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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