The Admixture Structure and Genetic Variation of the Archipelago of Cape Verde and Its Implications for Admixture Mapping Studies

Abstract

Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.

Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome

“…Differences between X-chromosomal and autosomal admixture estimates are sometimes used to demonstrate the occurrence of sex bias, even without estimating sex-specific contributions [21, 23, 24, 26, 27, 37]. Higher estimated admixture from a population S 1 for X chromosomes than for autosomes is taken as evidence of a female bias from S 1 and a male bias from a second population S 2 .…”

Association of genetic variants with skin pigmentation phenotype among populations of west Maharashtra, India

“…In particular, the advent of large‐scale SNP genotyping technologies has led to several GWAS that have helped to elucidate genetic variants that underlie normal variation in pigmentation phenotype. However, the majority of these have focused on European (Candille et al, ; Liu et al, ; Nan et al, ; Sulem et al, ; Zhang et al, ), or sometimes admixed populations (Beleza et al, ). Only a single GWAS has focused on the genetic architecture of pigmentation variation in South Asian populations (Stokowski et al, ).…”

Autosomal Admixture Levels Are Informative About Sex Bias in Admixed Populations

“…More recently, as the Y chromosome and mitochondrial genome each represent single nonrecombining loci that provide an incomplete genomic perspective, sex-biased admixture has been examined by comparisons of autosomal DNA to the X chromosome (Lind et al 2007; Wang et al 2008; Bryc et al 2010a,b; Cox et al 2010; Beleza et al 2013; Verdu et al 2013). …”