530,000 years old Spanish hominins were closely related to Denisovans

Mystery of Sima de los Huesos ‘proto-Neanderthal’ mitochondrial genome.

Sima de los Huesos – ‘the 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. Human remains dating to the Middle Pleistocene were first discovered there in 1976, and systematic excavation has been in progress since 1984. Investigation of the cramped site has proved to be long and difficult – it is located more than 500 m (⅓ mile) from the mouth of the Cueva Mayor and is hard to access, necessitating at times crawling on the stomach. 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. Many of the remains are of adolescents and young adults, though, the pattern of mortality was probably quite normal for the time, and a similar peak in adolescence has been found at a site at Krapina in Croatia. There is no evidence for violence and the deaths could simply be the result of hunting accidents and childbirth complications. Hunting accidents were probably not uncommon among inexperienced young hunters and women likely fell pregnant soon after commencing menstruation (Pettitt, 2005).
Uranium-series dating suggests that the remains are least 530,000 years old (Bischoff, et al., 2007), and display a mixture of Homo heidelbergensis and Neanderthal features. For this reason, the  Sima de los Huesos hominins are often described as ‘proto-Neanderthal’ (Klein, 2009), although it has also been argued that they were a species distinct from both Neanderthals and Homo heidelbergensis rather than an intermediate between the two (Tattersall, 2002).

In a newly-published study, researchers at the Max Planck Institute for Evolutionary Anthropology have reported the sequencing of the almost-complete mitochondrial genome of one of the Sima de los Huesos hominins. The mitochondrial DNA was extracted from a thigh bone. An estimated age of 400,000 years was obtained by comparison with other, younger ancient DNA sequences dated by direct means. This is rather more recent than the uranium series dates for the site, but still by far the oldest hominin DNA ever recovered. The previous record-holder was no more than 100,000 years old.

Given the geographical location of the Sima de los Huesos and the apparent affinities of the hominins to Neanderthals, it was expected that the material would show affinity to genetic sequences obtained from later Neanderthal remains. Instead, it more closely resembled ancestral Denisovan mitochondrial DNA (Meyer, et al., 2013).

The Denisovan genome, first identified Denisova Cave in the Altai Mountains of southern Siberia, has been found in the modern populations of New Guinea and Island Southeast Asia, implying that the Denisovan range had once extended from the deciduous forests of Siberia to the tropics. This is a wider ecological and geographic region than any other hominin species, with the exception of modern humans (Reich, et al., 2011); but could their range have extended all the way to Europe?

It is likelier that the Sima de los Huesos hominins were the common ancestors of both the Neanderthals and the Denisovans. Mitochondrial lineages originally present in both lineages subsequently disappeared from the Neanderthals, but persisted in the Denisovans. They could have been lost from the Neanderthal line as a result of a population bottleneck of the type known to have affected later Neanderthal populations (Dalén, et al., 2012).

References:

1. Pettitt, P., in The Human Past, edited by Scarre, C. (Thames & Hudson, London, 2005), pp. 124-173.

2. Bischoff, J. et al., High-resolution U-series dates from the Sima de los Huesos hominids yields 600 +/-66 kyrs: implications for the evolution of the early Neanderthal lineage. Journal of Archaeological Science 34, 763-770 (2007).

3. Klein, R., The Human Career, 3rd ed. (University of Chicago Press, Chicago, IL, 2009).

4. Tattersall, I., in The Speciation of Modern Homo sapiens, edited by Crow, T. (Oxford University Press, Oxford, 2002), pp. 49-59.

5. Meyer, M. et al., A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature (Published online) (2013).

6. Reich, D. et al., Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania. American Journal of Human Genetics 89, 1-13 (2011).

7. Dalén, L. et al., Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Molecular Biology and Evolution 29 (8), 1893-1897 (2012).

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Mesolithic hunter-gatherers persisted in Central Europe for 2,000 years after arrival of farmers

Study indicates that foragers maintained way of life alongside farming communities.

Farming spread across Europe from Southwest Asia between 6500 and 4000 BC, but interactions between the indigenous Mesolithic hunter-gatherers and incoming Neolithic farmers are poorly understood. The general view is that hunter-gathering disappeared soon after the arrival of agriculture, but whether the hunter-gatherers took up farming themselves or simply died out remains uncertain.

In order to investigate relationships between foragers and farmers, researchers examined Mesolithic and Neolithic samples from Blätterhöhle, a cave site near Hagen in North Rhine-Westphalia, Germany (Bollongino, et al., 2013). The cave contained the remains of around 450 Neolithic and Mesolithic individuals. It is likely that it was a burial ground, and that these individuals were deposited there deliberately. Radiocarbon dating has revealed two phases of occupation: a Mesolithic occupation from 9210 to 8340 BC, and a Late Neolithic occupation from 3986 to 2918 BC.

Stable isotope analysis and ancient mitochondrial DNA extraction was carried out on the bones and teeth of 29 individuals. Isotopic ratios of sulphur, nitrogen and carbon in human remains can provide an insight into the diet of an individual while they were alive. Mitochondrial DNA can trace maternal ancestry.

Of the 29 individuals sampled, 25 yielded usable mitochondrial DNA; five from the Mesolithic occupation and 20 from the Late Neolithic occupation. The five Mesolithic-era individuals all belonged to mitochondrial haplogroup U, in common with other pre-Neolithic hunter-gatherers of central, eastern and northern Europe. More unexpectedly, twelve of the Neolithic-era individuals also belonged to haplogroup U. This haplogroup is rare among Late Neolithic farmers, and suggests a surprising persistence of Mesolithic maternal ancestry. The remaining eight individuals belonged to typical Neolithic haplogroups.

Stable isotope analysis indicated the existence of three distinct groups. The first, comprising the Mesolithic-era individuals, subsisted on a diet of wild foods typical of that found at other inland Mesolithic sites. The second group comprised Late Neolithic individuals with a diet of domesticated animals typical of German Neolithic sites. The third group was also from the Late Neolithic, but diet was unusual: low in plant and animal protein and high in freshwater fish.

The members of this third group all belonged to mitochondrial haplogroup U, whereas members of the contemporary second group were a mixture of Mesolithic and Neolithic haplogroups. Thus it appears that a group of fisher-foragers were living alongside a group of farmers in the fourth millennium BC, which is around 2,000 years after agriculture reached central Europe. That both groups used the Blätterhöhle cave site at the same time indicates that they were near-neighbours.

Ethnographic data shows that such communities do live side by side, commonly exchanging food; for example cereals for fish. While forager women do marry into farming communities, the reverse is very rare as women from farming communities regard it as marrying down. The mitochondrial results are consistent with the ethnographic picture: no Neolithic haplogroups were found among the fisher-foragers; but the Mesolithic haplogroup U was present among the farmers.

It is unclear just how prevalent such forager communities were in Late Neolithic Europe, but the Blätterhöhle results are the strongest indication yet that such genetically-distinct communities persisted long after the arrival of farming. The ultimate fate of these communities remains uncertain. The authors of the study suggest that some groups may have eventually changed over to farming, although it has been suggested that incoming farmers would rapidly appropriate all the prime farmland, making such a switch problematic (Bellwood, 2005).

References:

1. Bollongino, R. et al., 2000 Years of Parallel Societies in Stone Age Central Europe. Science 342, 479-481 (2013).

2. Bellwood, P., First Farmers (Blackwell Publishing, Oxford, 2005).