Molecular Biology and Genetics
Statistics of barcoding coverage
|Specimen Records:||8,818||Public Records:||8,464|
|Specimens with Sequences:||19,169||Public Species:||3|
|Specimens with Barcodes:||8,677||Public BINs:||2|
|Species With Barcodes:||3|
Locations of barcode samples
Red Deer Cave people
The Red Deer Cave people are the youngest known prehistoric population who do not look like modern humans. Fossils dated between 14,500 and 11,500 years old were found in Red Deer Cave and Longlin Cave in China. Having a mix of archaic and modern features, they are tentatively thought to be a separate species of humans that became extinct without contributing to the gene pool of modern humans. Evidence shows large deer were cooked in the Red Deer Cave giving the people their name.
In 1979, the partial skull of a cave dweller was found in Longlin Cave in the Guangxi Zhuang region of China. Further human remains were excavated from Maludong (Red Deer Cave) in Yunnan Province. Fossils of the Red Deer Cave dwellers were radiocarbon dated between 14,500 and 11,500 years of age, using charcoal found in the fossil deposits. During the period the Red Deer Cave people lived, all other prehistoric human species such as Neanderthals were thought to have died out. The Red Deer Cave humans would therefore be more recent than Homo floresiensis (dubbed "Hobbits") dated to 13,000 years ago.
In spite of their relatively recent age, the fossils exhibit features of more primitive humans. The Red Deer Cave dwellers had distinctive features that differ from modern humans: flat face, broad nose, jutting jaw with no chin, large molars, prominent brows, thick skull bones, and moderate-size brain.
Status as a separate species 
Although the physical features of the Red Deer Cave people suggest that they may be a previously undiscovered species of prehistoric human, the scientists who discovered them are reluctant to classify them as a new species. Chris Stringer of the Natural History Museum in London has suggested that they could be a result of mating between Denisovans and modern humans. Other scientists remain skeptical, suggesting that the unique features are within the variations expected for human populations.
Attempts to extract DNA have been so far unsuccessful but are continuing. Only once this is done will it be possible to determine the relationship between this group and other modern humans.
See also 
- Deborah Smith (2012-03-15). "Scientists stumped by prehistoric human whose face doesn't fit". Brisbane Times.
- Barras, Colin (2012-03-14). "Chinese human fossils unlike any known species". New Scientist. Retrieved 2012-03-15.
- Curnoe, D.; Xueping, J.; Herries, A. I. R.; Kanning, B.; Taçon, P. S. C.; Zhende, B.; Fink, D.; Yunsheng, Z. et al. (2012). "Human remains from the Pleistocene-Holocene transition of southwest China Suggest a complex evolutionary history for East Asians". In Caramelli, David. PLoS ONE 7 (3): e31918. doi:10.1371/journal.pone.0031918. PMC 3303470. PMID 22431968.
- James Owen (2012-03-14). "Cave Fossil Find: New Human Species or "Nothing Extraordinary"?". National Geographic News.
Homo is the genus of great apes that includes modern humans and species closely related to them. The genus is estimated to be about 2.3 to 2.4 million years old, possibly having evolved from australopithecine ancestors, with the appearance of Homo habilis. Several species, including Australopithecus garhi, Australopithecus sediba, Australopithecus africanus and Australopithecus afarensis, have been proposed as the direct ancestor of the Homo lineage. Each of these species have morphological features that align them with Homo, but there is no consensus on which actually gave rise to Homo.
The most salient physiological development between the earlier Australopith species and Homo is the increase in cranial capacity, from about 450 cm3 (27 cu in) in A. garhi to 600 cm3 (37 cu in) in H. habilis. Within the Homo genus, cranial capacity again doubled from H. habilis through Homo ergaster or H. erectus to Homo heidelbergensis by 0.6 million years ago. The cranial capacity of H. heidelbergensis overlaps with the range found in modern humans.
The advent of Homo was thought to coincide with the first evidence of stone tools (the Oldowan industry), and thus by definition with the beginning of the Lower Palaeolithic; however, recent evidence from Ethiopia now places the earliest evidence of stone tool usage at before 3.39 million years ago. The emergence of Homo coincides roughly with the onset of Quaternary glaciation, the beginning of the current ice age.
Homo sapiens (modern humans) is the only surviving species in the genus, all others having become extinct. Homo neanderthalensis, traditionally considered the last surviving relative, died out about 24,000 years ago, though recent discoveries suggest that two other species, Homo floresiensis and the Red Deer Cave people, may have lived much more recently. The other extant Homininae—the chimpanzees and gorillas—have a limited geographic range. In contrast, the evolution of humans is a history of migrations and admixture. According to genetic studies, modern humans bred with "at least two groups" of ancient humans: Neanderthals and Denisovans. Humans repeatedly left Africa to populate Eurasia and finally the Americas, Oceania, and the rest of the world.
The word homo is Latin, in the original sense of "human being", or "man" (in the gender-neutral sense). The word "human" itself is from Latin humanus, an adjective cognate to homo, both thought to derive from a Proto-Indo-European word for "earth" reconstructed as *dhǵhem-.
Species status of Homo rudolfensis, H. ergaster, H. georgicus, H. antecessor, H. cepranensis, H. rhodesiensis and H. floresiensis remains under debate. H. heidelbergensis and H. neanderthalensis are closely related to each other and have been considered to be subspecies of H. sapiens. Recently, nuclear DNA from a Neanderthal specimen from Vindija Cave has been sequenced, as well, using two different methods that yield similar results regarding Neanderthal and H. sapiens lineages, with both analyses suggesting a date for the split between 460,000 and 700,000 years ago, though a population split of around 370,000 years is inferred. The nuclear DNA results indicate about 30% of derived alleles in H. sapiens are also in the Neanderthal lineage. This high frequency may suggest some gene flow between ancestral humans and Neanderthal populations.
|Species||Lived when (mya)||Lived where||Adult height||Adult mass||Cranial capacity (cm³)||Fossil record||Discovery / publication of name|
|Denisova hominin||0.04||Russia||1 site||2010|
|H. antecessor||1.2 – 0.8||Spain||1.75 m (5.7 ft)||90 kg (200 lb)||1,000||2 sites||1997|
|H. cepranensis||0.5 – 0.35||Italy||1,000||1 skull cap||1994/2003|
|H. erectus||1.8 – 0.2||Africa, Eurasia (Java, China, India, Caucasus)||1.8 m (5.9 ft)||60 kg (130 lb)||850 (early) – 1,100 (late)||Many||1891/1892|
|H. ergaster||1.9 – 1.4||Eastern and Southern Africa||1.9 m (6.2 ft)||700–850||Many||1975|
|H. floresiensis||0.10 – 0.012||Indonesia||1.0 m (3.3 ft)||25 kg (55 lb)||400||7 individuals||2003/2004|
|H. gautengensis||>2 – 0.6||South Africa||1.0 m (3.3 ft)||1 individual||2010/2010|
|H. habilis||2.3 – 1.4||Africa||1.0–1.5 m (3.3–4.9 ft)||33–55 kg (73–120 lb)||510–660||Many||1960/1964|
|H. heidelbergensis||0.6 – 0.35||Europe, Africa, China||1.8 m (5.9 ft)||90 kg (200 lb)||1,100–1,400||Many||1908|
|H. neanderthalensis||0.35 – 0.03||Europe, Western Asia||1.6 m (5.2 ft)||55–70 kg (120–150 lb) (heavily built)||1,200–1,900||Many||(1829)/1864|
|H. rhodesiensis||0.3 – 0.12||Zambia||1,300||Very few||1921|
|H. rudolfensis||1.9||Kenya||700||2 sites||1972/1986|
|Red Deer Cave people||0.0145–0.0115||China||Very few||2012|
|H. sapiens idaltu||0.16 – 0.15||Ethiopia||1,450||3 craniums||1997/2003|
|0.2 – present||Worldwide||1.4–1.9 m (4.6–6.2 ft)||50–100 kg (110–220 lb)||1,000–1,980||Still living||—/1978|
Migration and admixture 
H. habilis, which is considered the first member of the genus Homo, might have given rise to H. ergaster (however questionable, as some finds suggest both species were contemporaneous). Some of H. ergaster migrated to Asia, where they are named Homo erectus, and to Europe with Homo georgicus. H. ergaster in Africa and H. erectus in Eurasia evolved separately for almost two million years and presumably separated into two different species. Homo rhodesiensis, who were descended from H. ergaster, migrated from Africa to Europe and became Homo heidelbergensis and later (about 250,000 years ago) Homo neanderthalensis and the Denisova hominin in Asia. The first Homo sapiens, descendants of H. rhodesiensis, appeared in Africa about 250,000 years ago. About 100,000 years ago, some H. sapiens sapiens migrated from Africa to the Levant and met with resident Neanderthals, with some admixture. Later, about 70,000 years ago, perhaps after the Toba catastrophe, a small group left the Levant to populate Eurasia, Australia and later the Americas. A subgroup among them met the Denisovans and, after further admixture, migrated to populate Melanesia. In this scenario, non-African people living today are mostly of African origin ("Out of Africa model"). However, there was also some admixture with Neanderthals and Denisovans, who had evolved locally (the "multiregional hypothesis"). Recent genomic results from the group of Svante Pääbo also show that 30,000 years ago at least three major subspecies coexisted: Denisovans, Neanderthals and anatomically modern humans. Today, only H. sapiens sapiens remains, with no other extant species or subspecies.
- Stringer, C.B. (1994). "Evolution of early humans". In Steve Jones, Robert Martin & David Pilbeam (eds.). The Cambridge Encyclopedia of Human Evolution. Cambridge: Cambridge University Press. p. 242. ISBN 0-521-32370-3. Also ISBN 0-521-46786-1 (paperback)
- McHenry, H.M (2009). "Human Evolution". In Michael Ruse & Joseph Travis. Evolution: The First Four Billion Years. Cambridge, Massachusetts: The Belknap Press of Harvard University Press. p. 265. ISBN 978-0-674-03175-3.
- Pickering, R., Dirks, P. H., Jinnah, Z., De Ruiter, D. J., Churchill, S. E., Herries, A. I., ... & Berger, L. R. (2011). Australopithecus sediba at 1.977 Ma and implications for the origins of the genus Homo. Science, 333(6048), 1421-1423.
- Asfaw, B., White, T., Lovejoy, O., Latimer, B., Simpson, S., & Suwa, G. (1999). Australopithecus garhi: a new species of early hominid from Ethiopia. Science, 284(5414), 629-635.
- McPherron, S. P., Z. Alemseged, C. W. Marean, J. G. Wynn, D. Reed, D. Geraads, R. Bobe, and H. A. Bearat. 2010. Evidence for stone-tool-assisted consumption of animal tissues before 3.39 million years ago at Dikika, Ethiopia. Nature 466:857-860.
- Mitchell, Alanna (January 30, 2012). "DNA Turning Human Story Into a Tell-All". NYTimes. Retrieved January 31, 2012.
- dhghem The American Heritage Dictionary of the English Language: Fourth Edition. 2000.
- Note: In 1959, Linnaeus was designated as the lectotype for Homo sapiens (Stearn, W. T. 1959. "The background of Linnaeus's contributions to the nomenclature and methods of systematic biology", Systematic Zoology 8 (1): 4-22, p. 4) which means that following the nomenclatural rules, Homo sapiens was validly defined as the animal species to which Linnaeus belonged.
- Linné, Carl von (1758). Systema naturæ. Regnum animale. (10 ed.). pp. 18, 20. Retrieved 19 November 2012.
- Biological Anthropology: 2nd Edition. 2009. Craig Stanford et al.
- Spoor F, Leakey M.G, Gathogo P.N, Brown F.H, Antón S.C, McDougall I, Kiarie C, Manthi F.K. & Leakey L.N. (2007), "Implications of new early Homo fossils from Ileret, east of Lake Turkana, Kenya", Nature 448(7154): p. 688-691.
- Green RE, Krause J, et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. doi:10.1126/science.1188021 PMID 20448178
- ^ Reich D, Green RE, Kircher M, et al. (December 2010). "Genetic history of an archaic hominin group from Denisova Cave in Siberia". Nature 468 (7327): 1053–60. doi:10.1038/nature09710. PMID 21179161.
- Reich D ., et al. Denisova admixture and the first modern human dispersals into southeast Asia and Oceania. Am J Hum Genet. 2011 Oct 7;89(4):516-28, doi:10.1016/j.ajhg.2011.09.005 PMID 21944045.
The Denisova hominin (/dɨˈnɪsəvə/) is the name given to the remains of a member of the genus Homo that may be a previously unknown species based on an analysis of its mitochondrial DNA (mtDNA). In March 2010, discovery was announced of bone fragments of a juvenile that lived about 41,000 years ago found in Denisova Cave (Altai Krai, Russia), a region also inhabited at about the same time by Neanderthals and modern humans. The mtDNA of the Denisova hominin is distinct from the mtDNAs of Neanderthals and modern humans. In December 2010, an international team of scientists determined the sequence from the nuclear genome of this group (known as the Denisovans) from this finger bone. According to their analysis, this group shares a common origin with the Neanderthals and interbred with the ancestors of modern Melanesians.
Anatomy and lineage
Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered thus far are the finger bone from which only mitochondrial genetic material was gathered. A tooth found in Denisova Cave carries a mtDNA very similar to that of the finger bone and shares no derived morphological features with Neanderthal or modern humans. The Siberian bone's mtDNA 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. Analysis of the specimen's genome shows it to be due to a common branch of ancestors with Neanderthal lineage, but, after they diverged from one another, Denisovans and Neanderthals had largely separated population histories.
In 2008, Russian archeologists 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), 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. The analysis indicated that modern humans, Neanderthals, and the Denisova hominin last shared a common ancestor around 1 million years ago. 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.
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. 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.
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.
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 time of divergence between Denisovans and Neanderthals is 640,000 years ago, and that between both these groups and 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.
Interbreeding with modern humans
In addition to genetic studies linking approximately 4% of non-African modern human DNA to Neanderthals, these tests comparing the Denisova hominin genome with those of six modern humans whose genome has been sequenced, a ǃKung from South Africa, a Nigerian, a French person, 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, 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.
- ^ a b 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
- ^ a b 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
- ^ a b c Katsnelson, Alla (March 24, 2010), "New hominin found via mtDNA", The Scientist, http://www.the-scientist.com/blog/display/57254/#ixzz0j820ioz1
- ^ a b 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.
- ^ 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
- ^ a b c 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
- 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/ .
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