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).


‘Iceman’ stomach bug points to more complex picture of early European settlement

Researchers obtain genome of Helicobacter pylori from 5,000-year-old stomach contents

The stomach bacterium Helicobacter pylori is found in roughly half of the world’s present-day population, although it causes symptoms in only around 10 to 15 percent of cases. The bacterium’s association with humans is very ancient, possibly originating in East Africa 58,000 years ago. Since then, various strains have emerged as humans dispersed around the world. Thus differing strains reflect differing geographical origins and are informative about past human migrations.

The European strain hpEurope is believed to have resulted from hybridization between two ancestral strains known as AE1 and AE2. It is thought that AE1 emerged in Central Asia and later evolved into the present-day strain hpAsia2. AE2 is thought to have arisen in Northeast Africa. The two strains have been thought to have hybridized in Southwest Asia 50,000 years ago, with the recombined strain arriving in Europe when populations expanded after the Last Glacial Maximum.

To test this model, researchers obtained a genome of the bacterium from the stomach contents of ‘Ötzi’, the frozen 5,000 year old corpse that was found in 1991 in the Ötztal Alps on the border between Austria and Italy. Despite the age of Ötzi’s remains, it was thought that any H. pylori present would be similar to the present-day hpEurope strain.

Instead, it turned out that Ötzi was carrying a strain that most closely resembled hpAsia2, which is rare in modern Europeans. This suggests that the hybridisation with the African H. pylori strain actually occurred more recently than 5,000 years ago, in turn implying that there was a Chalcolithic migration from Africa. The study presents interesting evidence that the history of human settlement of Europe during this period is more complex than previously believed.

Maixner, F., Krause-Kyora, B., Turaev, D., Herbig, A. & Hoopmann, M., The 5300-year-old Helicobacter pylori genome of the Iceman. Science351 (6269), 162-165 (2016).

Ancient DNA reveals more extensive Neolithic back migrations to Africa from Eurasia

Sequenced genome of 4,500-year-old Ethiopian male provides genetic baseline for researchers

Modern humans are generally accepted to have originated in Africa, and the genomes of native Africans is therefore of great importance in reconstructing early migrations as our species dispersed around the world as it provides a baseline against which later events can be viewed. A problem for geneticists is the back migrations from Europe and Southwest Asia that have occurred within historical times, which act as a confounding factor when working with genetic data from present-day populations.

One way by which the problem could be solved is to obtain ancient DNA from prehistoric human remains, but this has proved difficult with only mitochondrial DNA being obtained up until now. However, in 2012, archaeologists excavated the burial of an adult male in Mota Cave, a riverside cave discovered the year before in the highlands of southwestern Ethiopia. Radiocarbon remains established that the remains were 4,500 years old, predating Eurasian migrations and the dispersal of Bantu farmers which spread agriculture across much of sub-Saharan Africa.

Conditions in the cave favoured the survival of ‘Mota’s’ DNA and it proved possible to sequence his genome. It was found that he was closely related to present-day Ethiopian populations, and in particular to the Ari, a group of Omotic speakers from southern Ethiopia, located to the west of the highland region where Mota lived. This was unsurprising and confirmed the view that there had been population continuity in this relatively isolated region over the last 4,500 years.

The researchers then searched for the source of the later Eurasian admixture by assuming that the present-day Ara genome is a genetic mix of Mota plus the source. It was found that the closest match was with Neolithic LBK farmers from Stuttgart and with present-day Sardinians. The latter are known to be the closest contemporary match to early Eurasian Neolithic farmers. The implication is that the genetic backflow into Africa came from the same source as the Neolithic expansion into Europe from Anatolia. These farmers were presumably responsible for the archaeologically-attested arrival of wheat, barley and other domesticated Southwest Asian crops in Africa around 3,000 years ago.

The next step was to use Mota as an African genetic baseline and the Neolithic LBK as the source of the Eurasian component to estimate the magnitude and geographic extent of historical migrations, without having to use present-day populations. It was found that the Eurasian genetic backflow was substantially higher than previously believed, with an additional 4 to 7 percent of the genome of most African populations tracing back to a Eurasian source. The geographical impact was also far greater than previous estimates suggest, extending all the way to West and South Africa. Even the Yoruba and Mbuti, often used as baselines in genetic studies, were found to have a significant Eurasian component, albeit less than in East Africa.

The Mota data has thus proved to be extremely informative about Neolithic migrations and obtaining even earlier African genomes would be highly desirable. Unfortunately, the African climate does not favour the preservation of DNA, but it is to be hoped that as sequencing techniques improve more ancient African genomes will become available.

Llorente, M. et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350 (6262), 820-822 (2015).

Peopling of the New World remains contentious

New genetic studies reach differing conclusions

It is generally accepted that the humans first reached the New World by crossing the land bridge between Siberia and Alaska during the last Ice Age. However, the number of migrations and their timing has been debated for many decades.

The Paleoamerican model states that the earliest Americans or Paleoamericans were replaced by a second, separate wave of migrants from which today’s Native Americans are descended. The model is based on apparent differences in craniofacial morphology between some early fossil remains and more recent Native American. Note that this hypothetical second migration is distinct from the much later migrations responsible for around half of Aleut-Eskimo ancestry, and a tenth of Na-Dene ancestry.

Two new studies, published respectively in the journals Science and Nature, have reached opposing conclusions. Publishing in Science, Raghavan and colleagues analysed whole genomes of 31 present-day people from the New World, Siberia and Oceania, 23 ancient New World genomes and single nucleotide polymorphism genotypes from 79 present-day people from the New World and Siberia. The ancient DNA included samples from a 4,000 year-old Saqqaq individual from Greenland and the 12,600 year-old Anzick-1 (Clovis culture) individual from Montana.

They found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the New World in a single migration from Siberia no earlier than 23,000 years ago and after no more than 8,000 years of isolation in Beringia. Around 13,000 years ago, these ancestral Native Americans diversified into two basal genetic branches: one that is now dispersed across North and South America and another restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians, including Siberians and, more distantly, Australo-Melanesians. But populations believed to be relict Paleoamericans including the Pericúes from Mexico and the Fuego-Patagonians, are not directly related to modern Australo-Melanesians, contrary to the predictions of the Paleoamerican Model.

The second study, published by Skoglund and his colleagues in Nature, featured genomic data from 63 Native Americans, who belonged to 21 diferent populations, and showed no discernable evidence of European or African ancestry. Results showed that some Amazonian Native Americans descend partly from a founding population with an ancestry more closely related to Aboriginal Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This genetic signature is not seen in present-day Northern and Central Native Americans, or in the Anzick-1 genome. The source population for this Australasian-related ancestry was named ‘Population Y’ after Ypykue´ra, which means ‘ancestor’ in the Tupi language family spoken by the Suruı´ and Karitiana.

The researchers suggested that Population Y had already admixed with a lineage related to First Americans by the time it reached Amazonia, and that it was the explanation for the differing craniofacial morphology noted above. However, no ancient DNA directly extracted from remains with this morphology, so the results did not prove that these people were Population Y. The absence of linkage disequilibrium in Population Y suggests that it arrived in the New World a long time ago. Furthermore, while it shows a distant genetic affinity to Andamanese, Australian and New Guinean populations, it is not particularly closely related to any of them, suggesting that its ultimate source in Eurasia no longer exists.

It is to be hoped that future ancient DNA studies provide further insight into the results of the Skoglund study.

Skoglund, P. et al., Genetic evidence for two founding populations of the Americas. Nature 525, 104-108 (2015).
Raghavan, M. et al., Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349(6250), 841, aab3884-1-10 (2015).



Early modern human from Romania had recent Neanderthal ancestor

Ancient DNA from Peştera cu Oase demonstrates inbreeding no more than four to six generations previously

The cave site of Peştera cu Oase (‘Cave with Bones’) in Romania has yielded some of the earliest fossil remains of modern humans in Europe. The remains of three individuals recovered from the site include a largely-complete lower jawbone (Oase 1), the near-complete skull of a 15-year-old adolescent, and a left temporal bone. The remains are around 40,000 years old and exhibit a mosaic of modern and archaic features. Modern features include the absence of browridges, a narrow nasal aperture, and a prominent chin; but there are also archaic features such as a wide dental arcade and very large molars. There is little doubt that they are modern humans and not Neanderthals, but some aspects of the morphology are consistent with Neanderthal ancestry.

Researchers have now recovered ancient DNA from the Oase 1 jawbone and sequenced the genome. They report that between 6 to 9 percent of the genome is of Neanderthal origin, a higher percentage than for any other modern human genome sequenced to date. Three chromosomal segments of Neanderthal DNA are of considerable length, suggesting that the Neanderthal contribution to the Oase 1 individual occurred so recently in their past that the chromosomal segments of Neanderthal origin had little time to break up due to recombination. The researchers turned their attention to seven segments of the genome that appeared to be of recent Neanderthal origin and from the genetic lengths of these, implied that Oase 1’s Neanderthal ancestor had lived no more than four to six generations earlier, or less than two hundred years.

The existence of such a recent Neanderthal ancestor casts doubts on theories that suggest that interbreeding occurred only very occasionally, or was confined to an early episode soon after modern humans first left Africa. However, the researchers failed to establish a clear relationship between the Oase 1 individual and later modern humans in Europe, suggests that they may have been a member of an early modern human population in Europe that eventually died out without contributing much to later European populations.

Fu, Q. et al., An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216-219 (2015).

Kennewick dispute set to reignite

Ancient DNA confirms Native American affinities

Kennewick Man died about 8,600 years ago and was between 40 to 55 years old at the time of his death. In 1996, his skull and some other skeletal parts were discovered in the Columbia River, Kennewick, Washington State. The find was of interest not just to anthropologists but also to Native Americans, who refer to him as the Ancient One. The Plateau people of the Pacific Northwest claimed an ancestral relationship and requested repatriation of the remains as provided for under US federal law (Native American Graves Protection and Repatriation Act or NAGPRA). The land where the remains were found is managed by the US Army Corps of Engineers, who announced that they were willing to hand over the remains. This in turn precipitated a lawsuit from scientists wishing to study the remains.

The plaintiffs’ claim was based on the morphology of the skull, which is long and narrow, with a narrow face, and a jutting chin. It is quite unlike the broad-headed, broad-faced appearance typical of Native Americans and resembles that of certain Pacific populations, in particular the Ainu and Polynesians. It was argued that Kennewick Man belonged to a population that reached America before the ancestors of the present-day Native Americans, and that the request for repatriation of the remains must therefore be rejected. In 2004, the plaintiffs’ claim was upheld by a judicial ruling.

However, subsequent discoveries have cast doubt on the claim that Native Americans are descended from migrants that replaced an earlier American population. Remains have been found that are even older than those of Kennewick Man, yet fall comfortably within the morphological range of present-day Native Americans. Other remains have yielded mitochondrial DNA belonging to haplogroups only found in Native American populations. Genetic studies have failed to find any evidence for a replacement of early Paleoindians by ancestors of today’s Native Americans.

It has been suggested that skull data has simply been misinterpreted. In one study, researchers applied statistical methods to skulls from all over the world, dating from around 15,000 years ago to the present day. They found that when shape variation was considered over a wide geographical range or over a long period of time, the skulls formed a continuum rather than discrete categories. The same pattern was also seen when New World skulls were considered on their own. The supposed Paleoindian and Native American forms were no more than extremes at opposite ends of a continuum, and most of the New World skulls fell well between the two extremes.

Following the 2004 ruling, study of Kennewick Man continued, but only now have researchers obtained ancient DNA from the remains. A team led by Morten Rasmussen has published its results in the journal Nature and they show that Kennewick Man is more closely related to present-day Native Americans than to any other population worldwide. Based on a comparison with Native American groups for whom genome-wide data is available, several groups are apparently descended from population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), which is one of the five groups claiming Kennewick Man.

A renewed claim for repatriation now seems inevitable.

Rasmussen, M., Sikora, M., Albrechtsen, A., Korneliussen, T. & Moreno-Mayar, J., The ancestry and affiliations of Kennewick Man. Nature 523, 455-458 (2015).
Jantz, R. & Owsley, D., Variation Among Early North American Crania. American Journal of Physical Anthropology 114, 144-156 (2001).

Is the steppe migration theory of Indo-European origins correct after all?

Genetic study challenges Anatolian farmer hypothesis

One of the longest-running debates in the study of prehistory is the origin of the Indo-European language family. This group includes languages spoken from Great Britain and Ireland to India the steppes of Central Asia, and a connection between them was established as far back as the late eighteenth century. It is assumed that all originated from a single mother tongue, Proto-Indo-European (PIE), but where was PIE spoken?

Until the 1980s, the favoured Indo-European homeland was the Pontic-Caspian steppes north of the Black Sea and Caspian Sea. In a series of papers published from the 1950s through to the 1970s, Lithuanian-born Marija Gimbutas identified the Proto-Indo-Europeans with the Kurgan culture, named for a Russian word for the burial mounds with which the culture is associated. The Kurgan people originated in the lower Volga basin and the lower Dnieper region around 4500 BC. They lived as nomadic pastors, with an economy based on sheep, goats, cattle and pigs. Gimbutas saw them as highly-mobile, warlike people who used ox-drawn wagons and horses for transport. Between 4400 and 2800 BC, the Kurgan people mounted a series of hostile incursions from the steppes into Europe, Anatolia, the Caucasus, India and Central Asia. The peaceful, settled Neolithic farmers living in the regions were no match for the invaders, whose language (PIE) and culture came to predominate.

Although some disputed the warlike nature of the Kurgan people, the steppe hypothesis was widely accepted. However, in 1987, British archaeologist Colin Renfrew put forward a rival view in which he claimed that PIE was spoken and dispersed by Neolithic farmers originating from Anatolia before 6500 BC. The spread of agriculture distributed their language over a vast area. From Anatolia, the expansion had moved into Greece and onwards across Europe in wave of advance, expanding generation by generation as populations grew. Renfrew offered a choice of two scenarios as to the spread of the Indo-Iranian sub-family of languages: the first proposed a simple wave of advance similar to that proposed for Europe. The second invoked a modification of the steppe-invader model. Once the European wave of advance reached the steppe, nomadic pastoralism developed and the pastors moved swiftly east across the steppes and into Iran and northern India. Renfrew later came down in favour of this second scenario.

The Renfrew model is supported by archaeological and genetic evidence for an agricultural expansion into Europe, with Neolithic farmers both replacing and intermarrying with existing Mesolithic hunter-gatherers. Further support has come from a 2012 study in which Bayesian statistics were applied to Indo-European languages. The results suggested that PIE originated in Anatolia and began to break up into its daughter tongues between 7500 and 6000 BC.

Despite the success of the Anatolian hypothesis, it is not without its faults. A common criticism is that PIE contains reconstructed words for the wheel and wheeled vehicles, which were not invented until long after the agricultural expansion into Europe.

The main weakness of the steppe model has been a lack of evidence for a major migration from the Eurasian steppe at that time. However, a study of ancient DNA obtained from just under a hundred Europeans living between 6000 and 1000 BC may address this issue. The results confirm that farmers reached Europe from Southwest Asia between 6000 and 5000 BC, but they also indicate a second, later migration. A close match was found between Yamnaya culture steppe pastors from Russia and Ukraine, dating to 3000 BC, and individuals of the Corded Ware culture of Northern Europe, dating to 2500 BC. The similarities indicate a large-scale migration into Europe from the east. While the language these migrants spoke is unknown, it probably originated in the Yamnaya homeland.

Consistent with these results is a new linguistic study suggesting that PIE originated around 4000 BC rather than between 7500 and 6000 BC. However, the methodology used has been criticised by the authors of the 2012 study.

It is also possible that the Yamnaya data represents a secondary migration of people descended from the original PIE-speaking Anatolian farmers, in which case the Yamnaya people might have spoken a derived Indo-European language ancestral to the present-day Balto-Slavic group rather than PIE itself.

Overall, the genetic results suggest that the true picture might be a synthesis of both Anatolian and steppe-migration models.

(W. Haak et al.; 2015)