Neanderthal genome sequencing yields surprising results

Scientists with the US Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and the Joint Genome Institute (JGI) have sequenced genomic DNA from fossilised Neanderthal bones with surprising results.

Their results show that the genomes of modern humans and Neanderthals are at least 99.5% identical, but despite this genetic similarity, and that the two species cohabitated the same geographic region for thousands of years, there is no evidence of any significant crossbreeding between the two.

Based on these early results, Homo sapiens and Homo neanderthalensis last shared a common ancestor approximately 700,000 years ago.

A team of researchers led by Edward Rubin, director of both JGI and Berkeley Lab's Genomics Division, reports the development of a "Neanderthal metagenomic library', which they used to characterise more than 65,000 DNA base pairs of Neanderthal origin.

According to the team of researchers, the current state of our knowledge concerning Neanderthals and their relationship to modern humans is largely inference and speculation based on archaeological data and a limited number of hominid remains. In this study, they demonstrated that Neanderthal genomic sequences can be recovered using a metagenomic library-based approach, and that specific Neanderthal sequences can be obtained from such libraries.

"We predict that in the near future anthropologists will be able to develop hypotheses about our extinct ancestors through the scanning of billions of base pairs of DNA sequences available on the web rather than only being able to study the limited number of bony remains and associated artifacts that are available in hard-to-access museum collections and field sites. Plus, the new techniques we have developed will have useful applications across a range of genomics efforts related to DOE's energy and environment missions," Rubin said.

Comparing Neanderthal to human and chimpanzee genomes showed that at multiple locations the Neanderthal DNA sequences matched chimpanzee DNA but not human.

"This enabled us to calculate for the first time when in pre-history Homo sapiens and Homo neanderthalensis coalesced to a single genome," Rubin said.

Comparative genomics in this study indicated that the common genetic ancestor of Neanderthal and modern humans lived about 706,000 years ago. The ancestors of all humans and Neanderthals split into two separate species some 330,000 years later. Rubin and his colleagues were also able to shed new light on the long-standing question of whether Neanderthals and humans mated during the thousands of years the two species cohabitated parts of Europe. Some scientists have suggested that rather than die out, Neanderthals as a species were bred out of existence by the overwhelming populations of Homo sapiens.

"While unable to definitively conclude that interbreeding between the two species of humans did not occur, analysis of the nuclear DNA from the Neanderthal suggests the low likelihood of it having occurred at any appreciable level," Rubin said.

With their metagenomic library-based approach to genome sequencing and analysis, Rubin and Noonan believe that in the future, scientists will be able to study specific sequences within the Neanderthal genome to determine the genetic changes that distinguished modern humans from our Neanderthal cousins. Among other advantages, this might help answer the most persistent mystery of all: Why did Neanderthals become extinct?