Let’s go back 520 years ago to the year 1494 on the island of Vieques, off the southeast coast of Puerto Rico’s mainland.

Tainos, the largest indigenous Caribbean population, were living a life based on the cultivation of root crops and fishing when upon the shores arrived Columbus and his fleet, having crossed the Atlantic Ocean for the second time in as many years. At that point in time everything changed.

What’s written on paper has told us much about what happened next. What’s written in the DNA of today’s Puerto Ricans can tell us some more.

(Photo by B. Anthony Stewart/National Geographic Creative)

National Geographic’s Genographic Project researches locations where different groups historically intermixed to create a modern day melting pot. Collaborating with 326 individuals from southeastern Puerto Rico and Vieques, the Genographic Project conducted the first genetic testing in the area with the goal to gain more information about their ancient past and learn how their DNA fits into the human family tree. The results, just published in the American Journal of Physical Anthropology, paint a picture of vast historic complexity dating back some 5,000 years, to the first Caribbean peoples.

Our Genographic team learned some key pieces of information that helped us gain more insight into the peopling of the Caribbean. Most surprisingly, we found that roughly 60% of Puerto Ricans carry maternal lineages of Native American origin. Native American ancestry, higher than nearly any other Caribbean island, originated from groups migrating to Puerto Rico from both South and Central America. Analysis of the Y Chromosome DNA found that no Puerto Rican men (0%) carried indigenous paternal lineages, while more than 80% were West Eurasian (or European).

This leads us to conclude that the Y chromosomes (inherited strictly paternally) of Tainos were completely lost in Puerto Rico, whereas the mitochondrial DNA (inherited strictly maternally) survived long and well. This stark difference has been seen in other former colonies (Brazil, Cuba, Jamaica), but the gender dichotomy appears strongest in the Spanish-speaking Americas. A look into the rest of the Puerto Rican genome using the Genographic Project’s custom genotyping tool, the GenoChip, sheds some light on what may have happened during Spanish colonial times to create this ancestral imbalance.

The average Puerto Rican individual carries 12% Native American, 65% West Eurasian (Mediterranean, Northern European and/or Middle Eastern) and 20% Sub-Saharan African DNA. To help explain these frequencies in light of the maternal and paternal differences, I used basic math and inferred that it would take at least three distinct migrations of hundreds of European men each (and practically no European women) to Puerto Rico, followed by intermixing with indigenous women. It also would necessitate the complete decimation of indigenous men (but not women), to account for those numbers. These results are surprising and also shed light into a dark colonial past that, until now, had remained somewhat unclear.

These types of analyses, not just across the Caribbean or the world, but across a specific population’s DNA, can have strong historical implications and at the same time help paint a new picture of world history. Learn more about how DNA can inform you about your own personal past, and help us uncover some new secrets of world history by joining The Genographic Project.