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Heritage, the interbreeding controversy, and brain capacity are described.
On November 16, 2006, Science Daily published an interview that suggested
that Neanderthals and ancient humans probably did not interbreed. Edward M.
Rubin, director of the U.S. Department of Energy’s Lawrence Berkeley
National Laboratory and the Joint Genome Institute (JGI), sequenced a
fraction (0.00002) of genomic nuclear DNA (nDNA) from a 38,000-year-old
Vindia Neanderthal femur bone. They calculated the common ancestor to be
about 353,000 years ago, and a complete separation of the ancestors of the
species about 188,000 years ago. Their results show the genomes of modern
humans and Neanderthals are at least 99.5% identical, but despite this
genetic similarity, and despite the two species having coexisted in the same
geographic region for thousands of years, Rubin and his team did not find
any evidence of any significant crossbreeding between the two. Rubin said,
“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
A main proponent of the interbreeding hypothesis is Erik Trinkaus of
Washington University. In a 2006 study published in Proceedings of the
National Academy of Sciences, Trinkaus and his co-authors report a
possibility that Neanderthals and humans did interbreed. The study claims to
settle the extinction controversy; according to researchers, the human and
neanderthal populations blended together through sexual reproduction.
Trinkaus states, "Extinction through absorption is a common phenomenon."
and "From my perspective, the replacement vs. continuity debate that raged
through the 1990s is now dead". 4 amino acid substitutions in mtDNA
translated changed COX2 protein of Cytochrome c oxidase subunit II.
Recently, Richard E. Green et al. from Max Planck Institute for Evolutionary
Anthropology published the full sequence of Neanderthal mitochondrial DNA
(mtDNA) and suggested that "Neandertals had a long-term effective population
size smaller than that of modern humans."  While reporting in Nature
Journal about the same publication, James Morgan asserted that the mtDNA
sequence contained clues that Neanderthals lived in "small and isolated
populations, and probably did not interbreed with their human neighbours." 
There is a possibility Neanderthals and Cro-Magnons interbred but left
little genetic evidence. There is an ongoing debate about whether the
hunter-gatherers of the middle stone age started farming when they came in
contact with agriculture, or were completely replaced by the farmers moving
in from the Middle East. If modern Europeans are mainly descendants of these
farming people with little or no genetic input from the foragers of the
middle stone age, then possible interbreeding between them and the
Neanderthals would not have had a great effect on the modern gene pool.