aDNA

Ancient genome 

from Africa 

sequenced 

for the first time 

Africa, Anthropology, ArchaeoHeritage, Archaeology, Breakingnews, Ethiopia, Genetics 


 The first ancient human genome from Africa to be sequenced has revealed that a wave of migration back into Africa from Western Eurasia around 3,000 years ago was up to twice as significant as previously thought, and affected the genetic make-up of populations across the entire African continent. The Mota cave is located in a mountainous region, and its entrance is about 6,000 feet  above sea level. 

Weather and the changing conditions of the only road that runs near  the cave -- a gravel surface -- made access complicated for the research team 

[Credit: Kathryn and John Arthur] 

The genome was taken from the skull of a man buried face-down 4,500 years ago in a cave called Mota in the highlands of Ethiopia -- a cave cool and dry enough to preserve his DNA for thousands of years. Previously, ancient genome analysis has been limited to samples from northern and arctic regions. The latest study is the first time an ancient human genome has been recovered and sequenced from Africa, the source of all human genetic diversity. The findings are published in the journal Science. The ancient genome predates a mysterious migratory event which occurred roughly 3,000 years ago, known as the 'Eurasian backflow', when people from regions of Western Eurasia such as the Near East and Anatolia suddenly flooded back into the Horn of Africa. 

Entrance to the Mota Cave in the Ethiopian highlands  

[Credit: Kathryn and John Arthur] 

The genome enabled researchers to run a millennia-spanning genetic comparison and determine that these Western Eurasians were closely related to the Early Neolithic farmers who had brought agriculture to Europe 4,000 years earlier. By comparing the ancient genome to DNA from modern Africans, the team have been able to show that not only do East African populations today have as much as 25% Eurasian ancestry from this event, but that African populations in all corners of the continent -- from the far West to the South -- have at least 5% of their genome traceable to the Eurasian migration. Researchers describe the findings as evidence that the 'backflow' event was of far greater size and influence than previously thought. The massive wave of migration was perhaps equivalent to over a quarter of the then population of the Horn of Africa, which hit the area and then dispersed genetically across the whole continent. 

The view looking out from the Mota cave in the Ethiopian highlands, where the remains containing the ancient genome were found  

[Credit: Kathryn and John Arthur] 

"Roughly speaking, the wave of West Eurasian migration back into the Horn of Africa could have been as much as 30% of the population that already lived there -- and that, to me, is mind-blowing. The question is: what got them moving all of a sudden?" said Dr Andrea Manica, senior author of the study from the University of Cambridge's Department of Zoology. Previous work on ancient genetics in Africa had involved trying to work back through the genomes of current populations, attempting to eliminate modern influences. "With an ancient genome, we have a direct window into the distant past. One genome from one individual can provide a picture of an entire population," said Manica. The cause of the West Eurasian migration back into Africa is currently a mystery, with no obvious climatic reasons. Archaeological evidence does, however, show the migration coincided with the arrival of Near Eastern crops into East Africa such as wheat and barley, suggesting the migrants helped develop new forms of agriculture in the region. 

In Mota cave, located in the Gamo highlands of Ethiopia, a group of NSF-supported  researchers excavation a rock cairn. They discovered under it a burial site  containing the remains of a 4,500-year skeleton  

[Credit: Kathryn and John Arthur] 

The researchers say it's clear that the Eurasian migrants were direct descendants of, or a very close population to, the Neolithic farmers that had had brought agriculture from the Near East into West Eurasia around 7,000 years ago, and then migrated into the Horn of Africa some 4,000 years later. "It's quite remarkable that genetically-speaking this is the same population that left the Near East several millennia previously," said Eppie Jones, a geneticist at Trinity College Dublin who led the laboratory work to sequence the genome. While the genetic make-up of the Near East has changed completely over the last few thousand years, the closest modern equivalents to these Neolithic migrants are Sardinians, probably because Sardinia is an isolated island, says Jones. "The famers found their way to Sardinia and created a bit of a time capsule. Sardinian ancestry is closest to the ancient Near East." "Genomes from this migration seeped right across the continent, way beyond East Africa, from the Yoruba on the western coast to the Mbuti in the heart of the Congo -- who show as much as 7% and 6% of their genomes respectively to be West Eurasian," said Marcos Gallego Llorente, first author of the study, also from Cambridge's Zoology Department. 

John Arthur, an NSF-supported archaeologist at the University  of South Florida St. Petersburg, excavates the Mota cave site  

[Credit: Kathryn and John Arthur]

 "Africa is a total melting pot. We know that the last 3,000 years saw a complete scrambling of population genetics in Africa. So being able to get a snapshot from before these migration events occurred is a big step," Gallego Llorente said. The ancient Mota genome allows researchers to jump to before another major African migration: the Bantu expansion, when speakers of an early Bantu language flowed out of West Africa and into central and southern areas around 3,000 years ago. Manica says the Bantu expansion may well have helped carry the Eurasian genomes to the continent's furthest corners. The researchers also identified genetic adaptations for living at altitude, and a lack of genes for lactose tolerance -- all genetic traits shared by the current populations of the Ethiopian highlands. In fact, the researchers found that modern inhabitants of the area highlands are direct descendants of the Mota man. Finding high-quality ancient DNA involves a lot of luck, says Dr Ron Pinhasi, co-senior author from University College Dublin. "It's hard to get your hands on remains that have been suitably preserved. The denser the bone, the more likely you are to find DNA that's been protected from degradation, so teeth are often used, but we found an even better bone -- the petrous." The petrous bone is a thick part of the temporal bone at the base of the skull, just behind the ear. "The sequencing of ancient genomes is still so new, and it's changing the way we reconstruct human origins," added Manica. "These new techniques will keep evolving, enabling us to gain an ever-clearer understanding of who our earliest ancestors were." The study was conducted by an international team of researchers, with permission from the Ethiopia's Ministry of Culture and Authority for Research and Conservation of Cultural Heritage. 

Source: University of Cambridge [October 08, 2015]

Zigolo infestante

Immagini di dettaglio del Cyperus rotundus, o Dente di cavallo, o Zigolo infestante.

Una concrezione calcarea dentale, in un corpo inumato nel Sudan Centrale, del 7.000 a.C.. 
Una pianta erbacea delle zone umide, oggi considerata infestante.
Un'Equipe internazionale di ricercatori.

Grazie a loro, sappiamo che anche prima di iniziare a produrre il proprio cibo, l'uomo conosceva già bene le varie proprietà delle piante.
Lo zigolo infestante (oggi solo un'erbaccia acquatica del gruppo Cyperus, tra cui il più famoso è il Papiro) contiene carboidrati, possiede proprietà aromatiche e medicinali, contiene fibre che potevano essere usate per costruire oggetti...
questo è - appunto - il motivo per il quale si formò una concrezione dentaria su quell'individuo risalente al periodo  Neolitico. I microcomponenti hanno permesso di 
 ricostruire una dieta differente da quella prevalentemente carnivora ed iperproteica prima ipotizzata per le popoazioni pre-agricoltura...
La capacità della pianta di inibire i batteri (Streptococcus Mutans) responsabili della carie dentaria rendono conto delle splendide dentature osservate nei reperti.
La zona del Sudan in cui si è avuto il rinvenimento è di estremo interesse: in una zona piuttosto ristretta essa contiene ben 5 sepolcreti di epoche differenti, dal Mesolitico, al Neolitico, al Meroitico. Non a caso gli Egizi furono eredi di molte delle conoscenze maturate in questa sede. Da questa pianta trassero medicine e profumi.

Tooth plaque 

provides unique insights 

into our prehistoric ancestors' diet 


An international team of researchers has found new evidence that our prehistoric ancestors had a detailed understanding of plants long before the development of agriculture.

 Researchers studied the dental calculus of skeletons, such as this one  of a young man, found at a prehistoric gravesite in central Sudan  
[Credit: Donatella Usai/Centro Studi Sudanesi and Sub-Sahariani (CSSeS)

 By extracting chemical compounds and microfossils from dental calculus (calcified dental plaque) from ancient teeth, the researchers were able to provide an entirely new perspective on our ancestors' diets. 

Their research suggests that purple nut sedge (Cyperus rotundus) -- today regarded as a nuisance weed -- formed an important part of the prehistoric diet. Crucially, the research, published in PLOS ONE and led by the Universitat Autonoma de Barcelona and the University of York, suggests that prehistoric people living in Central Sudan may have understood both the nutritional and medicinal qualities of this and other plants. The research was carried out at Al Khiday, a pre-historic site on the White Nile in Central Sudan. 
It demonstrates that for at least 7,000 years, beginning before the development of agriculture and continuing after agricultural plants were also available the people of Al Khiday ate the plant purple nut sedge. 
The plant is a good source of carbohydrates and has many useful medicinal and aromatic qualities. Lead author Karen Hardy, a Catalan Institute for Research and Advanced Studies (ICREA) Research Professor at the Universitat Autonoma de Barcelona (UAB) and an Honorary Research Associate at the University of York, said: "Purple nut sedge is today considered to be a scourge in tropical and sub-tropical regions and has been called the world's most expensive weed due to the difficulties and high costs of eradication from agricultural areas. By extracting material from samples of ancient dental calculus we have found that rather than being a nuisance in the past, its value as a food, and possibly its abundant medicinal qualities were known. More recently, it was also used by the ancient Egyptians as perfume and as medicine. 

The hardened dental calculus on prehistoric teeth suggests that people  ate purple nutsedge, a weedy plant rich in carbohydrates 

[Credit: Buckley S, et al. PLoS ONE]

 "We also discovered that these people ate several other plants and we found traces of smoke, evidence for cooking, and for chewing plant fibres to prepare raw materials. These small biographical details add to the growing evidence that prehistoric people had a detailed understanding of plants long before the development of agriculture." 

Al Khiday is a complex of five archaeological sites which lie 25 km south of Omdurman; one of the sites is predominantly a burial ground of pre-Mesolithic, Neolithic and Later Meroitic age. 
As a multi-period cemetery, it gave the researchers a useful long-term perspective on the material recovered. 
The researchers found ingestion of the purple nut sedge in both pre-agricultural and agricultural periods. 
They suggest that the plant's ability to inhibit Streptococcus mutans, a bacterium which contributes to tooth decay, may have contributed to the unexpectedly low level of cavities found in the agricultural population. 
Dr Stephen Buckley, a Research Fellow at the University of York's BioArCh research facility, conducted the chemical analyses. He said: "The evidence for purple nut sedge was very clear in samples from all the time periods we looked at. This plant was evidently important to the people of Al Khiday, even after agricultural plants had been introduced." 

One of the prone extended burials at the Al Khiday prehistoric site 

 [Credit: Donatella Usai/Centro Studi Sudanesi and Sub-Sahariani (CSSeS)] 

Dr Donatella Usai, from the Instituto Italiano per l'Africa e l'Oriente in Rome led the excavation and Dr Tina Jakob from Durham University's Department of Archaeology, performed the analysis of the human remains at Al Khiday. Anita Radini, an Archaeobotanist at the University of Leicester Archaeological Service (ULAS) and a PhD candidate at BioArCh, University of York, contributed to the analysis of microfossils found in the dental calculus samples. Dr Usai said: "Al Khiday is a unique site in the Nile valley, where a large population lived for many thousands of years. This study demonstrates that they made good use of the locally available wild plant as food, as raw materials, and possibly even as medicine."

Dr Hardy added: "The development of studies on chemical compounds and microfossils extracted from dental calculus will help to counterbalance the dominant focus on meat and protein that has been a feature of pre-agricultural dietary interpretation, up until now. The new access to plants ingested, which is provided by dental calculus analysis, will increase, if not revolutionise, the perception of ecological knowledge and use of plants among earlier prehistoric and pre-agrarian populations." 


Source: University of York 

[July 16, 2014]

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Razzismo, 13.000 anni fa?

Con una buona dose di sensazionalismo giornalistico, è stata annunciata (da ricercatori franco-inglesi) l'identificazione di quella che potrebbe essere stata  la prima 'guerra di razza' del Mondo, ai confini del Sahara, 13.000 anni fa: sono stati scoperti numerosi scheletri, per la maggior parte dei quali la causa di morte era stata una freccia con punta di selce.Una ricerca parallela (di ricercatori anglo- americani) si è concentrata sulla provenienza di costoro, cioé sulle caratteristiche etniche di queste vittime. Sono giunte alla conclusione che si tratta di gente di provenienza sub-sahariana, antenati degli attuali negri africani.Identità e provenienza dei vincitori dello scontro, coloro che li hanno uccisi, è un po' più difficile da stabilirsi, ma è ragionevole ipotizzare che si trattasse di quelle popolazioni levantine/europee/nord-africane, che vivevano sulle coste mediterranee, che avevano già elaborato personali criteri di appartenenza a gruppi etnici differenti.I due gruppi dovevano avere ormai aspetti, usi, costumi e lingue differenti, pur appartenendo ambedue alla medesima specie (homo sapiens).Tanto per specificarlo: i sub-sahariani avevano arti inferiori più lunghi, torace relativamente corto, mascella e mandibola sporgenti e fronte rotondeggiante. Il gruppo dei vincitori aveva invece gambe relativamente più corte, torso lungo, e viso proporzionalmente più piatto. Ambedue i gruppi erano formati da soggetti robusti e muscolarmente molto sviluppati.Se l'interpretazione è corretta, ci troviamo possibilmente di fronte ad uno dei primi conflitti 'identitari' del pianeta, quando ancora non si era consolidato un andamento prevalente in senso Est/Ovest.
July 14, 2014

Armed conflict in the Sahara, ~13 thousand years ago

An interesting story from the Independent:

Scientists are investigating what may be the oldest identified race war 13,000 years after it raged on the fringes of the Sahara. French scientists working in collaboration with the British Museum have been examining dozens of skeletons, a majority of whom appear to have been killed by archers using flint-tipped arrows.

...

Parallel research over recent years has also been shedding new light as to who, in ethnic and racial terms, these victims were. 

Work carried out at Liverpool John Moores University, the University of Alaska and New Orleans’ Tulane University indicates that they were part of the general sub-Saharan originating population – the ancestors of modern Black Africans. 

The identity of their killers is however less easy to determine. But it is conceivable that they were people from a totally different racial and ethnic group – part of a North African/ Levantine/European people who lived around much of the Mediterranean Basin. 

The two groups – although both part of our species, Homo sapiens – would have looked quite different from each other and were also almost certainly different culturally and linguistically. The sub-Saharan originating group had long limbs, relatively short torsos and projecting upper and lower jaws along with rounded foreheads and broad noses, while the North African/Levantine/European originating group had shorter limbs, longer torsos and flatter faces. Both groups were very muscular and strongly built.

Back to Africa

Esiste il Consenso sulla teoria "Out of Africa": l'uomo moderno deriverebbe da un'unica culla africana, dalla quale si sarebbe poi sparso in tutto il mondo. All'ingresso dell'Eurasia (diciamo in Mesopotamia) si sarebbe incontrato con il Neanderthal, che lo aveva preceduto nel viaggio. L'uomo moderno si sarebbe anche incrociato con il Neanderthal, scambiandosi parti di DNA, tanto che si affermava che era questo il sistema per distinguere un Eurasiatico da un Africano. Non è così, almeno: non del tutto. Recenti studi genetici avrebbero dimostrato anche l'avvenuto 'ritorno' di occidentali eurasiatici in Africa, fino alla punta meridionale del continente, circa 3000 anni fa. Tanto che i Khoisan avrebbero nel loro pool genetico una percentuale di DNA Neanderthaliano, talvolta elevata.

Humanity's forgotten return to Africa revealed in DNA 

Call it humanity's unexpected U-turn. One of the biggest events in the history of our species is the exodus out of Africa some 65,000 years ago, the start of Homo sapiens' long march across the world. Now a study of southern African genes shows that, unexpectedly, another migration took western Eurasian DNA back to the very southern tip of the continent 3000 years ago. 

Not so isolated: Khoisan tribes have European DNA [Credit: Times] 

According to conventional thinking, the Khoisan tribes of southern Africa, have lived in near-isolation from the rest of humanity for thousands of years. In fact, the study shows that some of their DNA matches most closely people from modern-day southern Europe, including Spain and Italy. Because Eurasian people also carry traces of Neanderthal DNA, the finding also shows – for the first time – that genetic material from our extinct cousin may be widespread in African populations. The Khoisan tribes of southern Africa are hunter-gatherers and pastoralists who speak unique click languages. Their extraordinarily diverse gene pool split from everyone else's before the African exodus.

 Ancient lineages 

"These are very special, isolated populations, carrying what are probably the most ancient lineages in human populations today," says David Reich of Harvard University. "For a lot of our genetic studies we had treated them as groups that had split from all other present-day humans before they had split from each other." So he and his colleagues were not expecting to find signs of western Eurasian genes in 32 individuals belonging to a variety of Khoisan tribes. "I think we were shocked," says Reich. The unexpected snippets of DNA most resembled sequences from southern Europeans, including Sardinians, Italians and people from the Basque region. Dating methods suggested they made their way into the Khoisan DNA sometime between 900 and 1800 years ago – well before known European contact with southern Africa. Archaeological and linguistic studies of the region can make sense of the discovery. They suggest that a subset of the Khoisan, known as the Khoe-Kwadi speakers, arrived in southern Africa from east Africa around 2200 years ago. Khoe-Kwadi speakers were – and remain – pastoralists who make their living from herding cows and sheep. The suggestion is that they introduced herding to a region that was otherwise dominated by hunter-gatherers. 

Genetics show a return to Africa starting around 3000 years ago, long before European colonialism [Credit: New Scientist]

 Khoe-Kwadi tribes Reich and his team found that the proportion of Eurasian DNA was highest in Khoe-Kwadi tribes, who have up to 14 per cent of western Eurasian ancestry. What is more, when they looked at the east African tribes from which the Khoe-Kwadi descended, they found a much stronger proportion of Eurasian DNA – up to 50 per cent. 
That result confirms a 2012 study by Luca Pagani of the Wellcome Trust Sanger Institute in Hinxton, UK, which found non-African genes in people living in Ethiopia. Both the 2012 study and this week's new results show that the Eurasian genes made their way into east African genomes around 3000 years ago. About a millennium later, the ancestors of the Khoe-Kwadi headed south, carrying a weaker signal of the Eurasian DNA into southern Africa. The cultural implications are complex and potentially uncomfortably close to European colonial themes. "I actually am not sure there's any population that doesn't have west Eurasian [DNA]," says Reich. "These populations were always thought to be pristine hunter-gatherers who had not interacted with anyone for millennia," says Reich's collaborator, linguist Brigitte Pakendorf of the University of Lyon in France. "Well, no. Just like the rest of the world, Africa had population movements too. There was simply no writing, no Romans or Greeks to document it." Twist in tale There's one more twist to the tale. In 2010 a research team – including Reich – published the first draft genome of a Neanderthal. Comparisons with living humans revealed traces of Neanderthal DNA in all humans with one notable exception: sub-Saharan peoples like the Yoruba and Khoisan. That made sense. After early humans migrated out of Africa around 60,000 years ago, they bumped into Neanderthals somewhere in what is now the Middle East. Some got rather cosy with each other. As their descendants spread across the world to Europe, Asia and eventually the Americas, they spread bits of Neanderthal DNA along with their own genes. But because those descendants did not move back into Africa until historical times, most of this continent remained a Neanderthal DNA-free zone. Or so it seemed at the time. Now it appears that the Back to Africa migration 3000 years ago carried a weak Neanderthal genetic signal deep into the homeland. Indeed one of Reich's analyses, published last month, found Neanderthal traces in Yoruba DNA In other words, not only is western Eurasian DNA ancestry a global phenomenon, so is having a bit of Neanderthal living on inside you. 

Author: Catherine Brahic | Source: New Scientist [February 23, 2014]

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Out of Africa

Genetic mutation may have allowed early humans to migrate throughout Africa

A genetic mutation that occurred thousands of years ago might be the answer to how early humans were able to move from central Africa and across the continent in what has been called "the great expansion," according to new research from Wake Forest Baptist Medical Center.

A genetic mutation that occurred thousands of years ago might be the answer to how early humans were able to move from central Africa and across the continent in what has been called "the great expansion," according to new research [Credit: iStockphoto]

By analyzing genetic sequence variation patterns in different populations around the world, three teams of scientists from Wake Forest Baptist, Johns Hopkins University School of Medicine and the University of Washington School of Medicine, Seattle, demonstrated that a critical genetic variant arose in a key gene cluster on chromosome 11, known as the fatty acid desaturase cluster or FADS, more than 85,000 years ago. This variation would have allowed early humans to convert plant-based polyunsaturated fatty acids (PUFAs) to brain PUFAs necessary for increased brain size, complexity and function. The FADS cluster plays a critical role in determining how effectively medium-chain PUFAs found in plants are converted to the long-chain PUFAs found in the brain.

This research is published online today in PLOS One.

Archaeological and genetic studies suggest that homo sapiens appeared approximately 180,000 years ago, but stayed in one location around bodies of water in central Africa for almost 100,000 years. Senior author Floyd H. "Ski" Chilton, Ph.D., professor of physiology and pharmacology and director of the Center for Botanical Lipids and Inflammatory Disease Prevention at Wake Forest Baptist, and others have hypothesized that this location was critical, in part, because early humans needed large amounts of the long-chain PUFA docosahexaenoic acid (DHA), which is found in shellfish and fish, to support complex brain function.

"This may have kept early humans tethered to the water in central Africa where there was a constant food source of DHA," Chilton said. "There has been considerable debate on how early humans were able to obtain sufficient DHA necessary to maintain brain size and complexity. It's amazing to think we may have uncovered the region of genetic variation that arose about the time that early humans moved out of this central region in what has been called the 'great expansion.'"

Once this trait arose, the study shows that it was under intense selective pressure and thus rapidly spread throughout the population of the entire African continent. "The power of genetics continually impresses me, and I find it remarkable that we can make inferences about things that happened tens of thousands of years ago by studying patterns of genetic variation that exist in contemporary populations," said Joshua M. Akey, Ph.D., lead scientist at the University of Washington.

This conversion meant that early humans didn't have to rely on just one food source, fish, for brain growth and development. This may have been particularly important because the genetic variant arose before organized hunting and fishing could have provided more reliable sources of long-chain PUFAs, Akey said.

To investigate the evolutionary forces shaping patterns of variation in the FADS gene cluster in geographically diverse populations, the researchers analyzed 1,092 individuals representing 15 different human populations that were sequenced as part of the 1000 Genome Project and 1,043 individuals from 52 populations from the Human Genome Diversity Panel database. They focused on the FADS cluster because they knew those genes code for the enzymatic steps in long-chain PUFA synthesis that are the least efficient.

Chilton said the findings were possible because of the collaboration of internationally recognized scientists from three distinct and diverse disciplines - fatty acid biochemistry (Wake Forest Baptist), statistical genetics (Johns Hopkins) and population genetics (University of Washington). This new information builds on Chilton's 2011 research findings published in BMC Genetics that showed how people of African descent have a much higher frequency of the gene variants that convert plant-based medium-chain omega-6 PUFAs found in cooking oils and processed foods to long-chain PUFAs that cause inflammation. Compared to Caucasians, African Americans in the United States have much higher rates of hypertension, type 2 diabetes, stroke, coronary heart disease and certain types of cancer. "The current observation provides another important clue as to why diverse racial and ethnic populations likely respond differently to the modern western diet," Chilton said.

This research was supported by National Institutes of Health grants, P50 AT002782 and a Clinical and Translational Science Award grant to The Johns Hopkins Medical Institutions. Additional support was received from the Wake Forest Health Sciences Center for Public Health Genomics. Additional support came from the Mary Beryl Patch Turnbull Scholar Program and the MOSAIC initiative of Johns Hopkins University.

Chilton has a financial interest in and is a consultant for Gene Smart Health. His potential conflict of interest is being institutionally managed by Wake Forest Baptist and outside sponsors, as appropriate. No other authors have a conflict of interest.

First author is Rasika Mathias, Sc.D, assistant professor of medicine and epidemiology, Johns Hopkins; contributing authors include Hannah C. Ainsworth and Susan Sergeant, both of Wake Forest Baptist; Wenqing Fu, U of W; Dara G. Torgerson, University of California San Francisco; and Ingo Ruczinski and Kathleen C. Barnes of Johns Hopkins.

Source: Wake Forest Baptist Medical Center [September 19, 2012]