Study confirms that Neanderthals and humans got it on

The genetic similarities between certain human populations and Neanderthals are striking. Indeed, many researchers think the Europeans and Asians inherited between 1 and 4 percent of their DNA from Neanderthals, yet scientists have struggled to demonstrate with a high degree of certainty that these genetic similarities are the result of interbreeding between these two species. Now, a pair of European scientists say that they have confirmed the human-Neanderthal reproduction hypothesis using statistical modeling — and these results, the researchers add, should go a long way to change the way we think of other human-like species.

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In the past, genetic similarities between Neanderthals and humans have been associated with two possible scenarios. The first hypothesis puts forth that idea that certain human populations — those that went on to become modern Eurasians — evolved in isolated patches in Africa that allowed them to stay genetically similar to Neanderthals after they split from their shared common ancestor. The interbreeding hypothesis, on the other hand, states that bouts of human-Neanderthal reproduction would have occurred after humans migrated out of Africa. So, to find out which hypothesis fit humanity's genetic history more closely, the scientists tested the two hypotheses using a statistics and an evolutionary model.

"A model that involves interbreeding is much more likely."

"We did a bunch of math to compute the likelihood of two different scenarios," says Laurent Frantz, study co-author and evolutionary biologist at Wageningen University in the Netherlands. "We were able to do that by dividing the genome in small blocks of equal lengths from which we inferred genealogy." This method allowed the researchers to support with a high degree of certainty that interbreeding occurred, Frantz says. "Our analysis shows that a model that involves interbreeding is much more likely than a model where there was sustained substructure in Africa." The scientist cautions that sustained substructure might still have occurred, "but it cannot be used to explain the genetic similarities" all on its own.

These results, published today in Genetics, go against a 2012 study, published in Proceedings of the National Academy of Sciences, which found that interbreeding was far less likely than the alternative. "There seemed to be something that has gone wrong [in that study] because it seems unparsimonious to me," Frantz says. "When we tested two hypotheses, we got a high support for a scenario where humans and Neanderthals interbred."

Shifting the conversation away from the brutality of human evolution

The researchers originally developed the statistical method to study the genetic history of insect and pig populations in Europe and Southeast Asia, respectively. But they think that it can also be used to study interbreeding events when there is a limited pool of genetic samples available. Furthermore, Frantz thinks that these results, along with those from previous studies, should serve to shift the conversation away from the brutality of human evolution.

"There have been a lot of arguments about what happened to these species," the researcher says. "Some think that we out competed [other hominids] or that they were killed by humans, but now we can see that it's not that simple." In all likelihood, some Neanderthals were recruited into certain human populations, he says, and shared in their daily lives. So thinking of humanity solely in terms of a struggle to destroy all that differs from our species is, at least partially, incorrect. There is little doubt now, Frantz says, that "human evolution is much more complex than we previously thought."

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 years.

Significance

Eye, hair, and skin pigmentation are highly variable in humans, particularly in western Eurasian populations. This diversity may be explained by population history, the relaxation of selection pressures, or positive selection. To investigate whether positive natural selection is responsible for depigmentation within Europe, we estimated the strength of selection acting on three genes known to have significant effects on human pigmentation. In a direct approach, these estimates were made using ancient DNA from prehistoric Europeans and computer simulations. This allowed us to determine selection coefficients for a precisely bounded period in the deep past. Our results indicate that strong selection has been operating on pigmentation-related genes within western Eurasia for the past 5,000 years.
Abstract

Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways—HERC2, SLC45A2, and TYR—using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2–10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 years.

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bluesbaby5050: Oldest ever human DNA found in Spain, raises new questions about

A fossil discovered in a Spanish cave has given researchers the oldest human DNA found to date. According to The New York Times, the DNA comes from a femur bone and is believed to be around 400,000 years old. But while it's helping to shed light on early human evolution, it's actually making matters more complicated. The fossil's anatomy reportedly made researchers believe at first that it came from an early Neanderthal, but the DNA appears to come from a separate branch of humans called Denisovans. Even more puzzling, until now Denisovan DNA has reportedly only been found in Siberia, at a site 4,000 miles away from this new discovery.

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"Now we have to rethink the whole story."

The discovery is being published today in Nature by researchers led from the Max Planck Institute for Evolutionary Anthropology in Germany. According to the Times, Denisovans were previously believed to have lived only in East Asia. They were also not believed to carry such a resemblance to Neanderthals. "Now we have to rethink the whole story," Juan Luis Arsuaga, a co-author of the paper, tells the Times. One possibility is that those living near the Spanish cave, Sima de los Huesos, were neither Denisovans nor Neanderthals, but actually an ancestor of both of them. The researchers are also considering whether such DNA may have initially been present in Neanderthals but disappeared later on in their evolution.

Until now, the oldest found DNA was 100,000 years old. "This would not have been possible even a year ago," Arsuaga tells the Times. DNA reaching so far back has previously only been found in permafrost, but USA Today reports that the cave was able to properly preserve it in a new environment. From there, the researchers were able to use an updated version of a DNA extraction technique that had been developed at the Max Planck Institute in 1997 to recover it, reports the Times. Though the fossil's DNA is opening up more questions, there's still more left to study: the femur bone was just one small part of the 28 skeletons found at Sima de los Huesos.

bluesbaby5050: Evolution revolution: how one skull may unite the early human fa

At a site in Dmanisi, Georgia, researchers have been finding the bones and tools of early human ancestors for years. Now, however, an unearthed skull is posing something of a problem. The top of its head is relatively small, resembling a humanlike species known as Homo habilis; but its jaw is fairly large, more closely resembling another species, Homo erectus. Naturally, a single skull can only come from a single species, but this one seems to be telling two separate stories.
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Researchers may otherwise have said they were separate species

In a paper published today in Science, researchers led by the Georgian National Museum describe how the approximately 1.8-million-year-old skull has begun raising questions about current classifications of these earlier humanlike species. "The brain case is very small, unexpectedly small," says Marcia Ponce de León, a co-author of the paper, during a call describing the findings. "At the same time we have the face. It is quite large, and the jaws are quite massive, and the teeth are big and large."

Had the two skull pieces been found at separate excavation sites, researchers almost certainly would have said that they came from two separate species. But instead, researchers are proposing something controversial: that many of our ancient ancestors are actually part of one single species, rather than a variety of them as they've long been classified.

Ponce de León says that the skull contains a "strange combination of features," one that hasn't been seen before in bones from human ancestors of that period. The research team has taken to colloquially calling those early inhabitants "early Homo," as an easy means of lumping all of the potential species together. After comparing the size of the new skull pieces to the size of other early Homo fossils, researchers recognized that the differentiation in shape and size — a major reason they've been considered separate species — wasn't actually so great after all. In fact, they were no farther apart than variations between modern humans.

"We can really look into and quantify the variation."

"Dmanisi is the first site where we can really look into and quantify the variation," Christoph Zollikofer, a co-author on the paper, said during the call. "We are pretty sure that the variation that we see in Dmanisi is within the species."

Combining those early members of the Homo genus into one single species isn't a done deal yet though. This is only one fossil — albeit one of the best ever found — and not every expert in the field will be convinced. Another of the paper's co-authors, Philip Rightmire, tells Science that the conclusion has already set off something of a "bomb" in their field, ostensibly causing a schism between those who agree with the findings and those who aren't sold on the idea of a singular species just yet.

As for the dig site in Dmanisi, there could be more to come. "[Dmanisi] is really a place that every paleoanthropologist dreams of," Ponce de León says. The paper's lead author, David Lordkipanidze, describes it as a medieval city set on a hilltop. Excavations at the location first uncovered animal bones, and since, at least five ancient skulls. Another 50,000 square meters have yet to be excavated. "[Dmanisi] may be a time capsule which preserves a system around 1.8 million years ago," Lordkipanidze says. "I can say for sure that we have still a lot to discover."

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