Modern humans interbred with Neanderthals 100,000 years ago

Ancient DNA from Altai Neanderthal female is first evidence of modern human contribution to Neanderthal genome

Ever since the first draft of the Neanderthal genome was published in 2010, it has been known that Neanderthals interbred with modern humans and it is now believed that around twenty percent of their genome survives in the present-day population. Subsequent work revealed the existence of a new human species in the Russian Altai, the Denisovans, and that parts of their genome also survive in the present-day population. It has also been established that the Altai Denisovans also interbred with Neanderthals in the region and with another as yet unidentified archaic species (probably Homo erectus). What has hitherto been absent up is evidence of gene flow from early modern humans into archaic genomes.

To address this issue, researchers investigated the previously-sequenced genome of a Neanderthal woman who lived in the Altai region 50,000 years ago. They found evidence of gene flow from modern humans into the ancestors of the Altai Neanderthal. The source was unclear, but was thought to be a modern population that either split from the ancestors of all present-day Africans, or was one of the early modern African lineages. It was estimated that the implied interbreeding occurred at least 100,000 years ago – well before the previously-reported gene flow from Neanderthals into modern humans outside Africa 47,000 to 65,000 years ago. However, they did not find evidence for similar gene flow from modern humans into either Denisovans or European Neanderthals.

The traditional view that modern humans did not leave Africa and the Levantine/Arabian region until around 60,000 years ago has been refuted by the discovery of teeth lying within the modern range at Fuyan Cave, China, dating to around 100,000 years ago. If modern humans were in China then it is entirely possible that they were also in the Altai at that time. Other possibilities are the Arabian Peninsula, where there is archaeological (though no fossil) evidence for a modern human presence as long ago as 127,000 years ago and Neanderthals were likely to also have been present; and the Levant where there is fossil evidence for both Neanderthals (Tabun) and modern humans (Skhul and Qafzeh) 120,000 to 110,000 years ago.

Reference:
Kuhlwilm, M. et al., Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, doi:10.1038/nature16544 (2015).

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Flores ‘hobbits’ arose from an archaic human species

Study confirms that Flores hominins are not Homo sapiens  

Since their headline-making discovery in 2003, the diminutive hominins from the Indonesian island of Flores have been generally accepted to be a distinctive human species, Homo floresiensis. Popularly referred to as ‘hobbits’, they are widely believed that they owe their small size to a phenomenon known as ‘insular dwarfism’. In the absence of dangerous predators and in a habitat where food is scarce, it was suggested that they ‘downsized’ from their ancestral condition as evolution favoured smaller, less ‘gas-guzzling’ individuals. The ancestral species is often claimed to be Homo erectus, but claims have also been made for more primitive hominins such as Homo habilis or even Australopithecus.

Not everybody accepted that Homo floresiensis was a new human species and among the sceptics was the late Teuku Jacob, an Indonesian anthropologist who claimed that the ‘hobbits’ were modern humans affected by a developmental disorder known as microcephaly. Some years after Jacob’s death, his former colleagues revived the theory, this time claiming that Homo floresiensis were modern humans suffering from Down syndrome.

A newly-published study describes the investigation of the cranial bones of the partial female skeleton LB 1 (popularly and perhaps inevitably known as ‘Flo’). A series of high-resolution scans were taken using an X-ray CT scanner. Comparative scans were also taken of microcephalic specimens used in earlier studies of LB 1. The scans were used to study the bone thickness distribution of the cranial vault and internal bone composition and structure. Cranial vault thickness (CVT) can be diagnostic of a hominin species attribution, and it was found to be thick for LB 1 in absolute terms and even more so in relative terms when the small cranial size is taken into account. By contrast, microcephalic skulls of modern humans are thinner than those of humans unaffected by the condition. It was found that Flo had suffered from a condition known as bilateral hyperostosis frontalis interna, and bore the healed scar of a head injury, but there was nothing to indicate that she had suffered from any developmental disorders of the type suggested by Jacob or his former colleagues.

The researchers showed that LB 1 displays characteristics related to the distribution of bone thickness and arrangements of cranial structures that are primitive traits for hominins, differing from the derived condition of modern humans. This was not seen with the microcephalic skulls.

The study thus rules out the possibility that LB 1 can be assigned to Homo sapiens, but leaves the issue of its true affinities unresolved.

Reference:

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Balzeau, A. & Charlier, P., What do cranial bones of LB1 tell us about Homo floresiensis? Journal of Human Evolution 93, 12-24 (2016).

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Half Moon

Taken on 15 Feb 2016 at 17:26 with Canon Power Shot SX530HS 1/320th sec at f/6.5 ISO 500.

Adverse effects of interbreeding with Neanderthals

Not all ‘imported’ genes were beneficial

Interbreeding with Neanderthals and Denisovans is believed to have introduced many beneficial genes into the modern genome, helping the immune systems of early modern humans to fight pathogens to which they had not previously been exposed. Other ‘imported’ genes include those involved with the production of keratin, a protein that is used in skin, hair and nails, and in East Asian populations, many genes involved with protection from the sun’s UV rays are of Neanderthal origin. It is likely that the transfer of these genes helped early modern humans to adapt to conditions away from their African homeland.

However, a newly-published study suggests that interbreeding with Neanderthals also had a down side. Researchers analysed the electronic health records (EHR) of 28,000 individuals of European origin and integrated the data with high resolution maps of Neanderthal haplotypes across individual modern human genomes. They carried out a large-scale assessment of the functional effects of DNA inherited from Neanderthals on health-related traits in these individuals. Particular use was made of genotype and phenotype data from the Electronic Medical Records and Genomics Network, which is a consortium that links EHR systems combined with patient genetic data from nine sites across the USA.

Genes of Neanderthal origin were found to be associated with smoking addiction, increased risk of depression, incontinence, bladder pain, urinary tract disorders, protein calorie malnutrition, and actinic keratosis (precancerous skin lesions resulting from exposure to the sun). One gene variant was associated with blood coagulation, increasing the risk of strokes. These results follow on from earlier work which implicated increased risk of Crohn’s disease and type 2 diabetes with Neanderthal genes.

Many of these genes would have been advantageous to Neanderthals: for example, the benefits of enhanced blood coagulation would have greatly outweighed the risk of strokes when injuries leading to significant loss of blood were a part of daily life and few people lived past forty. In other cases, genes were probably once advantageous but adverse effects were triggered by the changes in diet following the coming of agriculture in Neolithic times.

Depression can be triggered by disturbed circadian rhythms. It is possible that Neanderthal brain chemistry and skin responses to sunlight were both linked to the lighting conditions and lifestyles of an era when artificial light consisted of torches and camp fires. In which case, the genes might only have become maladaptive with the advent of widespread artificial lighting.

The methodology used by the researchers is likely to provide further insight into the genetic impact of these ancient encounters between Neanderthals and modern humans.

References:

Simonti, C. et al., The phenotypic legacy of admixture between modern humans and Neandertals. Science 351 (6274), 737-741 (2016).

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Milner Hall yields first hominin fossils

Fossils recovered at ‘Cradle of Humankind’ site

Sterkfontein is a set of limestone caves near Krugersdorp, South Africa. It is one of the most important hominin fossil-bearing sites in the world and finds include the female australopithecine Mrs Ples, discovered in 1947 and recently voted No.95 in a list of 100 Great South Africans. Sterkfontein has yielded stone tools in addition to hominin fossils and it is now part of the Cradle of Humankind, a World Heritage Site named by UNESCO in 1999. Most of the finds have been made in Members 4 and 5 of the cave’s sedimentary sequence, but rather less well known is the large underground chamber known as Milner Hall.

It is from Milner Hall that the discovery is reported of a hominin adult upper right molar (M1) tooth and a proximal phalanx finger bone, probably from a left hand. The chamber has previously yielded only stone tools, and association with these suggests that the fossils are 2.18 million years old.

The tooth is broadly closer to Homo than to Australopithecus or Paranthropus. It most closely resembles the Olduvai OH 6 first molar assigned to Homo habilis and a first molar assigned to the recently-proposed Homo naledi. The shape and size of the tooth’s cusps align it to early Homo.

The finger bone is larger and more robust than that of any hominin so far discovered in South Africa. It resembles the Olduvai Homo habilis fossil OH 7, but is much larger. It is markedly curved, within the range of Australopithecus afarensis and suggesting adaptation for tree-climbing, but it lacks other features associated with arborealism, such as a strongly developed flexor apparatus and a mediolaterally expanded diaphysis; these features are present in A. afarensis, Homo habilis and present-day chimpanzees. The finger bone possesses an enigmatic mixture of primitive, derived and unique characteristics. It is not clear whether or not it belonged to the same individual and its taxonomic affinities are at this stage uncertain.

References:

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Stratford, D., Heaton, J., Pickering, T., Caruana, M. & Shadrach, K., First hominin fossils from Milner Hall, Sterkfontein, South Africa. Journal of Human Evolution 91, 167-173 (2016).x

Study refutes claim for early cat domestication in China

Quanhucun ‘cats’ were a different feline species

Genetic studies suggest that the domestic cat (Felis silvestris catus) is descended from the Near Eastern Wildcat (Felis silvestris lybica), a subspecies of the widely-distributed Old World Wildcat. The latter has been associated with humans since the early Neolithic, initially as a commensal that preyed on rodents and other pests in early faming settlements. A cat burial from Cyprus, dating to 7350 BC, shows that cats were valued by humans by this time, but domestication was a much later development. The Cypriot cat was large even for a wildcat and well above the size range for a domestic cat.

In 2014, archaeologists claimed to have found evidence for cat domestication in China from around 3500 BC. The Neolithic site of Quanhucun in Shaanxi Province is associated with millet farmers, who had evidently employed cats to tackle the constant threat of rats and mice to their grain. Stable isotope analysis indicates that the many rats and mice whose remains were found fed on the millet, but in turn they were preyed upon by the cats. The cats were within the modern size range, suggesting that they were domesticated although China lies well beyond the geographical range of the Near Eastern Wildcat. The discovery opened up the possibility that domesticated cats had made their way eastwards from Southwest Asia, or that the Quanhucun cats were domesticated locally from an East Asian subspecies of the Old World Wildcat.

It now turns out that neither was the case. An assessment of the remains by another group of researchers has found that the Quanhucun cats were not domesticated Near Eastern Wildcats but leopard cats (Prionailurus bengalensis), a small wildcat native to the region. The Quanhucun cats seem to have been a domestication of a completely different species of wildcat, but it was evidently not successful in the long term. Domesticated Near Eastern Wildcats reached China around 500 BC, and it is from these that all present-day Chinese cats are descended.

References:

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1.  Vigne, J. et al., Earliest “Domestic” Cats in China Identified as Leopard Cat (Prionailurus bengalensis). PLoS One 11 (1) (2016).

2.  Hu, Y. et al., Earliest evidence for commensal processes of cat domestication. PNAS 111 (1), 116-120 (2014).x

Death at Lake Turkana

Evidence of inter-group violence between East African hunter-gatherers 10,000 years ago

Inter-group violence has long played a part in human affairs, but just how long is unclear. Over the last thirty years, evidence has accumulated that massacres were a frequent occurrence in Neolithic Europe. Mass graves have been found at a number of sites associated with the Linearbandkeramik (LBK) culture dating to around 5,000 BC. In all cases, the victims appeared to have been attacked and killed with weapons associated with farming groups suggesting internecine conflict between LBK groups rather than attacks by local hunter-gatherers.

Evidence has now emerged of much earlier inter-group violence involving hunter-gatherers at Nataruk, west of Lake Turkana, Kenya. At the time in question, the lake extended around 30 km (18 miles) beyond its present limits and Nataruk would have been located near its western margins.

In 2012, the remains of at least 27 individuals were discovered, partly or completely exposed upon the surface of a gravel bar ridge. Most were found fully exposed and fragmented, surviving in varying states of preservation and erosion; 12 individuals were partly preserved articulated in situ. Among these, no burial pit was identified, and no preferred orientation or position of head, face, or body was noted. The total number of individuals at the site is unknown, as only those partly exposed were excavated. The remains included 21 adults (8 men, 8 women, the others of unknown sex) and 6 children. One of the women was in the third trimester of pregnancy.

Excavations also revealed stone tools similar to other Later Stone Age assemblages in the area; and fragments of bone harpoons typical of Early Holocene hunter-fishers of Lake Turkana. The skeletal remains lacked collagen so radiocarbon dates were obtained from associated sediments and shells, and an optically stimulated luminescent date was obtained from lake sediments. Based on these, it was estimated that the Nataruk human remains dated to between 9,500 and 10,500 years ago; consistent with dates obtained for shells, harpoons, and charcoal from sites in the immediate vicinity, and corresponding to a period of early Holocene high water levels in Lake Turkana.

10 of the 12 skeletons found in situ show evidence of major trauma that would have proved fatal in the immediate-to-short term, including five or possibly six cases of head and/or neck probably caused by arrows; five cases of head injury inflicted by a blunt instrument; two cases of knee fracture; two cases of multiple fractures to the right hand; and once case of fractured ribs. Only two of these skeletons show no obvious injury. Four of the skeletons, including both that lacked injuries may have been bound hand and possibly foot at time of death. Three artefacts were found within or embedded in two of the bodies: an obsidian bladelet embedded in a male skull; and a chert lunate and obsidian trapeze, found inside the pelvic and thoracic cavities of a male skeleton. Both the injuries and the embedded projectile points are considered to be diagnostic of inter-group conflict, although there was no evidence of scalping or other trophy-taking, which often observed in prehistoric warfare.

West Turkana at this time supported a substantial hunter-gatherer population. The Nataruk massacre might have resulted from a raid for territory, women, children and stored food. The pursuit of these resources would in later agricultural times make violent attacks upon settlements and the need to defend against these an ever present fact of life. Alternatively, it might have been a simple antagonistic response as two groups came into contact.

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n either case, the deaths at Nataruk are a depressing testimony to the antiquity of inter-group violence and warfare.

References:

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Lahr, M. et al., Inter-group violence among early Holocene hunter-gatherers of West Turkana.; Kenya. Nature 529, 394-398 (2016).

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Humans were in the Arctic 45,000 years ago

Evidence for a human presence inside the Arctic Circle 15,000 years earlier than previously believed

In 2012, archaeologists recovered the remains of a woolly mammoth from frozen sediment on a coastal bluff on the eastern shore of Yenisei Bay, 1.8 km (1.1 miles) north of the Sopochnaya Karga weather station, at 71°54′19.2″N 82°4′23.5″E. The mammoth had clearly been killed by humans, and radiocarbon dating has established that the remains are 45,000 years old.

Previously, the earliest evidence for a human presence inside the Arctic Circle is the Yana Rhinoceros Horn site on the Lower Yana River at 71°N. Artefacts recovered at this site include spear shafts made from rhinoceros and mammoth horn, and a variety of stone tools. The site dates to around 30,000 years ago.

However, the Sopochnaya Karga evidence suggests that humans had mastered the challenging conditions of the Arctic well before this date. Damage and injuries to the mammoth’s ribs, shoulder blades, tusks and lower jawbone were consistent with it having been attacked and killed with thrusting spears and light projectile weapons, and subsequently butchered.

The hunters are assumed to be modern humans, though in the absence of fossil evidence this cannot be confirmed. There is fossil and ancient DNA evidence confirming that modern humans were at Ust’-Ishim in western Siberia 45,000 years ago, but this site lies well to the south at 57°N.

Reference:

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Pitulko, V. et al., Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains. Science 351 (6270), 260-263 (2016).x

RIP David Bowie

The scene at the David Bowie mural in Brixton a few days after the shock news of the legendary musician's death.

‘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.

Reference:

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Maixner, F., Krause-Kyora, B., Turaev, D., Herbig, A. & Hoopmann, M., The 5300-year-old Helicobacter pylori genome of the Iceman. Science 351 (6269), 162-165 (2016).

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Did Chinese Homo erectus survive into the Late Pleistocene?

14,000-year-old hominin thigh bone has archaic affinities.

In 2012, human remains differing from the modern condition were reported from two sites 300 km (185 miles) apart in southwest China: Longlin Cave in Guangxi Province, and Maludong (‘Red Deer Cave’) in Yunnan Province. The Longlin remains have been radiocarbon dated to 11,500 years old, and those from Maludong to 14,000 years old. The Longlin remains included a partial skull, a temporal bone fragment probably belonging to the skull, a partial lower jawbone and some fragmentary postcranial bones. The cheek bones of the skull are broad and flared sideways; the browridges conspicuous; the chin less prominent than in Homo sapiens; and the remains are very robust. The Maludong remains include a skullcap, two partial jawbones and a partial thighbone.

Popularly reported as the Red Deer Cave people, the hominins were at first thought to represent a single population, but newly-published work suggests that the Longlin skull has affinities to early modern humans. The bony labyrinth (the bony outer wall of the inner ear) of the temporal bone fragment is modern in appearance and it is possible that the skull’s unusual shape might be the result of interbreeding between archaic and modern humans. It has been suggested that Longlin was located in a ‘hybrid zone’ – a border between relict archaic and modern populations. Similar hybrid zones occur with some non-human primate populations.

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The Maludong thighbone is now claimed to show affinities to archaic humans, in particular those from the Early Pleistocene. There is a scarcity of later archaic human remains in East Asia, and the authors of the new report are reluctant to assign the thighbone to a particular archaic human species. However, the likeliest possibility is that the thighbone represents a late survival of Homo erectus in China. Regardless of species, the implications of these new findings is that isolated populations of archaic humans were still in existence in China as late as 11,500 years ago and that some of these populations were interbreeding with modern humans.

References:

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1.  Curnoe, D. et al., Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians. PLoS One 7 (3) (2012).

2.  Curnoe, D., Ji, X., Taçon, P. & Yaozheng, G., Possible Signatures of Hominin Hybridization from the Early Holocene of Southwest China. Scientific Reports 5, 12408 (2015).

3.  Curnoe, D. et al., A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS One (2015).

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New dates for Monte Verde pushes back arrival of first humans in South America

Chilean site was first occupied at least 18,500 years ago

Monte Verde in southern Chile is a peat bog in the terraces of Chinchihuapi Creek in the Maullín river basin, midway between the Pacific coast and the Andean mountains. There is well-preserved evidence of human occupation including wooden tent remains, foundations and floors of huts, hearths, wooden lances, mortars, and large numbers of stone tools. The site was apparently occupied all year round. A wide range of coastal and mountain habitats were exploited including marshes, wetlands, forests, estuaries, and rocky and sandy shorelines.

Evidence of habitation was not thought to pre-date the 14,600 year horizon identified at the site MV-II, although there was evidence of an earlier cultural horizon (MV-I). The MV-II dates in themselves made Monte Verde attractive to opponents of the long-running ‘Clovis First’ orthodoxy, which holds that the culture originally identified at Clovis, New Mexico represents the earliest human settlement of the New World. The Clovis culture is noted for its distinctive leaf-shaped spear points, which were first found in the 1930s. Clovis sites dating from 13,250 years ago are widespread across the United States and Central America to as far south as Panama. Assuming that the first Americans reached the New World via the Beringia land bridge that linked Alaska with Siberia during the last Ice Age, a human presence in South America 14,600 years ago is problematic to Clovis First.  

However, even earlier dates have now been obtained for Monte Verde. Archaeologists carried out spatially-intermittent excavations and core drillings across an area lying between MV-II and the two sites of CH-I and CH-II, located on the south side of the creek, 500 m upstream of MV-II. These revealed stone tools, faunal remains, and evidence of fires widespread across the study area albeit vertically and horizontally discontinuous. These appear to represent ephemeral seasonal activities carried out over a long period of time between shallow channels of a now-buried braided system of streams that fed into the river. Radiocarbon and Optically Stimulated Luminescence dating has yielded a range of dates from 18,500 to 14,500 years ago, with implications that humans reached the New World much earlier than previously believed.

Reference:

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Dillehay, T. et al., New Archaeological Evidence for an Early Human Presence at Monte Verde, Chile. PLoS One 10 (11) (2015).

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Homo erectus origin likely for Flores ‘hobbits’

Dental study rejects modern human or earlier hominin connection with Homo floresiensis

The origin of the diminutive ‘hobbits’ of Flores, Indonesia have been controversial since they were announced as a new human species, Homo floresiensis, in 2003. The most widely accepted view is that they are descended from a group of Homo erectus that reached Flores at least a million years ago and underwent a phenomenon known as insular dwarfism whereby a combination of low risk of predators and a relative scarcity of food means that smaller individuals are favoured from an evolutionary point of view and thus individuals within a population will ‘downsize’ over the course of many generations.

However, there are two alternative viewpoints. The first is that the Homo floresiensis remains simply represent modern humans affected by a condition such as microcephaly or cretinism. The second view accepts that the Flores hominins are indeed descended from an archaic species, but posit that it is something more primitive than Homo erectus – possibly Homo habilis or an australopithecine. It is argued that the absence of fossil evidence for such early hominins leaving Africa is not evidence of absence from Eurasia.

In a newly-published study, researchers carried out extensive comparisons using linear metric analyses, crown contour analyses, and other trait-by-trait morphological comparisons of the molar, premolar and canine teeth of Homo floresiensis against an extensive sample of teeth from present-day modern, prehistoric modern, and archaic humans. Three methods were used: metric analyses based on crown length and breadth data; comparisons of crown contour using normalized Elliptic Fourier Analysis (EFA); and non-metric and linear metric comparisons of individual morphological traits not recorded by the first two methods.

The researchers found suggest that the Homo floresiensis teeth do share derived characteristics with those of Early Pleistocene Homo erectus from East Africa and Java, and with the Dmanisi hominins from Georgia; but none of the ‘hobbit’ teeth exhibit the very primitive morphology associated with Homo habilis or australopithecines. Such characteristics include the occasional absence of a P3 buccal groove, a distally positioned P3 lingual cusp, a more circular P4 crown, the presence of a P4 transverse crest, non-parallelogram M2 crown shape, a mesiodistal short M2 crown, a M1 mid-trigonid crest, equivalent M1 and M2 sizes, and a moderately wide upper dental arcade. The findings rule out the claim that Homo floresiensis evolved from a hominin that was more primitive than Homo erectus.

Nor was a good match found with the modern samples. In comparison to Homo floresiensis, the teeth of Homo sapiens are derived for nine out of 26 character states, contradicting the suggestion that the dentition of Homo floresiensis is wholly modern.

Overall, the results suggest that Homo erectus is the ancestral species; however the dentition of Homo floresiensis did continue to evolve and possesses some unique features not seen in any other hominin species. These include the large (relative) size and the unique occlusal morphology of the P3 that otherwise exhibits primitive morphologies; and the extremely short first molars. In view of the general trend of molar shortening during the evolution of Homo over time, this condition in Homo floresiensis is actually more derived than in Homo sapiens.

It must be assumed that these evolutionary changes reflected the unique habitat of Flores, but regardless they demonstrate the distinctiveness of Homo floresiensis as a species.

Reference:

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Kaifu, Y. et al., Unique Dental Morphology of Homo floresiensis and Its Evolutionary Implications. PLoS One 10 (11) (2015).x

Bronze Age origins of bubonic plague

Study finds evidence of Yersinia pestis bacterium in 5,000-year-old human teeth

Three pandemics of bubonic plague have occurred in historical times: the first began with Plague of Justinian from AD 541 to 544, continuing intermittently until AD 750 AD; the second began with the Black Death from AD 1347 to 1351, continuing in waves including the Plague of 1665-66 into the eighteenth century; and the third which started in China in the mid-nineteenth century and triggered a series of outbreaks worldwide during the first half of the last century. The Black Death alone killed 30 to 50 percent of the European population. Deaths totalled at least 75 million, more than the number of deaths during World War I and II combined.

The cause of this deadly disease was identified as the flea-borne bacterium Yersinia pestis in 1894 by Swiss biologist Alexandre Yersin. More recently, genetic studies have suggested that it diverged from the more widespread but less virulent Yersinia pseudotuberculosis anywhere between 2,600 and 28,000 years ago.

In a newly-published study, researchers investigated the origins of Y. pestis by sequencing ancient bacterial genomes obtained from the teeth of Bronze Age people across Eurasia dating from 2,800 to 5,000 years ago. Their findings indicate that the flea-borne strain that caused the historic period plague pandemics evolved from a less virulent strain that was present in human populations long before any records of plague outbreaks.

The strains infecting Bronze Age Eurasian populations lacked the Yersinia murine toxin (ymt) gene, which encodes a phospholipase D protecting the bacterium inside the flea gut, so enabling fleas to act as vectors. Similarly, mutations associated with the development of bubonic plague and evading mammalian immune systems had not yet occurred. Not until around 3,000 years ago did highly virulent, flea-borne strains emerge.

The researchers also estimated the divergence from Y. pseudotuberculosis at 55,000 years ago, twice as early as previous maximum estimates. The Bronze Age strains began to diverge from one another 5,800 years ago. Although they could not cause bubonic plague, they could still cause pneumonic and septicemic plague and these might have been responsible for population declines between the late fourth and early third millennium BC. Large scale population movements and social changes during the Bronze Age might have facilitated plague outbreaks, but not on the scale of the historical era flea-borne pandemics.

Reference:

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Rasmussen, S., Allentoft, M., Nielsen, K., Orlando, L. & Sikora, M., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell 163, 571-582 (2015).x

Modern humans were in China 100,000 years ago

Assignment of fossil teeth from Fuyan Cave to Homo sapiens is ‘unequivocal’

Ever since genetic evidence emerged to support the ‘recent Out of Africa’ model of modern human origins, the orthodox view is that until around 60,000 years ago modern humans were confined to Africa and a short range extension into Southwest Asia. The latter is thought to have been brought to an end as colder, more arid climatic conditions set in around 90,000 years ago. The model has been challenged by archaeological evidence suggesting that modern humans were established on the Arabian Peninsula 125,000 years ago and had reached India 77,000 years ago.

What has up until now been lacking is unequivocal fossil evidence significantly earlier than around 45,000 years old. Controversial evidence had previously been reported from two sites in southern China. An age of up to 139,000 years old has been claimed for the Liujiang Skull, discovered in 1958, but the exact geological position of the find was not documented and the skull could actually be as little as 30,000 years old. A lower jawbone and two molar teeth from Zhirendong (‘Homo sapiens cave’) in Guizhou Province have been securely dated to 106,000 years old, but it is not certain that these remains belonged to a modern human.

However, the discovery has now been reported of 47 teeth at the newly-excavated site of Fuyan Cave in Daoxian, Hunan Province. Uranium series dating of associated stalagmite fragments gave a minimum age of 80,000 years old for the teeth and faunal dating gave a maximum age of 120,000 years old. The teeth were compared with those of Late Pleistocene humans from Europe, Asia and Africa and were found to fall consistently within the Homo sapiens size range. They are generally smaller than other Late Pleistocene samples from Asia and Africa, and are closer to European Late Pleistocene samples and the teeth of present-day people. They resemble the latter far more closely than they do the teeth of Neanderthals or Homo erectus.

The announcement adds a radical new dimension to the history of modern human dispersals in Eurasia.

Reference:

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Liu, W. et al., The earliest unequivocally modern humans in southern China. Nature 526, 696-699 (2015).x

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.

Reference:

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

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Congenital defect is possible further evidence of inbreeding by Neanderthals at El Sidrón

High incidence of congenital clefts of the arch of the atlas observed among remains from Spanish site

The Atlas (C1) vertebra is the first cervical vertebra of the spine, immediately below the skull. It takes its name from the Greek Titan Atlas, who is popularly (but incorrectly) supposed to have held the world on his shoulders. Congenital defects of the anterior or posterior arches are rare in modern populations, occurring at frequencies of 0.087 to 0.1 percent and 0.73 to 3.84 percent respectively. The condition does not normally lead to clinical symptoms.

El Sidrón is a cave site in Asturias, northern Spain that has yielded extensive Neanderthal remains and stone tools since these were first discovered there in 1994. Over 2,400 human fossils have been recovered, representing at least thirteen individuals including seven adults, three adolescents, two juveniles and one infant. The remains are 49,000 years old. Ancient DNA has previously been obtained from the remains, indicating a small patrilocal (mature males remain within their family birth group, but females come from outside) group with low genetic diversity. Dental hypoplasias indicate that around half of the group members had experienced episodes of growth arrest due to malnutrition.

Researchers now report that two out of just three well-preserved atlases from the site present respectively a defect of the posterior arch and the anterior arch. Such a high incidence of a rare condition could be interpreted as further evidence of low genetic diversity of the group, and as a possible indicator of inbreeding. The picture that emerges from El Sidrón is of a small, barely-viable Neanderthal group struggling for survival in extremely harsh conditions.

References:Ríos, L. et al., Possible Further Evidence of Low Genetic Diversity in the El Sidrón (Asturias, Spain) Neandertal Group: Congenital Clefts of the Atlas. PLoS One 10 (9), e0136550. (2015).

Hitherto-unknown early human species discovered deep inside Rising Star Cave, South Africa

A team led by Lee Burger has announced the discovery of a new species of early human.

Professor Berger, an American palaeoanthropologist working at the University of the Witwatersrand, Johannesburg, is known for Australopithecus sediba, announced in 2010 and at the time was the first new hominin species to be discovered in South Africa for decades. The discovery was when Matthew, Lee’s nine-year-old son, discovered a hominin collar bone embedded in a rock at Malapa, part of a now-eroded cave system near to Sterkfontein and Swartkrans, where many important hominin finds have been made.

Berger felt other cave systems in South Africa had the potential to yield hominin fossils, so in 2013 he recruited a team of cavers to search the Rising Star cave system, 50 km (30 miles) northwest of Johannesburg. The cave has been well explored over the years, but the team came across a narrow 18 cm (7 in.)-wide shaft that dropped vertically for 12 m (39 ft.) into an unexplored chamber. The cavers descended into the chamber and saw a fossil skull and jawbone lying on the floor of the cave. Berger believed that there were hominin fossils and obtained funding from the National Geographic for an expedition.

But to access what became known as Dinaledi Chamber (‘chamber of stars’) was problematic. Before they could even reach the narrow shaft leading down to the chamber, researchers, researchers would have to pass through another tiny shaft known as Superman’s Crawl and then climb a steep section known as Dragon’s Back. Berger placed an advertisement on Facebook for ‘small, skinny’ scientists believing at best there might be three or four people in the world who would fit the criteria. In the event, within days 57 suitable candidates had applied from which he chose six, all women. Within a month, the Rising Star Expedition had set up camp at the cave system and excavations commenced. Working in six-hour shifts, the six women soon recovered more fossil material than had been found in the whole of South Africa in the previous 90 years. Meanwhile, back on the surface, a large team began preparing and cataloguing the fossils, making full use of social media to report progress. A total of 1,550 fossils were recovered, comprising 15 individuals, including males, females and infants.

Berger then invited thirty young postdoctoral researchers from fifteen countries to help him evaluate the haul at a workshop in Johannesburg. They were accompanied by twenty of Berger’s more senior colleagues, who had worked with him on the Australopithecus sediba discovery. This unusual move did not please everybody and some questioned the wisdom of handing over such important fossils to inexperienced researchers.

The findings have now been announced. The remains represent a new human species, Homo naledi, named for the word ‘star’ in the local Sotho language. The new species is comparable in height and weight to a small-bodied modern human or a large australopithecine, with an estimated stature of around 1.5 m (5 ft.) and weighing 40 to 55 kg (88 to 121 lb.). The brain is tiny, ranging from 465 to 560 cc, overlapping entirely with the range of values known for australopithecines. The reconstructed skeleton exhibits both humanlike and apelike features, but in a combination that has not been seen with other hominins. The feet and lower limbs are humanlike, but the upper thighbone, pelvis and shoulders are apelike. The hands and wrists are humanlike, though the fingers are curved suggesting that it spent some of its time in the trees as well as on the ground. Overall, Homo naledi is the most primitive, small-brained hominin ever to have been included in Homo, but the shape of cranium and lower jawbone and the dentition suggest that it is human rather than an australopithecine.

Unfortunately, no dates have yet been published for the fossils. They are presumably too old to be radiocarbon dated, but there is no readily-datable material in the chamber. Calcium carbonate flowstones have been found to have been contaminated with materials from associated muds, making them unsuitable for uranium series dating. All we currently have to go on is the primitive characteristics such as the small brains. These suggest that Homo naledi emerged close to the base of the human family tree 2.5 to 2.8 million years ago. But until we have dates for the fossils, or other fossils turn up that can be dated, it will be difficult to say just where Homo naledi fits into the overall picture of human evolution.

Also troublesome is the question of how the fossils reached Dinaledi Chamber in the first place. There is a near-absence of non-hominin fossils in Dinaledi Chamber – yet these are abundant in the adjacent Dragon’s Back. This rules out the remains having being swept into Dinaledi Chamber by a flash flood, as this would have left a mixture of hominin and non-hominin remains in both chambers. Carnivores are also ruled out: even if there was a carnivore that preyed exclusively on Homo naledi, why would it drag its prey into such an inaccessible location? In any case, none of the bones showed any evidence of having been gnawed by carnivores. Nor does it seem that the hominins fell down a shaft leading into the cave from the surface: there is no evidence that any such shaft had ever existed. The fossils accumulated over time, so it can also be ruled out that a single group entered the chamber for some reason and then become trapped there.

The only obvious explanation is that the remains were deliberately placed in the chamber as part of a post-mortem ritual, although there is no evidence for such rituals until much later. Mass deposition of corpses is first seen at the cave site of Sima de los Huesos in Spain, 430,000 years ago. Even this was nothing more than a hygienic disposal of the corpses rather than any form of ritual. Also, unlike Homo naledi, the brain size of the Sima people was only slightly below that of modern people. In any case, even hygienic disposal seems unlikely as there is no evidence that Rising Star was ever inhabited, and there would surely be no need to use such an inaccessible chamber.

Taken at face value, the evidence from Dinaledi Chamber suggests that early humans were far more behaviourally complex than has long been believed. However, it is probably too soon to jump to conclusions and all that can safely be said is that we don’t yet know how the fossils reached the cavern.

References:

1. Berger, L., Hawks, J., de Ruiter, D. & Churchill, S., 2015. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife.

2. Dirks, P. et al., 2015. Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa. eLife.

Radiocarbon dates used to trace possible origins of domesticated rice

Seven models tested against extensive archaeological database

Rice is one of the world’s most important cereal crops, and has supported dense human populations in Asia since Neolithic times. The origin and spread of domesticated rice is understandably of great interest to students of Asian prehistory and researchers have employed a variety of methods, including genetics, phytolith studies, from the presence of charred grains in archaeological excavations, and from rice husks in Neolithic pottery.

In a newly-published study researchers have made use of an extensive database of radiocarbon data from 400 sites spanning 470 phases of occupation in mainland East, Southeast and South Asia. The researchers modelled the likely spread of rice agriculture using an algorithm known as Fast Marching, which was used to estimate least-cost distances based on simple geographical features and suitability of regions for rice agriculture. Existing knowledge of archaeological evidence for rice was used to infer backwards towards probable areas of origin for rice cultivation. The researchers also used goodness of fit to test various previously-published hypotheses of the origin of rice agriculture against the overall archaeological rice database.

The unconstrained search for the most likely origin identified a region between the Lower and Middle Yangtze, specifically the northeast of Jiangxi Province, where there is little archaeobotanical evidence for early rice agriculture. However, the algorithm was trying to find the best-fitting single source and was unable to identify multiple origin scenarios. In such cases, it will highlight an area in between the various true origins.

The next step was to test seven previously-published hypotheses, labelled L1 to L7 in the study:

L1 Ganges, Burma and northern Vietnam
L2 Ganges, Northern Thailand and lower Yangtze
L3 Middle Yangtze and northern Bay of Bengal
L4 Pearl River delta
L5 Middle Yangtze
L6 Lower Yangtze
L7 Middle and Lower Yangtze

Of these, the last model, favouring two independent origins in the Middle and the Lower Yangtze, gave the best fit with the data and is also the most consistent with the unconstrained search. The authors of the report claim that the L7 ‘dual Yangtze’ model is so well supported over the second-best match, the L6 Lower Yangtze scenario, that the situation is compared to randomly drawing 125 million white balls out of an urn and asking whether this is sufficient evidence that the urn contains only white balls, versus containing an equal amount of white and black balls.

Whether such optimism is justified, only time and further studies will tell. However, the results agree with the conclusions of many archaeologists who have recently focused on the Middle and Lower Yangtze basin. There is currently no reason to favour either over the other as a more likely source region of rice domestication episode. Instead, multiple, distinct domestication episodes seems the most plausible hypothesis in the current state of our evidence. Cultural differences between the Neolithic traditions of the Lower and Middle Yangtze, including the earliest preserved field systems, makes it unlikely that rice agriculture diffused between the two regions.

References:

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Silva, F. et al., Modelling the Geographical Origin of Rice Cultivation in Asia Using the Rice Archaeological Database. PLoS One 10 (9), e0137024. (2015).x

Mass grave at Schöneck-Kilianstädten reveals Neolithic massacre

 Chilling discovery at LBK site in Germany

Schöneck-Kilianstädten is a Neolithic mass grave in Hesse, Germany, which was discovered by chance in 2006 during road building works. The site is associated with the Linearbandkeramik (Linear Pottery) Culture or LBK, a Neolithic farming culture that emerged in Hungary around 5600 BC. The LBK is named for its distinctive pottery with banded incised decoration, and it is noted for its characteristic settlements comprised of clusters of massive timber-built longhouses, sometimes measuring up to 70 m (230 ft.) in length.

The LBK was a widespread phenomenon. LBK farmers spread rapidly across Central Europe, their dispersal probably aided by boats. They reached the Rhineland by 5300 BC, followed by the Paris Basin and they also spread eastwards as far as Ukraine and Moldova. Despite its success, evidence has emerged over the last thirty years that relations between LBK farming groups were not always positive.

A mass grave known as the Death Pit at Talheim, Germany, was found in 1983. It contained the remains of 34 individuals, including women and children, most of whom showed evidence of violence. Victims had been hacked or bludgeoned to death with stone adzes and three had been struck by arrows. The use of Neolithic stone tools as murder weapons suggests that the attackers were neighbouring LBK farmers rather than local hunter-gatherers, though the motive remains unknown.

Another example of internecine violence between LBK communities was found at the site of Schletz, Austria, where the remains of 67 individuals were found in an enclosure that was probably built as a defensive structure in an ultimately unsuccessful attempt to keep hostile neighbours at bay. Here again, the victims were bludgeoned to death with stone adzes, ruling out a clash with local hunter-gatherers.

However, the most disturbing find to date is a mass grave discovered by chance during road building work at Schöneck-Kilianstädten, Germany, in 2006. The grave dates to around 5000 BC and it has now been reported that it held the remains of at least 26 individuals including 13 predominantly male adults, one young adult and twelve children, mostly aged no more than six years old. The youngest was just six months old. The bodies had been dumped in the burial pit without any of the grave goods that normally accompanies LBK burials.

Again, the skulls showed signs of violence, but there was an additional find. Around half of the shin bones recovered from the grave had been freshly broken and while the corpses could have been systematically mutilated after death, the more sinister possibility is that individuals were tortured before they were killed.

These three sites, widely separated geographically but all dating to the later stages of the LBK, paint a grim picture of widespread violence in Neolithic Europe.

Reference:

Meyer, C., Lohr, C., Gronenborn, D. & Alt, K., 2015. The massacre mass grave of Schöneck-Kilianstädten reveals new insights into collective violence in Early Neolithic Central Europe. PNAS, 8 September, 112(36), pp. 11217-11222.