Denisova hominin

"Woman X" redirects here. For other uses, see X woman.

Denisova hominins (/dɨˈniːsəvə/), or Denisovans, are Paleolithic-Era members of the genus Homo that may belong to a previously unknown species. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female that lived about 41,000 years ago, found in Denisova Cave in Altai Krai, Russia, a region also inhabited at about the same time by Neanderthals and perhaps modern humans.^[1][2] A tooth and toe bone belonging to different members of the same population have since been found.

Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be distinct from the mtDNAs of Neanderthals and modern humans.^[3] Subsequent studies on the nuclear genome from this specimen, as well as mtDNA from the tooth, determined that this group shares a common origin with Neanderthals and interbred with the ancestors of some present-day Melanesians^[4]and Australian Aborigines^[5]. Similar analysis of a toe bone discovered in 2011 is underway.^[6]

Discovery

Tourists in front of the Denisova Cave, where "Woman X" was found.

In 2008, Russian archeologists from the Institute of Archaeology and Ethnology of Novosibirsk working at the site of Denisova Cave in the Altai Mountains of Siberia uncovered a small bone fragment from the fifth finger of a juvenile hominin, dubbed the "X-woman" (referring to the maternal descent of mitochondrial DNA^[7]), or the Denisova hominin. Artifacts, including a bracelet, excavated in the cave at the same level were carbon dated to around 40,000 BP.

A team of scientists led by Johannes Krause and Swedish biologist Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced mtDNA extracted from the fragment. Because of the cool climate in the location of the Denisova Cave, the discovery benefited from DNA's ability to survive for longer periods at lower temperatures.^[2] The analysis indicated that modern humans, Neanderthals, and the Denisova hominin last shared a common ancestor around 1 million years ago.^[3] Some studies suggest that modern humans coexisted with Neanderthals in Europe, and the discovery raises the possibility that Neanderthals, modern humans and the Denisovan hominin may have co-existed.^[8][9]

The DNA analysis further indicated that this new hominin species was the result of an early migration out of Africa, distinct from the later out-of-Africa migrations associated with Neanderthals and modern humans, but also distinct from the earlier African exodus of Homo erectus.^[3] Professor Chris Stringer, human origins researcher at London's Natural History Museum and one of the leading proponents of the recent single-origin hypothesis, remarked: "This new DNA work provides an entirely new way of looking at the still poorly understood evolution of humans in central and eastern Asia." Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene.^[7]

Later in 2010, a second paper from the Svante Pääbo group reported the prior discovery, in 2000, of a third upper molar from a young adult, dating from about the same time (the finger was from level 11 in the cave sequence, the tooth from level 11.1). The tooth differed in several aspects from those of Neanderthals while having archaic characteristics similar to the teeth of Homo erectus. They again performed mitochondrial DNA analysis on the tooth and found it to have a different but similar sequence to that of the finger bone, indicating a divergence time about 7,500 years before, and suggesting it belonged to a different individual from the same population.^[10] In 2011, a toe bone was discovered in the same layer of the Denisova cave and hence contemporary with the finger bone.

Anatomy

Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered thus far are the finger bone and tooth from which genetic material has been gathered, and a toe bone. The tooth shares no derived morphological features with Neanderthal or modern humans.^[10] An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, although a critic suggested the morphology was inconclusive. It is currently undergoing DNA analysis by Pääbo.^[6]

Mitochondrial DNA analysis

The mtDNA from the finger bone differs 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.^[2] This suggested a divergence time around one million years ago. mtDNA from the tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population.^[10]

Nuclear genome analysis

In the same second 2010 paper, the authors report the isolation and sequencing of nuclear DNA from the Denisova finger bone. This specimen showed an unusual degree of DNA preservation and low level of contamination. They were able to achieve near-complete genomic sequencing, allowing a detailed comparison with Neanderthal and modern humans. From this analysis, they concluded that in spite of the apparent divergence of their mitochondrial sequence, the Denisova population along with Neanderthal shared a common branch from the lineage leading to modern African humans. The estimated average time of divergence between Denisovan and Neanderthal sequences is 640,000 years ago, and that between both of these and the sequences of modern Africans is 804,000 years ago. They suggest that the divergence of the Denisova mtDNA results either from the persistence of a lineage purged from the other branches of humanity through genetic drift or else an introgression from an older hominin lineage.^[10]

Interbreeding with modern humans

Genetic study confirms that approximately 4% of non-African modern human DNA relates to Neanderthals. Tests comparing the Denisova hominin genome with those of six modern humans: a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese showed that between 4% and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. The genes were possibly introduced during the early migration of the ancestors of Melanesians into Southeast Asia. This history of interaction suggests that Denisovans once ranged widely over eastern Asia.^[10]

Later research suggests that modern-day descendants of Denisovans range wider afield than Melanesia. Mark Stoneking, molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology, led the research team which found genetic evidence that, in addition to Melanesians, Australian Aborigines, and some small, scattered groups of people in Southeast Asia, such as the Negrito Mamanwa in the Philippines, share varying levels of Denisovan ancestry. However, not all Negritos were found to possess Denisovan genes; Andaman Islanders and Malaysian Jehai, for example, were found to have no Denisovan inheritance. With their results, they challenged the belief that the Denisovans interbred in mainland Asia before spreading to the island from southeast Asia, Melanesia, and Australia. They said that their data "can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself."^{[11] [12][5]}

In August 2011, Denisovan and Neandertal archaic HLA types were found to represent more than half the HLA alleles of modern Eurasians.^[13] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population.

Further reading

• Fox, Maggie (2010-03-24), "Possible new human ancestor found in Siberia", Reuters, http://www.reuters.com/article/idUSTRE62N4VS20100324 .
• Ghosh, Pallab (2010-12-22), Ancient humans, dubbed 'Denisovans', interbred with us, BBC News online, http://www.bbc.co.uk/news/science-environment-12059564, "The study shows that Denisovans interbred with the ancestors of the present day people of the Melanesian region north and north-east of Australia. Melanesian DNA comprises between 4% and 6% Denisovan DNA." 
• Hawks, John (2010-12-22), "The Denisova genome FAQ", John Hawks Weblog, http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/denisova-nuclear-genome-reich-2010.html .
• Rincon, Paul (2010-03-25), DNA identifies new ancient human dubbed 'X-woman', BBC News online, http://news.bbc.co.uk/1/hi/sci/tech/8583254.stm .
• Wade, Nicholas (2010-03-24), "Bone May Reveal a New Human Group", The New York Times, http://www.nytimes.com/2010/03/25/science/25human.html .
• Zimmer, Carl (2010-03-24), Hybrid speculation (blog), Discover, http://blogs.discovermagazine.com/loom/2010/03/24/the-x-womans-fingerbone/ .
• Zimmer, Carl (2010-12-22), Meet the Denisovans, the newest members of the human tree of life (blog), Discover, http://blogs.discovermagazine.com/loom/2010/12/22/meet-the-denisovans-the-newest-members-of-the-human-tree-of-life/ .
• Barras, Colin (2011-08-13), "Stone Age toe could redraw human family tree", New Scientist, http://www.newscientist.com/article/mg21128254.000-stone-age-toe-could-redraw-human-family-tree.html .

References

1. ^ Brown, David (March 25, 2010), "DNA from bone shows new human forerunner, and raises array of questions", Washington Post, http://www.washingtonpost.com/wp-dyn/content/article/2010/03/24/AR2010032401926_pf.html 
2. ^ ^{a b c} Krause, Johannes; Fu, Qiaomei; Good, Jeffrey M.; Viola, Bence; Shunkov, Michael V.; Derevianko, Anatoli P. & Pääbo, Svante (2010), "The complete mitochondrial DNA genome of an unknown hominin from southern Siberia", Nature 464 (7290): 894–897, doi:10.1038/nature08976, PMID 20336068 
3. ^ ^{a b c} Katsnelson, Alla (March 24, 2010), "New hominin found via mtDNA", The Scientist, http://www.the-scientist.com/blog/display/57254/#ixzz0j820ioz1 
4. ^ Carl Zimmer (22 December 2010). "Denisovans Were Neanderthals' Cousins, DNA Analysis Reveals". NYTimes.com. http://www.nytimes.com/2010/12/23/science/23ancestor.html?hp. Retrieved 22 December 2010. 
5. ^ ^{a b} Callaway, Ewen (September 22, 2011), First Aboriginal genome sequenced, Nature News, http://www.nature.com/news/2011/110922/full/news.2011.551.html 
6. ^ ^{a b} Barras, Colin (13 August 2011), "Stone Age toe could redraw human family tree", New Scientist, http://www.newscientist.com/article/mg21128254.000-stone-age-toe-could-redraw-human-family-tree.html 
7. ^ ^{a b} Sample, Ian (March 24, 2010), "New species of human ancestor found in Siberia", The Guardian, http://www.guardian.co.uk/science/2010/mar/24/new-human-species-siberia 
8. ^ Scientists Discover an Ancient Human Relative
9. ^ Researchers Discover New Lineage of Ancient Human
10. ^ ^{a b c d e} Reich, David; Green, Richard E.; Kircher, Martin; Krause, Johannes; Patterson, Nick; Durand, Eric Y.; Viola, Bence; Briggs, Adrian W. et al. (2010), "Genetic history of an archaic hominin group from Denisova Cave in Siberia", Nature 468 (7327): 1053–1060, doi:10.1038/nature09710, PMID 21179161 
11. ^ Reich et al., Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania, The American Journal of Human Genetics (2011), doi:10.1016/j.ajhg.2011.09.005 , http://www.sciencedirect.com/science/article/pii/S0002929711003958 
12. ^ Choi, Charles (September 22, 2011), Now-Extinct Relative Had Sex with Humans Far and Wide, LiveScience, http://www.livescience.com/16171-denisovans-humans-widespread-sex-asia.html 
13. ^ Laurent Abi-Rached, et. al. (2011-08-25). "The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans". Science 334 (6052). doi:10.1126/science.1209202. Archived from the original on Aug 2011. http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1122&context=publichealthresources.