When the Spanish colonized Colombia in the sixteenth century, they brought with them many new influences: their religion and culture, slaves from West Africa, and European diseases that decimated the local Amerind population. Colombia's history of colonization, together with the obstacle to human mobility imposed by the Andes, made Carvajal-Carmona et al. question whether Colombian populations could be used to map complex traits. This is because the country's past combines two potential sources of linkage disequilibrium (LD) — recent founding by a small number of individuals and population admixture.

The authors studied 80 individuals descended from the northwestern Colombian province of Antioquia — a region settled by the Spanish in the seventeenth century. These individuals were typed for mitochondrial DNA (mtDNA) and Y-chromosome markers to identify the origins of their ancestors. Their findings — that 94% of Antioquian Y chromosomes are European and 90% of the Antioquian mtDNA gene pool is Amerind in origin — are perhaps not surprising given the colonial history of the region. These results confirm that local Amerind women predominantly had children with Spanish colonists and that this, combined with disease and colonial attack, almost eliminated the Amerind male gene pool from today's Antioquian population. A comparison of Antioquian Y-chromosome allele frequencies with those from the Iberian peninsula and northern Africa (because Spain was under Moorish rule between the eighth and fifteenth centuries) showed that the European founders were predominantly from southern Spain, but also that a fraction of founders came from the northern Basque region and that others had a Sephardic ancestry.

Previous blood-group data had showed the genetic background of Antioquians to be predominantly (∼70%) white. The researchers suggest that this could be accounted for by there having been more male founders than female ones. Furthermore, colonial culture pressured Spanish men into having families with mixed-race rather than with Amerind women, further reducing the incorporation of additional Amerind female founders into the expanding population.

So does the Antioquian population have LD levels that would make it useful for mapping complex traits? It remains an open question. Although the mtDNA data indicate that it was isolated for some time, the level of founder diversity suggests that a strong population bottleneck did not occur at founding. However, the researchers remain hopeful that the presence of population sub-isolates within this large region may yet prove this founding admixture to be a fruitful blend.