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Scientists decode oldest DNA of extinct human

Dec. 5, 2013
Courtesy of the Max Planck In­sti­tute 
for Ev­o­lu­tion­ary An­thro­po­l­ogy
and World Science staff

Re­search­ers say they have de­cod­ed a key part of the DNA for a 400,000-year-old ex­tinct hu­man re­lat­ed to a spe­cies of an­ces­tral hu­mans called Deni­so­vans.

The sci­en­tists were able to study DNA so old that pre­vi­ous sam­ples of si­m­i­lar age could only be re­trieved from per­ma­nently fro­zen ground. This sam­ple in­stead came from a cave in North­ern Spain.

The Si­ma de los Hue­sos ho­minins, shown here in an artist's con­cep­tion, lived an es­ti­mat­ed 400,000 years ago dur­ing the Mid­dle Pleis­to­cene. (Cred­it: Javier Trueba, Ma­drid Sci­en­tif­ic Films)


The re­search­ers said they de­ter­mined the al­most com­plete “mi­to­chon­drial genome,” a large sec­tion of hu­man DNA which is­n’t en­closed in the cell nu­cle­us like most of the rest. Mi­to­chon­drial DNA is ma­ter­nally trans­mit­ted and com­monly used for an­ces­try stud­ies.

The Span­ish ca­ve, known as the “bone pit” or Si­ma de los Hue­sos, has yielded the world’s larg­est as­sembly of an­cient hu­man fos­sils from the Mid­dle Pleis­to­cene era. 

Mat­thi­as Mey­er and col­leagues of the Max Planck In­sti­tute for Ev­o­lu­tion­ary An­thro­po­l­ogy in Leip­zig, Ger­ma­ny, de­vel­oped new meth­ods for de­cod­ing highly de­grad­ed an­cient DNA. They then teamed up with Span­ish pa­le­on­tol­ogist Juan-Luis Ar­suaga and used the tech­niques on a cave bear from the site. Lat­er the group sam­pled some bone pow­der from a thigh bone of a ho­minin, or ex­tinct hu­man rel­a­tive, found there. They com­pared its mi­to­chon­d­rial DNA with that of Ne­an­der­thal peo­ple, Deni­so­vans, pre­s­ent-day hu­mans, and apes.

Based on “miss­ing muta­t­ions,” the re­search­ers cal­cu­lat­ed that the Si­ma ho­minin lived about 400,000 years ago and shared a com­mon an­ces­tor not with Ne­an­der­thals but with Deni­so­vans—an ex­tinct group from Asia re­lat­ed to the Ne­an­der­thals—a­bout 700,000 years ago. 

The re­sult is al­so “un­ex­pect­ed” since the ske­l­e­ton shows Ne­an­der­thal-like fea­tures, said Mey­er. The bones, at­trib­ut­ed to a spe­cies known as Ho­mo hei­del­ber­gen­sis, may be re­lat­ed to the popula­t­ion an­ces­tral to both Ne­an­der­thals and Deni­so­vans, he said. This “points to a com­plex pat­tern of ev­o­lu­tion in the or­i­gin of Ne­an­der­thals and mod­ern hu­mans,” added Svante Pääbo, di­rec­tor at the Max Planck In­sti­tute.

The find­ings are pub­lished in the Dec. 4 is­sue of the re­search jour­nal Na­ture

“Our re­sults show that we can now study DNA from hu­man an­ces­tors that are hun­dreds of thou­sands of years old,” Pääbo said. “This opens prospects to study the genes of the an­ces­tors of Ne­an­der­thals and Deni­so­vans. It is tre­men­dously ex­cit­ing.”


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Researchers say they have decoded a key part of the DNA for a 400,000-year-old extinct human related to a species of ancestral humans called Denisovans. The scientists were able to study DNA so old that previous samples of similar age could only be retrieved from permanently frozen ground. This sample instead came from a cave in Northern Spain. The researchers said they determined the almost complete “mitochondrial genome,” a large section of human DNA that isn’t enclosed in the cell nucleus like most of the rest. Mitochondrial DNA is maternally transmitted and commonly used for ancestry studies. The Spanish cave, known as the “bone pit” or Sima de los Huesos, has yielded the world’s largest assembly of human-related fossils from the Middle Pleistocene era. Matthias Meyer and colleagues of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, developed new methods for decoding highly degraded ancient DNA. They then teamed up with Spanish paleontologist Juan-Luis Arsuaga and used the techniques on a cave bear from the site. Later they sampled some bone powder from a thigh bone of a hominin, or extinct human relative, found there. They compared its mitochondrial DNA with that of Neanderthal people, Denisovans, present-day humans, and apes. Based on “missing mutations,” the researchers calculated that the Sima hominin lived about 400,000 years ago and shared a common ancestor not with Neanderthals but with Denisovans—an extinct group from Asia related to the Neanderthals—about 700,000 years ago. The result is also “unexpected” since the skeleton shows Neanderthal-like features, said Meyer. The bones, attributed to a species known as Homo heidelbergensis, may be related to the population ancestral to both Neanderthals and Denisovans, he said. This “points to a complex pattern of evolution in the origin of Neanderthals and modern humans,” added Svante Pääbo, director at the Max Planck Institute The findings are published in the Dec. 4 issue of the research journal Nature. “Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old,” Pääbo said. “This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting.”