Neanderthal genome reveals early human interbreeding and inbreeding

The most complete sequence to date of the Neanderthal genome, using DNA extracted from a woman's toe bone that dates back 50,000 years, reveals a long history of interbreeding among at least four different types of early humans living in Europe and Asia at that time, according to University of California, Berkeley, scientists.

Population geneticist Montgomery Slatkin, graduate student Fernando Racimo and post-doctoral student 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 recognized 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 research team estimates that between 1.5 and 2.1 percent 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 genomes of Australian aborigines, New Guineans and some Pacific Islanders are about six percent Denisovan genes, according to earlier studies. The new analysis finds that the genomes of Han Chinese and other mainland Asian populations, as well as of native Americans, contain about 0.2 percent 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.

“The paper really shows that the history of humans and hominins during this period was very complicated,” said Slatkin, a UC Berkeley professor of integrative biology. “There was lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered.”

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 (the offspring of two siblings who married siblings).

Further analyses suggest that the population sizes of Neanderthals and Denisovans were small and that inbreeding may have been more common in Neanderthal groups than in modern populations.

As part of the new study, Racimo was able to identify 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.

- MNT