Most complete Neanderthal genome shows inbreeding

The most complete sequence to date of the Neanderthal genome suggests they inbred with their family members while occasionally interbreeding with modern humans, a new study has found.
The study, that used DNA extracted from a woman's toe bone that dates back 50,000 years, also reveals a long history of interbreeding among at least four different types of early humans living in Europe and Asia at that time.
University of California, Berkeley, scientists Montgomery Slatkin, Fernando Racimo and Flora Jay were part of an international team of anthropologists and geneticists who generated a high-quality sequence of the Neanderthal genome and compared it with the genomes of modern humans and a recently recognised group of early humans called Denisovans.

The comparison shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago. Neanderthals and Denisovans split about 300,000 years ago.
Though Denisovans and Neanderthals eventually died out, they left behind bits of their genetic heritage because they occasionally interbred with modern humans.
The team estimates between 1.5 and 2.1 per cent of the genomes of modern non-Africans can be traced to Neanderthals.

Denisovans also left genetic traces in modern humans, though only in some Oceanic and Asian populations.
The analysis finds that the genomes of Han Chinese and other mainland Asian populations, as well as of native Americans, contain about 0.2 per cent Denisovan genes.

The genome comparisons also show that Denisovans interbred with a mysterious fourth group of early humans also living in Eurasia at the time.
That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia a million or more years ago.
In another analysis, Jay discovered that the Neanderthal woman whose toe bone provided the DNA was highly inbred.
The woman's genome indicates that she was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins, scientists said.

Researchers also identified at least 87 specific genes in modern humans that are significantly different from related genes in Neanderthals and Denisovans, and that may hold clues to the behavioural differences distinguishing us from early human populations that died out.
The study was published in the journal Nature.