To learn more about DNA and genetics in general we recommend a site called DNA from the Beginning, found at http://www.dnaftb.org/dnaftb/. This site offers a wealth of information about both topics.

Ancient DNA has been successfully extracted several times from hominin fossils; they were all Neanderthal bones. The primary challenge is that when an organism dies, water, oxygen and microbes start degrading DNA. Within 50,000 to 100,000 years, all the DNA is gone. Therefore, extracting DNA from any hominins older than Neanderthals and Homo sapiens is currently impossible. Also, the DNA that is extracted is fragmentary and damaged. Another concern is contamination of the ancient DNA with modern DNA.

Hominin mitochondrial DNA, or mtDNA, was first extracted from a Neanderthal in 1997. The bone was from the first Neanderthal fossil recognized by scientists, from a cave in the Neander valley in Germany. To avoid contamination, the extraction was performed in a lab where no modern DNA had been processed. A small sample of the bone was ground up to extract the mtDNA. Polymerase chain reaction (PCR) was used to amplify the mtDNA segments before sequencing it.

The sequences obtained showed substantial differences from modern human mtDNA and various experiments were conducted to exclude the possibility that the sequence was the result of contamination. The results of these tests showed that the mtDNA had come from the Neanderthal fossil. Researchers then began to compare the sequence to modern human and chimpanzee sequences. Most human sequences differ from each other by 8.0 ± 3.1 substitutions, while the human and chimpanzee sequences differ by 55.0 ± 3.0 substitutions. The Neanderthal and modern human sequences differed by 27.2 ± 2.2 substitutions.

In 2000, a second successful Neanderthal extraction was published. This sequence came from the well-dated remains of a Neanderthal infant found in the northern Caucasus. The remains date to approximately 29,000 years ago, which is around the time that Neanderthals were thought to have been replaced by modern humans. The analysis of the infant sequences corroborated the earlier results by showing more sequence differences than found within modern human samples. This sequence showed 22 substitutions compared with modern sequences.

The third Neanderthal sequence (published in 2000) came from the Vindija fossil remains, which date to approximately 33,000 years ago. The three sequences do not contain enough divergence for Homo sapiens to be included within a Neanderthal group. Therefore, the Neanderthals would not have contributed significantly to the modern gene pool.

The analysis shows an evolutionary divergence between modern human mtDNA and Neanderthal mtDNA prior to 550,000 years ago. Upon breaking down the 994 modern human sequences used into different geographical localities, researchers found that the Neanderthal sequences were no more similar to modern human sequences from any one locality. If Neanderthals had evolved into modern humans in Europe, then a greater similarity between Neanderthal and European sequences would be expected. However, this is not the case, and the genetic evidence corroborates fossil and archaeological evidence showing a distinct separation between Neanderthals and populations ancestral to modern Homo sapiens.