Scientists have identified a clutch of subtle genetic changes that have shaped our minds and bodies into the unique form that sets humans apart from chimpanzees and the rest of the animal kingdom.

The work by researchers in the US represents a landmark in a search that has occupied philosophers and scientists for millennia and one that goes to the heart of understanding what it means to be human.

The findings offer up the humbling conclusion that the secret of human success may owe more to what we lost along the path of evolution, rather than anything we gained.

When the human genome was first deciphered more than a decade ago, some scientists expected to find extra genes that explained why humans had an intellectual edge over their closest living relatives and other species. But since diverging from chimpanzees around seven million years ago, it turns out that our human ancestors lost several hundred snippets of DNA, which together led to traits that are uniquely human, the researchers claim.

In ditching these chunks of DNA, our ancient ancestors lost facial whiskers and short, tactile spines on their penises. The latter development is thought to have paved the way for more intimate sex and monogamous relationships. The loss of other DNA may have been crucial in allowing humans to grow larger brains.

Intriguingly, hardly any of the lost DNA was from genes, which make the proteins that are the building blocks of life. Instead, the missing DNA came from areas of the genome that regulate where and when certain genes are active.

"Like someone looking for their keys under a lamp post, the genes were the easiest place to look for differences between humans and chimpanzees, and in many respects those have been studied pretty well," said Philip Reno, a co-author on the study at Penn State University.

"But there is a larger unknown in the form of these other regions of DNA, and in those we are only just beginning to find ways to pull out the differences between humans and chimpanzees."

In the years since the human genome project was completed it has become clear that humans and chimps share around 96% of their DNA. Of the three billion pairs of "letters" that make up the human genetic code, genes account for less than 2%.

The US team compared the complete human genome with sequences from the chimp, macaque and mouse. They found that humans lack 510 short sections of DNA that are present in the other animals. Intriguingly, only one missing piece of DNA affected a human gene directly. The vast majority of lost DNA disrupted parts of the genome that control how genes are expressed.

One missing section of DNA was found to block a gene that, in other animals, stifles the growth of brain cells. Losing that DNA may have been a pivotal moment in human development, as it allowed parts of the human brain to expand into the most complex organ known.

Writing in the journal Nature, the researchers describe how our ancestors lost another piece of DNA that gives rise to both facial whiskers and sensitive spines on the tip of the penis, both of which are found in chimpanzees and other non-human primates.

Penile spines – which make the penis more sensitive and speed ejaculation – are more common in animals that face intense competition for mates, and where females are likely to mate with many males in rapid succession.

The loss of penile spines may have allowed our ancient ancestors to copulate for longer, a development thought to have nurtured monogamous couples and paved the way for more complex social structures.

When the scientists checked their genetic discoveries against the Neanderthal genome, they found the same chunks of DNA were missing, meaning the DNA was lost more than 800,000 years ago, which is when our human ancestors split from the Neanderthal lineage.

The scientists are still working out what many of the lost sections of DNA do, but expect to find more evidence of how humans differ genetically from chimpanzees.

"There are going to be many different features that make humans unique and I don't think we're close to describing all the links between genes that make us different from chimpanzees," said Reno. "We are just getting the initial picture."