More than 10,000 years ago, our ancestors began to expand their organization of food production—purposefully promoting certain plants and animals they found tasty or useful. Over time, they domesticated those species, inserting human preferences into the process of natural selection.

We know today that agriculture and domesticated species arose separately in different regions around the world. Grains, beans, and livestock appear to be some of the earliest species domesticated in Southwest Asia, for example. But many questions remain about why humans shifted from hunting and gathering to agriculture and how the process of domesticating species unfolded—a process that, in cases like wheat and rice, appears to have taken more than a thousand years.

A special section in this week’s Proceedings of the National Academy of Sciences delved into what science has discovered about domestication and how to provide answers to our remaining questions about the lives of prehistoric people and their relationship with the plants and animals around them.

In one of the examples explored in PNAS, scientists turned to chickens in their search for answers to an age old question.

Building the modern chicken

It's not the question you’re probably thinking of. The jury’s still out on which came first, as well as motivations for road crossing. Instead, scientists were looking to see if certain traits commonly found in modern chickens were the same traits selected for when ancient humans began the domestication process.

To study the origins of these traits, the scientists compared the DNA in modern chickens to samples obtained from archeological sites ranging from 200 years BC to the 18th century.

In chickens, traits that are considered hallmarks of domestication include yellow skin. This is commonly found in most modern breeds, and it is caused by a recessive allele in the gene that breaks down orange-yellow compounds known as carotenoids. However, it’s absent in the chicken's primary ancestor, the Red Jungle Fowl, which still lives in Asia and looks a lot like a chicken. Another key trait associated with domestication is a mutation in a thyroid hormone receptor—the jungle fowl lacks it, but almost all modern chicken breeds have it.

In the past, many researchers concluded that these traits must have been selected long ago by our ancestors as they first domesticated chickens. But the in-depth genetic analysis showed that they only became common in chicken breeds relatively recently—within the past couple hundred years.

The significance here goes far beyond chicken genetics. It’s so tempting to trust neat little evolutionary stories—all the chickens have the same hormonal mutation, that must have been one of the things our ancestors selected for long, long ago—when it very well might be random chance. The genetic process of domestication can’t just be assumed from modern data.

Looking beyond genes

To really understand the origins of a domesticated species, you need more than genes; you need some sense of the people who did the domestication and the environment in which they lived. To pinpoint that environment, it helps to use more than one type of data. That’s what a team of researchers tracking the origins of the chili pepper in Mexico found. They used archeology, ecology, genetics, and linguistics to zoom in on the original hot pepper.

It was possible to narrow down the potential sites of origin by looking at the ancient languages and determining whether or not they had a word for chili pepper. Further refinement came from looking at the natural range and habitat of the wild ancestor chili pepper bush. These approaches identified a number of likely locations. Genetic tests comparing the similarity of domesticated plants to wild ancestors indicated a slight different region, a bit further north along Mexico’s Atlantic coast.

Combining the different data sets led the scientists to conclude that central east Mexico as the likely site of initial cultivation. But the study shows again that domestication is a more complicated process to study than perhaps previously thought. Each method indicated slightly different likely areas of origin, suggesting that only pursuing one method probably won't provide conclusive results.

It’s easy to draw “incomplete and sometimes biased picture of the past,” note the authors who introduce the special section on domestication. But domesticating plants and animals, inventing agriculture—these drove a powerful shift in the course of human history. And they happened in multiple places and multiple times. Why? Why give up gathering for growing? There's plenty of theories and pictures of the past, but studying domestication provides the data.

Today, we get most of our calories from a few key successful species—how much of their success was dumb luck or the spot-on instincts of our ancestors? The authors expect advances in research in the coming decade. Along with better understanding of "the interplay between past ecology, climate, plant phenotypic responses, and human activities,” these innovations should help answer the remaining, nagging questions about human history and the foods that made us who we are.

PNAS, 2014. DOI: 10.1073/pnas.1308939110, 10.1073/pnas.1308933111 (About DOIs).