The Neolithic Revolution involved the advent of agriculture, which finally allowed people to settle down in ever-larger groups and focus on things other than procuring calories—things like developing written language and forming social cliques. It was one of the most profound events in the collective history of humanity.

But it wasn't just social change. It was a change in the evolutionary environment that shaped the human genome. The genetic variation found in different populations on the globe today provides hints to the ways we all adapted. But analyzing ancient DNA could allow us to identify traits as they adapted in real time.

Alas, ancient human DNA has been pretty sparse. Now, an international team of geneticists, archaeologists, and anthropologists has assembled a database of genomes from 230 West Eurasians who lived between 6500 and 300 BCE and found evidence of selection at genetic loci involved in diet, pigmentation, immunity, and height.

The database consists of previously published and new samples. Critically, it includes the genomes of 26 Anatolian Neolithic farmers, examined for the first time here. (Their DNA was obtained from the inner-ear region of the petrous bone, which yields twice as much DNA as teeth.) To study selection, the researchers compared over a million sites in the chromosomes that are known to vary within human populations. The researchers looked at both the ancient DNA and in genome-wide sequencing data from four populations of European ancestry in the 1,000 Genomes Project.

By far the strongest signal for selection is at the SNP responsible for lactase persistence, a variant that allows adults to digest milk sugars, located on chromosome 2. The allele first appears in an individual who lived in central Europe around 4,000 years ago.

Other diet-related alleles selected for include two that decrease blood plasma triglyceride levels, which come from a meat-rich diet. Two others regulate circulating vitamin D levels, and another two are associated with celiac disease. One of these celiac-associated SNPs occurs in the gene encoding the ergothionine transporter, which helps import a relative of key amino acids. This is hypothesized to have undergone a selective sweep to protect against ergothionine deficiency in those switching from hunter-gatherer to more agricultural diets.

After lactase, the next strongest signal contributes to light skin pigmentation. This SNP, on chromosome 5, is almost fixed in present-day Europeans but was much less frequent in the ancient genomes. Alleles for light eye color were also selected for, although not nearly as markedly.

There was also a strong signal for selection at the major histocompatibility complex (MHC) locus on chromosome 6. MHC proteins are essential in adaptive immunity and for preventing autoimmune reactions. Adaptive immunity may have become more critical to humans who were living in the larger and larger groups, enabled by agriculture; perhaps autoimmune disorders are part of the price humanity must pay for the enhanced immune vigilance necessary for living en masse.

This study suggests that the height differences between current northern and southern Europeans has been doubly selected for: early Neolithic migrants to southern Europe were under selection for decreased height compared to other contemporaneous populations, while the steppe populations that eventually migrated to northern Europe were selected to be taller than others.

Natural selection is a force that shapes all living things, fitting them into their environments and allowing them to survive environmental stressors. Selection and adaptation have been witnessed and recorded as they occur in many species: finches in the Galapagos, cichlids in the East African Great Lakes, and of course MRSA and other pathogenic bacteria as they learn to evade our antibiotics. Humans work no differently from these other forms of life; now that we can purify and analyze DNA throughout history, we can see how our genes evolved to help us adapt to our environments.

Nature, 2015. DOI: 10.1038/nature16152 (About DOIs).