Neanderthal Y Chromosome Not Seen in Men

Modern men have no traces of Neanderthal DNA on their Y chromosome, the first-ever analysis of the male Neanderthal sex chromosome has revealed.

The disappearance of the Neanderthal Y chromosome may be due to genetic incompatibilities between the two species that led to miscarriages, suggests a study published today in the American Journal of Human Genetics.

The Y chromosome is passed exclusively from father to son.

Until now, all sequencing of the Neanderthal genome had been done on females because those happened to be the specimens that provided enough good-quality DNA, the study's lead author, Dr. Fernando Mendez of Stanford University, said.

"Characterising the Neanderthal Y chromosome helps us to better understand the population divergence that led to Neanderthals and modern humans," he said.

"It also enables us to explore possible genetic interactions between archaic and modern variants within hybrid offspring."

It is widely known that modern non-Africans have around 2.5 to 4 per cent Neanderthal DNA in their genes, but the Y chromosome is special, Dr Mendez said.

"Either you get the whole Y chromosome, or you get nothing," he said.

Analysis compared ancient and modern Y chromosomes Dr Mendez and his colleagues compared the Y chromosome of a 49,000 year-old Neanderthal male found in El Sidron in Spain, with the Y chromosome from two modern humans.

Their analysis supports earlier data that estimated Neanderthals and modern humans diverged from their common ancestor around 588,000 years ago.

They also found the Neanderthal Y chromosome was distinct from any Y chromosome observed in modern humans, suggesting the lineage is extinct.

The researchers then searched for evidence that would explain why the Neanderthal Y chromosome disappeared.

"The Y chromosome has a number of genes that are specific for male functions, like making sperm, so we said maybe we'd find something in one of those, but we didn't," Dr Mendez said.

These genes did contain mutations that distinguished Neanderthals from modern humans, but none would have adversely affected their function.

But the team identified mutations on three genes on the Neanderthal Y chromosome connected to immune factors called the minor histocompatibility antigens.

When these antigens, which are only found in males, are mismatched they can cause women to reject organ transplants from men as well as have miscarriages after the birth of their first child, Mendez said.

This may have had serious consequences for the offspring of Neanderthal and modern human interbreeding; a male foetus could have sensitised his mother's immune system so any subsequent male offspring would be at greatly increased risk of being miscarried.

"If they have fewer boys than other couples, then systematically boys are likely to have fewer boys," said Mendez.

Over time the Neanderthal Y chromosome would be lost in favour of the modern human Y chromosome.

However, Mendez stressed this was still only a hypothesis.

"The amount of Neanderthal DNA in modern humans nowadays is relatively low so it could have been lost by drift," he said.

But reduced fertility or viability of hybrid offspring with Neanderthal Y chromosomes is consistent with an observation known as Haldane's rule.

"Haldane's rule says basically that when you have a cross of differential populations, the male offspring are the ones that have more trouble," Mendez said.

Mendez said he hoped other Neanderthal samples would reveal more about the Neanderthal man.

More From ABC Science:

Genetic map reveals impact of interbreeding with cavemen DNA indicates humans left Africa and had sex with Neanderthals earlier than thought Genetic map reveals impact of interbreeding with ancient Denisovans and Neanderthals This story originally appeared on ABC Science.

The Neanderthal Y chromosome was distinct from any Y chromosome observed in modern humans.

Back in the Beginning

To put a human face on our ancestors, scientists from the Senckenberg Research Institute used sophisticated methods to form 27 model heads based on tiny bone fragments, teeth and skulls collected from across the globe. The heads are on display for the first time together at the Senckenberg Natural History Museum in Frankfurt, Germany. This model is Sahelanthropus tchadensis, also nicknamed "Toumai," who lived 6.8 million years ago. Parts of its jaw bone and teeth were found nine years ago in the Djurab desert in Chad. It's one of the oldest hominid specimens ever found.

Australopithecus afarensis

With each new discovery, paleoanthropologists have to rewrite the origins of man's ancestors, adding on new branches and tracking when species split. This model was fashioned from pieces of a skull and jaw found among the remains of 17 pre-humans (nine adults, three adolescents and five children) which were discovered in the Afar Region of Ethiopia in 1975. The ape-man species, Australopithecus afarensis, is believed to have lived 3.2 million years ago. Several more bones from this species have been found in Ethiopia, including the famed "Lucy," a nearly complete A. afarensis skeleton found in Hadar.

Australopithecus africanus

Meet "Mrs. Ples," the popular nickname for the most complete skull of an Australopithecus africanus, unearthed in Sterkfontein, South Africa in 1947. It is believed she lived 2.5 million years ago (although the sex of the fossil is not entirely certain). Crystals found on her skull suggest that she died after falling into a chalk pit, which was later filled with sediment. A. africanus has long puzzled scientists because of its massive jaws and teeth, but they now believe the species' skull design was optimal for cracking nuts and seeds.

Paranthropus aethiopicus

The skull of this male adult was found on the western shore of Lake Turkana in Kenya in 1985. The shape of the mouth indicates that he had a strong bite and could chew plants. He is believed to have lived in 2.5 million years ago and is classified as Paranthropus aethiopicus. Much is still unknown about this species because so few reamins of P. aethiopicus have been found.

Paranthropus boisei

Researchers shaped this skull of "Zinj," found in 1959. The adult male lived 1.8 million years ago in the Olduvai Gorge of Tanzania. His scientific name is Paranthropus boisei, though he was originally called Zinjanthropus boisei -- hence the nickname. First discovered by anthropologist Mary Leakey, the well-preserved cranium has a small brain cavity. He would have eaten seeds, plants and roots which he probably dug with sticks or bones.

Homo rudolfensis

This model of a sub-human species -- Homo rudolfensis -- was made from bone fragments found in Koobi Fora, Kenya, in 1972. The adult male is believed to have lived about 1.8 million years ago. He used stone tools and ate meat and plants. H. Rudolfensis' distinctive features include a flatter, broader face and broader postcanine teeth, with more complex crowns and roots. He is also recognized as having a larger cranium than his contemporaries.

Homo ergaster

The almost perfectly preserved skeleton of the "Turkana Boy" is one of the most spectacular discoveries in paleoanthropology. Judging from his anatomy, scientists believe this Homo ergaster was a tall youth about 13 to 15 years old. According to research, the boy died beside a shallow river delta, where he was covered by alluvial sediments. Comparing the shape of the skull and teeth, H. ergaster had a similiar head structure to the Asian Homo erectus.

Homo heidelbergensis

This adult male, Homo heidelbergensis, was discovered in in Sima de los Huesos, Spain in 1993. Judging by the skull and cranium, scientists believe he probably died from a massive infection that caused a facial deformation. The model, shown here, does not include the deformity. This species is believed to be an ancestor of Neanderthals, as seen in the shape of his face. "Miquelon," the nickname of "Atapuerca 5", lived about 500,000 to 350,000 years ago and fossils of this species have been found in Italy, France and Greece.

Homo neanderthalensis

The "Old Man of La Chapelle" was recreated from the skull and jaw of a Homo neanderthalensis male found near La Chapelle-aux-Saints, in France in 1908. He lived 56,000 years ago. His relatively old age, thought to be between 40 to 50 years old, indicates he was well looked after by a clan. The old man's skeleton indicates he suffered from a number of afflictions, including arthritis, and had numerous broken bones. Scientists at first did not realize the age and afflicted state of this specimen when he was first discovered. This led them to incorrectly theorize that male Neanderthals were hunched over when they walked.

Homo floresiensis

The skull and jaw of this female "hobbit" was found in Liang Bua, Flores, Indonesia, in 2003. She was about 1 meter tall (about 3'3") and lived about 18,000 years ago. The discovery of her species, Homo floresiensis, brought into question the belief that Homo sapiens was the only form of mankind for the past 30,000 years. Scientists are still debating whether Homo floresiensis was its own species, or merely a group of diseased modern humans. Evidence is mounting that these small beings were, in fact, a distinct human species.

Homo sapiens

Bones can only tell us so much. Experts often assume or make educated guesses to fill in the gaps in mankind's family tree, and to develop a sense what our ancestors may have looked like. Judging from skull and mandible fragments found in a cave in Israel in 1969, this young female Homo sapien lived between 100,000 and 90,000 years ago. Her bones indicate she was about 20 years old. Her shattered skull was found among the remains of 20 others in a shallow grave.