Scientists believe men once had small spines on their genitalia such as those found in chimpanzees, cats and mice.
Analysis of the genomes of humans, chimpanzees and macaques indicates that a DNA sequence thought to play a role in the production of these spines have been deleted in humans, but has been preserved in other primates.
It suggests another genetic deletion may have led to the expansion of specific regions of the human brain.
The study is in the journal Nature.
The researchers at Stanford, Georgia and Pennsylvania State universities in the US wanted to trace evolutionary changes in human DNA.
They compared the human genome with those of the chimpanzee and macaque, and came up with 510 stretches of DNA that have been conserved in our primate relatives but deleted in humans.
Nearly all these DNA regions appear to play a regulatory role in the function of nearby genes.
The researchers then focused on two deletions, linking one to penile spines and another to the growth of specific areas of the brain.
They then tested the effects of the deleted sequences in human skin and neural tissue, and found further evidence to support their claims.
"We're trying to find the molecular basis of being human," said Professor David Kingsley of Stanford University, one of the authors of the study.
"That's a really ambitious goal; but we live at this unique time where we have the complete genome sequence of ourselves and our closest relatives, so you can systematically go through and find all the ways that we differ from other organisms."
Penile spines are barb-like structures found in many mammals. Their role remains under debate, and they may play different roles in different species.
They may increase stimulation for the male during mating. They might also play a part in inducing female ovulation in a small number of species, but there is evidence that they can cause damage to the female too.
Then there is the suggestion that they might have evolved to remove "mating plugs" - material that some male species deposit in the female genital tract to block other males' attempts to fertilise the same female.
"It's been proposed these structures can help remove the copulatory plugs left by other males; so in some mammals with multi-male mating systems, there's quite a little arms race going on for fertilisation," said Professor Kingsley.
The researchers believe the loss of these spines in humans may be related to changes in human courtship.
The loss of spines, they say, would result in less sensitivity and longer copulation, and may be associated with stronger pair-bonding in humans and greater paternal care for human offspring.