Hans Jonatan left Denmark in 1802 and eventually started a new life as an immigrant in Iceland. But he was an unusual Icelander. Unlike most Icelanders—and even most immigrants to Iceland—Hans Jonatan was mixed-race and a former slave. By piecing together genetic information from his descendants, scientists in Iceland have now reconstructed a substantial portion of Jonatan's own genome and genetic history.

Jonatan's history has been a subject of fascination, not only because he was an unexpected person to find in 19th-century Iceland, but because of his role in Danish legal history. His journey started in the Caribbean, where he was born to an enslaved mother in the then-Danish colony of St. Croix. Jonatan and his mother were brought along when the plantation-owning family returned to Denmark, but Jonatan managed to escape and ended up joining the Danish Navy.

When he was eventually caught and imprisoned, his lawyer argued for his emancipation on the grounds that slavery was illegal in Denmark, albeit still legal in Danish colonies. Jonatan lost the case, and the judge ordered that Jonatan should be returned to the Caribbean. He escaped again and disappeared from Denmark, turning up in 1805 in Iceland.

Filling in the gaps

Many details are missing from Jonatan’s story. For instance, it’s not clear exactly how he ended up in Iceland. The identity of his parents is also hazy. Historical records suggest that his father was European. His mother, Emilia Regina, was likely to have been a first- or second-generation slave, but the precise details of her origins are unknown.

While these questions have been difficult for historical records to answer, genetics might have the tools to answer some of them. But genetic data, while powerful, is also wildly complicated and messy. Piecing together the ancestry of someone who lived 200 years ago requires a lot of information, most of which we don't typically have access to.

As luck would have it, Iceland is a place that happens to have an abundance of that kind of unusual information. Because the country is so geographically isolated, it is also unusually genetically isolated; its small population also lends itself to detailed genealogical record-keeping.

Using this spectacular record-keeping, a team of scientists identified 182 of Jonatan's descendants in present-day Iceland. The researchers searched through these individuals' genetic data and found 674 stretches of genetic information that matched up with genomic data we've obtained from African DNA.

Narrowing down the data

"Because of the relative isolation of Icelanders," the team writes in a paper in Nature Genetics, "genuine African fragments in descendants of [Jonatan] are likely to originate only from [Jonatan himself]." That's as opposed to another, unidentified African source. But there's an important question here: are these fragments genuinely African? All human DNA is similar enough that it can be hard to tell.

To test this, the researchers looked at whether the fragments they found could definitely be considered African. They discovered that a small percentage of them were shared with Icelanders who otherwise seemed to have no African heritage. “Such fragments are... probably not truly African,” they write—the databases that link genetic features to specific regions of the world are still under development, and many of the details are still being ironed out.

For the remaining fragments, the scientists used only those that could be verified as truly representing descent from Jonatan by cross-referencing the genetic data with the genealogical records of the family tree. What they were left with essentially amounted to a collection of 593 puzzle pieces of African DNA: two from this great-grandson here, one from that great-great-granddaughter there, and another from that great-grandson that is mostly a duplicate but carries a small amount of extra data.

Once all those puzzle pieces were assembled, they amounted to a substantial portion of the overall picture: approximately 38 percent of Emilia Regina’s genome. The data suggested that Jonatan's mother's origins lay in Nigeria, Cameroon, or Benin and that, specifically, she was most closely related to the Yoruba people from Benin.

To see whether the historical claim of Jonatan's European paternity held water, the researchers also looked through the male line from Jonatan to his present-day descendants. They found a genetic signature that is “essentially absent from African populations” and found mostly in Europe.

“Virtual ancient DNA”

The homogeneity of the Icelandic population and their detailed family data allowed this reconstruction as a test case of what might be possible. In principle, though, the researchers argue that this kind of work might succeed in other cases, too, if there is also good genealogical and genetic data.

“Ancestor genome reconstruction of this kind can be viewed as a virtual ancient DNA study,” they write, “whereby genotype information is retrieved from a long-dead individual without the need for DNA samples from physical remains.”

But going back further than 10 generations is unlikely to produce any useful results, and the instances when this technique is possible are likely to be limited. When it is feasible, though, it will certainly be a powerful way to fill in the missing historical details of remarkable stories like Jonatan's.

Nature Genetics, 2018. DOI: 10.1038/s41588-017-0031-6 (About DOIs).