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 a University of California, Berkeley, team of scientists.
     The team of anthropologists and geneticists 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 Neantherthals. Denisovans also left genetic traces in modern humans: the genomes of Australian aborigines, New Guineans and some Pacific Islanders are about 6 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, the fossils of which indicate their presence 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 Montgomery Slatkin, a UC Berkeley professor of integrative biology. "There was a lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered."
     In another analysis, post-doctoral student Flora 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.
     Slatkin noted that no one is sure how long the various now-extinct groups lasted, but there is evidence that Neanderthals and modern humans coexisted in Europe and Asia for at least 30,000 years. "We don't know if interbreeding took place once, where a group of Neanderthals got mixed in with modern humans, and it didn't happen again, or whether groups lived side by side, and there was interbreeding over a prolonged period," he said.

Edited from Popular Archaeology (18 December 2013)