Neanderthal genome project

File:Neandertaler reconst.jpg

Reconstruction of an adult Neanderthal

In July 2006, the Max Planck Institute for Evolutionary Anthropology in Germany and 454 Life Sciences in the United States announced that they would be sequencing the Neanderthal genome over the next several years. At roughly 3.2 billion base pairs, the Neanderthal genome is about the size of the modern human genome; according to preliminary sequences, modern human and Neanderthal DNA appear to be 99.5% identical. The researchers recovered ancient DNA of Neanderthals by extracting the DNA from the femur bone of a 38,000-year-old male Neanderthal specimen from Vindija Cave, Croatia, and also other bones found in Spain, Russia, and Germany. Only about half a gram of the bone samples was required for the sequencing, but the project faced many difficulties, including the contamination of the samples by the bacteria that had colonized the Neanderthal's body and humans who handled the bones at the excavation site and at the laboratory.

In 2006, two research teams working on the same Neanderthal sample published their results, "Green et al." in Nature, and "Noonan et al." in Science. The results were received with some criticism, mainly surrounding the issue of a possible admixture of Neanderthals into the modern human genome. The speech-related gene FOXP2 with the same mutations as in modern humans was discovered in ancient DNA in the El Sidron 1253 and 1351c specimens, suggesting Neanderthals might have shared some basic language capabilities with modern humans.

In February 2009, the research team, led by geneticist Svante Pääbo, announced that they had completed the first draft of the Neanderthal genome, which covers about 63% of the entire base pairs. New results suggested that adult Neanderthals were lactose intolerant. As for the possibility of cloning a Neanderthal, Pääbo commented, "Starting from the DNA extracted from a fossil, it is and will remain impossible."

Project results

Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany

The group of "Green et al." used a new sequencing technique that amplifies single molecules for characterization and obtained over a quarter-million unique sequences. Co-author Svante Pääbo directly sequenced the Neanderthal nuclear DNA genome. Since direct sequencing is random, one must wait for specific sequences for genes that might be different between modern humans and Neanderthals to show in the process. Direct sequencing destroys the original sample, so in principle, the metagenomic library approach will retain a clone of the Neanderthal DNA forever, for future targeted research.

The group of "Noonan et al." (including Rubin) used a different technique, one in which the Neanderthal DNA is inserted into bacteria, which make multiple copies of a single fragment. It is a slower technique and only 65,000 bases were sequenced, but the same DNA can be obtained from the bacteria as needed and thus allows for a higher degree of error correction. They demonstrated that Neanderthal genomic sequences can be recovered using a metagenomic library-based approach. All of the DNA in the sample is "immortalized" into metagenomic libraries. A DNA fragment is selected, then propagated in microbes. The Neanderthal DNA can be sequenced or specific sequences can be studied.

Overall, their results were remarkably similar. One group suggested there was a hint of mixing between human and Neanderthal genomes, while the other found none, but both recognize that the data set is just not large enough to give a definitive answer.

The publication of "Noonan et al." revealed Neanderthal DNA sequences matching chimpanzee DNA, but not modern human DNA at multiple locations, thus enabling the first accurate calculation of the date of the most recent common ancestor of H. sapiens and H. neanderthalensis. The research team estimates the most recent common ancestor of their H. neanderthalensis samples and their H. sapiens reference sequence lived 706,000 (divergence time), estimating the separation of the human and Neanderthal ancestral populations to 370,000 years ago (split time).

Earlier mitochondrial DNA research led by Svante Pääbo in 1997 had indicated archaic Homo sapiens and Neanderthals broke into separate lineages approximately 500,000 years ago (split time).

"Green et al." calculated a divergence time of 516,000 years ago and do not indicate a split, while they claim the average divergence time between alleles within humans is thus 459,000 years with a 95% confidence interval between 419,000 and 498,000 years:

"Neanderthal genetic differences to humans must therefore be interpreted within the context of human diversity."

"Noonan et al.", on the other hand, found no evidence of Neanderthal admixture to the modern human genome, but they cannot preclude admixture of up to 20% with a certainty better than 95%, and hence do not claim to present a definite answer to the question.

Criticism

Svante Pääbo, the director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology and the Neanderthal genome project

A review of the data by Wall and Kim in 2007, reanalyses the data obtained from the published papers of Noonan et al. and Green et al., and holds the results are inconsistent with each other. The review proposes serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.

The reanalyses confirmed both results to the Human-Neanderthal DNA Sequence Divergence Time (common ancestor), that is 706 kya (thousands of years ago) to the Noonan et al. analysis and 516 kya to the Green et al. analysis. The modern European-Neanderthal population split time was estimated at 35 kya for the Green et al. data, and 325 kya for the Noonan et al. data. Before, no split time was estimated by the Green et al. study, and according to Wall and Kim the split time originally estimated by Noonan et al. was even higher: 440 kya (the Noonan et al. paper mentions 370 kya).

While Noonan et al. were unable to definitively conclude that interbreeding between the two species of humans did not occur, they proclaim little likelihood of it having occurred at any appreciable level. The study opts for a 0% contribution of Neanderthal DNA to the modern European gene pool, based on the 95% confidence interval that indicates a margin between 0% and 20% contribution. The reanalyses of Wall and Kim yielded interbreeding margins between 0% and 39% to the data of Noonan et al., and margins between 81% and 100% to the data of Green et al. These vastly inconsistent results could only be reconciled by assuming a very recent split time between the two populations of 60 kya or less. However, such a recent split time would not be consistent with the estimated modern European-Neanderthal population split time from the Noonan et al. data.

The key assumption of Noonan et al. is that the 38,000 years of fossilisation suffered by the Neanderthal DNA should have the genome analysis focus on ancient DNA fragments of about 50 to 70 base pairs in length. Green et al. do not make such an assumption; they generalized towards the exclusion of modern human nuclear DNA contamination by finding little evidence of modern human mtDNA contamination. Such mitochondrial DNA tends to remain preserved longer than nuclear DNA. However, Wall and Kim noted a length dependence of the results, having the small fragments pointing to a divergence time similar to the results of Noonan et al. and the large fragments much more similar on average to modern human DNA - even to the extent of indicating an estimated human-Neanderthal sequence divergence time that is less than the estimated divergence time of two extant members of one referenced population in West Africa. Although Wall and Kim hold modern human contamination to be size-biased, since Neanderthal DNA would be expected to have a tendency to be degraded into short fragments, they noted that length dependence of the results means that alignment issues alone are unlikely to be a sufficient explanation, since longer fragments would be easier to align and thus the data from longer fragments should be more accurate. Still they mark this as a signal of potential contamination in the data of Green et al. No similar signal of potential contamination was found in the data of Noonan et al.

Contamination in the data of Green et al. should have decreased the Neanderthal-specific sequence divergence in this study. Since this is not the case, the assumption of contamination also would indicate a higher sequencing error rate in the Green et al. data, since sequence errors would look the same as Neanderthal-specific mutations. It should be noted that these Neanderthal-specific mutations already were considered prone to error due to post-mortem DNA damage in both studies, and were excluded from the results.

In summary, Wall and Kim consider a model with 78% contamination more likely than a model with no contamination and 94% admixture.

See also

• Neanderthal
• Neanderthal extinction hypotheses

Further reading

• Green, Richard E. (2008-08-08). "A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing" (PDF). Cell. 134. Elsevier: 416–426. doi:10.1016/j.cell.2008.06.021. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)

External links

• "Genetic algorithm model shows that modern humans out-competed the Neanderthal" Short summary of a peer review paper 2008
• "Last of the Neanderthals" National Geographic, October 2008
• MSNBC "Neanderthal genome project launches" 22 November 2006.
• BBC News Paul Rincon, "Neanderthal DNA secrets unlocked" 15 November 2006
• "Welcome to Neanderthal genomics" 17 November 2006
• "Neanderthal Genome Sequencing Yields Surprising Results and Opens a New Door to Future Studies" 15 November 2006