The arrival of the first Spanish conquistadores in the Americas in the late 15th century marked a major turning point in the social and the genetic history of the continent. Aside from asserting their political and economic authority, the European invaders also quickly established their reproductive superiority over their indigenous counterparts, and in so doing plotted a new genetic course for the inhabitants of the New World. A new study in the journal PLOS ONE reveals how this encounter led to the virtual extermination of certain native genes – particularly those passed along the paternal line – and continues to shape the genetic makeup of modern-day Panamanians.

In the aftermath of the Spanish colonization of the Americas, large numbers of indigenous men were killed in violent conflicts with the new arrivals, while many who survived were sent to work in mines throughout the Spanish empire. As such, they were denied access to the women of their communities, leading to a drop-off in reproduction.

Meanwhile, the colonial authorities often took native women as sexual partners, resulting in the emergence of a Mestizo population, carrying a mix of Native American and European genes. Over the years, as European men continued to mate with Mestizo women while indigenous males were deprived of sexual rights, native genes passed along by these females persisted through the generations, although others that can only be passed on by native men did not.

Accordingly, a genetic study conducted in 2012 revealed that some 83 percent of Panama’s population harbor mitochondrial DNA (mtDNA) of Native American ancestry. Mitochondria are structures found in cells that convert energy from food into a usable form, and contain DNA that is only passed along the maternal line.

However, new research looking at 408 Panamanian men has found that, although the majority carried Native American mitochondrial DNA, only 22 percent harbored Y-chromosomes of Native American origin.

Since Y-chromosomes are only found in males and are always inherited along the paternal line, this data suggests that while the female component of Native American DNA has been retained in the Panamanian population, the male component has significantly decreased.

Participants in the study were recruited from nine different provinces as well as one autonomous indigenous territory, and despite the fact that nearly all had Native American mtDNA, 60 percent carried Y-chromosomes originating in West Eurasia and North Africa. The rest had their origins in sub-Saharan Africa and South Asia.

Interestingly, the proportion of men carrying European Y-chromosomes varied from province to province, reflecting the geographical movements of the Spanish conquistadores. For instance, Native American Y-chromosomes were found to be much more prevalent along the Caribbean coast than elsewhere in the country, largely due to the fact that the colonial centers of power tended to be located on Panama’s Pacific coast. Furthermore, sub-Saharan African Y-chromosomes were most common in a region of dense jungle called Darien, where many escaped slaves fled to during the colonial era.