Neanderthal genome project

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The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.

It was initiated by 454 Life Sciences, a biotechnology company based in Branford, Connecticut in the United States and is coordinated by the Max Planck Institute for Evolutionary Anthropology in Germany. In May 2010 the project published their initial draft of the Neanderthal genome based on the analysis of four billion base remain in modern humans outside Africa.[1][2][3]

In December 2013, a high coverage genome of a Neanderthal was reported for the first time. It stemmed from a Neanderthal female bone fragment found in a cave in the Altai mountains of Siberia from around 50,000–100,000 years ago.[4][5]

Findings[edit]

The researchers recovered ancient DNA of Neanderthals by extracting the DNA from the femur bones of three 38,000 year-old female Neanderthal specimens from Vindija Cave, Croatia, and other bones found in Spain, Russia, and Germany.[6] Only about half a gram of the bone samples (or 21 samples each 50–100 mg[1]) 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.[7]

In February 2009, the Max Planck Institute's team led by Pääbo announced that they had completed the first draft of the Neanderthal genome.[7] An early analysis of the data suggested in "the genome of Neanderthals, a human species driven to extinction" "no significant trace of Neanderthal genes in modern humans".[8] New results suggested that some adult Neanderthals were lactose intolerant.[9] On the question of potentially cloning a Neanderthal, Pääbo commented, "Starting from the DNA extracted from a fossil, it is and will remain impossible."[7]

In May 2010, the project released a draft of their report on the sequenced Neanderthal genome. Contradicting the results discovered while examining mitochondrial DNA, they demonstrated a range of genetic contribution to non-African modern humans ranging from 1% to 4%. From their Homo sapiens samples in Eurasia (French, Han Chinese and Papuan) the authors stated that it is likely that interbreeding occurred in the Levant before Homo sapiens migrated into Europe.[10] This finding is disputed because of the paucity of archeological evidence supporting their statement. The fossil evidence does not conclusively place Neanderthals and modern humans in close proximity at this time and place.[11] According to preliminary sequences from 2010, 99.7% of the nucleotide sequences of the modern human and Neanderthal genomes are identical, compared to humans sharing around 98.8% of sequences with the chimpanzee.[12] (For some time, studies concerning the commonality between chimps and humans modified the commonality of 99% to a commonality of only 94%, showing that the genetic gap between humans and chimpanzees was far larger than originally thought,[13][14] but more recent knowledge states the difference between humans, chimpanzees, and bonobos at just about 1.0%–1.2% again.[15][16])

Additionally, in 2010, the discovery and analysis of Mitochondrial DNA (mtDNA) from the Denisova hominin in Siberia revealed that it differed from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. Analysis of the specimen's nuclear DNA was then still under way and expected to clarify whether the find is a distinct species.[17][18] Even though the Denisova hominin's mtDNA lineage predates the divergence of modern humans and Neanderthals, coalescent theory does not preclude a more recent divergence date for her nuclear DNA.

A rib fragment from the partial skeleton of a Neanderthal infant found in the Mezmaiskaya cave in the northwestern foothills of the Caucasus Mountains was radiocarbon-dated in 1999 to 29,195±965 B.P., and therefore belonging to the latest lived Neanderthals. Ancient DNA recovered for a mtDNA sequence showed 3.48% divergence from that of the Feldhofer Neanderthal, some 2,500 km to the west in Germany and in 2011 Phylogenetic analysis placed the two in a clade distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool.[19]

In 2015, Israel Hershkovitz of Tel Aviv University reported that a skull found in a cave in northern Israel, is "probably a woman, who lived and died in the region about 55,000 years ago, placing modern humans there and then for the first time ever", pointing to a potential time and location when modern humans first interbred with Neanderthals.[20]

In 2016, the project found that Neanderthals bred with modern humans multiple times, and that Neanderthals interbred with Denisovans only once, as evidenced in the genome of modern-day Melanesians.[21]

History 2006-2007[edit]

In 2006, two research teams working on the same Neanderthal sample published their results, Richard Green and his team in Nature,[22] and James Noonan's team in Science.[23] The results were received with some scepticism, mainly surrounding the issue of a possible admixture of Neanderthals into the modern human genome.[24]

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

In 2006, Richard Green's team had used a then new sequencing technique developed by 454 Life Sciences that amplifies single molecules for characterization and obtained over a quarter of a million unique short sequences ("reads"). The technique delivers randomly located reads, so that sequences of interest – genes that differ between modern humans and Neanderthals – show up at random as well. However, this form of direct sequencing destroys the original sample so to obtain new reads more samples must be destructively sequenced.[25]

Noonan's team, led by Edward Rubin, used a different technique, one in which the Neanderthal DNA is inserted into bacteria, which make multiple copies of a single fragment. 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.[clarification needed][25]

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 teams recognized that the data set was not large enough to give a definitive answer.[24]

The publication by Noonan, and his team 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 years ago (divergence time), estimating the separation of the human and Neanderthal ancestral populations to 370,000 years ago (split time).

"Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor ~706,000 years ago, and that the human and Neanderthal ancestral populations split ~370,000 years ago, before the emergence of anatomically modern humans."

— Noonan et al. (2006)[23]

Earlier mitochondrial DNA research led by geneticist Svante Pääbo in 1997 had indicated present day Homo sapiens and Neanderthals mtDNA split into separate lineages approximately 500,000 years ago.[citation needed]

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. These two dates (both ~500,000) were calculated with assumption on non-selective pressure. If positive selection forced mtDNA changes then the split time may be shorter. In this study, the team stated:

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

[citation needed]

On the other hand, Noonan et al. found no evidence of Neanderthal admixture to the modern human genome, but they did not preclude admixture of up to 20% with a certainty better than 95%, and hence did not claim to present a definite answer to the question.[citation needed]

In 2007, speech-related gene FOXP2 mutations identical to those in modern humans were discovered in Neanderthal DNA from the El Sidrón 1253 and 1351c specimens,[26] suggesting Neanderthals might have shared some basic language capabilities with modern humans.[9]

See also[edit]

General:

References[edit]

  1. ^ a b Green RE, Krause J, Briggs AW, et al. (May 2010). "A draft sequence of the Neandertal genome" (PDF). Science. 328 (5979): 710–722. doi:10.1126/science.1188021. PMC 5100745Freely accessible. PMID 20448178. 
  2. ^ The Neanderthal in Us
  3. ^ "Neandertal DNA may raise risk for some modern human diseases". Science News. Retrieved 2016-02-15. 
  4. ^ Zimmer, Carl (18 December 2013). "Toe Fossil Provides Complete Neanderthal Genome". New York Times. Retrieved 18 December 2013. 
  5. ^ Prüfer, Kay; et al. (18 December 2013). "The complete genome sequence of a Neanderthal from the Altai Mountains". Nature. 505: 43–49. Bibcode:2014Natur.505...43P. doi:10.1038/nature12886. PMC 4031459Freely accessible. PMID 24352235. Retrieved 18 December 2013. 
  6. ^ "Scientists Decode Majority of Neanderthal Man's Genome". Deutsche Welle. 13 February 2009. 
  7. ^ a b c McGroarty, Patrick (12 February 2009). "Team in Germany maps Neanderthal genome". The Associated Press. 
  8. ^ Wade, Nicholas (12 February 2009). "Scientists in Germany Draft Neanderthal Genome". The New York Times. Retrieved 20 May 2010. 
  9. ^ a b Inman, Mason (12 February 2009). "Neanderthal Genome "First Draft" Unveiled". National Geographic News. 
  10. ^ Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S (7 May 2010). "Draft full sequence of Neanderthal Genome". Science. Science Mag. 328: 710–22. doi:10.1126/science.1188021. PMC 5100745Freely accessible. PMID 20448178. 
  11. ^ Wade, Nicholas (6 May 2010). "Signs of Neanderthals Mating With Humans". The New York Times. 
  12. ^ Than, Ker (6 May 2010). "Neanderthals, Humans Interbred—First Solid DNA Evidence". National Geographic Society. Retrieved 9 May 2010. 
  13. ^ Cohen, Jon (29 June 2007). "Relative Differences: The Myth of 1%" (PDF). AAAS. 
  14. ^ "Humans and Chimps: Close But Not That Close". Scientific American. 2006-12-19. Retrieved 2006-12-20. 
  15. ^ Wong, Kate (1 September 2014). "Tiny Genetic Differences between Humans and Other Primates Pervade the Genome". Scientific American. Retrieved 12 October 2016. 
  16. ^ Gibbons, Ann (13 June 2012). "Bonobos Join Chimps as Closest Human Relatives". Science/AAAS. 
  17. ^ Brown, David (March 25, 2010). "DNA from bone shows new human forerunner, and raises array of questions". Washington Post. 
  18. ^ Krause J, Fu Q, Good JM, et al. (April 2010). "The complete mitochondrial DNA genome of an unknown hominin from southern Siberia". Nature. 464 (7290): 894–897. doi:10.1038/nature08976. PMID 20336068. 
  19. ^ Igor V. Ovchinnikov; Anders Götherström; Galina P. Romanova; Vitaliy M. Kharitonov; Kerstin Lidén; William Goodwin (30 March 2000). "Molecular analysis of Neanderthal DNA from the northern Caucasus". Letters to Nature. Nature 404. 404: 490–493. doi:10.1038/35006625. Retrieved 13 March 2011. 
  20. ^ Skull discovery suggests location where humans first had sex with Neanderthals The Guardian, 28 January 2015
  21. ^ Vernot B., Tucci S., Kelso J., Schraiber J. G., Wolf A. B., Gittelman R. M., Dannemann M., Grote S., McCoy R. C., Norton H., Scheinfeldt L. B., Merriwether D. A., Koki G., Friedlaender J. S., Wakefield J., Paabo S., Akey J. M. (2016). "Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals". Science. 352: 235–239. doi:10.1126/science.aad9416. 
  22. ^ Green, Richard E.; et al. (16 November 2006). "Analysis of one million base pairs of Neanderthal DNA" (PDF). Nature. 444 (7117): 330–336. doi:10.1038/nature05336. PMID 17108958. 
  23. ^ a b Noonan, James P.; et al. (17 November 2006). "Sequencing and Analysis of Neanderthal Genomic DNA" (PDF). Science. 314 (5802): 1113–1118. doi:10.1126/science.1131412. PMC 2583069Freely accessible. PMID 17110569. 
  24. ^ a b Timmer, John (2006-11-17). "Welcome to Neanderthal genomics". 
  25. ^ a b Lynn Yarris (15 November 2006). "Neanderthal Genome Sequencing Yields Surprising Results and Opens a New Door to Future Studies". Lawrence Berkeley National Laboratory. Retrieved 2009-02-16. 
  26. ^ Krause J, Lalueza-Fox C, Orlando L, et al. (November 2007). "The derived FOXP2 variant of modern humans was shared with Neandertals". Curr. Biol. 17 (21): 1908–1912. doi:10.1016/j.cub.2007.10.008. PMID 17949978. 

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