Archaic admixture in Africans

"
Well established is that modern Africans have greater genetic diversity, overall, than the modern populations of other continents," Parham said.
"This greater diversity is likely due to what was inherited from earlier forms of Homo, combined with interbreeding between different forms of Homo."

http://news.discovery.com/human/neanderthals-interbreeding-humans-110825.html

Its a blog. Its not science

Neanderthal-type species once roamed Africa, DNA shows
By Brian Vastag, Published: July 26The Washington Post

July 26

The human family tree just got another — mysterious — branch, an African “sister species” to the heavy-browed Neanderthals that once roamed Europe.

While no fossilized bones have been found from these enigmatic people, they did leave a calling card in present-day Africans: snippets of foreign DNA.

There’s only one way that genetic material could have made it into modern human populations.

“Geneticists like euphemisms, but we’re talking about sex,” said Joshua Akey of the University of Washington in Seattle, whose lab identified the mystery DNA in three groups of modern Africans.

These genetic leftovers do not resemble DNA from any modern-day humans. The foreign DNA also does not resemble Neanderthal DNA, which shows up in the DNA of some modern-day Europeans, Akey said. That means the newly identified DNA came from an unknown group.

“We’re calling this a Neanderthal sibling species in Africa,” Akey said. He added that the interbreeding probably occurred 20,000 to 50,000 years ago, long after some modern humans had walked out of Africa to colonize Asia and Europe, and around the same time Neanderthals were waning in Europe.
The find offers more evidence that for thousands of years, modern-looking humans shared the Earth with evolutionary cousins that later died out. And whenever the groups met, whether in Africa or Europe, they did what came naturally — they bred. In fact, hominid hanky-panky seems to have occurred wherever humans met others who looked kind of like them — a controversial idea until recently.

In 2010, researchers from the Max Planck Institute for Evolutionary Anthropology in Germany announced finding Neanderthal DNA in the genomes of modern Europeans.

Barrel-chested people whose thick double brows, broad noses and flat faces set them apart from modern humans, Neanderthals disappeared about 25,000 or 30,000 years ago.

Another mysterious group of extinct people recently identified from a 30,000-year-old finger bone in Siberia — known as the Denisovans — also left some of their DNA in modern-day Pacific Islanders.

And while modern humans and the newly found “archaic” Africans might be classified as distinct species, they produced viable offspring. Likewise, donkeys and horses, lions and tigers.

One skull found in Nigeria with puzzling “primitive” features may represent a survivor of these mystery people — or a hybrid with anatomically modern humans — said Chris Stringer of the Natural History Museum in London, who was not involved in the new work.

“You can argue, are these really different species?” Stringer said.

Stringer added that he was not surprised to see genetic evidence for another humanlike group in Africa that interbred with anatomically modern people, who are thought to have emerged in Africa about 200,000 years ago.

Still, without a definitive fossil, it’s impossible to say what these people looked like. But one thing is clear: This enigmatic group left its DNA all across Africa. The researchers found it in the forest-dwelling pygmies of central Africa and in two groups of hunter-gatherers on the other side of the continent — the Hadza and Sandawe people of Tanzania.

Starting a decade ago, a team led by Sarah Tishkoff and Joseph Lachance of the University of Pennsylvania drew blood from five individuals in each of the three groups. Using the latest genetic technology, Tishkoff spent $150,000 to read, or sequence, the DNA of these 15 people. The research was reported Wednesday in the journal Cell.

In addition to finding evidence of the now-extinct humans, the team discovered a huge range of genetic diversity between the three groups. The human genome contains about 3 billion letters, or base pairs, of DNA. Before this study, scientists had found that about 40 million of these letters vary across human populations.

But in the 15 Africans, Tishkoff and Lachance found 3 million more genetic variants — a huge treasure trove of human diversity. Among this stunning variety, Tishkoff says they have pinpointed some of the genes responsible for the short stature of the pygmies, who average less than 5 feet in height. She also found that immune system genes and genes for taste and smell varied wildly between the three groups — confirming Africa as the seat of the widest range of human diversity.

The oldest modern human skull, found in Ethi­o­pia, dates to 195,000 years ago. For more than 150,000 years, then, humans shared the planet with cousin species.

Despite all the amorous advances, however, only one group survived: us.

Akey said: “As we were conquering the world, we also conquered similar human populations that were dying out.”

September 8th, 2012; Vol.182 #5 / Article

DNA hints at African cousin to humans
Gene profiles suggest people interbred with a now-extinct species on the continent not that long ago

By Tina Hesman Saey


Expeditions to Africa may have brought back evidence of a hitherto unknown branch in the human family tree. But this time the evidence wasn’t unearthed by digging in the dirt. It was found in the DNA of hunter-gatherer people living in Cameroon and Tanzania.

Buried in the genetic blueprints of 15 people, researchers found the genetic signature of a sister species that branched off the human family tree at about the same time that Neandertals did. This lineage probably remained isolated from the one that produced modern humans for a long time, but its DNA jumped into the Homo sapiens gene pool through interbreeding with modern humans during the same era that other modern humans and Neandertals were mixing in the Middle East, researchers report in the August 3 Cell.

The evidence for ancient interbreeding is surprisingly convincing, says Richard “Ed” Green, a genome biologist at the University of California, Santa Cruz. “There is a signal that demands explanation, and archaic admixture seems to be the most reasonable one at this point,” he says.

Scientists have discovered that some people with ancestry outside Africa have DNA inherited from Neandertals or Denisovans, a mysterious group known only through DNA derived from a fossil finger bone found in a Siberian cave (SN: 6/5/10, p. 5; SN: 1/15/11, p.10).

But those researchers had DNA from fossils to guide their research. This time, researchers led by Sarah Tishkoff at the University of Pennsylvania in Philadelphia didn’t have fossil DNA, or even fossils.

Tishkoff’s group took DNA donated by 15 African hunter-gatherers — five Pygmies from Cameroon and five Hadza and five Sandawe from Tanzania— and compiled complete genetic blueprints for each person.
Population geneticist Joshua Akey of the University of Washington and his colleagues helped analyze the data.

Using a statistical analysis, the team determined that about 2 percent of the DNA from the hunter-gatherers came from an unknown species of hominid that split from modern human ancestors about 1.1 million years ago. These long-lost human cousins must have then interbred with modern humans sometime before the common ancestral lineage of the three hunter-gatherer groups separated about 30,000 to 70,000 years ago, Akey says.

A separate study posted online July 23 on arXiv.org examined patterns of single DNA unit changes, known as SNPs, in 22 African groups. That study, by Joseph Pickrell of Harvard Medical School and colleagues, also presents evidence that some African groups, including the Hadza, may harbor DNA from unknown extinct hominids.

Other researchers aren’t convinced that the DNA remnants identified are the genetic remains of a new species of human cousin. The DNA could have come from a genetically distinct group of modern humans that has since died out due to changes in their environment, diseases or confrontations with rival groups of humans, says Jean-Jacques Hublin, a paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Relatively recent interbreeding isn’t the only explanation for the presence of this newly discovered DNA, says anthropological geneticist Paul Verdu of Stanford University. He thinks the DNA may be the genetic stamp left by a common ancestor of modern humans and another species.
The DNA may have morphed so much in non-African groups, just by chance, that it is now unrecognizable.

Early humans in Africa mated with a mystery species of human that may have been related to Neanderthals that later inhabited Europe, genetic studies show.

No fossil evidence of the previously unknown humans exists, researchers said, but they left their mark in bits of foreign DNA in modern-day African populations.

The existence of that genetic material in modern human populations is proof of interbreeding between the two species, probably 20,000 to 50,000 years ago, they said.

"Geneticists like euphemisms, but we're talking about sex," Joshua Akey of the University of Washington in Seattle told The Washington Post.

Akey's lab identified the mystery DNA in three groups of modern Africans.

"We're calling this a Neanderthal sibling species in Africa," Akey said.

The time of the interbreeding would have been long after some modern humans had walked out of Africa to colonize Asia and Europe, he said, and around the same time Neanderthals were on the decline in Europe.

Present-day Europeans show no evidence of the foreign DNA, suggesting the mystery people were likely confined to Africa, he said.

While modern humans and the newly found "archaic" Africans might be classified as distinct species, they managed to produce viable offspring, Akey said.

"They had to be similar enough in appearance to anatomically modern humans that reproduction would happen," Akey said.

However, with no fossils in hand, he acknowledged, it's impossible to say what these people looked like.

The consensus today is that the Skhul-Qafzeh hominins were a dead-end, although a significant portion of the sub-Saharan gene pool seems to come from them or from a related population.

Human Y Chromosome Much Older Than Previously Thought

Mar. 4, 2013 — The discovery and analysis of an extremely rare African American Y chromosome pushes back the time of the most recent common ancestor for the Y chromosome lineage tree to 338,000 years ago. This time predates the age of the oldest known anatomically modern human fossils.

University of Arizona geneticists have discovered the oldest known genetic branch of the human Y chromosome -- the hereditary factor determining male sex.

The new divergent lineage, which was found in an individual who submitted his DNA to Family Tree DNA, a company specializing in DNA analysis to trace family roots, branched from the Y chromosome tree before the first appearance of anatomically modern humans in the fossil record.

The results are published in the American Journal of Human Genetics.

"Our analysis indicates this lineage diverged from previously known Y chromosomes about 338,000 ago, a time when anatomically modern humans had not yet evolved," said Michael Hammer, an associate professor in the University of Arizona's department of ecology and evolutionary biology and a research scientist at the UA's Arizona Research Labs. "This pushes back the time the last common Y chromosome ancestor lived by almost 70 percent."

Unlike the other human chromosomes, the majority of the Y chromosome does not exchange genetic material with other chromosomes, which makes it simpler to trace ancestral relationships among contemporary lineages. If two Y chromosomes carry the same mutation, it is because they share a common paternal ancestor at some point in the past. The more mutations that differ between two Y chromosomes the farther back in time the common ancestor lived.

Originally, a DNA sample obtained from an African American living in South Carolina was submitted to the National Geographic Genographic Project. When none of the genetic markers used to assign lineages to known Y chromosome groupings were found, the DNA sample was sent to Family Tree DNA for sequencing. Fernando Mendez, a postdoctoral researcher in Hammer's lab, led the effort to analyze the DNA sequence, which included more than 240,000 base pairs of the Y chromosome.

Hammer said "the most striking feature of this research is that a consumer genetic testing company identified a lineage that didn't fit anywhere on the existing Y chromosome tree, even though the tree had been constructed based on perhaps a half-million individuals or more. Nobody expected to find anything like this."

About 300,000 years ago, the time the Neanderthals are believed to have split from the ancestral human lineage. It was not until more than 100,000 years later that anatomically modern humans appear in the fossil record. They differ from the more archaic forms by a more lightly built skeleton, a smaller face tucked under a high forehead, the absence of a cranial ridge and smaller chins.

Hammer said the newly discovered Y chromosome variation is extremely rare. Through large database searches, his team eventually was able to find a similar chromosome in the Mbo, a population living in a tiny area of western Cameroon in sub-Saharan Africa.

"This was surprising because previously the most diverged branches of the Y chromosome were found in traditional hunter-gatherer populations such as Pygmies and the click-speaking KhoeSan, who are considered to be the most diverged human populations living today."

"Instead, the sample matched the Y chromosome DNA of 11 men, who all came from a very small region of western Cameroon," Hammer said. "And the sequences of those individuals are variable, so it's not like they all descended from the same grandfather."

Hammer cautions against popular concepts of "mitochondrial Eve" or "Y chromosome Adam" that suggest all of humankind descended from exactly one pair of humans that lived at a certain point in human evolution.

"There has been too much emphasis on this in the past," he said. "It is a misconception that the genealogy of a single genetic region reflects population divergence. Instead, our results suggest that there are pockets of genetically isolated communities that together preserve a great deal of human diversity."

Still, Hammer said, "It is likely that other divergent lineages will be found, whether in Africa or among African-Americans in the U.S. and that some of these may further increase the age of the Y chromosome tree."

He added: "There has been a lot of hype with people trying to trace their Y chromosome to different tribes, but this individual from South Carolina can say he did it."

The study came about by combined efforts of a private business, Family Tree DNA, the efforts of a citizen scientist, Bonnie Schrack, and the research capabilities at the UA.