Tag: Human evolution

How did African humans survive the 74 ka Toba volcanic supereruption?

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The largest volcanic eruption during the 2.5 million year evolution of the genius Homo, about 74 thousand years (ka) ago, formed a huge caldera in Sumatra, now filled by Lake Toba. A series of explosions lasting just 9 to 14 days was forceful enough to blast between 2,800 to 6,000 km3 of rocky debris from the crust. An estimated 800 km3 was in the form of fine volcanic ash that blanketed South Asia to a depth of 15 cm. Thin ash layers containing shards of glass from Toba occur in marine sediments beneath the Indian Ocean, the Arabian and South China Seas. Some occur as far off as sediments on the floor of Lake Malawi in southern Africa. A ‘spike’ of sulfates is present at around 74 ka in a Greenland ice core too. Stratospheric fine dust and sulfate aerosols from Toba probably caused global cooling of up to 3.5 °C over a modelled 5 years following the eruption. To make matters worse, this severe ‘volcanic winter’ occurred during a climatic transition from warm to cold caused by changes in ocean circulation and falling atmospheric CO2 concentration, known as a Dansgaard-Oeschger event.

There had been short-lived migrations of modern humans out of Africa into the Levant since about 185 ka. However, studies of the mitochondrial DNA (mtDNA) of living humans in Eurasia and Australasia suggest that permanent migration began about 60 ka ago. Another outcome of the mtDNA analysis is that the genetic diversity of living humans is surprisingly low. This suggests that human genetic diversity may have been sharply reduced globally roughly around the time of the  Toba eruption. This implies a population bottleneck with the number of humans alive at the time to the order of a few tens of thousands (see also: Toba ash and calibrating the Pleistocene record; December 2012). Could such a major genetic ‘pruning’ have happened in Africa? Over six field seasons, a large team of geoscientists and archaeologists drawn from the USA, Ethiopia, China, France and South Africa have excavated a rich Palaeolithic site in the valley of the Shinfa River, a tributary of the Blue Nile in western Ethiopia. Microscopic studies of the sediments enclosing the site yielded glass shards whose chemistry closely matches those in Toba ash, thereby providing an extremely precise date for the human occupation of the site: during the Toba eruption itself (Kappelman, Y. and 63 others 2024. Adaptive foraging behaviours in the Horn of Africa during Toba supereruption. Nature, v. 627; DOI: 10.1038/s41586-024-07208-3).

Selection of possible arrowheads from the Shinfa River site (Credit: Kappelman et al.; Blue Nile Survey Project)

The artifacts and bones of what these modern humans ate suggest a remarkable scenario for how they lived. Stone tools are finely worked from local basalt lava, quartz and flint-like chalcedony found in cavities in lava flows. Many of them are small, sharp triangular points, some of which show features consistent with their use as projectile tips that fractured on impact; they may be arrowheads, indeed the earliest known. Bones found at the site are key pointers to their diet. They are from a wide variety of animal, roughly similar to those living in the area at present: from monkeys to giraffe, guinea fowl to ostrich, and even frogs. There are remains of many fish and freshwater molluscs. Although there are no traces of plant foods, clearly those people who loved through the distant effects of Toba were well fed. Although a period of global cooling may have increased aridity at tropical latitudes in Africa, the campers were able to devise efficient strategies to obtain victuals. During wet seasons they lived off terrestrial prey animals, and during the driest times ate fish from pools in the river valley. These are hardly conditions likely to devastate their numbers, and the people seem to have been technologically flexible. Similar observations were made at the Pinnacle Point site in far-off South Africa in 2018, where Toba ash is also present. Both sites refute any retardation of human cultural progress 74 ka ago. Rather the opposite: people may have been spurred to innovation, and the new strategies may have allowed them to migrate more efficiently, perhaps along seasonal drainages. In this case that would have led them or their descendants to the Nile and a direct route to Eurasia; along ‘blue highway’ corridors as Kappelman et al. suggest.

Yet the population bottleneck implied by mtDNA analyses is only vaguely dated: it may have been well before or well after Toba. Moreover, there is a 10 ka gap between Toba and the earliest accurately dated migrants who left Africa – the first Australians at about 65 ka. However, note that there is inconclusive evidence that modern humans may have occupied Sumatra by the time of the eruption.  Much closer to the site of the eruption in southeast India, stone artifacts have been found below and above the 74 ka datum marked by the thick Toba Ash. Whether these were discarded by anatomically modern humans or earlier migrants such as Homo erectus remains unresolved. Either way, at that site there is no evidence for any mass die-off, even though conditions must have been pretty dreadful while the ash fell. But that probably only lasted for little more than a month. If the migrants did suffer very high losses to decrease the genetic diversity of the survivors, it seems just as likely to have been due to attrition on an extremely lengthy trek, with little likelihood of tangible evidence surviving. Alternatively, the out-of-Africa migrants may have been small in number and not fully representative of the genetic richness of the Africans who stayed put: a few tens of thousand migrants may not have been very diverse from the outset.

An evolutionary bottleneck and the emergence of Neanderthals, Denisovans and modern humans

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The genetic diversity of living humans, particularly among short, repetitive segments of DNA, is surprisingly low. As they are passed from generation to generation they have a high chance of mutation, which would be expected to create substantial differences between geographically separated populations. In the late 1990s and early 2000s some researchers attributed the absence of such gross differences to the human gene pool having been reduced to a small size in the past, thereby reducing earlier genetic variation as a result of increased interbreeding among survivors. They were able to assess roughly when such a population ‘bottleneck’ took place and the level to which the global population fell. Genetic analysis of living human populations seemed to suggest that around 74 ka ago the global human population fell to as little as 10 thousand individuals. A potential culprit was the catastrophic eruption of the Toba supervolcano in Sumatra around that time, which belched out 800 km3 of ash now found as far afield as the Greenland and Antarctic ice caps. Global surface temperature may have fallen by 10°C for several years to decades. Subsequent research has cast doubt on such a severe decline in numbers of living hummans; for instance archaeologists working in SE India found much the same numbers of stone tools above the Toba ash deposit as below it (see: Toba ash and calibrating the Pleistocene record: December 2012). Other, less catastrophic explanations for the low genetic diversity of modern humans have also been proposed. Nevertheless, environmental changes that placed huge stresses on our ancestors may repeatedly have led to such population bottlenecks, and indeed throughout the entire history of biological evolution.

An improved method of ‘back-tracking’ genetic relatedness among living populations, known as fast infinitesimal time coalescence or ‘FitCoal’, tracks genomes of individuals back to a last common ancestor. In simple language, it expresses relatedness along lineages to find branching points and, using an assumed mutation rate, estimates how long ago such coalescences probably occurred. The more lineages the further back in time FitCoal can reach and the greater the precision of the analysis. Moreover it can suggest the likely numbers of individuals, whose history is preserved in the genetics of modern people, who contributed to the gene pool at different branching points. Our genetics today are not restricted to our species for it is certain that traces of Neanderthal and Denisovan ancestry are present in populations outside of Africa. African genetics also host ‘ghosts’ of so-far unknown distant ancestors. So, the FitCoal approach may well be capable of teasing out events in human evolution beyond a million years ago, if sufficient data are fed into the algorithms. A team of geneticists based in China, Italy and the US has recently applied FitCoal to genomic sequences of 3154 individual alive today (Hu, W.and 8 others 2023. Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science, v. 381, p. 979-984; DOI I: 10.1126/science.abq7487). Their findings are startling and likely to launch controversy among their peers.

Their analyses suggest that between 930 and 813 ka ago human ancestors passed through a population bottleneck that involved only about 1300 breeding individuals. Moreover they remained at the very brink of extinction for a little under 120 thousand years. Interestingly, the genetic data are from people living on all continents, with no major differences between the analyses for geographically broad groups of people in Africa and Eurasia. Archaeological evidence, albeit sparse, suggests that ancient humans were widely spread across those two continental masses before the bottleneck event. The date range coincides with late stages of the Mid-Pleistocene climatic transition (1250 to 750 ka) during which glacial-interglacial cycles changed from 41 thousand-year periods to those that have an average duration of around 100 ka. The transition also brought with it roughly a doubling in the mean annual temperature range from the warmest parts of interglacials to the frigid glacial maxima: the world became a colder and drier place during the glacial parts of the cycles.

Genomes for Neanderthals and Denisovans suggest that they emerged as separate species between 500 and 700 ka ago. Their common ancestor, possibly Homo heidelbergensis, H. antecessor or other candidates (palaeoanthropologists habitually differ) may well have constituted the widespread population whose numbers shrank dramatically during the bottleneck. Perhaps several variants emerged because of it to become Denisovans, Neanderthals and, several hundred thousand years later, of anatomically modern humans. Yet it would require actual DNA from one or other candidate for the issue of last common ancestor for the three genetically known ‘late’ hominins to be resolved. But Hu et al. have shown a possible means of accelerated hominin evolution from which they may have emerged, at the very brink of extinction.

Oxygen-isotope record and global temperature changes over the last 5 million years, green lines showing the times dominated by 41 and 100 ka climatic cycles. The mid-Pleistocene climatic transition is shown in pink (Credit: Robert A Rohde)

There is a need for caution, however. H. erectus first appeared in the African fossil record about 1.8 Ma ago and subsequently spread across Eurasia to become the most ‘durable’ of all hominin species. Physiologically they seem not to have evolved much over at least a million years, nor even culturally – their biface Acheulean tools lasted as long as they did. They were present in Asia for even longer, and apparently did not dwindle during the mid-Pleistocene transition to the near catastrophic levels as did the ancestral species for living humans. The tiny global population suggested by Hu et al. for the latter also hints that their geographic distribution had to be very limited; otherwise widely separated small bands would surely have perished over the 120 ka of the bottleneck event. Yet, during the critical period from 930 to 813 ka even Britain was visited by a small band of archaic humans who left footprints in river sediments now exposed at Happisburgh in Norfolk. Hu et al. cite the scarcity of archaeological evidence from that period – perhaps unwisely – in support of their bottleneck hypothesis. There are plenty of other gaps in the comparatively tenuous fossil and archaeological records of hominins as a whole.

The discovery of genetic evidence for this population bottleneck is clearly exciting, as is the implication that it may have been the trigger for evolution of later human species and the stem event for modern humans. Hopefully Hu et al’s work will spur yet more genetic research along similar lines, but there is an even more pressing need for field research aimed at new human fossils from new archaeological sites.

See also: Ashton, N. & Stringer, C. 2023. Did our ancestors nearly die out? Science (Perspectives), v. 381, p. 947-948; DOI: 10.1126.science.adj9484.

Ikarashi, A. 2023. Human ancestors nearly went extinct 900,000 years ago. Nature, v. 621; DOI: 10.1038/d41586-023-02712-4

Di Vicenzo, F & Manzi, G. 2023. An evolutionary bottleneck and the emergence of Neanderthals, Denisovans and modern humans. Homo heidelbergensis as the Middle Pleistocene common ancestor of Denisovans, Neanderthals and modern humans. Journal of Mediterranean Earth Sciences, v, 15, p. 161-173; DOI: 10.13133/2280-6148/18074

A book on archaeology, radiocarbon dating, ancient DNA, and how modern humans evolved

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Since 2001 Tom Higham, now Professor of Scientific Archaeology at the University of Vienna, helped develop new ways of refining radiocarbon dating at Oxford University’s Research Lab for Archaeology and the History of Art. Specifically his lab learned how to remove contamination of ancient samples by recent carbon and to reduce the detection limit of their accelerator mass spectrometer for the 14C atoms that remained from when they were in living organisms. The Oxford Radiocarbon Accelerator Unit pushed sample dates to the absolute limit of the method: around 50 thousand years. Being among the very best, the ORAU had a path beaten to its doors by archaeologists from across the world keen to get the most believable dates for their samples. Equally, Higham engaged in the field work itself and in the interpretation of other data from sites, such as ancient DNA. An outcome of Higham’s energetic efforts over two decades is his book The World Before Us: How Science is Revealing a New Story of Our Human Origins (paperback edition 2022, Penguin Books,ISBN-10: ‎0241989051). One reviewer commented ‘The who, what, where, when and how of human evolution’.

The World Before Us is not only comprehensive and eminently clear for the lay-reader, but it is more exciting than any science book that I have read. For the moment, it is the latest ‘word’ on early, anatomically modern humans and on the closely related Neanderthals and Denisovans. Its core is about how these three key groups ‘rubbed along’ once they met  in the Late Pleistocene. As an amateur interested in palaeoanthropology, I have tried to keep pace with all the developments in the field since 2001 through Earth-logs, but Higham shows just how much I have missed that is important to the human story. If you have followed my many posts on human evolution and migrations with interest, read his book for a great deal more and a coherent story of how things stand.

The ancestry of our opposable thumbs

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Since the appearance of smart phones and the explosion of social media our thumbs have found a new niche; typing while holding a mobile. At a desktop keyboard, most of us don’t use thumbs very much, unless we have mastered fast touch typing, but for a huge variety of manual tasks thumbs are essential. The first makers of sophisticated stone tools must have been able to grip between fingers and thumb to manipulate the materials from which they were made and to perform the various stages in creating a razor sharp edge. To do that, as most of us are aware, the tip of the thumb must be capable of touching the tips of all four fingers; an opposable thumb is essential for the ‘precision grip’. Being able to tell when opposable thumbs evolve depends, of course, on finding hand-bone fossils. Being made of many bones disarticulated hands are a lot more fragile than long bones or those of the skull. Complete fossil hands are rare, as are feet, but a number have been found more or less complete. Whichever hominin had evolved opposable thumbs, their potential would have given them a considerable advantage over those that hadn’t.

The main muscles that control the movements of modern human fingers and thumb (Credit: Wikipedia)

Simply comparing the shapes of fossilised bones of fingers and thumbs with those of modern humans and other living primates has, so far, not proved capable of resolving with certainty which hominin groups either did or did not have opposable thumbs. The key lies in the muscles that operate them. It has become commonplace to reconstruct faces and even whole bodies from fairly complete skeletal remains by modelling musculature from the positioning and shape of the points of attachment of muscles to bone. But that become increasingly difficult for the small-scale and intricate attachments in hands. The critical muscle for opposable thumbs is known as the Opponens pollicis (the Latin for thumb is Digitus pollex); a small triangular muscle that operates in conjunction with three others (with pollicis in their Latin names).

Fotios Karakostis and six colleagues from German, Swiss and Greek universities have devised software that can model muscles in 3-D (F.A. Karakostis et al. 2021. Biomechanics of the human thumb and the evolution of dexterity. Current Biology, v.31,  online; DOI: 10.1016/j.cub.2020.12.041). Based on the anatomy of human and chimpanzee hand muscles and the positions of their attachment to individual bones, they have been able to establish a series of parameters that clearly distinguish the morphological and probably functional characteristics of the thumbs of these living primates. Complete sets of thumb bones from four Neanderthal skeletons show that they were significantly, but only slightly, different from anatomically modern humans. Those from three species of Australopithecus (africanus, sediba and afarensis) lie between ours and chimps’, with significantly closer affinity to chimpanzees. It seems that australopithecines of whatever age were not equipped with opposable thumbs and were possible tool producers and users with the very limited capabilities of modern chimps; holding, pounding and poking. A single set of hominin thumb bones from about two million years ago that were found in the famous Swartkrans Cave in South Africa show just as close affinity in thumb opposability to humans as do Neanderthals. So at 2 Ma there was a hominin species sufficiently dextrous to make and use sophisticated tools. The problem is, the bones are not directly associated with others and have been ascribed by different authors either to H. habilis or Paranthropus robustus. Interestingly, this paranthropoid has also been suggested (controversially) to have been the first known hominin to use fire, and it also used digging sticks. No one has ever suggested that the genus Homo descended from a paranthropoid ancestor or vice versa; these massively jawed beings did coexist with early humans in East Africa for over a million years. The other hominin who left hands in the geological record was Homo naledi; a controversial species because it was found in a barely accessible cave chamber, and took a while to date. This context gave rise to the notions that it was the direct ancestor of humans and that it buried its dead in a special place. However, it turned out to be relative recent, at about 280 ka (see: Homo naledi: an anti-climax; May 2017). Homo naledi does seem to have had opposable thumbs, but there is no associated evidence to suggest either tool making or use.

Fascinating as the methodology outlined by Karakostis et al. is, their findings do not take early human capabilities very much further than what is already known. Tools were made and used as far back as 3.3 Ma ago, and we know that H. habilis was doing this by about 2.6 Ma; i.e. long before the first evidence for opposable thumbs, and who had them first is uncertain. What is clear is that sophisticated tools, such as the bifacial Acheulian artifacts whose manufacture demands great dexterity, only appeared after the potential for nimble dexterity (about 1.8 Ma). The same goes for the first migration out of Africa, at about the same time, which demanded resourcefulness that may have sprung from the ability to manipulate natural materials effectively and carefully

See also: Handwerk B. 2012. How dexterous thumbs may have helped shape evolution two million years ago. (Smithsonian Magazine, 28 January 2021); Bower, B. 2021. Humanlike thumb dexterity may date back as far as 2 million years ago. (Science News, 28 January 2021)

A protein clue to H. antecessor’s role in human evolution

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Homo_antecessor child
Forensic reconstruction of the remains of a Homo antecessor child from Gran Dolina Cave in northern Spain (credit Élisabeth Daynès, Museo de la Evolución, Burgos, Spain)

The older a fossil, no matter how well preserved it is, the less chance it has to contain enough undegraded DNA for it to be extracted and sequenced using the most advanced techniques. At present the oldest fossil DNA not to have passed its ‘sell-by’date is that of a 560 to 780 thousand year-old horse’s legbone found in Canadian permafrost. For human remains the oldest mtDNA is that of a ~430 ka individual from the Sima de los Huesos in northern Spain (see: Mitochondrial DNA from 400 thousand year old humans; Earth-logs December 2013). But there is another route to establishing genetic relatedness from the amino-acid sequences of proteins recovered from ancient individuals (see: Ancient proteins: keys to early human evolution?). Fossil teeth have proved to be good repositories of ancient protein and are the most commonly found hominin fossils.

A key species for unravelling the origins of the three most recent human groups (ourselves, Neanderthals and Denisovans) is thought to be Homo antecessor who inhabited the Gran Dolina Cave in the Atapuerca Mountains in northern Spain between about 1.2 Ma and 800 ka ago (see: Human evolution: bush or basketwork? Earth-logs, January 2014). Palaeoanthropologists excavated 170 skeletal fragments from six individuals in the most productive layer at Gran Dolina. Incomplete facial bones suggest a ‘modern-like’ face, although the remains as a whole are insufficient to reconstruct the oldest Europeans with sufficient detail to place them in anatomical relation to the younger groups. But there are several teeth. One of them, a permanent molar, has yielded informative proteins (Welker, F. and 26 others 2020. The dental proteome of Homo antecessor. Nature, v. 580, p. 235-238; DOI: 10.1038/s41586-020-2153-8) and has been dated to between 772 to 949 ka.

Amino acids in the dental proteins, sequenced using mass spectrometry, were compared with those of other hominins. Because protein sequences are coded by an animal’s genome they are a ‘proxy’ for DNA. The outcome is that the Gran Dolina proteins are roughly equally related to Denisovans, Neanderthals and ourselves, suggesting that, although the younger three groups are closely related, H. antecessor is an ‘outlier’. Being significantly older, it is likely to be the common ancestor of all three. Another species with close anatomical affinities is H. heidelbergensis (700 to 300 ka) found in Africa as well as in Europe. Its mtDNA (see: Mitochondrial DNA from 400 thousand year old humans; Earth-logs December 2013) matches that of Denisovans better than it does Neanderthals, yet without protein and full-genome analysis all that can be concluded is that it may be an intermediary between H. antecessor and the well known interbreeding triad of more recent times.

We are getting closer to a documented web of interrelationships between humans in general whose time span from 2 Ma ago is now well established. The remaining genetic link to be documented is that to H. erectus, the longest lived and most travelled of all ancient humans. Frido Welker and co-workers also had a shot at the proteomics of one of the first humans known to have migrated from Africa, using an isolated, presumably H. erectus, molar found at the 1.77 Ma site at Dmanisi in the Caucasus foothills of Georgia. Although inconclusive in placing that precociously intrepid group firmly in the human story, the fact that dental proteins were discovered is cause for optimism.

See also: Campbell, M. 2020. Protein analysis of 800,000-year-old human fossil clarifies dispute over ancestors (Technology Networks, 1 April 2020)

Further back in the Eurasian human story

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About 800 to 950 thousand years (ka) ago the earliest human colonisers of northern Europe, both adults and children, left footprints and stone tools in sedimentary strata laid down by a river system that then drained central England and Wales. The fossil flora and fauna at the Happisburgh (pronounced ‘Haze-burra’) site in Norfolk suggest a climate that was somewhat warmer in summers than at present, with winter temperatures about 3°C lower than now: similar to the climate in today’s southern Norway. At that time the European landmass extended unbroken to the western UK, so any hunter-gatherers could easily follow migrating herds and take advantage of seasonal vegetation resources. These people don’t have a name because they left no body fossils. A group known from their fossils as Homo antecessor had occupied Spain, southern France and Italy in slightly earlier times (back to 1200 ka). Since the discovery of their unique mix of modern and primitive traits, they have been regarded as possible intermediaries between H. erectus and H. heidelbergensis – once supposed to be the predecessor of Neanderthals and possibly anatomically modern humans (AMH). Since the emergence about 10 years ago of ancient genomics as the prime tool in examining human ancestry the picture has been shown to be considerably more complex. Not only had AMH interbred with Neanderthals and Denisovans, those two groups were demonstrably interfertile too, and a complex web of such relationships had been pieced together by 2016. But there has been a new development.

700 ka Homo erectus from Java: a possible Eurasian ‘super-archaic’ human (credit: Gibbons 2020)

Population geneticists at the University of Utah, USA, have devised sophisticated means of making more of the detailed ATCG nucleotide sequences in ancient human DNA, despite there being very few full genomes of Neanderthals and Denisovans (Rogers, A.R. et al. 2020. Neanderthal-Denisovan ancestors interbred with a distantly related hominin. Science Advances, v. 6, article eaay5483; DOI: 10.1126/sciadv.aay5483). In Earth-logs you may already have come across the idea of the ancestral ‘ghosts’ that are represented by unusual sections of genomes from living West African people. Those sections seem likely to have resulted from interbreeding with an unknown archaic population – i.e. neither Neanderthal nor Denisovan. It now seems that both Neanderthal and Denisovan genomes also show traces of such introgression with ‘ghost’ populations during much earlier times. The ancestors of both these groups separated from the lineage that led to AMH perhaps 750 ka ago. Rogers et al. refer to the earliest as ‘neandersovans’ and consider that they split into the two groups after they entered Eurasia, at some time before 600 ka – perhaps around 740 ka. This division may well have occurred as a result of a population of ‘neandersovans’ having spread over the vastness of Eurasia and growing genetic isolation. The reanalysis of both sets of genomes show evidence of a ‘neandersovan’ population crash before the split. Thereafter, the early Neanderthal population may have risen to around 16 thousand then slowly declined to ~3400 individuals.

A ‘state-of-play’ view of human interbreeding in Eurasia since 2 Ma ago (credit: Gibbons 2020)

However, the ‘neandersovans’ did not enter a new continent devoid of hominins, for as long ago as 1.9 Ma archaic H. erectus had arrived from Africa.  Both Neanderthal and Denisovan genomes record the presence of sections of ‘super-archaic’ DNA, which reflect early  interbreeding with earlier Eurasian populations. Indeed, Denisovans seem to have repeated their ancestors’ sexual exploits, once they became a genetically distinct group.  From the ‘ghost’ DNA fragments Rogers et al. conclude that the ‘super-archaics’ separated from other humans about two million years ago. They were descended from the first ‘Out-of-Africa’ wave of humans, represented by the fossils humans from Dmanisi in Georgia (see First out of Africa, November 2003 and An iconic early human skull,  October 2013 in Earth-logs Human evolution and migrations). A measure of the potential of novel means of analysing available ancient human DNA is the authors’ ability even to estimate the approximate population size of the interbreeding ‘super-archaic’ group at 20 to 50 thousand. Long thought to be impossible, it now seems possible to penetrate back to the very earliest human genetics, and the more DNA that can be teased out of other Neanderthal and Denisovan fossils the more we will know of our origins.

See also: Gibbons, A. 2020. Strange bedfellows for human ancestors. Science, v. 367, p. 838–839; doi:10.1126/science.367.6480.838

Ancient proteins: keys to early human evolution?

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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)

 

Multiregional human evolution in Africa

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Africa is not only a large continent, but is subdivided into many different climatic zones and ecosystems and these have changed drastically over the last 2 Ma. It is further subdivided by terrain features, such as the courses of major rivers, large plateaus, tectonic rift systems and the mountains that frequently define their flanks. Getting around Africa is not easy today, was more difficult before modern transport, and many geomorphic provinces may have been mutually inaccessible in the distant past. For instance, the Sahara Desert forms a major barrier to travellers on foot because access to surface water is non-existent except at widely spaced oases. Without boats or rafts the Nile and Congo cannot be crossed for a thousand miles or more. Migration was perhaps a very rare event outside of periods of widespread humid climates or when great environmental stress forced people either to move or perish. Despite these physical and ecological divisions and barriers palaeoanthropologists have, until recently, tended to regard the evolution of Homo sapiens and earlier human and hominin species as having occurred within single populations: a linear view forced on them by scanty fossil remains and limited methodologies. Logically, when human numbers were small Africa probably had several isolated population Physical isolation would have engendered genetic isolation in which our ancestors evolved for tens of thousand years.

Anatomically modern human (AMH) remains found at Jebel Irhoud in Morocco turned out to be 315 ka old, displacing those from Ethiopia (190 ka) as the earliest known examples of AMH. Several more archaic H. sapiens fossils have turned up in southern Africa and as far afield as the Middle East, suggesting that the early evolution of AMH was in an Africa-wide context rather than in one area – the rift system of Ethiopia and Kenya – from which a new species radiated outwards. This breadth of finds has encouraged Eleanor Scerri of Oxford University and her many international colleagues to resurrect what was once a widely discarded hypothesis; a multiregional model of modern human origins, originally proposed to have arisen from pre-sapiens groups in Eurasia by Milford Wolpoff but which was sunk once genetic connections among living humans turned out to be rooted in Africa. (Scerri, E.M.L. and 22 others 2018. Did our species evolve in subdivided populations across Africa, and why does it matter? Trends in Ecology & Evolution, v. 33, p. 582-594; (PDF) doi: 10.1016/j.tree.2018.05.005). Scerri et al’s model is sited in Africa and the paper’s authors include several leading palaeoanthropologists who once opposed multiregionalism and established the Recent African Origin hypothesis on the back of the early genetic data.

early homo
Different early AMH cranium shapes: left Jebel Irhoud, Morocco (315 ka), right Qafzeh, the Levant (85 ka) (credit: Scerri et al, 2018; Figure 1)

From region to region in Africa, the oldest AMH crania show significant differences from each other, but within a distinct combination of features that clearly distinguish us from our fossil relatives and ancestors, such as Homo heidelbergensis from Zimbabwe and the primitive-looking H. naledi found in a South African cave in 2015. Improved dating now shows that the Zimbabwean H. heidelbergensis and H.naledi remains are roughly the same age as the Jebel Irhoud AMH specimens. The first has long been held as the progenitor of AMH and descended from H. antecessor, perhaps the common ancestor for AMH, Neanderthals and Denisovans about 700 ka ago. The three human species cohabited Africa early in the evolutionary history of AMH. It is now abundantly clear from ancient and modern genomes that AMH, Neanderthals and Denisovans interbred in Eurasia. The proximity in time and space of earlier African AMH to two more ancient human species opens up a similar possibility earlier in the emergence of all living humans. There is evidence for that too: Yoruba people living in West Africa, whose genomes have been analysed, carry up to 8% of genetic ancestry that originated in an unidentified ancient population that was non-sapiens. At present, DNA analysis with the same high precision and information content from other living Africans has not been performed, and deterioration of ancient DNA in African climates has so far thwarted genomic studies of ancient African fossils.

The new view of our origins points to repeated hybridisation involving other coexisting human species, as well as evolution in isolation, from the outset. It continued through later times while Neanderthals and Denisovans survived. Even recent human genetic history is peppered with intermingling of a great variety of migrants passing through all the habitable continents. Another issue: In the earliest times, were cultures exchanged as well as genes? The first appearance of AMH coincides with that of a new stone technology (Levallois technique), moving away from the earlier dominance by handaxes towards more delicate, leaf-shaped points, that characterise the African Middle Stone Age. Similar techniques reached Europe with the Neanderthals. Was this an invention of the earliest AMH or a joint venture?

You can find an excellent review of these issues in the September 2018 issue of Scientific American (Wong, K. 2018. Last hominin standing.  Scientific American, v. 319(3), p. 56-61) along with several other articles on human evolution.

A revised and updated edition of Steve Drury’s book Stepping Stones: The Making of Our Home World can now be downloaded as a free eBook

Early modern humans in Sumatra before the Toba eruption

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In late July 2017 news emerged that modern humans first reached Australia at least 65 thousand years ago. Confirming that the date of departure from Africa to end up in SE Asia and Australasia was  considerable earlier than previously believed, deposits in Sumatra that contain remains of early Home sapiens have yielded even older ages (Westaway, K.E. and 22 others 2017. An early modern human presence in Sumatra 73,000–63,000 years ago. Nature v. 548 online; doi:10.1038/nature23452). This resulted from a re-examination of material from the Padang Caves first excavated more than a century ago by Eugène Dubois, famous for his discovery in Java of the first H. erectus remains. A richly fossiliferous breccia in the Lida Ajer cave yielded a fauna characteristic of a rainforest biome and included two teeth that Dubois considered to be human. Several later palaeontologists confirmed his identification as have hominin specialists in the present Australian-Indonesian-American-British-Dutch-German team. The fossil assemblage has long suggested great antiquity for the site, but only now has it been dated precisely. The dating employed three methods: optically stimulated luminescence dating of quartz grains from the breccia (85±25 to 62±5  ka); uranium-series dating of speleothem including fragments of hollow ‘soda-straw’ stalactites(84±1 to 71±7 ka); uranium-series dating of gibbon and orangutan teeth found together with the human teeth (86±13 to 76±7 ka). Statistical analysis of the age data suggests 73 to 63 ka for the fauna, with a maximum age for deposition of the breccia of 84±1 ka.

Satellite image of Lake Toba, the site of a VE...
Satellite image of Lake Toba in NW Sumatra (at centre), the site of the largest volcanic eruption during the history of human evolution ~71,600 years ago (credit: Wikipedia)

Stone tools which may have been carried by anatomically modern humans into the area have previously been used to suggest a minimum date of the arrival of migrants, though they may have been carried by ­H. erectus. Remarkably, such tools have been found beneath a thick bed of volcanic ash found throughout southern Asia and in Indian Ocean sediment cores. This has been dated at 71.6 ka and represents the explosive collapse of the caldera now containing Lake Toba in NW Sumatra that was the largest volcanic event in the entire history of the genus Homo. The new age data from Lida Ajer suggests that modern humans were present in its vicinty before the eruption, a view also supported by ‘molecular-clock’ dating of the range of mitochondrial DNA carried by living SE Asian people (79 to 75 ka). So, despite the stupendous magnitude of the Toba eruption is seems likely that some of the migrants survived.  Together with the dating of the earliest Australians the Sumatran evidence is at odds with the view, widely held by palaeoanthropologists, that the ‘Out of Africa’ exodus began by crossing the Straits of Bab el Mandab between 74 and 58 ka when global sea-level fell markedly during marine oxygen-isotope Stage 4 (MIS4). A problem with that hypothesis has been that climatic and ecological conditions in southern Asia during MIS4 were unfavourable. But is seems that modern humans were already there and capable of adapting to both the climate shift and to the devastation undoubtedly caused by Toba.

Stepping Stones eBook

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Title

A revised and updated edition of Stepping Stones: The Making of Our Home World by Steve Drury, first published in 1999, has been released as a free eBook on the book’s web site https://earthstep.wordpress.com/. The revision incorporates the hundreds of commentaries on geoscientific advances written since 2000 by Steve for earth-pages. It is a personal view of the evolution of the Earth System and the emergence of humanity from it. First published by Oxford University Press, Stepping Stones was widely acclaimed by  fellow Earth scientists and general readers.