West Africa.”
The authors state this as an assumption.
Skin color in Cape Verde is 80% heritable.
“If skin color in Cape Verde is 80% heritable, the four major loci and individual ancestry explain most of that variation”
The paper relies on this without support.
HapMap CEU and YRI individuals adequately represent the European and African ancestral populations of Cape Verde.
“Data from CEU and YRI HapMap individuals [19] was used to partition each Cape Verdean individual's ancestry into “European” and “African” components.”
The authors state this as an assumption.
The Cape Verdean population has two ancestral populations (European and West African).
“assuming two ancestral populations”
The authors state this as an assumption.
Residual non-genetic variance is independent of any genotype or ancestry.
“The residual non-genetic variance was assumed to be independent of any genotype or ancestry, such that the total variance in each simulated phenotype matches that observed for skin pigmentation in Cape Verde.”
The authors state this as an assumption.
The simulated phenotype has a genetic architecture with three major loci, each with the same effect as SLC24A5 and perfectly ancestrally informative.
“The phenotypes were simulated assuming a genetic architecture with three major loci, each of which has the same effect as SLC24A5 and is perfectly ancestrally informative.”

6 of 6

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Effect sizes are attributed to the wrong figure
Minor
The text directs readers to Figure 6a for skin-color effect sizes, but the captions identify Figure 7a as the effect-size panel; Figure 6 concerns allele frequencies and haplotypes.
Figure 6 names a different HERC2 SNP
Minor
The Figure 6 caption identifies the eye-color SNP as rs1291382, whereas Table 1 identifies it as rs12913832. The caption appears to omit a digit.

2 of 2

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FAIRsharing record for: Human Genetic Variation Database
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Authors: Beleza, S., Johnson, N. A., Candille, S. I., Absher, D. M., Coram, M. A., Lopes, J., Campos, J., Araújo, I. I., Anderson, T. M., Vilhjálmsson, B. J., Nordborg, M., Correia e Silva, A., Shriver, M. D., Rocha, J., Barsh, G. S., & Tang, H.
Affiliations: Universidade do Porto (PT)
Stanford University (US)
Stanford Medicine (US)
HudsonAlpha Institute for Biotechnology (US)
University of Cape Verde (CV)
Gregor Mendel Institute of Molecular Plant Biology (AT)
Pennsylvania State University (US)
Corresponding author: Beleza, Sandra
Barsh, Gregory S.
ORCID: Beleza, Sandra
Absher, Devin M.
Coram, Marc A.
Campos, Joana
Araújo, Isabel Inês
Vilhjálmsson, Bjarni J.
Nordborg, Magnus
Shriver, Mark D.
Rocha, Jorge
Barsh, Gregory S.
Tang, Hua
Venue: PLoS Genetics
Publisher: Public Library of Science (PLoS)
Published: 2013-03-21
Volume: 9
Issue: 3
Pages: e1003372
ISSN: 1553-7390 (ISSN-L)
1553-7404
DOI: 10.1371/journal.pgen.1003372
PMC: PMC3605137
OpenAlex: W2129233990
Cited by: 161
References: 55
Citations by year: 2026: 6 · 2025: 7 · 2024: 8 · 2023: 10 · 2022: 12 · 2021: 20 · 2020: 11 · 2019: 9 · 2018: 13 · 2017: 20 · 2016: 11 · 2015: 15 · 2014: 12 · 2013: 7
FWCI: 8.70
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS Genetics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: Fundação para a Ciência e a Tecnologia
National Human Genome Research Institute (T32HG000044)
National Institute of General Medical Sciences (GM073059, T32GM007790, R01GM073059)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: skin color, eye color, admixed populations, Cape Verde, SLC24A5, OCA2, HERC2, TYR, SLC45A2, genetic ancestry, heritability
MeSH terms: Eye Color, Genotype, Hair Color, Haplotypes, Humans, Skin Pigmentation, Albinism, Oculocutaneous, Polymorphism, Single Nucleotide, Black People, White People, Cabo Verde

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Genetic Architecture of Skin and Eye Color in an African-European Admixed Population

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