Ancient DNA reveals differences between Neanderthal and modern human lineages

Study also confirms that Neanderthal populations were small and isolated

 Researchers have analysed genetic sequences from Neanderthal remains found in Spain, Croatia and southern Siberia. The results indicated that the genetic diversity of Neanderthals is very low in comparison to that of modern humans, suggesting that they lived in small, scattered populations.

Genes associated with skeletal morphology were found to be more changed in the lineage leading to Neanderthals than they were in the lineage leading to modern humans, implying that Neanderthals underwent more skeletal changes than modern humans.

Conversely, genes associated with pigmentation and behavioural characteristics were to be more changed in the modern lineage. The team researchers also identified amino acid substitutions in Neanderthals and modern humans. These can change the structure and function of proteins, and may underlie phenotypic differences (differences in observable characteristics) between the two species.

Reference:
Castellano, S., et al Patterns of coding variation in the complete exomes of three Neandertals, PNAS (2014); published ahead of print April 21, 2014, doi:10.1073/pnas.1405138111

Link:
http://www.pnas.org/content/early/2014/04/16/1405138111.short?rss=1

Ancient Egyptians tamed cats 2,000 years before earliest generally accepted evidence

Sacrificial burial from Predynastic Hierakonpolis dates to 3800 – 3600 BC

The remains of six cats were found in a circular pit in an elite graveyard: an adult male, an adult female and two pairs of kittens. The cats were sacrificed as part of a funerary ritual. The ages of the kittens suggest that they belonged to two different litters; furthermore the adult female was too young to have been the mother.

The relationship of the male cat to the kittens cannot be determined. If all these animals were taken from the wild, then four different captures would have been required (the male, the female and each pair of kittens). It is unlikely that this could have been accomplished in short period prior to the sacrifice. Furthermore, the slightly different ages of the kittens suggest they were born outside the natural reproductive cycle of Egyptian wild cats, with a single birth season on spring. It therefore seems likely that the cats were bred in captivity or at least in close association with humans.

The traditional view is that domesticated cats first appeared in Egypt during the Middle Kingdom around 4000 BC or possibly 300 years earlier during the latter part of the Old Kingdom, but this finding pushes the date back to the Predynastic Naqada IC-IIB period (3800 – 3600 BC).

However, the earliest evidence for an association between humans and cats is a 9,500 year old burial from Cyprus containing the remains of a human and a cat.

Open Access http://dx.doi.org/10.1016/j.jas.2014.02.014

Reference:

1. van Neer, W., Linseele, V., Friedman, R. & de Cupere, B., More evidence for cat taming at the Predynastic elite cemetery of Hierakonpolis (Upper Egypt). Journal of Archaeological Science 45, 103-111 (2014).

Fifty years of Homo habilis

 The first human species - or was it?

Fifty years ago, the British anthropologist Louis Leakey and two colleagues reported the discovery of a new human species, Homo habilis (‘handy man’), in the journal Nature. Homo habilis lived at least 1.9 million years ago and remains the earliest-known widely-recognised human species to this day. The new species was described from fossils recovered at Olduvai Gorge, Tanzania between 1960 and 1964, but the story of its discovery began more than three decades earlier in 1931, when Leakey first investigated this now world-famous site.

Leakey believed that humans had evolved from African apes, as Darwin had originally suggested. By the early twentieth century however, this view had fallen out of favour and an Asian origin was widely favoured. The earliest-known human species at that time was Homo erectus, which had been discovered in late nineteenth century and was then known only in Asia. Although Neanderthals had been discovered some decades before that, Homo erectus was the first human species to be discovered that lived significantly before Homo sapiens and its brain was only around two-thirds the size of a modern brain.

However, in 1924, Australian anthropologist Raymond Dart had studied an apelike fossil found at a lime quarry at Taung, near Johannesburg, South Africa. He noted that the spinal column entered the skull through the centre rather than the back, suggesting that it was a biped and therefore a very early human – although its brain was no larger than that of a chimpanzee. Dart named it Australopithecus africanus (southern ape from Africa). The discovery switched the focus back to Africa, and in the decades that followed, australopithecines were also found in East and Central Africa. What was missing was a human ancestor intermediate between the australopithecines and Homo erectus.

Leakey became interested in Olduvai Gorge when fossilised human remains were found there, though ironically these later turned out to be a comparatively recent burial. Olduvai Gorge is probably the best-known fossil site in the world, and is now a UNESCO World Heritage site. A steep-sided ravine in Eastern Serengeti, it was formed when a stream carved its way through sedimentary rock, revealing seven main archaeological layers going back two million years. It was originally known as Oldoway Gorge; but it and Olduvai are mispronunciations of the local name Oldupai Gorge, which in turn comes from the Maasai word for the wild sisal plant growing in the gorge.

The 1931 expedition failed to discover any fossils, but a number of stone tools were found. These included a rudimentary stone chopping tool that was made by chipping flakes off a stone cobble to produce a weighty, sharp-edged cutting tool capable of cutting into animal carcasses. The tool is now on display in the British Museum, which at 1.8 million years old is the oldest object in the museum’s collection. Leakey classed the find as Oldowan, for the then still-current name Oldoway Gorge. The tool was found in Bed I, the lowest, earliest archaeological level at the site; more sophisticated stone hand-axes were found in higher, later levels. Leakey believed that the site recorded a sequence leading from the simple chopping tools in the lowest levels to the far more sophisticated tools in the higher Bed IV. The search was now on for the maker of the Oldowan tools, but Leakey’s work was interrupted by the breakup of his marriage and the outbreak of the Second World War.  

In 1951, he returned to Olduvai Gorge with his second wife, Mary, and in 1959, after several fruitless seasons, the Leakeys were finally rewarded with the discovery of the fossil skull of a young adult in the same archaeological layer that had yielded the stone cobble tool. It was small-brained and large jawed, with massive chewing teeth. The new species was designated Zinjanthropus boisei; ‘Zinj’ is an ancient Arabic word for the coast of East Africa, and the name also honours expedition sponsor Charles Boise. The skull was given the affectionate nickname of ‘Dear Boy’ by Mary Leakey. Now known as Paranthropus boisei, ‘Dear Boy’ belonged to an offshoot of the australopithecine lineage that is thought to have been an evolutionary dead end. Could this have been the maker of the cobble tools? It seemed doubtful.

The Leakeys were then joined in the field by their son Jonathan, and in November 1960 Jonathan and Mary found a lower jawbone with 13 teeth still in place, together with finger, hand and wrist bones. Over the next three years further fossils were recovered and analysed with the help of primatologist John Napier and anthropologist Phillip Tobias. They came from a species with a larger brain and smaller teeth than ‘Dear Boy’. Louis Leakey believed that this was this was the real toolmaker. The new species was announced in the journal Nature in April 1964 and given a name proposed by Raymond Dart – Homo habilis.

Compared to the australopithecines, the skull of Homo habilis was less massively-built, and the upper and lower jaws were within the size range of both Homo erectus and modern humans. The feet were humanlike, as were the thumb joints – but it was shorter in stature and much smaller-brained than a modern human. Males averaged 5 ft. 1 in and females 4 ft. 1 in; the brain size of around 600 cc was far less than the 1350 cc average for a modern human, or even the 750 cc human minimum proposed by British anthropologist Sir Arthur Keith in the late 1940s. This figure lies midway between the largest gorilla brain and the smallest modern human brain. Homo habilis was nevertheless significantly taller and bigger-brained than the australopithecines. However, the limb proportions were still apelike, with proportionately long arms and short legs, suggesting that Homo habilis retained some apelike tree-climbing abilities.

The Olduvai fossils are 1.8 million years old. Most remains are from East Africa; but the skull STW 53 from Sterkfontein, South Africa, may also be Homo habilis. The oldest tentative fossil evidence for Homo habilis to date is AL 666-1, a 2.33-million-year-old upper jawbone recovered at Hadar, Ethiopia, but the oldest uncontested Homo habilis remains are only 1.9 million years old. The most recent Homo habilis fossil currently known is a 1.44-million-year-old partial upper jawbone from Koobi Fora, Kenya. These dates – if both correct – imply that the species survived for almost a million years. Homo habilis is not known to have left Africa, but it has been suggested that it might have been the ancestor of Homo floresiensis, the so-called ‘hobbit people’ from the Indonesian island of Flores.

The Oldowan stone tool tradition associated with Homo habilis was the most primitive of all stone tool traditions. We now know that such tools were also made by some of the later australopithecines and might have a response to deteriorating climate as the Earth entered the current series of ice ages 2.5 million years ago. It is possible that as the climate deteriorated, preferred food types became unavailable and australopithecines added more meat to their diet. The increased need to butcher carcasses led to the development of stone tools. Early Homo erectus also used Oldowan tools before switching to the more advanced hand-axes seen in the upper levels at Olduvai Gorge. However, many Homo erectus groups, particularly in the Far East, persisted with the Oldowan stone cobble tools.

Plaster casts of the inside of Homo habilis braincases have shown that the sulcal and gyral patterns (ridges and furrows that give the human brain its wrinkled look) were more humanlike than apelike. The frontal and parietal lobes are enlarged, and that the Broca’s Area was expanded in comparison to the same region in australopithecines and modern apes. The frontal lobes, which control higher brain functions including planning and reasoning, are located at the front of the brain. Behind them, on the top and on each side of the brain are the parietal lobes, which carry out a wide range of functions including spatial awareness and the processing of sensory information.

Broca’s Area is named for nineteenth century physician Paul Broca who demonstrated a connection with speech. Damage leads to Broca’s aphasia, where patients are unable to speak in a grammatically correct manner. This suggests some linguistic abilities, though recent research shows that the Broca’s Area is also associated with tool-making. It is possible that its expansion was linked to enhanced tool-making skills as well as or possibly instead of the use of language.

However, the late australopithecines that made stone tools had brains no larger than their forebears, so tool-making alone doesn’t explain why Homo habilis needed a bigger, better brain. Bigger brains might sound like a good idea, but the same could be said of owning a Rolls-Royce. The problem in both cases is that they are expensive to run, and there is a pretty good case for trying to get by without. Brain tissue requires over 22 times as much energy as an equivalent amount of muscle tissue. In a modern human, the brain uses around 16 percent of the body’s energy budget despite making up just 2 percent of the body’s overall mass. While the energy costs of the smaller Homo habilis brain were less than those of a modern human brain, they were still considerable.

A possible answer is the social brain hypothesis, a theory which links the brain size of primates to the size of their social group. The enhanced brainpower is needed to keep track of the complex social relationships that are normal in many primate societies – not just human ones. Larger, more co-operative social groupings in Homo habilis society might have been an evolutionary response to the deteriorating climate and reduced availability of food.

Just where Homo habilis belongs in the human family tree remains contentious, even half a century after its discovery was announced. Even its membership of the human league is now questioned, with some seeing it as the anthropological equivalent of the now ex-planet Pluto and arguing that it should be reclassified as an australopithecine.

Although most textbooks describe Homo habilis as the ancestor of Homo erectus, the view has been called into question. Recent fossil finds indicate that Homo habilis persisted alongside Homo erectus for hundreds of thousands of year at Koobi Fora, Kenya. This makes it unlikely that the latter evolved from the former, and instead it has been proposed that both shared a common ancestor about two million years ago. If it were to turn out that the disputed AL 666-1 upper jawbone was something other than Homo habilis, then this scenario would become likely as the oldest examples of the two species would then be practically the same age. Another possibility is that the true ancestor of Homo erectus is the recently-discovered australopithecine species Australopithecus sediba. Australopithecus sediba lived in South Africa two million years ago, with limb proportions said to be more humanlike than Homo habilis.

Do the fossils assigned to Homo habilis even represent a single species? The variation in Homo habilis fossils is considerable and it has been suggested that these actually represent two species. Some examples have a broader, flatter face and larger teeth than others, and it is has been proposed that these be assigned to a second species known as Homo rudolfensis. On the other hand, it has been claimed that the degree of variation between skulls assigned to Homo habilis, Homo rudolfensis and Homo erectus is actually no more than that between five early Homo erectus skulls found at Dmanisi, Georgia, and it has accordingly been suggested that all three are actually the same species. The problem with this view is that it does not explain the more apelike limb proportions of Homo habilis.

It is this detail together with the small brain size that has led some to believe that Homo habilis should be reclassified as an australopithecine. Quite simply, it is too unlike Homo sapiens to be regarded as a human species. However, there is no consensus on the issue. Studies have been conducted to determine whether it can be included in Genus Homo on the basis of anatomical characteristics shared with other members, but these have proved inconclusive.

If Homo habilis individuals could somehow have been aware that they would one day become the subject of such deliberations, it is unlikely that they would have been overly concerned. It should not be forgotten that they might have existed for as long as a million years, which is a testament to their success as a species.

Ancient DNA study provides additional insight into Neolithic transition in Scandinavia

Hunter-gatherers were absorbed into farming communities

A newly-published genetic study of ancient DNA obtained from prehistoric human remains in Sweden has provided a fresh insight into the transition to agriculture in Scandinavia.

The ability to obtain DNA from the remains of prehistoric people has in recent years added a new dimension to the long-running quest to understand the demographics of the transition from hunter-gathering to farming in Neolithic Europe. Studies based on living populations have been unable to provide definitive answers, as ancient genetic signals are often blurred by far more recent events.

Researchers at Stockholm University and Uppsala University obtained genetic material from the remains of six hunter-gatherers and four farmers from the Scandinavian Neolithic, dating to around 5,000 years ago, together with a late Mesolithic hunter-gatherer from 7,500 years ago. The samples were obtained from mainland Sweden and the Swedish island of Gotland.

It was found that the genetic diversity of the hunter-gatherers was far lower than that of the farmers and of any present-day Eurasian populations, suggesting that their population sizes were very small. Fluctuating climatic conditions and/or restricted carrying capacities might have affected hunter-gatherer population sizes. It is also possible that the genetic diversity of the hunter-gatherers never recovered from population crashes occurring during the Last Glacial Maximum when European populations were confined to a few ice-free refugia.

A significant finding was that the hunter-gatherer and farming populations were genetically distinct from one another, confirming the view that agriculture was spread across Europe by migrating farmers, rather than by indigenous hunter-gatherers simply taking up farming. In other words, it was farmers and not just farming that spread.

The researchers also found evidence for genetic admixing between the hunter-gathering and farming communities – but it was one way. Hunter-gatherers apparently married into the farming communities, but not the other way round. Thus the expanding farming communities assimilated indigenous hunter-gatherers.

The study, published in the journal Science, is part of a recently-launched initiative to investigate ancient human remains in Scandinavia. Known as the Atlas project, it is being conducted by researchers at Stockholm University and Uppsala University.

References:

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1.  Skoglund, P. et al., Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. Science (2014).

Bronze Age pastoralists played key role in spread of crops in Central Asia

New archaeobotanical data highlights cereal cultivation by mobile groups during period 2800 to 1200 BC.

Mobile pastoralism first appeared on the steppes of Central Asia during the fourth millennium BC, and was established by the early part of the third millennium BC. Nomadic groups were also responsible for introducing copper, tin, ceramics and bronze metallurgy into the Inner Asian Mountain Corridor between the Altai and Pamir mountain ranges.

However, much less is known of the Central Asian herders’ use of domesticated cereals and the integration of farming into their mobile economies. Botanical evidence for farming on the steppes and mountains of Central Asia has not been previously documented prior to 800 BC, leading to the traditional view that there was a sharp division between nomadic pastors and sedentary farmers in Eurasia and elsewhere.

This view has now been challenged by newly-published archaeobotanical data from four Bronze Age sites in the region. The highland steppe sites of Tasbas and Begash in eastern Kazakhstan, and Ojakly and the unnamed site of 1211/1219 in the Murgab Delta region of Turkmenistan are all believed to have been used as seasonal camps by mobile pastoralists as part of their annual round. Features of these sites include semi-subterranean houses and storage areas.

At Tasbas, wheat and unidentifiable cereal grains were recovered from a funerary urn dating from between 2840 to 2500 BC; and wheat, barley and broomcorn millet dating from between 2450 to 2100 BC were found at Begash. This is the earliest evidence for the use of domestic crops in the region. By 1450 – 1250 BC, cereals were present in far greater quantities at Tasbas: barley, wheat, broomcorn millet and foxtail millet, together with peas. The high density of seeds found in soil suggests that the crops were cultivated locally and not obtained by trading with farmers. Barley chaff used as binder in mud bricks also suggests local cultivation.

The two sites in Turkmenistan date to between 1700 and 1500 BC and have yielded broomcorn millet, barley and wheat. By this time, sedentary farming communities had emerged in the region, and both sites lay close to specialised farming villages. It is likely that the pastoralists obtained their barley and wheat from these, but the farmers did not grow broomcorn millet. Thus it appears likely that the mobile pastoralists were responsible for introducing this crop into the region.

In conclusion, the wheat and broomcorn millet at the two Kazakh sites is earliest evidence for spread of crops into the region – wheat from southern Central Asia and broomcorn millet from East Asia. The seasonal migrations of the pastoralists who used these sites resulted in extensive interactions between local communities throughout the mountainous regions of Central Asia. These interactions resulted in the spread in both directions of crops and agriculture between China and Central Asia among sedentary and mobile groups by the second millennium BC.

The findings indicate that domesticated crops reached Central Asia 2,000 years earlier than previously believed, and highlight the key role of mobile pastoralists in transmitting crop repertoires and transforming agricultural economies in the region. They break down the sharp divide previously thought to exist between nomads and farmers in prehistoric Central Asia.

References:

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1.  Spengler, R. et al., Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia. Proceedings of the Royal Society B 291 (1783) (2014).

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Fishing was rapidly abandoned by first farmers in Britain and Ireland

Lipid residue study finds evidence for dramatic change in diet during Neolithic transition

Agriculture reached Britain and Ireland around 4000 BC, but the means by which the transition from hunting, fishing and gathering occurred has been debated for many years. One view is that indigenous Mesolithic people acquired domesticated crops and animals from continental Europe, but retained much of their existing lifestyle. Another is that Neolithic farmers arrived from the continent and spread rapidly. This latter scenario proposes that a rapid acculturation of indigenous Mesolithic people followed.

Previous work has considered stable carbon isotope signatures of bone collagen extracted from Mesolithic and Neolithic human remains. The results suggested that in coastal environments, the Mesolithic diet included a significant amount of marine protein, but that of the Neolithic farmers was predominantly terrestrial-based. However, doubts have been expressed about the sensitivity of the bone collagen stable isotope analysis to low-protein diets; quantities of less than 20 percent marine protein in the diet would be undetectable. Possible Neolithic shell middens from Scotland and Ireland suggest that seafood continued to be eaten.

To address this uncertainty, researchers analysed lipid residues recovered from Neolithic pottery sherds from coastal sites in Britain, the Scottish Isles, and Ireland. To extend the chronological period, material was also included from sites dating to the Bronze Age through to the Viking period. The results confirmed the near-complete absence of marine protein from the Neolithic diet and the strong presence of dairy products. This remained the case during the Bronze Age, and it was not until Viking times did marine protein again become a significant dietary item.

Similar studies in the Baltic region indicate a different pattern. There, hunting, gathering and fishing continued alongside farming. The contrasting patterns occurring at the same time in different regions suggest geographically-distinct ecological, demographic and cultural influences dictating the adoption of agriculture. The rapid shift to an intensive dairy economy is consistent with the low frequency of lactose intolerance among modern inhabitants of northwest European archipelagos. The evolutionary processes driving lactase persistence in adults would have been driven by the increasing importance of dairy products in the diet.

References:

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1.  Cramp, L. et al., Immediate replacement of fishing with dairying by the earliest farmers of the northeast Atlantic archipelagos. Proceedings of the Royal Society B 281 (2014).

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Copper awl points to non-local origin for metallurgy in southern Levant

Artefact was imported centuries before Late Chalcolithic.

The southern Levant became a major centre for metallurgy in Southwest Asia during the Late Chalcolithic period from 4500 to 3800 BC. Artefacts from this period include eight massive gold rings weighing a total of almost 1 kg (2.2 lb.) from the Nahal Qanah Cave, Israel, and prestige copper items from a cave at Nahal Mishmar near the Dead Sea, which display lost wax casting technology.

However, the origins of this metalworking tradition have remained obscure until recently. Now a newly-published report has suggested that the roots of southern Levantine metallurgy might be found in an earlier, non-local tradition. Tel Tsaf in the Jordan Valley was excavated between 2004 and 2007. The main period of occupation of the site occurred during the Middle Chalcolithic, and dates to between 5100 and 4600 BC. The mud-brick complex included courtyard buildings and grain silos, two of which had been repurposed as graves. Artefacts from the site included elaborately painted pottery and over 2,500 beads made of ostrich egg-shells and stone. Many artefacts were of non-local origin, including obsidian items from Anatolia or Armenia, a shell from the Nile and pottery from northern Syria or Mesopotamia. Animal remains included large numbers of cattle and pigs and the capacity of the grain silos has been estimated at around 15 to 30 tons. Wealth and food surpluses were being accumulated at Tel Tsaf far in excess of anything else known in the region during this period; and the site had access to long-distance exchange networks throughout Southwest Asia.

From one of the silo-graves was recovered a badly-corroded copper awl. The awl is a 41 mm (1.6 inch) pin made from cast copper, with a rounded cross-section. The maximum diameter is 5 mm (0.2 inch), narrowing to 1 mm (0.04 inch) near the tip. The burial held the remains of a woman aged around forty, and other grave goods included an ostrich-shell bead necklace with 1,668 beads.

Chemical analysis indicated the metal composition of the awl included 6 percent tin and 0.8 percent. Although corrosion may have altered the chemical composition of the awl, the presence of tin suggests that it was not of local origin. Copper items of such a composition have not been found in the Late Chalcolithic or the Early Bronze Age of the southern Levant, nor does it match the composition of local native copper. It is thought that the alloy is natural, as it unlikely that artificial copper/tin alloys were being produced at this stage. Tin bronze is not known from the region until the Middle Bronze Age, around the second millennium BC. Thus the awl not only predates all previously-known metal artefacts in the southern Levant by several centuries, it also predates all known tin bronze items in the region by around 3,000 years.

Assuming that the awl is not of local origin, then it must have reached Tel Tsaf via long-distance exchange networks. Metallurgy must have diffused to the southern Levant from the north. At first, artefacts were imported and it was not until some centuries later that they were produced locally. Thus it can be seen that the elaborate Late Chalcolithic metallurgy of the southern Levant developed from an earlier, non-local tradition.

That the awl was found in an elaborate grave suggests that at this stage, metal items were seen as rare and prestigious. The residents of the courtyard building where the grave was found apparently belonged to a family or group that controlled the local cultivation and storage of grain as well as long-distance trade. Their wealth may have either led to or been the result of a trade in luxury items obtained from sources very remote from Tel Tsaf.

References:

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1.  Garfinkel, Y., Klimscha, F., Shalev, S. & Rosenberg, D., The Beginning of Metallurgy in the Southern Levant: A Late 6th Millennium CalBC Copper Awl from Tel Tsaf, Israel. PLoS One 9 (3), e92591 (2014).x