A progression of sketches shows how a skull and genetic clues were combined to come up with the look of a 7,000-year-old hunter-gatherer who lived in Spain. Pelopanton / CSIC

A 7,000-year-old man whose bones were left behind in a Spanish cave had the dark skin of an African, but the blue eyes of a Scandinavian. He was a hunter-gatherer who ate a low-starch diet and couldn't digest milk well — which meshes with the lifestyle that predated the rise of agriculture. But his immune system was already starting to adapt to a new lifestyle.

Researchers found all this out not from medical records, or from a study of the man's actual skin or eyes, but from an analysis of the DNA extracted from his tooth.

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The study, published online Sunday by the journal Nature, lays out what's said to be the first recovered genome of a European hunter-gatherer from a transitional time known as the Mesolithic Period, which lasted from 10,000 to 5,000 years ago. It's a time when the hunter-gatherer lifestyle was starting to give way to a more settled existence, with farms, livestock and urban settlements.

The remains of the Mesolithic male, dubbed La Braña 1, were found in 2006 in the La Braña-Arintero cave complex in northwest Spain. In the Nature paper, the researchers describe how they isolated the ancient DNA, sequenced the genome and looked at key regions linked to physical traits — including lactose intolerance, starch digestion and immune response.

The biggest surprise was that the genes linked to skin pigmentation reflected African rather than modern European variations. That indicates that the man had dark skin, "although we cannot know the exact shade," Carles Lalueza-Fox, a member of the research team from the Spanish National Research Council, said in a news release. At the same time, the man possessed the genetic variations that produce blue eyes in current Europeans.

That combination makes for a rare genetic profile, but perhaps it was more typical of the Mesolithic Period. To find out, the researchers say they'll need to analyze more genomes from that time — starting with La Braña 2, another male whose skeleton was found in the Spanish cave.

The skeleton of the male known as La Braña 1 lies in a Spanish cave, as seen after its discovery in 2006. J.M. Vidal Encina

More about ancient genomes:

In addition to Lalueza-Fox, the authors of "Derived Immune and Ancestral Pigmentation Alleles in a 7,000-Year-Old Mesolithic European" include Iñigo Olalde, Morten E. Allentoft, Federico Sanchez-Quinto, Gabriel Santpere, Charleston W. K. Chiang, Michael DeGiorgio, Javier Prado-Martinez, Juan Antonio Rodriguez, Simon Rasmussen, Javier Quilez, Oscar Ramirez, Urko M. Marigorta, Marcos Fernandez-Callejo, Maria Encina Prada, Julio Manuel Vidal Encinas, Rasmus Nielsen, Mihai G. Netea, John Novembre, Richard A. Sturm, Pardis Sabeti, Tomas Marques-Bonet, Arcadi Navarro and Eske Willerslev.

Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the NBC News Science Facebook page, following @b0yle on Twitter and adding +Alan Boyle to your Google+ circles. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.