Time to give thanks for your genome: A new study finds that at some point in our evolutionary history, humans lost a stretch of DNA that would have otherwise promoted the growth of spines on the penis.

The genetic loss is just one of millions that separates us from our closest primate relative, the chimpanzee, researchers report in the March 10 issue of the journal Nature. The team also reported the disappearance of a growth-suppressing genetic switch. That loss may have contributed to the enlargement of the human brain.

Many studies have emphasized the similarities between humans and chimpanzees; we share 96 percent of our genomes, according to a 2005 study published in Nature. But that still leaves millions of genetic differences that explain the discrepancies between us and our primate cousins.

"The biggest question is, 'What is the molecular biology of becoming human?'" study co-author David Kingsley, a developmental biologist at Stanford University, told LiveScience.

What makes humans special

To find out, Kingsley and his colleagues compared the chimpanzee genome, sequenced in 2005, with the human genome, sequenced in 2001. They found millions of differences, but narrowed it down to a more manageable set of 510 segments of DNA that are present across many other animals, including chimps, but disappear in humans. Because the sequences are so well-preserved across species, they're likely to be functional (not so-called "junk DNA"), Kingsley said. And because they're missing in humans, they're likely to be the keys to what makes us special.

"The challenge is to match some of the differences between the genomes to the differences between the species," study co-author Gill Bejerano, a professor of computer science and developmental biology at Stanford, told LiveScience.

To do that, the researchers had to "roll up [their] sleeves and head for the lab," Bejerano said. The subset of 510 genes of interest still required whittling down, so the team recruited researchers from fields such as neuroscience and physical anthropology. The hunt was on for genes with known functions that could be linked to a physical change in humans.

Big brains and smooth penises

Of the 510 genes the researchers looked at, only one was a protein-coding gene, meaning it held the recipe for making a specific protein in the body. The rest mapped to noncoding parts of the genome, which often play the role of regulators, ensuring that the protein-coding genes get switched on and off at the right times.

Two particular categories of gene showed a propensity for nearby DNA losses, the researchers found. The first were genes related to neural development. One, the researchers found, normally suppresses cell growth. Humans still have this gene, but a nearby snippet of regulatory DNA is gone. In other animals, that snippet controls the expression of the gene in parts of the brain.

Thus, the loss of the gene in humans "may be one of the events that contributed to the expanded cell production in the developing brain," Kingsley said. In other words, the genetic change might be one reason humans have such big brains.

The second category of genes with absentee regulatory neighbors was a group of androgen receptor genes. Androgens are male hormones, responsible for the development of, among other things, penile spines in animals.

Penile spines are exactly what they sound like: small spines on the head of the penis of many animals. Plenty of animals sport the spikes, including a type of beetle called the bean weevil whose hard, sharp spikes scar the female beetle's reproductive tract during sperm delivery. Many rodents, primates, such as marmosets, and even pythons whose Y-shaped hemipenis is often spined in order to grip the walls of the female's opening, known as a cloaca. [Penis Myths Debunked]

In species with penile spines, Kingsley said, females tend to mate with multiple males. Penile spines may have evolved to clear out a competitor's sperm – or to abrade the female's vagina, making her less likely to mate with others. Either way, Bejerano said, "the loss of the spines is most often seen in species that have gone more the monogamous way."

Mice whose androgen receptor gene is disrupted don't develop penile spines, Kingsley said. The same may be true of humans, who have lost 60,000 base pairs of DNA right next to that gene. (A base pair consists of two nucleotide molecules that sit opposite one another on complementary strands of DNA.)

"Humans have thrown away the molecular switch from a key gene that's required to form the spine," Kingsley said.

Setting humans apart

The researchers still have a list of 508 promising genes to investigate, Kingsley said, and experiments are ongoing to suss out the functions of many. Plenty of the millions of genetic differences not examined in this project are likely also important, Bejerano said.

"We think that the 510 [differences] we highlight here are important, but by no means are they the only 510 differences that may have contributed to who we are today," he said.

The researchers are also working to recreate the loss of the brain growth regulatory gene in mice. The change in size of the mouse brains should reveal how important that singular genetic loss was to the evolution of larger brains, Kingsley said.

The availability of full gene sequences also makes it possible to compare humans with other relatives, Kingsley said. The Neanderthal genome, for example, shows the same loss of both the brain growth and penile spine regulatory genes. That makes sense, Kingsley said, given that Neanderthals are known to have large brains and may have interbred with humans.

"We live at this time when the complete genome sequences of ourselves and our closest relatives are being isolated," Kingsley said. "You can now, for the first time, troll through the entire genome and enumerate all the ways we're different from other organisms."

You can follow LiveScience Senior Writer Stephanie Pappas on Twitter @sipappas.