Modern humans left Africa almost 200,000 years ago

But should we be surprised?

With an age range of 120,000 to 90,000 years old, the fossils from the Levantine sites of Skhul and Qafzeh have long been the oldest known anatomically modern human remains from outside Africa. The recent find of an upper jawbone and associated dentition at Misliya Cave in Israel has now been independently dated by uranium series (U-Th), combined uranium and electron spin resonance (U-ESR), and thermoluminescence (TL) methods to yield an age range of 194,000 to 177,000 years old. The jawbone and teeth are associated with the Homo sapiens clade, meaning that they predate the Skhul and Qafzeh remains by more than 50,000 years. (Hershkovitz, et al., 2018)

The Misliya Cave remains were associated with large numbers of Levallois (mode 3) stone tools, characteristic of the Middle Palaeolithic.

While the findings have understandably generated a good deal of excitement, should we be unduly surprised? The Sahara and Sinai deserts can only be crossed during interglacials, when warm, wet climatic conditions cause these normally inhospitable regions to green, and the Levant effectively becomes a northeasterly extension of Africa. The date range of the Skhul and Qafzeh remains suggest that these people left Africa during the Eemian interglacial (Marine Isotope Stage 5e) 126,000 to 110,000 years ago. Similarly, the upper end of the age range of Misliya Cave remains lies within the warm, wet Marine Isotope Stage 7 which lasted from 245,000 to 186,000 years ago.

Until recently, the earliest anatomically modern humans were believed to be those from Omo, Kenya, now thought to be 195,000 years old (though originally thought to be more recent). Accordingly, it was not thought that modern humans could have left Africa prior to the Eemian. Recent discoveries from China and the Arabian Peninsula have overturned the longstanding view that the Levant was the extent of our species’ excursions beyond Africa prior to around 65,000 years ago. However, the Eemian was still thought to represent the upper limit.

The re-dating of the Jebel Irhoud remains from Morocco last year has changed the picture. The remains were found at a cave site 100 km (60 miles) from Marrakech in the early 1960s and were originally thought to be no more than 40,000 years old. The puzzle was that while the facial features are modern, the brain case is still long and low, a characteristic of archaic humans and suggesting that they really belonged to a much earlier lineage of Homo sapiens. This eventually turned out to be the case. In 2007, the remains were found to be much older at 160,000 years old with US-ESR methods – but even this turned out to be a gross underestimate. Excavations carried out between 2004 and 2011 enabled radiation dosages to be estimated more accurately, yielding a TL date of 286,000 ± 32,000 years old – making the Jebel Irhoud the earliest representatives of our species by some considerable way.

With modern humans having existed throughout Marine Isotope Stage 7, it is unsurprising that some of them reached the Levant, and entirely possible that some went further. This raises the possibility that some of these pioneers encountered and interbred with Neanderthals, which would explain a 2017 genetic study which suggested that Neanderthals and modern humans were interbreeding as long ago as the period between 460,000 and 219,000 years ago (Posth, et al., 2017). The upper end is clearly an overestimate, but the lower end could point to interbreeding in the Levant, where Neanderthals are known to have been present. While there is no suggestion at this stage that modern humans reached Europe prior to 46,000 years ago, such a discovery would call into question the attribution of recent discoveries, such as the stone circle Bruniquel Cave in southwest France reported in 2016 to be 176,500 years old, and accordingly assumed to be the work of Neanderthals. (Jaubert, et al., 2016)

References:
Hershkovitz, I. et al., 2018. The earliest modern humans outside Africa. Science, Volume 359, pp. 456-459.
Jaubert, J. et al., 2016. Early Neanderthal constructions deep in Bruniquel Cave in southwestern France. Nature, 2 June, Volume 534, pp. 111-114.
Posth, C. et al., 2017. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nature Communications, 4 July, Volume 8, p. 16046.

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

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

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

Evidence of interbreeding between archaic and modern humans – or just highly diverse morphology?

50,000-year-old Tam Pa Ling lower jawbone is a mosaic of archaic and modern features

Tam Pa Ling (‘Cave of the Monkeys’) is a cave site in Huà Pan Province, Laos. A fully-modern partial human skull (TPL1) was recovered in December 2009, followed a year later by a complete human lower jawbone (TPL2). The upper jawbone of TPL1 does not match with TPL2, so the two represent different individuals. The fossils are estimated to be from 46,000 to 63,000 years old, establishing an early presence of modern humans in Southeast Asia.

A newly-published study of the more recent discovery suggests that the TPL2 lower jawbone, though essentially modern, possesses a number of archaic attributes. The most obvious sign of modern affinities is the clear presence of a chin. However, viewed from the side, the jawbone is very robust, particularly at the position of the first and second mandibles. In this respect, TPL2 is closer to the archaic than the modern human condition.

While this mosaic could be evidence of modern humans interbreeding with archaic populations – possibly Denisovans or Homo erectus – the authors of the report take the view that early modern humans in the region simply possessed a large range of morphological variation.

Reference:
Demeter, F. et al., Early Modern Humans and Morphological Variation in Southeast Asia: Fossil Evidence from Tam Pa Ling, Laos. PLoS One 10 (4), e0121193 (2015).

 

 

Neolithic was brought to Europe by maritime colonists

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

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

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

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

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

References:

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

 Link:
 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004401

13,000 year old skull and mtDNA reinforces continuity between Paleoindians and Native Americans

Teenaged girl ‘Naia’ shared craniofacial features with earliest-known Americans, but genetic profile is common among today’s Native Americans 

The first people to reach the New World arrived around 15,000 years ago, having migrated across the Beringia land bridge that then linked Siberia to Alaska. The Paleoindians, as they are known, possessed craniofacial features that differ markedly to those of present-day Native Americans. Their skulls were long and narrow, the face narrow and the forehead prominent. By contrast, present-day Native Americans are broad-faced, with rounder skulls. A facial reconstruction of Kennewick Man – an 8,400 year old skull found in the Columbia River, Kennewick, WA – is said to bear startling a resemblance to the actor Sir Patrick Steward.

It has therefore been suggested that there were two migrations to the New World, with the Paleoindians arriving first and later being replaced by the ancestors of the present-day Native Americans. However, others argue that the differences arose in situ, possibly as a result of changes in diet when the Paleoindians adopted agriculture during the period between 8,000 and 2,000 years ago. Another possibility is that the changes are simply the result of genetic drift.

The ‘two migrations’ theory has received a significant setback with the recovery of a near-complete human skeleton of a female aged 15 to 16 years from Hoyo Negro, a submerged collapsed chamber in the Sac Actun cave system in the Yucatan Peninsula, Mexico. The skeleton has been nicknamed ‘Naia’ (Greek for ‘water nymph’), and it has been dated to between 12,000 and 13,000 years old. Naia’s craniofacial features are typical of the Paleoindian morphology, but mitochondrial DNA extracted from a molar teeth has been identified as belonging to the haplogroup D1, which occurs only among present-day Native Americans. This is consistent with the view that there was continuity between Paleoindians and present-day Native Americans.

Researchers now intend to sequence Naia’s nuclear DNA, which they hope will shed further light on the origins of the first Americans.

References:

1. Chatters, J. et al., Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science 344, 750-754 (2014).