Neanderthal genome shows high levels of inbreeding

Matt Celesky

A 50,000 year old Neanderthal toe bone provided the most thorough neanderthal genome sequenced yet, and showed that the individual was highly inbred. Today’s announcement comes from Svante Pääbo of UC Berkeley along with an extensive international team and was published today in Nature.

Genetic analysis of the bone that was discovered in the Altai Mountains of Siberia turned out to be the most detailed genome ever recovered for a Neanderthal. With this information, they found that the toe belonged to a female who was heavily inbred

Her parents were likely very closely related, and this could have come from a variety of relationships. It is possible that her parents were half siblings with the same mother, an uncle and a niece (or an aunt and a nephew), or a grandparent and a grandchild. The researchers also found evidence that this was not an isolated incident, as many of her ancestors were similarly related. The inbreeding might have been due to the fact that Neanderthals typically lived in very small populations when compared to other earlier human species.

Because the genome was so complete, the study compared 87 similar genes between modern humans, Denisovans, and Neanderthals. The team found that there were significant differences between modern humans and the two extinct species and the differences discovered may help researchers understand why our species persisted where theirs went extinct a long time ago. 

The research also reconfirms earlier reports of Neanderthals interbreeding among different human species, including modern humans, Denisovans, and a fourth group that has not yet been identified, though it was not rampant. Researchers speculate that humans and Neanderthals coexisted for about 30,000 years in the late Pleistocene. Unfortunately, the extent of the relationship cannot be determined with current evidence. Though it is clear there was not extensive interbreeding, it becomes less clear how it happened in the first place. It is possible that an ancient Neanderthal group got involved with humans as an isolated incident, or breeding might have occurred sporadically over time. 

As genetic sequencing of ancient genomes becomes more refined and if we are able to obtain similarly-complete sequences from Neanderthals in different areas, researchers will be able to determine if all Neanderthals were as heavily inbred as this individual was. If most Neanderthals lived this way, it is possible that inbreeding depression may have been at least partially responsible for the species’ demise, as they would not have had a wide range of alleles to deal with environmental pressures.

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