Continental populations of the world vary considerably in their predisposition to diseases and in the allele frequencies of important pharmacogenetic loci, probably as a result of genetic drift, but also because of adaptation to local selective factors such as climate and available nutrients. In many countries, skin color has traditionally been used in clinical and pharmacological studies as a phenotypic proxy for geographical ancestry. Brazil is no exception.
The Brazilian population was formed by extensive admixture from three different ancestral roots: Amerindians, Europeans and Africans. This resulted in a great variability of skin pigmentation, with no discontinuities between Black and White. For instance, in a single small fishing village in Brazil, Harris and Kotak 
identified dozens of designations for varied shades of skin pigmentation.
However, the Instituto Brasileiro de Geografia e Estatística (IBGE), which is responsible for the official census of Brazil, has employed only few pre-established color categories, which are based on self-classification. Since 1991 they number five: White (“branca”), Brown (“parda”), Black (“preta”), Yellow (amarela) and Indigenous (“indígena”). Brown (“pardo”) emerged as a synthesis of a variety of classifications, such as “caboclo”, “mulato”, “moreno”, “cafuzo”, and other denominations that express the admixed character of the Brazilian population 
In general, there is academic support for the IBGE classification system, which is the only source of information on color categories at a national level 
. It reflects the fact that in Brazil social “racial” categorization depends not on ancestry, but on the physical appearance of the individual 
In 2008 IBGE ascertained a population of circa
190 million Brazilians who, based on self-classification, could be segregated into the following proportions for color: 48.4% White, 43.8% Brown, 6.8% Black, 0.6% Yellow, 0.3% Indigenous and 0.1% with no declaration (http://www.sidra.ibge.gov.br/bda/tabela/listabl.asp?z=t&c=262
). The first three of these categories (White, Brown and Black) encompass 99.1% of the Brazilian population and will be the focus of this study. It is important to realize that in Brazil, color (in Portuguese, cor
) denotes the Brazilian equivalent of the English term race (raça
) and is based on a complex subjective phenotypic evaluation that takes into account, not only skin pigmentation, but also hair pigmentation and type, eye melanization and facial features such as nose and lip shape 
With an area of 8,511,960 Km2
, Brazil has a territory of continental size (the fifth largest in the world) and different regions have diverse population histories. For instance, the North had a large influence of the Amerindian root, the Northeast had a history of strong African presence due to slavery and the South was mostly settled by European immigrants. These different compositions were quite evident in our studies of mtDNA haplotypes of White Brazilians 
When we look into the Brazilian census data on the proportion of each color category according to region, we indeed can see noticeable differences (). In the North and Northeast there is a strong predominance of Brown individuals (64.0% and 58.0%, respectively) while in the Southeast and South, White Brazilians constitute the largest category (62.4% and 83.6%, respectively). The Center-West, the least populous region, includes the heterogeneous Federal District (i.e. Brasilia) and displays more even proportions of White and Brown individuals (49.7% and 43.7%, respectively). Such high level of regional structure is peculiar, especially when we consider that our previous work has shown only a feeble relationship between color and ancestry in Brazilians 
2008 IBGE data for the regions and states sampled in this study.
We have already shown that a set of 40 short insertion-deletion (indel) polymorphisms was sufficient for an adequate characterization of human population structure at the global level 
. We furthermore demonstrated the resolution power of these markers in discriminating among Europeans, Africans and Amerindians by plotting in a triangular graph our results with the samples of Europeans, Africans and Amerindians of the HGDP-CEPH Diversity Panel 
. Three totally divergent clusters that correspond to the European, African and Amerindian populations were obtained without any overlap — each group clustered in one of the vertices of the triangular plot 
In the present study we used these loci to estimate the Amerindian, European and African genomic ancestry of 934 Brazilians from the four most populous geographical regions of the Country, self-categorized as White, Brown and Black.