Genomic ancestry and ethnoracial self-classification based on 5,871 community-dwelling Brazilians (The Epigen Initiative)

TLDR

Brazil’s lack of segregation laws has produced a highly admixed population, making ethnoracial classification complex and previous studies have reported conflicting links between genomic ancestry and self‑reported race. The study genotyped 370,539 SNPs in 5,851 community‑dwelling Brazilians from Pelotas, Bambui, and Salvador to quantify the correlation between genomic ancestry and self‑classified race. European ancestry dominated Pelotas and Bambui (median ~85 %), African ancestry was highest in Salvador (median ~50 %), and the association between self‑reported race and African ancestry varied by site (pseudo‑R² 0.50, 0.22, 0.13), with an S‑shaped positive link for Blacks, inverse for Whites, and a bell‑shaped pattern for Mixed, indicating that self‑classification is shaped by both genetic and non‑biological factors.

Abstract

Abstract Brazil never had segregation laws defining membership of an ethnoracial group. Thus, the composition of the Brazilian population is mixed and its ethnoracial classification is complex. Previous studies showed conflicting results on the correlation between genome ancestry and ethnoracial classification in Brazilians. We used 370,539 Single Nucleotide Polymorphisms to quantify this correlation in 5,851 community-dwelling individuals in the South (Pelotas), Southeast (Bambui) and Northeast (Salvador) Brazil. European ancestry was predominant in Pelotas and Bambui (median = 85.3% and 83.8%, respectively). African ancestry was highest in Salvador (median = 50.5%). The strength of the association between the phenotype and median proportion of African ancestry varied largely across populations, with pseudo R 2 values of 0.50 in Pelotas, 0.22 in Bambui and 0.13 in Salvador. The continuous proportion of African genomic ancestry showed a significant S-shape positive association with self-reported Blacks in the three sites and the reverse trend was found for self reported Whites, with most consistent classifications in the extremes of the high and low proportion of African ancestry. In self-classified Mixed individuals, the predicted probability of having African ancestry was bell-shaped. Our results support the view that ethnoracial self-classification is affected by both genome ancestry and non-biological factors.