Genetic study suggests that Sima hominins were proto-Neanderthals

430,000-year-old nuclear genome sequences confirms affinities  

Sima de los Huesos (‘Pit of Bones’)is a small muddy chamber lying at the bottom of a 13 m (43 ft.) chimney, lying deep within the Cueva Mayor system of caves in the Sierra de Atapuerca of northern Spain. Hominin remains were first reported there in the 1970s, and to date the remains of 28 individuals have been recovered. The Sima hominins lived around 430,000 years ago and while conventionally described as Homo heidelbergensis, they share some derived features with Neanderthals. This has led some to suggest that they are very early Neanderthals.

In 2014, mitochondrial DNA was obtained from the thighbone of one of the Sima hominins. It was expected that it would show affinities to later sequences obtained from Neanderthals, but instead it suggested that the Sima hominins were more closely related to Denisovans. However, mitochondrial DNA does not reveal the full picture of relationships among populations, so researchers set about the more difficult task of obtaining nuclear sequences from the Sima remains.

Genetic material was recovered from an incisor and a molar tooth, a fragment of a thighbone and a shoulder blade. Useful sequences were obtained from the incisor tooth and the thighbone fragment. The results have shown that the Sima hominins were, after all, more closely related to Neanderthals than they were to Denisovans. The Sima hominins were thus either early Neanderthals or closely related to the ancestors of Neanderthals after diverging from a common ancestor shared with the Denisovans. The age of the Sima remains is compatible with earlier estimates that the Neanderthal/Denisovan split occurred between 381,000 and 473,000 years ago. Based on the correctness of these estimates, modern humans diverged from Neanderthals 550,000 to 765,000 years ago – too early for later examples of Homo heidelbergensis such as Arago or Petralona to belong to a population ancestral to both Neanderthals and modern humans. The true common ancestor may be Homo antecessor, which was present in Spain from 1.2 million to 800,000 years ago and might have been responsible for the hominin footprints discovered at Happisburgh, England, in May 2013. However, this species has yet to be identified in Africa and may be a European variant of Homo erectus that migrated from Asia.

The Denisovan affinities of the mitochondrial DNA are still unexplained. One possibility is that the common ancestor carried mitochondrial lineages present in both, but later eliminated from the Neanderthals. The authors noted that this requires an explanation for the presence of two deeply divergent mtDNA lineages in the same archaic group, one that later recurred in Denisovans but disappeared from the Neanderthals; and one that became fixed in Neanderthals. The required explanation might be later population bottlenecks that are known to have affected Neanderthal populations. However, the authors preferred explanation is that the mitochondrial genomes of later European Neanderthals was acquired by interbreeding with hominins from Africa. This might explain the absence of Neanderthal-derived morphological traits in some European Middle Pleistocene hominins such as Ceprano and Mala Balanica.

Meyer, M. et al., Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature (Published online) (2016).


Sima de los Huesos hominins are proto-Neanderthals

New study supports ‘accretion’ model

A new study, published in the journal Science, has provided support for the ‘accretion’ model of Neanderthal evolution. ‘Classic’ Neanderthals, i.e. humans possessing the full suite of Neanderthal characteristics, do not appear in the fossil record until 130,000 years ago. However, French palaeoanthropologist Jean-Jacques Hublin has proposed that Neanderthal characteristics appeared gradually over time, in a piecemeal fashion.

Thus, for example if Feature X appeared in one population and Feature Y in another, then interbreeding between the two populations would have resulted in a population possessing both Features X and Y. Over time, populations gradually acquired the full suite of Neanderthal characteristics by a process of accretion, resulting in a gradual transition from Homo heidelbergensis to Neanderthal. The accretion model explains ‘proto-Neanderthal’ features seen on certain fossils dating to the period prior to the appearance of the ‘classic’ Neanderthals. These include a 400,000-year-old fragmentary skull from Swanscombe in England and the 225,000-year-old Steinheim skull from Stuttgart, Germany.

Much of the evidence we have regarding Neanderthal origins comes from a single site in the Sierra de Atapuerca of northern Spain, near the city of Burgos: a Middle Pleistocene human burial pit known as Sima de los Huesos. The name translates – rather appropriately – as ‘the Pit of Bones’. Sima de los Huesos is a small muddy chamber lying at the bottom of a 13 m (43 ft.) chimney, lying deep within the Cueva Mayor system of caves. Investigation of the site has proved to be long and difficult. The most immediate problems are logistical. The cramped site is located more than 500 m (⅓mile) from the mouth of the Cueva Mayor and is hard to access, necessitating at times crawling on the stomach. Another problem is the disturbance to the site caused by the many generations of souvenir and fossil hunters. Systematic excavation commenced in 1984 and has continued ever since. To date, over 2,000 fragmentary hominin fossils have been recovered, including three skulls. In total, the remains are thought to represent at least 32 individuals of both sexes. It is likely that the site was simply used for the hygienic disposal of the dead, because there is no evidence to suppose that any of the individuals were deliberately killed and the bones show no sign of injuries caused by spears or clubs.

Study of this enormous collection of bones is still in progress, and is likely to continue for some time yet as the site yields further fossils. However, it has become clear that the fossils show a mixture of Homo heidelbergensis and Neanderthal characteristics, just as would be expected if the accretion model is correct. The key question is how old is the site? Uranium series dates obtained in 2007 suggested that they were at least 530,000 years old, making the Sima people older than some Homo heidelbergensis remains from southern Europe and the Balkan region that show no incipient Neanderthal characteristic features.

The new study considered 17 crania, including seven new specimens. The sample shows a consistent morphological pattern with derived Neanderthal features present in the face and anterior of the cranial vault, many of which are adaptations to aid chewing of food. This suggests that facial modification was the first step in the evolution of the Neanderthal lineage, consistent with the accretion model evolution, with different anatomical features evolving at different rates.

The researchers also used a variety of techniques including combined electron spin resonance/uranium series to obtain a revised date of 430,000 years old, which gives a far better fit with the accretion model.

Arsuaga, J. et al., Neandertal roots: Cranial and chronological evidence from Sima de los Huesos. Science 344 (6190), 1358-1363 (2014).