Friday, 27 June 2014

Neanderthals ate their greens

Analysis of 60,000 – 45,000 year old coprolites provides insight into Neanderthal diet

Neanderthal dietary reconstructions have, to date, been based on archaeological evidence, stable isotope data and studies of dental calculus. These suggest that they were predominantly meat eaters, although plant foods made a contribution to their diet. Hitherto, there has been no direct evidence for an omnivorous diet.

A new study, published in the open access journal PLoS One has presented direct evidence of Neanderthal diet using faecal biomarkers, which are a valuable analytical tool for identifying diet. Researchers applied gas chromatography and mass spectroscopy techniques to coprolites (fossil faeces) from the Neanderthal site of El Salt at Alicante, Spain. The coprolites were recovered from sediments gathered from a number of levels at the site, which was repeatedly occupied by Neanderthals between 60,000 and 45,000 years ago.

The team focussed on chemical processes associated with the action of bacteria in the gut. They found a high proportion of coprostanol, which the gut bacteria produce from cholesterol and which is associated with the consumption of meat. However, they also recorded significant quantities of 5β-stigmastanol, which is associated with plant consumption.

Further tests were necessary to confirm that the coprolites were of human origin. The conversion of cholesterol into coprostanol is not unique to humans, but related molecules were also identified in proportions that ruled out other omnivores.

1.  Ainara Sistiaga, A., Mallol, C., Galván, B. & Everett Summons, R., The Neanderthal Meal: A New Perspective Using Faecal Biomarkers. PLoS One 9 (6), e101045 (2014).


Friday, 20 June 2014

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 ( mile) 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.


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

Sunday, 15 June 2014

Interbreeding between Neanderthals and modern humans

What we know now

Whether or not modern humans interbred with Neanderthals is a question that has long been of interest to both scholars and lay people alike, but it was not until May 2010 that strong evidence emerged that the answer to the question was ‘yes, probably’.

A project to sequence the Neanderthal genome was commenced in 2006 at the Max Planck Institute for Evolutionary Anthropology (Green, et al., 2006; Green, et al., 2008), and in May 2010, researchers published a first draft of the Neanderthal genome (Green, et al., 2010). With the initial announcement came the dramatic news that made headlines around the world. It turned out that between one and four percent of the genome of modern non-Africans was derived from Neanderthals. In other words, the answer to the million dollar question was ‘yes, they did interbreed – but not in Africa’. The researchers compared the Neanderthal genome with those of five present-day individuals: two indigenous Africans (one San from South Africa and one Yoruba from West Africa) and three Eurasians (one from Papua New Guinea, one from China and one from France). The results showed that Neanderthals were more closely related to non-Africans than to Africans. This is not particularly surprising, as Neanderthals are not known to have lived in Africa. Any interbreeding has generally been supposed to have occurred within the known range of the Neanderthals, in Europe and western Asia. What was unexpected was that no difference was found between Papua New Guinean, Chinese and European individuals in terms of their degree of relatedness to Neanderthals.

The implication is that the interbreeding must have occurred before the ancestors of the present-day Asian, Australasian and European populations diverged from one another – presumably in Southwest Asia soon after modern humans first left Africa, and long before they reached Europe. If the population that left Africa was small, only limited interbreeding would be necessary to leave the Neanderthal contribution fixed in the modern non-African genome for all time, as numbers increased during the subsequent peopling of the world.

Interbreeding was not the only way to interpret these initial results, and the authors of the report said that they could not rule out the possibility that their results reflected substructure in the early modern human populations. In fact, a later independent study favoured this possibility, using a mathematical model to represent a connected string of regional populations spanning Africa and Eurasia. After the string split, the Eurasian and African parts of the range subsequently evolved into Neanderthals and modern humans respectively. For the latter, groups geographically closest to the split (i.e. in North Africa) remained more closely related to Neanderthals than those further south. It was assumed that the non-African world was subsequently populated by a dispersal of one of these northerly groups from Africa (Eriksson & Manica, 2012).

Subsequent work by independent researchers ruled out this substructure scenario (Sankararaman, et al., 2012; Yang, et al., 2012), and appeared to back the view that there had been a single episode of interbreeding very early on in the Out of Africa expansion that led to the peopling of the non-African world (Yotova, et al., 2011). The findings that some Africans do after all carry a Neanderthal genetic signature (Sánchez-Quinto, et al., 2012; Wall, et al., 2013) is not a major problem, as this can be accounted for in terms of a pre-Neolithic ‘Back to Africa’ migration of modern humans from Southwest Asia (Olivieri, et al., 2006; González, et al., 2007; Hodgson, et al., 2014).

A complication is that studies have found no trace of a Neanderthal component in mitochondrial DNA (Caramelli, et al., 2003; Serre, et al., 2004; Caramelli, et al., 2008). On the ‘brief encounter’ picture, this could mean crossbred women were sterile, and thus their mitochondrial DNA was never passed to subsequent generations. Another possibility is that interbreeding between Neanderthals and modern humans was very rare, with only one such event every couple of centuries. The reason could be limited biological compatibility, or it could be that the two mostly avoided interspecific mating. Such a low rate of interbreeding would account for the absence of Neanderthal mitochondrial DNA from the present-day gene pool, but it would still be sufficient to account for the observed levels of Neanderthal DNA in the nuclear genome. However, it would require interbreeding to occur across the whole of the Neanderthal range, not just in Southwest Asia (Currat & Excoffier, 2011; Neves & Serva, 2012).

Between 2012 and 2014, further studies showed that the original conclusion that all non-African populations were related equally to Neanderthals was incorrect, and that the proportion of Neanderthal ancestry in East Asians is 20 to 40 percent higher than it is in Europeans. This implies that interbreeding could not all have happened at a single time and place; some of it must have happened after the ancestral East Asian and European populations separated (Meyer, et al., 2012; Wall, et al., 2013; Vernot & Akey, 2014). Given that Neanderthals lived in Europe but are not known from East Asia, this is unexpected. However, their known range extents to the Altai region north of the Himalayas and a subsequent episode of interbreeding might have occurred there. Alternatively, it is possible that the Neanderthal range actually extended further south, as we know to have been the case for the Denisovans.

The latest work suggests that around 20 percent of the Neanderthal genome survives in the present-day population, albeit individuals each only possess a small fraction of this amount (Vernot & Akey, 2014). 

Many useful Neanderthal genes have been incorporated into the modern genome; for example those involved with the production of keratin, a protein that is used in skin, hair and nails. Possibly the Neanderthal versions of these genes were more suited to the harsh conditions of Ice Age Europe (Sankararaman, et al., 2014). In East Asian populations, many genes involved with protection from UV are of Neanderthal origin (Ding, et al., 2014).

Some deleterious genes also have a Neanderthal connection, including those implicated in Type 2 diabetes and Crohn’s disease. Significantly, Neanderthal DNA was largely absent from the X chromosome and genes associated with modern testes. The implication is that Neanderthal DNA in these regions led to reduced male fertility, or sterility (Sankararaman, et al., 2014), consistent with the view that Neanderthals and modern humans were at the limits of biological compatibility.

These results show that natural selection had a significant role, with both positive and negative selection determining Neanderthal gene frequencies. It is entirely possible that selective factors could be at least partially responsible for the higher incidence of Neanderthal DNA in East Asian populations.
It is now clear that the interactions between Neanderthal and modern populations were complex; and that we are still at a very early stage of understanding them.

1. Green, R. et al., Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330-336 (2006).

2. Green, R. et al., A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134, 416–426 (2008).

3. Green, R. et al., A Draft Sequence of the Neandertal Genome. Science 328, 710-722 (2010).

4. Eriksson, A. & Manica, A., Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. PNAS 109 (35), 13956–13960 (2012).

5. Sankararaman, S., Patterson, N., Li, H., Pääbo, S. & Reich, D., The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genetics 8 (10) (2012).

6. Yang, M., Malaspinas, A., Durand, E. & Slatkin, M., Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity. Molecular Biology and Evolution 29 (10), 2987–2995 (2012).

7. Yotova, V. et al., An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations. Molecular Biology and Evolution 28 (7), 1957-1962 (2011).

8. Sánchez-Quinto, F. et al., North African Populations Carry the Signature of Admixture with Neandertals. PLoS One 7 (10) (2012).

9.  Wall, J. et al., Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194, 199-209 (2013).

10. Olivieri, A. et al., The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa. Science 314, 1757-1770 (2006).

11. González, A. et al., Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 8 (223) (2007).

12. Hodgson, J., Mulligan, C., Al-Meeri, A. & Raaum, R., Early Back-to-Africa Migration into the Horn of Africa. PLoS Genetics 10 (6), e1004393 (2014).

13. Caramelli, D. et al., Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. PNAS 100 (11), 6593–6597 (2003).

14.  Serre, D. et al., No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS Biology 2 (3), 0313-0317 (2004).

15.  Caramelli, D. et al., A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences. PLoS One 3 (7) (2008).

16.  Currat, M. & Excoffier, L., Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. PNAS 108 (37), 15129-15134 (2011).

17.  Neves, A. & Serva, M., Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. PLoS One 7 (10) (2012).

18.  Meyer, M. et al., A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 338, 222-226 (2012).

19. Vernot, B. & Akey, J., Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science 343, 1017-1021 (2014).

20.  Sankararaman, S. et al., The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354–357 (2014).

21.  Ding, Q., Hu, Y., Xu, S., Wang, J. & Jin, L., Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians. Molecular Biology and Evolution 31 (3), 683-695 (2014).

Monday, 9 June 2014

Neolithic was brought to Europe by maritime colonists

Ancient and modern mitochondrial DNA study links PPNB to modern populations of Cyprus and Crete

In recent years, ancient DNA has been obtained from Neolithic human remains, and this has provided a more reliable picture of the genetic impact of the European Neolithic than was possible with genetic studies of living populations. However, researchers have been hampered by the lack of data from the original farmers of Southwest Asia.

In a new study, published in the open access journal PLoS One Genetics, researchers report the successful extraction of mitochondrial DNA from fifteen out of 63 skeletons recovered from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja’de El Mughara, dating from between 8700 to 6600 BC. 

The genetic profiles were compared with data obtained from human remains associated with the LBK and Cardial/Epicardial European Neolithic cultures. The researchers also looked for possible signatures of the original Neolithic expansion in the gene pools of present-day Southwest Asian and southern European populations, and tried to infer possible routes of the expansion by comparison with the ancient samples. They were able to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain.

They also observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete. However, no such link was found to modern populations of western Anatolia, suggesting that the Neolithic was first introduced into Europe by maritime colonists.


1. Fernández, E. et al., Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS One Genetics 10 (6), e1004401 (2014).


Tuesday, 3 June 2014

KwaZulu-Natal findings refutes technological hiatus during African Middle Stone Age

Post-Howieson’s Poort Sibudan tradition was not ‘unstructured and unsophisticated’

Archaeologists have long believed that the later part of the African Middle Stone Age (MSA) was characterised by conservative technologies punctuated by the appearance of technologically-sophisticated but short-lived technocomplexes such as the Stillbay and Howieson’s Poort traditions of South Africa. These traditions are noted for finely-worked stone points, microliths, tools made from bone, and innovative technologies including pressure flaking and compound adhesives. Various theories involving population collapses have been put forward to account for their disappearance and the reversion to comparatively unsophisticated prepared-core industries.

However, it has been suggested that this phenomenon may be more apparent than real, as the Stillbay and Howieson’s Poort eras have been studied far more closely than the supposed hiatus periods that followed. Recent work at the archaeological site Sibudu, KwaZulu-Natal supports the view. Archaeologists have identified a new technocomplex, which they have named the Sibudan, from the six uppermost lithic assemblages at the site. The new technocomplex dates from around 58,000 years ago, placing its’ beginning just after the end of the Howieson’s Poort era.

While the Sibudan has technological parallels with other contemporary MSA industries, it is typologically and technologically distinct. The six stratified tool assemblages are linked by common features, which identify them as a distinct tradition. Many of these features are considered to be hallmarks of a sophisticated stone tool-making technology, including characteristic tool assemblages with standardised forms and reduction cycles, and the production of standardised blades with soft stone hammers. Overall, the Sibudan refutes the notion that post-Howieson’s Poort stone-knapping technologies were rudimentary or unsophisticated.
The report is published in the open access journal PLoS One.


1.  Will, M. B. G. & Conard, N., Characterizing the Late Pleistocene MSA Lithic Technology of Sibudu, KwaZulu-Natal, South Africa. PLoS One 9 (5), e98359 (2014).