Early human migrations in southern Africa

Comparing the DNA profiles of living people who are indigenous to different parts of the world has achieved a lot as regards tracing the migrations of their ancestors and amalgamations between and separations from different genetic groups along the way. Most such analyses have centred on alleles in DNA from mitochondria (maternal) and Y chromosomes (paternal), and depend on the assumption that rates of mutation (specifically those that have neither negative nor positive outcomes) in both remain constant over tens of thousand years and genetic intermixing through reproduction. Both provide plausible hypotheses of where migrations began, the approximate route that they took and the timing of both departures from and arrival at different locations en route. Most studies have focused on the ‘Out of Africa’ migration, which began, according to the latest data, around 80 ka ago. Arrival times at various locations differ considerably, from around 60 ka for the indigenous populations of Australia and New Guinea, roughly 40 ka for Europe and ~12 ka for the Americas. Yet an often overlooked factor is that not all migrating groups have descendants that are alive today. For instance, remains of anatomically modern humans (AMH)have been found in sediments in the Levant as old as 177 ka (see: Earliest departure of modern humans from Africa, January 2018), and between 170 to 210 ka in southern Greece (See: Out of Africa: The earliest modern human to leave). Neither have yielded ancient DNA, yet nor are their arrival times compatible with the ‘route mapping’ provided by genetic studies of living people. Such groups became extinct and left no traceable descendants, and there were probably many more awaiting discovery. Maybe these mysteries will be penetrated by DNA from the ancient bones, should that prove possible.

The recorded history of AMH within Africa began around 286 to 315 ka in Morocco (see: Origin of anatomically modern humans, June 2017) and their evolutionary development may have spanned much of the continent, judging by previously discovered fossils in Ethiopia and South Africa that are older than 200 ka. Again, ancient DNA has not been extracted from the oldest fossils; nor is that likely to be possible because the double helix breaks down quickly in hot and humid climates. Genetic data from living Africans are growing quickly. An additional 198 African mtDNA genomes reported recently have pushed up the total available for analysis, the bulk of them being from eastern and southern Africa (Chan, E.K.F. and 11 others 2019. Human origins in a southern African palaeo-wetland and first migrations. Nature, v. 575, p. 185-189; DOI: 10.1038/s41586-019-1714-1). The study focuses on data from the KhoeSan ethnic group, restricted to areas south of the Zambezi River, who speak a language with distinctive  click consonants. Some KhoeSan still practice a hunter-gatherer lifestyle. Previous genetic studies showed the KhoeSan to differ markedly from other inhabitants of southern Africa, and they are widely regarded as having inhabited the area for far longer than any other groups. A sign of this emerges from their mtDNA in a genetic lineage signified as L0. Comparing KhoeSan mtDNA with the wider genetic database allowed the researchers to plot a ‘family tree’. Measures of the degree of difference between samples push back the origin of L0 and the KhoeSan themselves to roughly 200 ka.

okavango
The Okavango Delta today during the wet season (Credit: Wikimedia Commons)

It turns out that the LO lineage has several variants, whose geographic distributions allow the approximate place of origin for the lineage and directions of later migration from it to be mapped. It seems that LO was originally indigenous to the modern Okavango Delta and Makgadikgadi salt flats of Botswana. People carrying the original (L0k) variant are estimated to have remained in the broad area for about 70 thousand years. During that time it was all lush, low-lying wetland around a huge, now vanished lake. The hydrology of the area was dramatically split by regional tectonic activity at around 60 ka. The lake simply evaporated to form the salt pan of the Makgadikgadi, leaving only the seasonal Okavango Delta as a destination for flood water. People carrying Lok stayed in the original homeland whereas other shifted. Migration routes to the northeast and towards the southwest and south are crudely mapped by the distribution of the other L0 variants among modern populations. They followed ‘green corridors’ between 130 and 110 ka, the collapse of the ecosystem leaving a small group of the founding population isolated from its descendants.

The paper claims that the former Botswana wetlands were the cradle of the first modern humans. Perhaps in southern Africa, but other, older AMH remains found far off and perhaps undiscovered elsewhere are more likely. But that can only be reconciled with the KhoeSan study by ancient DNA from fossils. Criticism of the sweeping claims in the paper has already been voiced, on these grounds and the study’s lack of data on paternal DNA or whole genomes from the sampled population.

See also: Gibbons, A. 2019. Experts question study claiming to pinpoint birthplace of all humans. Science (online); DOI: 10.1126/science.aba0155

Tracing hominin evolution further back

The earliest hominin known from Africa is Sahelanthropus tchadensis, announced in 2002 by Michel Brunet and his team working in 7 Ma old Miocene sediments deposited by the predecessor to Lake Chad in the central Sahara Desert. Only cranial bones were present. From the rear the skull and cranial capacity resembled what might have been regarded as an early relative of chimpanzees. But its face and teeth look very like those of an australopithecine. Sadly, the foramen magnum – where the cranium is attached to the spine – was not well preserved, and leg bones were missing. The position of the first is a clue to posture; forward of the base of the skull would suggest an habitual upright posture, towards the rear being characteristic of knuckle walkers. Some authorities, including Brunet, believe Sahelanthropus may have been upright, but others strongly contest that. The angle of the neck-and-head ball joint of the femur (thigh bone), where the leg is attached to a socket on the pelvis to form the hip joint is a clue to both posture and gait. The earliest clear sign of an upright, bipedal gait is the femur of a fossil primate from Africa – about a million years younger than Sahelanthropus, found in the Tugen Hills of Kenya. Orrorin tugenensis was described from 20 bone fragments, making up: a bit of the other femur, three hand bones; a fragment of the upper arm (humerus); seven teeth; part of the left and right side of a lower jawbone (mandible). Apart from the femur that retains a neck and head and signifies an upright gait, only the teeth offer substantial clues. Orrorin has  a dentition similar to humans apart from ape-like canines but significantly smaller in size – all known hominins lack the large canines, relative to other teeth. Despite being almost 2 Ma older than Ardipithecus ramidus, the first clearly bipedal hominin, Orrorin is more similar to humans than both it and Australopithecus afarensis, Lucy’s species.

Oreopithecus_bambolii_1
Near-complete skeleton of Oreopithecus bambolii from Italy (credit: Wikipedia Commons)

DNA differences suggest that human evolution split from that of chimpanzees about 12 Ma ago. Yet the earlier Miocene stratigraphy of Africa has yet to provide a shred of evidence for earlier members of either lineage or a plausible last common ancestor of both. In 1872, a year after publication of Charles Darwin’s The Descent of Man parts of an extinct primate were found in Miocene sediments in Tuscany and Sardinia, Italy. In 1950 an almost complete skeleton was unearthed and named Oreopithecus bambolii (see Hominin evolution becoming a thicket, January 2013). Despite dozens of specimens having been found in different localities, the creature was largely ignored in subsequent debate about human origins, until 1990 when it was discovered that not only could Oreopithecus walk on two legs, albeit differently from humans, it had relatively small canine teeth and its hands were like those of hominins, capable of a precision grip. Dated at 7 to 9 Ma, it may lie further back on the descent path of hominins; but it lived in Europe not Africa. Now the plot has thickened, for another primate has emerged from a clay pit in Bavaria, Germany (Böhme, M. and 8 others 2019. A new Miocene ape and locomotion in the ancestor of great apes and humans. Nature, online publication; DOI: 10.1038/s41586-019-1731-0).

Danuvius
Bones from 4 Danuvius guggenmosi individuals. Note the diminutive sizes compared with living apes (Credit: Christoph Jäckle)

Danuvius guggenmosi lived 11.6 Ma ago and its fossilised remains represent four individuals. Both femurs and a tibea (lower leg), together with the upper arm bones are preserved. The femurs and vertebrae strongly suggest that Danuvius could walk on two legs, indeed the vertebral shapes indicate that it had a flexible spine; essential for balance by supporting the weight of the torso over the pelvis. It also had long arms, pointing to its likely hanging in and brachiating through tree canopies. Maybe it had the benefit of two possible lifestyles; arboreal and terrestrial. Its discoverers do not go that far, suggesting that it probably lived entirely in trees using both forms of locomotion in ‘extended limb clambering’. It may not have been alone, another younger European primate found in the Miocene of Hungary, Rudapithecus hungaricus, may also have had similar clambering abilities, as might have Oreopithecus.

There is sure to be a great deal of head scratching among palaeoanthropologists, now that three species of Miocene primate seem – for the moment – to possess  ‘prototype specifications’ for early entrants on the evolutionary path to definite hominins. Questions to be asked are ‘If so, how did any of them cross the geographic barrier to Africa; i.e. the Mediterranean Sea?’, ‘Did the knuckle-walking chimps evolve from a bipedal common ancestor shared with hominins?, ‘Did bipedalism arise several times?’. The first may not have been as difficult as it might seem (see Africa_Europe exchange of faunas in the Late Miocene, July 2013). The Betic Seaway that once separated Iberia from NW Africa, in a similar manner to the modern Straits of Gibraltar, closed during the Miocene after a ‘mild’ tectonic collision that threw up the Betic Cordillera of Southern Spain. Between 5.6 and 5.3 Ma there was a brief ‘window of opportunity’ for the crossing, that ended with one of the most dramtic events in the Cenozoic Era; the Zanclean Flood, when the Atlantic burst through what is now the Straits of Gibraltar cataclysmically to refill the Mediterranean .

See also: Barras, C. 2019. Ancient ape offers clues to evolution of two-legged walking. Nature, v. 575, online; Kivell, T.L. 2019. Fossil ape hints at how walking on two feet evolved. Nature, v. 575, online; DOI: 10.1038/d41586-019-03347-0

Life with the Neanderthals

From Robinson Crusoe’s discovery of Friday’s footprint on his desert island to Mary Leakey’s unearthing of a 3.6 Ma old trackway left by two adults and a juvenile of the hominin species Australopithecus afarensis at Laetoli in Tanzania, such tangible signs of another related creature have fostered an eerie thrill in whoever witnesses them. Other ancient examples have turned up, such as the signs of mud trampled by 800 ka humans (H. antecessor?) at Happisburgh, Norfolk, UK (see Traces of the most ancient Britons, February 2014). From a purely scientific standpoint, footprints provide key evidence of foot anatomy, gait, travel speed, height, weight, and the number of individuals who contributed to a trackway. At Le Rozel on the Cherbourg Peninsula in Normandy, France – about 30 km west of the D-Day landing site at Utah beach – Yves Roupin, an amateur archaeologist, discovered a footprint on the foreshore in the 1960s close to the base of a thick sequence of late-Pleistocene dune sediments exposed below a rocky cliff. Fifty years later, rapid onset of wind and tidal erosion threatened to destroy the site, so excavations and scientific analysis began. This involved excavation of thick overburden on an annual basis to expose as much of five footprint-bearing horizons as possible (about 90 m2).

Le Rozel
The Le Rozel excavation, with weighted plastic sheets to protect the site from erosion between visits (credit: Dominique Cliquet)

More and more prints emerged, each photographed and modelled in 3-D, with the best being preserved as casts using a flexible material, similar to that used by dentists (Duveau, J. eyt al. 2019. The composition of a Neandertal social group revealed by the hominin footprints at Le Rozel (Normandy, France). Proceedings of the National Academy of Sciences. 9 September 2019; DOI: 10.1073/pnas.1901789116). At the end of the excavation hundreds of prints had been found and recorded. They had been preserved in wet sand, probably deposited in an interdune pond. Luminescence dating of sand grains revealed that the footprints were produced around 80 ka ago, 35 ka before Europe was occupied by anatomically modern humans. Scattered around the site are numerous fossils of butchered prey animals, together with stone tools typical of Neanderthal technology.

Such a large number of footprints presented a unique opportunity to analyse the social structure of the Neanderthal group that produced them, for they came in many different sizes. During the very short period in which they were produced and buried by wind-blown sand, an estimated 10 to 13 individuals had crossed and re-crossed the site – there may have been more individuals who didn’t happen to cross the wet patch But the evidence suggests that children and adolescents, one of whom may have been as young as 2 years, predominated. Two or three with the biggest feet were probably adults as tall as 1.9 metres – about 20 cm taller that the average for modern human males. That is surprising for Neanderthals who are widely believed to have been more stocky. The fact that footprints occur in 5 horizons suggests that the band, or perhaps family, found the site to be good for occupation. Wider hypotheses are a little shaky. Did Neanderthals have large families? Does the predominance of children and adolescents indicate that they died young? But perhaps children stayed close to habitations with just a few ‘minders’, while other adults went off hunting and foraging. Were the kids playing?

Australopithecus anamensis; a face to fit the name

Ethiopian palaeoanthropologist Yohannes Haile-Selassie of the Cleveland Museum of Natural History, Ohio, USA has been involved in the search for early human ancestors in the Awash Valley of the Afar Depression in Ethiopia since 1990. The Middle Awash Project, founded by his mentor Tim White, has been enormously successful over the years. That is because most members from the top down are persistent, inured to heat and sharp sighted. Haile-Selassie is a case in point. In 2016 near a place called Miro Dora, he and a local worker independently spotted two parts of what turned out to be a near-complete cranium of an australopithecine (Au. anamensis) (Haile-Selassie, Y. et al. 2019. A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia. Nature, v. 572, published online; DOI: 10.1038/s41586-019-1513-8). When it was dated at about 3.8 Ma, using the 40Ar/39Ar method and magnetic reversal stratigraphy (Saylor, B.Z. and 13 others 2019. Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia. Nature, v. 572, published online; DOI: 10.1038/s41586-019-1514-7), his find caused quite a stir.

anamensis
The near-complete cranium of an Au. anamensis found in the Afar Depression of NE Ethiopia. Note the lateral fflattening caused by sedimentary burial. (Credit: Cleveland Museum of Natural History)

Fragmentary hominin fossils, including a complete lower jaw, found near Lake Turkana, Kenya in 1994 were sufficiently different from other, known australopithecines to warrant their recognition as a new species, Australopithecus anamensis. Seeming more ape-like than the famous ‘Lucy’ fossil Au. afarensis and also older – 3.9 to 4.2 Ma compared with 3.0 to 3.8 Ma for Lucy’s species –  Au anamensis  has long been regarded as a possible ancestor of afarensis, or even a more primitive member if the same species. The new, almost perfect cranium – except for some distortion during burial – cohabited the Afar Depression with Au. afarensis, for as long as 100 ka, and is sufficiently different to retain its species status. Because many palaeoanthropologists consider Au. afarensis to be early in the evolutionary line that lead to humans, the new find seems to throw a spanner in this linear hypothesis. However, there is another possibility that may resolve the issue.

During the Pliocene, Afar was a very diverse place with many volcanoes, lava flows and minor rift systems. It is possible that geographic complexity separated and isolated small groups allowing them to diverge genetically, in the manner of island faunas. Australopithecus afarensis may have arisen from such isolation, going on to outcompete its ‘parent’ species Au anamensis whose numbers progressively dwindled. Nevertheless, the emerging diversity of coexisting hominin populations in the Pliocene seriously challenges linear evolutionary hypotheses aimed at understanding the origin of our own genus (see Taking stock of hominid evolution February 2002 and Hominid evolution: a line or a bush? May 2006).

See also: Video of the discovery and summary of subsequent research

Barras, C. 2019. Rare 3.8-million-year-old skull recasts origins of iconic ‘Lucy’ fossil. Nature, v. 572, p. ; DOI: 10.1038/d41586-019-02573-w

Spoor, F. 2019. Elusive cranium of early hominin found. Nature, v. 572, p. ; DOI: 10.1038/d41586-019-02520-9

 

Symbolic art made by Denisovans (?)

The deep soil by a permanent spring in a vegetable allotment on the edge of the small town of Lingjing near Xuchang City in Henan Province, China has provided a wealth of stone artefacts and bone fragments to a depth of 10 m (see Denisovan(?) remains in the garden, March 2017). Optically stimulated luminescence (OSL) dating of mineral grains shows that the last time that the deepest soils were exposed to sunlight was between 78 to 123 ka. Long before the first arrival of anatomically modern humans (AMH) in China the site had been much as it is today, a human habitation site. Among the bones were fragments of the crania from five human individuals, perhaps either Homo erectus descended from the earliest arrivals in China or more recent Denisovans closely related to the Neanderthals of western Eurasia. Reconstruction of the two most complete crania hinted at the second possibility by resemblance to Neanderthal anatomy yet the complete lack of evidence that Neanderthals travelled so far to the east.

denisovan arft
Top: lines etched through ochre veneer on a rib bone from Lingjing, China; bottom: hashed lines carved on a faceted block of hematite from Blombos Cave (Credit: Li et al 2019; Fig. 3 and Chris Henshilwood)

So far there have been no reports of DNA from these enigmatic fossils, but some of the bones from the deepest layers show etched, roughly parallel lines (Li, Z et al. 2019. Engraved bones from the archaic hominin site of Lingjing, Henan Province. Antiquity, v. 370, p. 886-900; DOI: 10.15184/aqy.2019.81). Analysis shows that they were deliberately made after the bones had been defleshed: the fragments have thin veneers of red ochre through which the deep scratches reveal white bone. They are not cut marks, but the scratches on previously reddened bone suggest some form of design. This is by no means the earliest symbolic art, for shells associated with Eugene Dubois’s ~500 ka old ‘Pithecanthropus’ (Homo) erectus remains from Trinil, Java are similarly engraved (see Art from half a million years ago. December 2014). Yet the Lingjing engravings predate the oldest know symbolic art from the Blombos Cave of South Africa that was produced by AMH who lived in about 75 ka ago. Neanderthal artistic ability has shown up at many sites (see Human evolution and migrations, March 2011; May 2016; February 2018)

An ability to express mental concepts of some kind in a durable way now seems to have characterised at least four human species over the last half-million years.

See also: Schuster, R. 2019. Prehistoric Art or Doodle? 110,000-year-old Engraved Bones Create New Mystery (Haaretz, 31 July 2019); Denisovan(?) remains in a Chinese garden (Earth-logs, March 2017)

Humans gorged on giant mole rats during Ethiopian glaciation

Until recently it was believed that humans only adapted to life at high elevations, such as those of the Tibetan Plateau, during the Holocene. Then it turned out that the DNA of modern Tibetans contains a mutated gene (EPAS1) that boosts haemoglobin production that underpins their comfortably living at above 4000 m. In quick succession it was discovered that modern humans were living in Tibet as early as 30 to 40 ka, the same gene was found in Denisovan DNA and then a jawbone of that earlier human emerged from a Tibetan cave. It has been estimated that ancestral Tibetans inherited the DNA segment from Denisovans at around 40 ka. The ancestral African homeland of our genus Homo has large highland tracts that rise above 4000 m, most notably Mount Kilimanjaro (5895 m, Tanzania), Mount Kenya (5199 m Kenya) and Mount Stanley (5109 m, Rwenzori, Uganda). Those three retain glaciers, albeit small ones. But during the last glacial maximum permanent ice fields also capped highland areas in Morocco, Ethiopia and South Africa. Today there are permanent or seasonal habitations above 4000 m in all these African settings because of warmer conditions, but DNA analyses of the inhabitants have yet to be tested for the EPAS1 genetic mutation.

erratic Bale
Glacial erratic in the Bale Mountains National Park, Ethiopia (credit: James Steamer)

Understandably, research into the former glaciation of highland areas in tropical Africa is a hot topic. One of the largest areas of glacial till and moraine in Africa lies on the >4000 m high Sanetti Plateau in the Bale Mountains of south-eastern Ethiopia. These mountains are the dissected remnants of a Miocene shield volcano and host a rich ecosystem; in fact the largest reserve of Afro-alpine flora and fauna. Like many mountains in tropical Africa, Bale helps rising moist air to condense as mists. The resulting rich ecology makes such mountain systems high-elevation ‘oases’ surrounded by semi-arid to arid savannah and desert. Because this was likely to have been equally true during the more arid conditions of the last glacial period areas such as Bale may have been refuges for humans during those times, despite the risk of altitude sickness (hypoxia). Aarchaeologist Götz Ossendorf of the University of Cologne, together with a large team from Germany, France, Ethiopia, Switzerland the USA, set out to test this hypothesis ( Ossendorf, G. and 21 others 2019. Middle Stone Age foragers resided in high elevations of the glaciated Bale Mountains, Ethiopia. Science, v. 365, p. 583–587; DOI: 10.1126/science.aaw8942).

Their main target was to excavate a rock shelter at around 3500 m, but outcrops of volcanic glass (obsidian) at 4200 m had clearly attracted human interest  as they are scattered with flaked tools and debitage from their manufacture. The upper sediment layers in the rock shelter yielded ashes, charcoal, a few pottery shards and a glass bead, together with evidence for herbivore droppings. Dates fall in the last 800 years; hardly surprising as the Bale Plateau is seasonally visited by local herders who use rock shelters as corrals for livestock. The lower levels, however, contain artefacts of the Middle Stone Age (MSA); the African terminology roughly equivalent to the Upper Palaeolithic in Eurasia. The MSA layer also contain coprolites, some of hyena in its upper parts but also massive amounts likely to be human that extend to the base of the cave sediments. Dated at 47 to 31 ka, the sediments bracket the age of maximum glacier extent.

giant_molerat
Alert giant mole rat in Ethiopia’s Bale Mountains (credit: M. Watson)

The lower cave sediments contain abundant animal bones and signs of several hearths. Some of the bones show signs of cooking from burn marks. Although several prey species occur, more than 90% of the bones are those of giant mole rats (Tachyoryctes macrocephalus). It is not difficult to conclude that the human population’s meat consumption was almost entirely of roasted mole rat. That is not surprising because the thin soils of the Bale Mountains support at least 29 mole rats per hectare, each adult weighing around a kilogram. Like the guinea pig (Cavia porcellus), which forms a major source of protein for people living today in the high Andes of Peru and Bolivia – an estimated 65 million being eaten annually by Peruvians, mole rats are extremely easy to catch; an attractive proposition for consumers surviving under the stress of hypoxia. They also reproduce at a phenomenal rate Today, Andean people domesticate guinea pigs for the table. Until other sites of human habitation during the Bale ‘ice age’ whether the MSA people lived permanently at high elevation or migrated there seasonally, to gorge on mole rats, cannot be resolved.

Out of Africa: The earliest modern human to leave

The 2017 discovery in Morocco of fossilised, anatomically modern humans (AMH) dated at 286 ka (see: Origin of anatomically modern humans, June 2017) pushed back the origin of our species by at least 100 ka. Indeed, the same site yielded flint tools around 315 ka old. Aside from indicating our antiquity, the Jebel Irhoud discovery expanded the time span during which AMH might have wandered into Eurasia, as a whole variety of earlier hominins had managed since about 1.8 Ma ago. Sure enough, the widely accepted earliest modern human migrants from Skhul and Qafzeh caves in Israel (90 to 120 ka) were superseded in 2018 by AMH fossils at Misliya Cave, also in Israel, in association with 177 ka stone artefacts (see Earliest departure of modern humans from Africa, January 2018). Such early dates helped make more sense of very old ages for unaccompanied stone tools in the Arabian Peninsula as tracers for early migration routes. Unlike today, Arabia was a fertile place during a series of monsoon-related cycles extending back to about 160 ka (see: Arabia : staging post for human migrations? September 2014; Wet spells in Arabia and human migration, March 2015). The ‘record’ has now shifted to Greece.

hominin sites
Key ages of early H. sapiens, Neanderthals and Denisovans (credit: Delson, 2019; Fig. 1)

Fossil human remains unearthed decades ago often undergo revised assessment as more precise dating methods and anatomical ideas become available. Such is the case for two partial human skulls found in the Apidima Cave complex of southern Greece during the late 1970s. Now, using the uranium-series method, one has been dated at 170 ka, the other being at least 210 ka old (Harvati, K. and 11 others 2019. Apidima Cave fossils provide earliest evidence of Homo sapiens in Eurasia. Nature, v. 571 online; DOI: 10.1038/s41586-019-1376-z). These are well within the age range of European Neanderthals. Indeed, the younger one does have the characteristic Neanderthal brow ridges and elongated shape. Albeit damaged, the older skull is more rounded and lacks the Neanderthals’ ‘bun’-like bulge at the back; it is an early member of Homo sapiens. In fact 170 ka older than any other early European AMH, and a clear contemporary of the long-lived Neanderthal population of Eurasia; in fact the age relations could indicate that Neanderthals replaced these early AMH migrants.

Given suitable climatic conditions in the Levant and Arabia, those areas are the closest to Africa to which they are linked by an ‘easy’, overland route. To reach Greece is not only a longer haul from the Red Sea isthmus but involves the significant barrier of the Dardanelles strait, or it requires navigation across the Mediterranean Sea. Such is the ‘specky’ occurrence of hominin fossils in both space and time that a new geographic outlier such as Apidima doesn’t help much in understanding how migration happened. Until – and if – DNA can be extracted it is impossible to tell if AMH-Neanderthal hybridisation occurred at such an early date and if the 210 ka population in Greece vanished without a trace or left a sign in the genomics of living humans. Yet, both time and place being so unexpected, the discovery raises optimism of further discoveries to come

See also: Delson, E. 2019. An early modern human outside Africa. Nature, v. 571 online; DOI: 10.1038/d41586-019-02075-9

Ancient proteins: keys to early human evolution?

A jawbone discovered in a Tibetan cave turned out to be that of a Denisovan who had lived and died there about 160,000 years ago (see: Denisovan on top of the world; 6 May, 2019). That discovery owed nothing to ancient DNA, because the fossil proved to contain none that could be sequenced. But the dentine in one of two molar teeth embedded in the partial jaw did yield protein. The teeth are extremely large and have three roots, rather than the four more common in modern, non-Asian humans, as are Denisovan teeth from in the Siberian Denisova Cave. Fortunately, those teeth also yielded proteins. In an analogous way to the genomic sequencing of nucleotides (adenine, thymine, guanine and cytosine) in DNA, the sequence of amino acids from which proteins are built can also be analysed. Such a proteomic sequence can be compared with others in a similar manner to genetic sequences in DNA. The Tibetan and Siberian dentine proteins are statistically almost the same.

collagen
Triple helix structure of collagen, colour-coded to represent different amino acids (credit: Wikipedia)

At present the most ancient human DNA that has been recovered – from an early Neanderthal in the Sima de los Huesos in Spain – is 430,000 years old (see: Mitochondrial DNA from 400 thousand year old humans; December 2013). Yet it is proving difficult to go beyond that time, even in the cool climates that slow down the degradation of DNA. The oldest known genome of any animal is that of mtDNA from a 560–780 thousand year old horse, a leg bone of which was extracted from permafrost in the Yukon Territory, Canada. The technologies on which sequencing of ancient DNA depends may advance, but, until then, tracing the human evolutionary journey back beyond Neanderthals and Denisovans seems dependent on proteomic approaches (Warren, M. 2019. Move over, DNA: ancient proteins are starting to reveal humanity’s history. Nature, v. 570, p. 433-436; DOI: 10.1038/d41586-019-01986-x). Are the earlier Homo heidelbergensis and H. erectus within reach?

It seems that they may be, as might even earlier hominins. The 1.8 Ma Dmanisi site in Georgia, now famous for fossils of the earliest humans known to have left Africa, also yielded an extinct rhinoceros (Stephanorhinus). Proteins have been extracted from it, which show that Stephanorhinus was closely related to the later woolly rhinoceros (Coelodonta antiquitatis). Collagen protein sequences from a 3.4 Ma camel preserved in the Arctic and even from a Tanzanian 3.8 Ma ostrich egg shell show the huge potential of ancient proteomics. Most exciting is that last example, not only because it extends the potential age range to that of Australopithecus afarensis but into tropical regions where DNA is at its most fragile. Matthew Warren points out potential difficulties, such as the limit of a few thousand amino acids in protein sequences compared with 3 million variants in DNA, and the fact that the most commonly found fossil proteins – collagens –  may have evolved very little. On the positive side, proteins have been detected in a 195 Ma old fossil dinosaur. But some earlier reports of intact diosaur proteins have been questioned recently (Saitta, E.T. et al. 2019. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. eLife, 8:e46205; DOI: 10.7554/eLife.46205)

 

Multiple invention of stone tools

Steadily, the record of stone tools has progressed further back in time as archaeological surveys have expanded, especially in East Africa (Stone tools go even further back, May 2015). The earliest known tools – now termed Lomekwian – are 3.3 million years old, from deposits in north-western Kenya, as are cut-marked bone fragments from Ethiopia’s Afar region. There is no direct link to their makers, but at least six species of Australopithecus occupied Africa during the Middle Pliocene. Similarly, there are various options for who made Oldowan tools in the period between 2.6 and 2.0 Ma, the only known direct association being with Homo habilis in 2.0 Ma old sediments from Tanzania’s Olduvai Gorge; the type locality for the Oldowan.

The shapes of stone tools and the manufacturing techniques required to make them and other artefacts, are among the best, if not the only, means of assessing the cognitive abilities of their makers. A new, detailed study of the shapes of 327 Oldowan tools from a 2.6 Ma old site in Afar, Ethiopia has revealed a major shift in hominin working methods (Braun, D.R. and 17 others 2019. Earliest known Oldowan artifacts at >2.58 Ma from Ledi-Geraru, Ethiopia, highlight early technological diversity. Proceedings of the National Academy, v. 116, p. 11712-11717; DOI: 10.1073/pnas.1820177116). The sharp-edged tools were made by more complex methods than the Lomekwian. Analysis suggests that they were probably made by striking two lumps of rock together, i.e. by a deliberate two-handed technique. On the other hand, Lomekwian tools derived simply by repeatedly bashing one rock against a hard surface, not much different from the way some living primates make rudimentary tools. But the morphology of the Ledi-Geraru tools also falls into several distinct types, each suggesting systematic removal of only 2 or 3 flakes to make a sharp edge. The variations in technique suggest that several different groups with different traditions used the once lake-side site.

oldowan
Various 2.6 Ma old Oldowan stone tools from Ledi-Geraru, Ethiopia (credit: Braun et al., 2019)

Ledi-Geraru lies about 5 km from another site dated about 200 ka earlier than the tools, which yielded a hominin jawbone, likely to be from the earliest known member of the genus Homo. A key feature that suggested a human affinity is the nature of the teeth that differ markedly from those of contemporary and earlier australopithecines. It appears that the tools are of early human manufacture. The ecosystem suggested by bones of other animals, such as antelope and giraffe was probably open grassland – a more difficult environment for hominin subsistence. The time of the Lomekwian tools was one of significantly denser vegetation, with more opportunities for gathering plant foods. Perhaps this environmental shift was instrumental in driving hominins to increased scavenging of meat, the selection pressure acting on culture to demand tools sharp enough to remove meat from the prey of other animals quickly, and on physiology and cognitive power to achieve that.

See also: Solly, M. 2019. Humans may have been crafting stone tools for 2.6 million years (Smithsonian Magazine)

Neanderthal demographics and their extinction

About 39 thousand years ago all sign of the presence of Neanderthal bands in their extensive range across western Eurasia disappears. Their demise occurred during a period of relative warmth (Marine-Isotope Stage-3) following a cold period at its worst around 65 ka (MIS-4). They had previously thrived since their first appearance in Eurasia at about 250 ka, surviving at least two full glacial cycles. Their demise occurred around 5 thousand years after they were joined in western Eurasia by anatomically modern humans (AMH). During their long period of habitation they had adapted well to a range of climatic zones from woodland to tundra. During their overlap both groups shared much the same food resources, dominated by large herbivores whose numbers burgeoned during the warm period, with the difference that Neanderthals seemed to have depended on ranges centred on fixed sites of habitation while AMH maintained a nomadic lifestyle. Having shared a common African ancestry about 400 thousand years ago, DNA studies  have revealed that the two populations interbred regularly, probably in the earlier period of overlap in west Asia from around 120 thousand years ago and possibly in Europe too after 44 ka. Considering their previous tenacity, how the Neanderthals met their end is something of a mystery. It may have been a result of competition for resources with AMH, which could be countered by the increase in food resources. Maybe physical conflict was involved, or perhaps disease imported with AMH from warmer climes. Genetic absorption through interbreeding of a small population with a larger one of AMH is a possibility, although DNA evidence is lacking. An inability to adapt to climate change contradicts the Neanderthals long record and their disappearance during MIS-3. Previous population estimates of changing Neanderthal populations in the Iberian Peninsula (see Fig. 2 in Roberts, M.F. & Bricher, S.E 2018. Modeling the disappearance of the Neanderthals using principles of population dynamics and ecology. Journal of Archaeological Science, v. 100, p.16-31; DOI: 10.1016/j.jas.2018.09.012) show decline from about 70,000 to 20,000 before MIS-4, then recovery to about 40,000 before the arrival of AMH at 44 ka followed by a decline to extinction thereafter. Roberts and Bricher developed a model for investigating demographics from archaeological evidence that is neutral as regards any particular hypothesis for Neanderthal extinction.

Nea family
Artistic reconstruction of Neanderthal family group (credit: Nikola Solic, Reuters)

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