Mitochondrial DNA from 400 thousand year old humans

The Sima de los Huesos (‘pit of bones’) site in the cave complex of Atapuerca in northern Spain has yielded one of the greatest assemblages of hominin bones. Well-preserved remains of at least 28 individuals date to the Middle Pleistocene (>300 ka). Anatomically the individuals have many Neanderthal-like features but also show affinities with earlier Homo heidelbergensis, who is widely considered to be the common ancestor for anatomically modern humans and Neanderthals, and perhaps also for the mysterious Denisovans. Most palaeoanthropologists have previously considered this Atapuerca group to be early Neanderthals, divergent from African lineages because they migrated to and became isolated in Europe.

English: Cranium 5 is one of the most importan...
Human cranium from the Sima de los Huesos, Atapuerca mountains (Spain). (credit: Wikipedia)

The riches of the Sima de los Huesos ossuary made it inevitable that attempts would be made to extract DNA that survived in the bones, especially as bear bones from the area had shown that mtDNA can survive more than 4300 ka. There has been an air of expectancy in hominin-evolution circles, and indeed among the wider public, since rumours emerged that the famous Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany had initiated genetic sequencing under the direction of Svante Pääbo: perhaps another ‘scoop’ to add to their reconstructing the first Neanderthal and Denisovan genomes. The news came out in the 5 December 2013 issue of Nature, albeit published on-line (Meyer, M. and 10 others 2013. A mitochondrial genome sequence of a hominin from Sima de los Huesos, Nature, v. 504; doi:10.1038/nature12788) with a discussion by Ewan Callaway (Callaway, E. 2013. Hominin DNA baffles experts Nature, v. 504, p. 16-17).

The bafflement is because the mtDNA from a femur of a 400 ka  individual does not match existing Neanderthal data as well as it does that of the Denisovan from Siberia by such a degree that the individual is an early Denisovan not a Neanderthal. Northern Spain being thousands of kilometres further west than the Denisova cave heightens the surprise.  Indeed, it may be on a lineage from an earlier hominin that did not give rise to Neanderthals. The full Neanderthal and Denisovan genomes suggest that they shared a common ancestor up to 700 ka ago. So the Sima de los Huesos individual presents several possibilities. It could be a member of an original population of migrants from Africa that occupied wide tracts of Eurasia, eventually to give rise to both Neanderthals and Denisovans. That genetic split may have arisen by the female line carrying it not surviving into populations that became Neanderthals – mtDNA is only present in the eggs of mothers. Mind you, that begs the question of who the Neanderthal females were. Another view is that the Sima de los Huesos individual may be descended from even earlier H. antecessor, whose 800 ka remains occur in a nearby cave. Pääbo’s team have even suggested that Denisovans interbred with a mysterious group: perhaps relics of the earlier H. antecessor colonists.

Established ideas of how humans emerged, based on bones alone and very few individuals to boot, are set to totter and collapse like a house of cards. Interbreeding has been cited three times from DNA data: modern human-Neanderthal; modern human-Denisovan and Denisovan with an unknown population. Will opinion converge on what seems to be obvious, that one repeatedly errant species, albeit with distinct variants, has been involved from far back in the human evolutionary journey?  There seems only one avenue to follow for an answer, which is to look for well preserved H. heidelbergensis. H. antecessor and H. erectus remains and apply ever improving techniques of genetic retrieval. Yet there is a chance that stretches of ancient DNA can be teased out of younger fossils.

Hybridisation in human evolution

A press release from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announces the completion of the most precise genome from a third Neanderthal individual. For the first time it is possible to distinguish copies of the genes inherited by the individual from both parents. The data release coincided with a review of genetic evidence for interbreeding between early Homo sapiens and other species.

The full item can be read at Earth-logs in the Human evolution and migrations archive for 2013

Modern human migration out of and within Africa relative to the domains of coeval archaic humans 1 = modern humans 2 = Neanderthals 3 = other archaic humans (credit: Wikipedia)

Denisovans scooped?

In late 2010 it emerged from genomic studies of a finger bone from Denisova Cave in eastern Siberia that a probably archaic human group had shared genes with ancestors of some modern humans who colonised West Pacific islands around 45 Ka ago, well before the last glacial maximum. Melanesians, including tpeople living in Papua-New Guinea have DNA that contains on average around 6% contributed from fertile interbreeding with Denisovans. This ancient groups are suggested by comparative studies of their and Neanderthal mitochondrial DNA to have split from them as lond as a million years ago. Now it seems possible that much more complete fossils of Denisovans may have been discovered in China (Curnoe, D. And 16 others 2012. Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians. PLoS ONE,

Skull from Red Deer Cave in Guanxi Province, southern China. Darren Curnoe

A block of sediment from Longlin Cave in Guanxi Province in southern China that was collected more than 30 years ago, has yielded skull fragments whose reconstruction reveals a most unusual individual, very different from anatomically modern humans, Neanderthals and from H. erectus. It had a wide flat face with highly prominent cheek bones, strong brow ridges and a diminutive chin.  Remains of three other individuals found by recent excavations in Maludong (Red Deer) Cave 300 km to the south of Longlin share similar characteristics. Yet there are similarities to moderns, for instance CT-scans show that the brain likely had a height and frontal lobes similar to ours, but different from Neanderthals.

These are not truly ancient fossils; radiocarbon and uranium-series dating give an age range from 14.3 to 11.5 ka, around the time of the Younger Dryas cold episode that preceded the Holocene. These two individuals lived when East Asia had long been home to fully modern humans.

The finds perhaps open a major new focus for human evolution, directed towards less-well studied older fossils from elsewhere in the East including those referred to by Jonathan Kingdon as ‘Mapas’ from both southern and northern China. Certainly it will boost palaeoanthropological research within China

Snippets on human evolution

Image copyright held by author, Chris Henshilw...
Artifacts from the Blombos Cave, South Africa, including deliberately etched block of hematite Image by Chris Henshilwood via Wikipedia

The news that most humans outside of Africa carry fragments of DNA that match with those of Neanderthals and the mysterious Denisovan archaic humans ( see Yes, it seems that they did… and Other rich hominin pickings in the May 2010 issue of EPN) has entered into popular culture; or soon will have! Similar dalliances with the ‘older folk’ seem also to have occurred among those humans who remained in Africa (Hammer, M.F. et al. 2011. Genetic evidence for archaic admixture in Africa. Proceedings of the National Academy of Sciences, v. 108, p. 15123-15128). The DNA of three groups in West Africa who maintain a hunter-gatherer lifestyles show regions that are not involved in coding for proteins that differ from the African norm. This suggests mating with an entirely separate and unknown group of hominins – probably archaic forms of humans – that produced fertile offspring, probably around 35 thousand years ago. The find spurred re-evaluation of bones with a mix of archaic and modern features that were discovered in a Nigerian cave in the 1960s (Harvati, K. et al. 2011. The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology. PLoS ONE, v.  6: e24024. doi:10.1371/journal.pone.0024024). The study confirms that the skulls are outside the fully modern human range, but display a close similarity with Neanderthal and H. erectus. The big surprise is that U-Th dating suggests they are quite recent, around 16 ka. The stage seems set for nor only a burst of exploration for human remains of less antiquity than early hominins but a ‘paradigm shift’ in our view of what constitutes a human species.

See also: Gibbons, A. 2011, African data bolster new view of modern human origins. Science, v. 334, p. 167.

Another interesting link with archaic humans who had the closest of relationships with some of our ancestors is that their union may have bolstered the resistance of migrants from Africa to Eurasian pathogens (Abi-Rached, L. and 22 others 2011. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science, v. 334, p. 89-94). The focus was on the human leucocyte antigen (HLA) group that is a vital part of our immune system in the form of ‘killer cells’. Part of modern Eurasian DNA that codes for the group (HLA-B*73 allele) appears in the Neanderthal and Denisovan genomes; indeed more than half the HLA alleles of modern Eurasians may have originated in this way, and have also been introduced into Africans subsequently.

Also at the front line of genomic research into human origins, DNA sequenced from a lock of hair given to an Edwardian anthropologist by a native Australian turns out to have an extreme antiquity compared with that of other Eurasian people descended from African migrants (Rasmussen, M. and 57 others. An aboriginal Australian genome reveals separate human dispersals into Asia. Science, v. 334, p. 94-98). The unique aspects of the Australian genome signify separation of a group of individuals from the main African population around 62-75 thousand years ago; significantly earlier than and different from ‘run of the mill’ migrants from whom modern Asians arose at between 25 to 38 ka. There is little doubt that native Australians are descended from the pioneers who first diffused from Africa either by crossing the Straits of Bab el Mandab or taking another route and they moved more speedily across southern Asia than other waves made possible by climate change and sea-level falls following the Eemian interglacial of 133-115 ka.

Despite the lingering Eurocentrist view that somehow fully modern human consciousness sprang into being at the time the famous French and Spanish cave art was painted, around 30 ka, increasing evidence points to an African origin for a sense of aesthetics and the ability to express it. The latest is the discovery of a 100 ka ‘paint box’ in a South African coastal cave (Henshilwood, C.S. et al. 2011. A 100,000-year-old ochre-processing workshop at Blombos Cave, South Africa. Science, v. 334, p. 219-223). The material consists of two large abalone shells containing traces of red and orange ochre, together with a hammer stone and grinder with adhering ochre, and fat-rich bones which ground-up would have produced a binder for the ochre. No art occurs in the cave and it might be supposed that the pigments were intended for face- or body adornment.