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Jean M
12-04-2013, 07:56 PM
Exciting news! This was posted on the New Papers thread, but I feel it deserves its own.

http://www.mpg.de/7637951/hominin_from_sima_de_los_huesos


Using novel techniques to extract and study ancient DNA researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have determined an almost complete mitochondrial genome sequence of a 400,000-year-old representative of the genus Homo from Sima de los Huesos, a unique cave site in Northern Spain, and found that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neandertals in Asia. DNA this old has until recently been retrieved only from the permafrost....

The fossils are classified as Homo heidelbergensis but also carry traits typical of Neandertals. .... From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. “The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features”, says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

If the Denisovan mtDNA is in fact an introgression from an older Hominin, it would make sense of this result.

Love the reconstruction painting by Kennis & Kennis.

Actual paper: Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell and Svante Pääbo, A mitochondrial genome sequence of a hominin from Sima de los Huesos
Nature, December 4, 2013 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12788.html

Jean M
12-04-2013, 08:18 PM
BBC covers the story http://www.bbc.co.uk/news/science-environment-25193442


The discovery of DNA in a 400,000-year-old human thigh bone will open up a new frontier in the study of our ancestors. That's the verdict cast by human evolution experts on an analysis in Nature journal of the oldest human genetic material ever sequenced. The femur comes from the famed "Pit of Bones" site in Spain, which gave up the remains of at least 28 ancient people.

But the results are perplexing, raising more questions than answers about our increasingly complex family tree. The early human remains from the cave site near the northern Spanish city of Burgos have been painstakingly excavated and pieced together over the course of more than two decades. It has yielded one of the richest assemblages of human bones from this stage of human evolution, in a time called the Middle Pleistocene.


Chris Stringer reacts on video.

Jean M
12-04-2013, 09:29 PM
Dienekes provides comments and a key tree from the paper: http://dienekes.blogspot.co.uk/2013/12/400-thousand-year-old-human-mtdna-from.html

999

parasar
12-05-2013, 01:29 AM
Matthias Meyer:

The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating:)

http://news.nationalgeographic.com/news/2013/12/131204-human-fossil-dna-spain-denisovan-cave/


Sima de los Huesos, has been studied since 1997 and hosts more than 6,000 ancient bone samples belonging to 28 ancient humans that lived roughly 400,000 years ago. The exact origin of the bone pile is unclear.

"Could a natural catastrophe or carnivore activities explain the accumulation of so many bodies?" asks anthropologist Juan-Luis Arsuaga, a co-author of the study and lead excavator at the cave for the past 30 years. "Or were there hominins that accumulated the corpses of their relatives and friends in such a dark and remote place: a pit in a cave?

"I would like to live to know the answer."

Rathna
12-05-2013, 09:52 AM
I counted 275 mutations. As to what? Probably rCRS. Thus if the ancientness of this mtDNA is of 400,000 years, they are 1451 years for mutation, thus much lower than what we think. Thus also mtDNA in a long period of time has numerous back mutations. I can not think that those A73G or A263G or T16311C or T16519C are the same of my K1a1b1e.
This is the reason that made my opposers lose their battle against me about the Y.

palamede
12-05-2013, 12:27 PM
I counted 275 mutations. As to what? Probably rCRS. Thus if the ancientness of this mtDNA is of 400,000 years, they are 1451 years for mutation, thus much lower than what we think. Thus also mtDNA in a long period of time has numerous back mutations. I can not think that those A73G or A263G or T16311C or T16519C are the same of my K1a1b1e.
This is the reason that made my opposers lose their battle against me about the Y.

Rathna, I am a precise rCRS (H2a2a1 without supplementary mutation) . According to your calculation, It seems you think I am a direct descendant of a Lady of Sima de los Huesos. It could be true because I love devouring my contemporaries at each lunch, but by the speech only.

I would have guessed the Lady and I were away (if 3500 years by mutation) from about 275 * 3500 = 962,500 years with a common grand-mother dating from about (962,500+400,000)/2 = 681,150 years ago, say more 700,000 years ago with back-mutations.

Rathna
12-05-2013, 01:55 PM
Rathna, I am a precise rCRS (H2a2a1 without supplementary mutation) . According to your calculation, It seems you think I am a direct descendant of a Lady of Sima de los Huesos. It could be true because I love devouring my contemporaries at each lunch, but by the speech only.

I would have guessed the Lady and I were away (if 3500 years by mutation) from about 275 * 3500 = 962,500 years with a common grand-mother dating from about (962,500+400,000)/2 = 681,150 years ago, say more 700,000 years ago with back-mutations.

1) Palamede, if you are rCRS*, this demonstrates that it was born in France rather than in Great Britain (I am waiting the FSM of DeMao, one of my points of the origin of R1b1* in Italy, who has an Irish mother and is close to rCRS*).
2) Your calculation of 700,000 YBP of these two lines (ours and that: someone thinks that her mt came from a Denisovian) could also be taken seriously.

Bernard
12-05-2013, 01:59 PM
This is a nice poster of the site of La Sima de los Huesos with the pit of bones: http://www.diariodeatapuerca.net/LaSimadelosHuesos.pdf

Jean M
12-05-2013, 07:26 PM
Razib Khan's take on the matter: Caveman rules: prepare to be surprised! http://www.unz.com/gnxp/caveman-rules-prepare-to-surprised/


The big surprise is that these proto-Neandertals carry a mtDNA lineage which is closer to that of the Siberian Denisovans than that of later Neandertals. That’s the specific finding, and if you read the reaction it is rather clear that this is confusing researchers who work in this area. But take a step back, imagine what a world without ancient DNA would be like. Yes, the broad conjectures would be supported (e.g., Out of Africa), but many specific details would be off. So praise the data! Sometimes complexity is closer to the truth, and this is one of those cases. These are good problems to have.

I couldn't agree more! :)

He recommends Ewen Callaway's take in it in Nature: Hominin DNA baffles experts: Analysis of oldest sequence from a human ancestor suggests link to mystery population. http://www.nature.com/news/hominin-dna-baffles-experts-1.14294


“I’ve got my own twist on it,” says Stringer, who has previously argued that the Sima de los Huesos hominins are indeed early Neanderthals (C. Stringer Evol. Anthropol. 21, 101–107; 2012). He thinks that the newly decoded mitochondrial genome may have come from another distinct group of hominins. Not far from the caves, researchers have discovered hominin bones from about 800,000 years ago that have been attributed to an archaic hominin called Homo antecessor, thought to be a European descendant of Homo erectus. Stringer proposes that this species interbred with a population that was ancestral to both Denisovans and Sima de los Huesos hominins, introducing the newly decoded mitochondrial lineage to both populations.

There is a podcast: Svante Pääbo talks to Ewen Callaway about the hominin DNA.

Ian B
12-06-2013, 12:27 AM
Jean, I was about to post this same info, it appeared in a story in todays newspaper. So it appears possible that there is another, as yet undiscovered, human species from which the Denisovans, and possibly the Neanderthals originated. Excellent stuff! Can hardly wait for further developments.

GailT
12-06-2013, 04:32 AM
They are working on testing mtDNA from more samples and also autosomal DNA, so hopefully we will get a better understanding of the population with more test results. As always, John Hawks has an interesting discussion of the new find (link) (http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/sima-de-los-huesos-dna-meyer-2013.html).

It makes me wonder if there is any hope that the Rising Star samples can be sequenced.