NEW YORK – Scientists are showing Neanderthals some love. This is new, and required them to overcome some unscientific prejudices. It was only a few years ago that many anthropologists insisted that Neanderthals can’t possibly have contributed to human ancestry because they were too ugly to appeal sexually to their modern human contemporaries.

Wrong. DNA evidence showed six years ago that many ancestors of modern humans made love with Neanderthals. Scientists now know in some detail how sex with Homo neanderthalensis contributed to the gene pool of today’s Homo sapiens.

Yet our Pleistocene cousins still have an image problem and scientists deserve much of the blame, said John Hawks, a University of Wisconsin anthropologist who has been one of their leading defenders in blog posts dubbed the Neanderthal Anti Defamation Files. Not only were they complicit in the ugliness frame-up, they also had deemed Neanderthals stupid. That doesn’t look smart now.

To be sure, the relationship between people and Neanderthals is complicated. About 350,000 years ago in Africa, two strains of prehistoric people diverged. One gradually evolved into bona fide modern Homo sapiens, probably around 200,000 years ago.

The Neanderthal branch left the cradle of humanity for Europe and Asia. Much later, some of the so-called modern humans also moved north, where the two branches encountered each other. The DNA evidence shows that they had evolved in somewhat different directions while they were apart, but not enough to prevent them from having sex and producing kids.

Science learned all this thanks to the ability to read Neanderthal DNA scraped from ancient bones. That advance allowed scientists to recognize telltale sequences in people today. Neanderthal DNA makes up between 1 percent and 5 percent of the DNA of people with European, Asian, Australian or Native American ancestry.

How do these bits of Neanderthal DNA affect those who carry it? To find out, scientists looked at genetic and medical data for a group of 28,000 people. The results, published last Thursday in the journal Science, showed that Neanderthal DNA was correlated with a host of different traits and susceptibility to health problems.

Some bits of Neanderthal DNA increased carriers’ risk of skin lesions known as actinic keratosis. Others cause blood to coagulate faster, thus slightly increasing the risk of stroke. Some increased the risk of depression; some decreased it. Some Neanderthal genes increased the risk of tobacco addiction in modern people.

That probably wasn’t a problem for Neanderthals. They knew how to control fire, but there’s no evidence they smoked, even after having sex with modern humans.

One finding of possible relevance to today’s obsession with paleo dieting was a bit of DNA that influences the ability to digest carbohydrates. Neanderthals were apparently not as well-suited to eating carbs as the modern humans.

There seemed to be slightly more negative than positive associations with Neanderthal DNA, but not enough to worry anyone, said geneticist Josh Akey, a collaborator on this study.

But there’s still a question of whether these genes should be considered embarrassing — suggesting the breaking of some species-barrier taboo. Scientists are still arguing about whether Neanderthals constituted a separate species. Biologists no longer believe in the rule that animals of different species never mate. There are too many exceptions — grizzlies and polar bears, lions and tigers, dogs and wolves. (And happy Valentine’s Day to them.)

Hawks, the Neanderthal-defending anthropologist, said Neanderthals had many of the traits that seem central to being human. That’s a new discovery, too. Until recently, no one had found evidence that they created art or jewelry or complex bone tools. It was therefore incorrectly thought that they were incapable of symbolism. Some scientists assumed that Neanderthals couldn’t talk.

And then people started finding Neanderthal beads, paint pigments and bone tools finely crafted for leather work, said Hawks. Beyond that, humans and Neanderthals share distinct physiological traits in the structure of vocal tracts and inner ears, apparently critical in the ability to speak and detect the common frequencies of speech.

Scientists have also revised their view of Neanderthal extinction — long attributed to some deficit on their part. Maybe nothing dramatic happened at all, said Hawks. They would have made up a small fraction of the world’s population, and when larger groups of modern humans joined them in Europe they might have simply been absorbed.

Which comes back to the question of who would want to absorb them. Neanderthals look weird when encountered in museum dioramas, but anthropologists point out that the so-called “modern humans” of 50,000 years ago looked nothing like Wilma Flintstone or Betty Rubble, let alone Raquel Welch in that caveman bikini.

For all we know, some of them were great cooks or singers. That we ridiculed Neanderthals so maliciously for so long says more about our shortcomings than theirs.

Faye Flam writes about science, mathematics and medicine. She has been a staff writer for Science magazine and a columnist for the Philadelphia Inquirer. She is author of “The Score: How the Quest for Sex has Shaped the Modern Man.”