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Neandertal DNA sequences and the origin of modern humans. Krings M,Stone A,Schmitz R W,Krainitzki H,Stoneking M,Pääbo S Cell DNA was extracted from the Neandertal-type specimen found in 1856 in western Germany. By sequencing clones from short overlapping PCR products, a hitherto unknown mitochondrial (mt) DNA sequence was determined. Multiple controls indicate that this sequence is endogenous to the fossil. Sequence comparisons with human mtDNA sequences, as well as phylogenetic analyses, show that the Neandertal sequence falls outside the variation of modern humans. Furthermore, the age of the common ancestor of the Neandertal and modern human mtDNAs is estimated to be four times greater than that of the common ancestor of human mtDNAs. This suggests that Neandertals went extinct without contributing mtDNA to modern humans. 10.1016/s0092-8674(00)80310-4
A draft sequence of the Neandertal genome. Science (New York, N.Y.) Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. 10.1126/science.1188021
The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined, the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans. 10.1038/nature08976
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Reich David,Green Richard E,Kircher Martin,Krause Johannes,Patterson Nick,Durand Eric Y,Viola Bence,Briggs Adrian W,Stenzel Udo,Johnson Philip L F,Maricic Tomislav,Good Jeffrey M,Marques-Bonet Tomas,Alkan Can,Fu Qiaomei,Mallick Swapan,Li Heng,Meyer Matthias,Eichler Evan E,Stoneking Mark,Richards Michael,Talamo Sahra,Shunkov Michael V,Derevianko Anatoli P,Hublin Jean-Jacques,Kelso Janet,Slatkin Montgomery,Pääbo Svante Nature Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans. 10.1038/nature09710
A high-coverage genome sequence from an archaic Denisovan individual. Meyer Matthias,Kircher Martin,Gansauge Marie-Theres,Li Heng,Racimo Fernando,Mallick Swapan,Schraiber Joshua G,Jay Flora,Prüfer Kay,de Filippo Cesare,Sudmant Peter H,Alkan Can,Fu Qiaomei,Do Ron,Rohland Nadin,Tandon Arti,Siebauer Michael,Green Richard E,Bryc Katarzyna,Briggs Adrian W,Stenzel Udo,Dabney Jesse,Shendure Jay,Kitzman Jacob,Hammer Michael F,Shunkov Michael V,Derevianko Anatoli P,Patterson Nick,Andrés Aida M,Eichler Evan E,Slatkin Montgomery,Reich David,Kelso Janet,Pääbo Svante Science (New York, N.Y.) We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans. 10.1126/science.1224344