Hairiness -- allowing adaptation to warmer environments -- was among gains

Roughly 500,000 year ago, the breeding populations that would evolve into humans (Homo sapiens) and Neanderthals (Homo neanderthalensis) separated.  Neanderthals came to dominate the mountainous, forest terrain of Europe, while humans spread out across the warm grasslands of Africa and the Middle East.
But the long estranged relatives would come into contact in an intimate way once more when mankind thrust its way into Europe roughly 80,000 years ago.  And by intimate, yes, we mean there was sex.
I. Understanding Our Shared Family Secret -- Neanderthal Sex
Ever since researcher and entrepreneur J. Craig Venter, Ph.D. became the first human to have his or her genome sequenced in 2007, the race was on to sequence the Neanderthal genome and find what secrets it might hold.
Led by led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany and its top ancient-DNA expert, Svante Pääbo, the project yielded a draft genome in May 2010, followed by a "finished" Neanderthal genome in March 2013. 
With the initial 2010 announcement, definitive proof of our ancestors' steamy romance with European Neanderthals was laid bare for the first time.  Today researchers are still worker to chronicle that mysterious engagement and what impacts it has on modern human genetics.
Harvard Medical School (HMS) geneticist Professor David Reich's lab -- working with collaborators at the Max Planck Institute -- is the latest to offer new insight into this relationship.

Professor David Reich
Professor David Reich, Harvard Medical School [Image Source: Harvard]

To hunt down Neanderthal genes, the researchers first sequenced 846 people of non-African heritage (who likely contained Neanderthal genes) and 176 people from sub-Saharan Africa (who likely did not receive Neanderthal genetics).  These sequences were then used to pinpoint the genes that the non-African humans (e.g. Europeans) shared with Neanderthals, but which weren't found in people of sub-Saharan African origin.
In total Professor Reich's team located 100,000 genes that originally belonged to the Neanderthal genome but penetrated the human genome, thanks to our frisky ancestors.

Roughly 2 percent of Europeans' DNA comes from Neanderthals. [Image Source: Mashable]

The researchers next examined individuals to look at how much Neanderthal DNA they had and what holes in the genome that DNA crammed into.  They found that on average non-Africans had roughly 2 percent Neanderthal-inherited DNA, but that these genes were not uniformly laid out.  Some stretches of the participants' DNA were rich in Neanderthal genes, while others were more like "deserts", devoid of Neanderthal genes.
II. Breeding With Neanderthals Had Genetic Downsides
HMS Professor Sriram Sankararaman, the first author of a new study on the work, comments:

It suggests the introduction of some of these Neanderthal mutations was harmful to the ancestors of non-Africans and that these mutations were later removed by the action of natural selection.

The location of the barren stretches -- mostly in the female "X" sex chromosome, and in genes on other chromosomes most-expressed in male testes germ cells -- show that it was likely difficult for the Neanderthals and their hopeful human mates to conceive children.  This is a common problem in genetics called "hybrid infertility" that occurs between species related closely enough to be sexually compatible, but different enough to suffer fertility issues.

Geico Caveman
Humans and Neanderthals are believed to have struggled with fertility issues.
[Image Source: Terez Owens]

The way the human genome stretched to accommodate genetics from the members of the Neanderthal species could lead not only to breakthroughs in understanding human evolution, but also in human health studies and finding ways to prevent infertility in crossbred livestock.
Professor David Reich, senior author of the study, comments:

Now that we can estimate the probability that a particular genetic variant arose from Neanderthals, we can begin to understand how that inherited DNA affects us.  We may also learn more about what Neanderthals themselves were like.  [The barren DNA stretches] suggest that when ancient humans met and mixed with Neanderthals, the two species were at the edge of biological incompatibility.  It is fascinating that these types of problems could arise over that short a time scale.

While past studies have suggested that interbreeding improved immunity and genetics related to disease resistance, it turns out that Neanderthals might have actually passed along some harmful genes, as well.  Studies suggested that genes associated with increased risk of lupus, biliary cirrhosis, Crohn’s disease, and smoking addiction were all inherited from the Neanderthals.

Lupus Harvard
Neanderthals also contributed genes that caused diseases such as Lupus
[Image Source: DermNet]

Likewise, Asians with some Neanderthal DNA saw an increased risk of type 2 diabetes versus Europeans or Africans.
III. Benefits, New Look Also Came With the Territory
But the study also looked at how the Neanderthal genes influenced genes affecting keratin, a fibrous protein found in hair, skin, and nails.  It indicated the Neanderthal donations might have made the human European colonists more hairy, allowing them survive harsh winters.
And while Neanderthals have traditionally been portrayed as dark haired, darker skinned primates, recent research indicates that quite the opposite may be the case.

Hairiness, blonde hair, and thick body hair are all thought to have been inherited from Neanderthals. [Image Source: OurPRG]

Researchers believe that darker skin and hair color came from the human gene lines, where as genes yielding red or blonde hair and lighter skin complexion came from Neanderthals.  Perhaps that explains like regions such as Scotland and Scandinavia where Neanderthals are believed to have survived the longest have the highest rates of red or blond hair and fair skin.

Neanderthal Red haired
Red hair and fair skin are also thought to have been inherited from Neanderthals.
[Image Source: BBC News]

A study on the work has been published in the prestigious peer-reviewed journal Nature.  A second paper has been published in the prestigious peer-reviewed journal Science.

The researchers next goals include making tests for the Neanderthal genes identified available to the public, enhancing the hunt for Neanderthal genomes by sequencing other Neanderthals' full gene sequences, and sequencing the DNA of Denisovans (Denisova hominins) -- another close relative of man that bread with early humans in Oceania.

The ongoing research is funded by the Max Planck Institute, the Howard Hughes Medical Institute (HHMI), the National Science Foundation, and the National Institutes of Health (NIH).

Sources: Nature, Science, Harvard Medical School

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