Homo naledi: an anti-climax

In September 2015 a barrage of publicity announced the remarkable unearthing of the remains of 15 diminutive hominins, dubbed Homo nadeli, from the floor sediments of an almost inaccessible South African cave, part of the equally hyped ‘Cradle of Humankind’ UNESCO World Heritage Site near Johannesburg. An international team of lithe women speleo-archaeologists was recruited for the excavation, for which the original discoverers were incapably burly. The remains included numerous examples of still articulated intricate bones, such as those of feet and hands, and none show signs of dismemberment by large scavengers. Indeed the discovery chamber was so far from the cave entrance that such animals probably were unaware of their presence. These features and the sheer complexity of the system strongly suggested that cadavers had been deliberately taken to the chamber; implying that the deep penetration had been accomplished using fire-brand illumination. What seized the headlines was the possibility of ritual burial, although sanitary disposal or panicked refuge from predators seem equally, if not more likely.

Lee Burger and the reconstructed skull of Homo naledi

Now yet more fossils have been reported from a separate chamber at a crawling distance about 150 m away from the original but closer to the system’s main entrance (~85 m). These add at least other 3 individuals to the H. nadeli association, with sufficient similarity to indicate that all 18 belong to H. naledi. This wealth of detail enabled the team of authors (Hawks, J. and 37 others 2017. New fossil remains of Homo naledi from the Lesedi Chamber, South Africa. eLife, v. 6, online; http://dx.doi.org/10.7554/eLife.24232) to perform a detailed comparative anatomic analysis of the species. The results are a mosaic, showing some post-cranial affinities with australopithecines, H. habilis, H.floresiensis, H. erectus, Neanderthals and anatomically modern humans, and others, such as the hands and shoulders, that are not well matched with other hominins. Their crania show a similar broad spectrum of resemblances, and as regards dentition they are distinctly primitive. They are also on the small-brained side of the hominin clade. Despite the astonishing abundance of fossil material, not a single artifact was found in the cave system, despite the apparent similarity of its hands to those of ourselves and Neanderthals.

With plenty of scope for speculation, H. nadeli remains enigmatic. The big question looming over the 2015 announcement of the species was its age, the discovers suggesting about 2 Ma, and placing on the direct line of human descent. On the same day as the fossil description there appeared a multi-method dating analysis (Dirks, P.H.G.M. and 19 others 2017. eLife, v. 6, online; http://dx.doi.org/10.7554/eLife.24231.001), which showed that with little doubt that the H. nadeli association was deposited between 236 ka and 335 ka; around the time when anatomically modern humans first emerged and stone tools had undergone a >2 Ma technological evolution. To me, the only sensible conclusion at present is that H. nadeli is another addition to the 6 species living and in some cases coexisting across the late Pleistocene world, and that expansion of ideas beyond that must await DNA analysis; a definite possibility considering the age of the fossils, their seemingly good preservation in a relatively dry cave system and the new possibility of cave soils as well as bones yielding genetic materials. The leader of the research team, Lee Berger of the University of the Witwatersrand now maintains, together with four other members of the research team, that H. nadeli may be a coelacanth-like survivor of Homo’s earliest diversification and that ‘we cannot exclude that this lineage was responsible for the production of Acheulean or Middle Stone Age tool industries’.

Barras, C. 2017. Homo naledi is only 250,000 years old – here’s why that matters. New Scientist, 6 May 2017 Issue

Sample, I. 2017. New haul of Homo naledi bones sheds surprising light on human evolution. The Guardian, 9 May 2017

Detecting the presence of hominins in ancient soil samples

Out on the plains countless herbivores fertilise the ground by continual urination and defecation. A friend’s sheep are doing just that in the small field that came with my current home while they are keeping the grass under control.  Millions of hectares of prime agricultural land in China are kept fertile through disposal of human night soil from ‘honey wagons’ every day; it is even fed to fishes in small ponds. Such a nice economy also donates the DNA of the animal and plant inhabitants to the soil system. In 2015 analysis of environmental DNA from permafrost in Siberia and Alaska produced ‘bar codes’ for the now vanished ecosystems of what was  mammoth steppe during the climate decline to the last glacial maximum and the subsequent warming. The study revealed mammoth and pre-Columbian horse DNA and changes in the steppe vegetation, from which it was concluded that the steppe underwent regional extinction pulses of its megafauna linked to rapid climate ups and downs connected with Dansgaard-Oeschger cycles. It was but a small step to see the potential for studying distribution and timing of various hominins’ occupation of caves from the soils preserved within them, without depending on generally very rare occurrences of human skeletal remains.

Tourists at the entrance to Denisova Cave, Rus...

Tourists at the entrance to Denisova Cave, Russia (credit: Wikipedia)

The Max Planck Institute for Evolutionary Anthropology in Leipzig, now famous for extracting DNA from Neanderthal, Denisovan and possibly H. antecessor fossils, has applied the environmental DNA approach to sediments from 7 caves in France, Belgium, Spain, Croatia and Russia that span the period from 550 to 14 ka (Slon, V. and 30 others 2017.  Neandertal and Denisovan DNA from Pleistocene sediments. Science, v. 356 (online publication); doi:10.1126/science.aam9695). The sites had previously yielded fossils and/or artefacts. All of them contained mitochondrial DNA from diverse large mammals, four including archaic human genetic material supplied by Neanderthal individuals and Denisovans in the case of the Denisova cave. A key finding was Neanderthal mtDNA in one sedimentary layer that contained no skeletal remains – decay of a body was probably not involved. In two cases the DNA was from more than one individual. A variety of tests showed that surprisingly large quantities of DNA survive in soil and that it is spread evenly in sediment rather than being present in spots – an indication of derivation from urine, excreta or decayed soft tissue.

Although the study does not add to knowledge of hominin genetics, it confirms that the methodology is sufficiently advanced and efficient to detect hominin presence in fossil-free sediment. So this approach seems set to become a standard for many sites, such as that from California reported in the previous post, which suggest a human influence, or any cave sediments for that matter. Although skeletal remains are essential for reconstruction of bodily characteristics, hominin phylogeny seems set to cut loose from fossils. Hitherto suspected species’ presence in the time period where DNA analysis is feasible may be detected, such as Asian H. erectus. It may become possible to map or extend the geographic ranges of Denisovans and Neanderthals. Perhaps species new to science will emerge.

More on late Pleistocene hominin genetics here

Wade, E. 2017. DNA from cave soil reveals ancient human occupants. Science, v. 356, p. 363.

Wade, E. 2017. DNA from cave soil reveals ancient human occupants. Science, v. 356, p. 363.

Pre-sapiens hominins reached North America?

In 1991-2 palaeontologists excavated a site near San Diego, California where broken bones had been found. These turned out to be the disarticulated remains of an extinct mastodon. One feature of the site was the association of several large cobbles with bones of large limbs that seemed to have been smashed either to extract marrow or as source of tool-making material. The cobbles showed clear signs or pounding, such as loss of flakes – one flake could be fitted exactly to a scar in a cobble – pitted surfaces and small radiating fractures. The damage to one cobble suggested that it had been used as an anvil, the others being hammer stones.  Broken pieces of rock identical to the hammer stones were found among the heap of bones. No other artefacts were found, and the bones show no sign of marks left by cutting meat from them with stone tools. The breakage patterns of the bones included spiral fractures that experimental hammering of large elephant and cow bones suggest form when bone is fresh. Other clear signs of deliberate breakage are impact notches and small bone flakes. Two detached, almost spherical heads of mastodon femora suggest that marrow was the target for the hammering and confirmed the breakage was deliberate.


Artist’s impression of American mastodon. (credit: Wikipedia)

Since the sediment stratum in which the remains occurred consists of fine sands and silt, typical of a low-energy river system, the chances that the cobbles had been washed into association with the mastodon are very small. The interpretation of the site is that it was the result of opportunistic exploitation of a partial carcase of a young adult mastodon by humans. In the early 1990s attempts were made to date the bones using the radiocarbon method, but failed due to insufficient preserved collagen. That the site may have been much older than the period of known occupation of North America by ancestors of native people (post 14.5 ka) emerged from attempts at optically stimulated luminescence dating of sand grains that can suggest the age of burial. These suggested burial by at least 60 to 70 ka ago. It was only when the uranium-series disequilibrium method was used on bone fragments that full significance of the site emerged. The results indicated that they had been buried at 130.7±9.4 ka (Holen, S.R. and 10 others 2017. A 130,000-year-old archaeological site in southern California, USA. Nature, v.  544, p. 479—493; doi:10.1038/nature22065 – full paper and supplements available free)

Not only is the date almost ten times that of the earliest widely accepted signs of Homo sapiens in the Americas, the earliest anatomically modern humans known to have left Africa are around the same age, but restricted to the Levant. The earliest evidence that modern humans had reached East Asia and Australasia through their eastward migration out of Africa is no more than 60 ka. The date from southern California is around the start of the interglacial (Eemian) before the one in which we live now. It may well have been possible then, as ~14 ka ago, to walk across the Bering Straits due to low sea level, or even by using coast-hugging boats – hominins had reached islands in the Mediterranean and the Indonesian peninsula certainly by 100 ka, and probably earlier. But whoever exploited the Californian mastodon marrow must have been cold-adapted to achieve such a migration. While the authors speculate about ‘archaic’ H. sapiens the best candidates would have been hominins known to have been present in East Asia: H. erectus, Neaderthals and the elusive Denisovans.

Surely there will be reluctance to accept such a suggestion without further evidence, such as tools and, of course, hominin skeletal remains. But these long-delayed findings seem destined to open up a new horizon for American palaeoanthropology, at least in California.

You can find more information on hominin migration here.


Zealandia: a hitherto undiscovered continent?

Mid-February 2017 saw the announcement in the world’s media of what was made out to be a previously unsuspected, drowned continent. No, not in the Atlantic, but surrounding New Zealand. For geoscientists this was not ‘fake news’, but neither was it a surprise. Precise bathymetry based on satellite data rather than more conventional soundings from ships had long shown a substantial area (4.9 million km2) of the Coral and Tasman Seas between Australia and New Zealand and the Pacific to the immediate south-east of New Zealand was considerably less deep than the mean for the world’s ocean floors. It shows up clearly on Google Earth.  The name ‘Zealandia’ had been suggested in 1995. The media flurry emerged from a paper published in the March/April 2017 issue of the Geological Society of America’s on-line newsletter (Mortimer, N. and 10 others 2017. Zealandia: Earth’s hidden continent. GSA Today, v. 27(3 March April 2107); doi:10.1130/GSATG321A.1), the phrase ‘hidden continent’ no doubt pulling in the hacks like mackerel to a piece of tin foil.

The extent of Zealandia shown by Google Earth – the paler the blue coloration the shallower the ocean floor

The 10 New Zealander authors with one Australian, based their definition of the anomalously shallow ocean floor as a continent on data accumulated over many years from geophysical surveys and spot sampling of rocks from dredging, drilling and field work on the area’s few islands as well as New Zealand itself. As well as being at a relatively high elevation – a mean of -1100 m compared with -3700 for the oceans as a whole – samples are  predominantly those expected from continental crust. In fact orogenic belts exposed in New Zealand can be traced lithologically and topographically on several large submerged ridges. Samples of its underlying mantle found as xenoliths in igneous rocks yield radiometric dates of 2.7 billion years. So it is an ancient entity, unlike oceanic crust none of which exceeds about 200 Ma. The ocean floor also exhibits a number of sedimentary basins dating back to the Cretaceous, which contain terrigenous clastic rocks and limestones that reach thicknesses of 2 to 10 km. Seismic surveys give an average P-wave speed of 6.5 km s-1 through the underlying crust, a density of 2830 kg m-3 and a crustal thickness between 30 and 46 km, none of which apply to mafic oceanic crust.

There are plenty of areas on the ocean floor that have such continental affinities, but they are small and referred to as microcontinents. To be dubbed ‘continent’ obviously involves an essence of mightiness, but for geologists the term also implies a lack of connection: hence Europe is a mere part of the Eurasian continent. The six geologically recognised continents (Africa, Eurasia, North America, South America, Antarctica, and Australia) are spatially isolated by geological and/or bathymetric features. Zealandia obeys that criterion, but only just: its NW end comes as close as 25 km to the crust of Australia, but the line of separation is a major fracture zone and 3600 m deep trough. However, Zealandia is considerably smaller than the recognised continents, but about the size of India and Arabia which some have regarded as having been a continent (India) and one in the process of formation (Arabia). Mortimer and co suggest that the size needed to be called a continent should be >1 million km2, which would clearly put New Zealand on a continent separate from Australia – long a source of irritation to Kiwis!

Setting aside any suggestion of some nationalist motives, Zealandia is very interesting. The very fact that it is uniquely drowned require some explanation. A great deal of evidence suggests that once being at the flank of Gondwanaland an extensional plate margin spalled it away around 85 Ma ago. In so doing tectonic forces substantially thinned the crust in a similar manner to what is presently happening on a smaller scale beneath the Afar Depression of Ethiopia. That would tend to result in widespread subsidence once any thermal buoyancy during rifting had cooled to increase crustal density. Such a process would explain the alternations of linear ridges and troughs that characterise this section of continental crust, but are less developed in the other continents.

More on continental growth and plate tectonics



Archaean continents derived from Hadean oceanic crust

As DNA is to tracing  human evolution and migration, so various isotope systems are to the evolution of the Earth. One of the most fruitful is the samarium-neodymium (Sm-Nd) system. The decay of 147Sm to 143Nd is used in dating rocks across the full range of Earth history, given coeval rocks with a suitable range of Sm/Nd ratios, because the decay has a long half life (1.06 x 1011 years). However, samarium has another radioactive isotope 147Sm with a half life that is a thousand times shorter (1.06 x 108 years). So it remains only as a minute proportion of the total Sm in rocks, most having decayed since it was formed in a pre-Solar System supernova. But its daughter isotope 142Nd is present in easily measurable quantities, having accumulated from 147Sm decay over the first few hundred million years of Earth’s history; i.e. during the Hadean and earliest Archaean Eons. It is this fact that allows geochemists to get an indirect ‘handle’ on events that took place in the Earth’s earliest, largely vanished history. The principle behind this approach is that when an ancient rock undergoes partial melting to produce a younger magma the rock that crystallizes from it inherits the relative proportions of Nd isotopes of its source and thereby carries a record of the earlier history.

English: An outcrop of metamorphosed volcanose...

Metamorphosed volcanosedimentary rocks from the Porpoise Cove locality, Nuvvuagittuq supracrustal belt, Canada. Possibly the oldest rocks on Earth. (credit: Wikipedia)

The eastern shore of Hudson Bay in Canada hosts the oldest tangible geology known, in form of some metamorphosed basaltic rocks dated at 4200 Ma old known as the Nuvvuagittuq Greenstone Belt – the only known Hadean rocks. They occur in a tiny (20 km2) patch associated with gneisses of tonalite-trondjhemits-granodiorite composition that are dated between 3760 and 3350 Ma. Engulfing both are younger (2800 to 2500 Ma) Archaean plutonic igneous rocks of felsic composition. Jonathan O’Neil and Richard Carlson of the University of Ottawa, Canada and the Carnegie Institution for Science, Washington DC, USA respectively, measured proportions of Nd isotopes in both sets of felsic igneous rocks (O’Neil, J. & Carlson, R.W. 2017. Building Archean cratons from Hadean mafic crust. Science, v. 355, p. 1199-1202; doi:10.1126/science.aah3823).

The oldest gneisses contained relative proportions of 142Nd commensurate with them having been formed by partial melting of the Hadean mafic rocks about a few hundred million years after they had been erupted to form the oldest known crust; no surprise there. However, the dominant components of the local continental crust that are about a billion years younger also contain about the same relative proportions of 142Nd. A reasonable conclusion is that the Archaean continental crust of NE Canada formed by repeated melting of mafic crust of Hadean age over a period of 1.5 billion years. The modern Earth continually replenishes its oceanic crust over about 200 Ma due to plate tectonics. During the Archaean mantle dynamics would have been driven faster by much higher internal heat production. Had this involved simply faster plate tectonics the outermost skin of mafic crust would have been resorbed into the mantle even faster. By the end of the Archaean (2500 Ma) barely any Hadean crust should have been available to produce felsic magmas. But clearly at least some did linger, adding more weight to the idea that plate tectonics did not operate during the Hadean and Archaean Eons. See Formation of continents without subduction below.

Yukon colonised during Last Glacial Maximum

For many years anthropologists were certain that the Americas remained outside the human realm until the great icecap of North America had begun to melt decisively. This view stemmed partly from the only conceived route being across the exposed floor of the Bering Sea when sea-level had fallen to leave it as a landmass known as Beringia. The other literal stumbling block had been the glacial blockage of the only lowland corridor from Alaska to the Great Plains which roughly follows the Alberta – British Columbia border in Canada. There is abundant evidence that the corridor did not become ice-free until about 13 ka, an important fact that for a long while bolstered the Clovis-First hypothesis, from the eponymous and highly distinctive stone tools that date back to just after that time. After a long, sturdy rearguard action by its devotees that view was transcended by finds of earlier tools with dates as old as 15.5 ka that extend close to the southernmost tip of South America. Studies of Y-chromosome DNA from living First Nations men that suggested that all early Americans stemmed from 4 separate colonising populations who may have entered via Beringia by different routes, including along the Pacific coast. A possible common ancestor of all native Americans has turned up from the mitochondrial and Y-chromosome DNA of a fossil skeleton from near Lake Baikal in Siberia who lived about 24 ka ago. But yet another twist has emerged from the Yukon Territory of Northern Canada.

Beringia Land Bridge. Animated gif of its prog...

Beringia Land Bridge. Animation of its development from 21.000 BC to modern times.(Photo credit: Wikipedia)

Since 1987 it has been known that animal bones with clear signs of butchery occurred in the Bluefish Cave on the Yukon – Alaska border. Dating of the bones by the 14C method seemed to support human occupation there during the Last Glacial Maximum; highly controversial at the time, in the absence of any other sites of that age in the whole Americas. The material has now been re-examined and dated by a more advanced radiocarbon method (Bourgeon, L. et al. 2017. Earliest human presence in North America dated to the Last Glacial Maximum: new radiocarbon dates from Bluefish Caves, Canada. PLoS ONE, v. 12; doi:10.1371/journal.pone.0169486). This work has confirmed the earlier view since the ages of bones range from 24 to 12 ka. But the discovery of what seems long-term occupation under the most arduous glacial conditions is not the only outcome of the research. One hypothesis for the genetic diversity among living indigenous people of the Americas is that their forebears, the first people of the Americas, may have been from genetically isolated populations stranded on Beringia, yet surviving eventually to migrate southward once climate warmed. The ‘Beringian standstill hypothesis’ suggest that the small population underwent genetic drift for about eight thousand years, their descendants inheriting the genetic diversity produced by this process. Bluefish Cave is probably where some of those pioneers waited-out the Ice Age

Formation of continents without subduction

The formulation of the theory of plate tectonics provided plausible explanations for the growth of continental crust over time, among many other fundamental Earth processes. Briefly expressed, once basalt capped oceanic lithosphere is forced downwards at plate boundaries where plates move towards one another, beyond a certain penetration cool, moist basalt undergoes a pressure-controlled change of state. Its chemical constituents reassemble into minerals more stable under elevated pressure. In doing so, one outcome involves dehydration reactions the other being that the bulk composition is recast mainly in the form of high-pressure pyroxene and the mineral garnet: the rock eclogite. The density of the basaltic cap increases above that of the mantle. Gravity acts to pull the subducting slab downwards, this slab-pull force being the main driver of plate motions globally. Water vapour and other fluids shed by dehydration reactions rise from the subducted slab into the wedge of overlying mantle to change its conditions of partial melting and the composition of the magma so produced. This is the source of arc magmatism that persists at the destructive plate margin to increase the volcanic pile’s thickness over time. When magma is able to pond at the base of the new crust its fractional crystallisation produces dense cumulates of high-temperature mafic silicates and residual melt that is both lighter and more enriched in silica. Residual magma rises to add to the middle and upper crust while the cumulate-rich lower crust becomes less gravitationally stable, eventually to spall downwards by delamination. Such a process helps to explain the bulk low density of continental crust built up over time together with the freeboard of continents relative to the ocean floor: a unique feature of the Earth compared with all other bodies in the Solar System. It also accounts for the vast bulk of continental crust having remained at the surface since it formed: it rarely gets subducted, if at all.

One suggested model for pre-plate tectonic continent formation (credit, Robert J Stern https://speakingofgeoscience.org/2013/04/28/when-did-plate-tectonics-begin-on-earth-and-what-came-before/)

Tangible signs that such subduction was taking place in the past – eclogites and other high-pressure, low-temperature metamorphosed basalts or blueschists – are only found after 800 Ma ago. Before that time evidence for plate tectonics is circumstantial. Some geologists have argued for a different style of subduction in earlier times, plates under riding others at low angles. Others have argued for a totally different style of tectonics in Earth early history, marked by changes in bulk chemical composition of the continental crust at the Archaean-Proterozoic boundary. A new twist comes from evidence in the Archaean Pilbara Craton of Western Australia (Johnson, T.E. et al. 2017. Earth’s first stable continents did not form by subduction. Nature, v. 543, p. 239-242; doi:10.1038/nature21383). The authors found that basalts dated at about 3.5 Ga have trace-element geochemistry with affinities to the primitive basalts of island arcs. That makes them a plausible source for slightly younger felsic plutonic rocks with a tonalite-trondhjemite-granodiorite (TTG) compositional range (characteristic of Archaean continental crust). If the basalts were partially melted to yield 30% of their mass as new magma the melt composition would match that of the TTG crust. This would be feasible at only 30 km depth given a temperature increase with depth of at least 25° C per kilometre; more than the average continent geothermal gradient today but quite plausible with the then higher heat production by less decayed radioactive isotopes of uranium, thorium and potassium 3.5 Ga ago. This would have required the basalts to have formed a 30 km thick crust. However, the basalts’ geochemistry requires their generation by partial melting of earlier more mafic basalts rather than directly from the mantle. That early Archaean mantle melting probably did generate vast amounts such primary magma is generally acknowledged and confirmed by the common occurrence of komatiitic lavas with much higher magnesium content than common basalts of modern constructive margins. In essence, Johnson et al. favour thermal reworking of primitive Archaean crust, rather than reworking in a plate tectonic cycle.

More on continental growth and plate tectonics

See also

When did Plate Tectonics begin on Earth, and what came before?

Neanderthals and dental hygiene

Teeth are the most likely parts of skeletons to survive for long periods because of their armour by a layer of enamel made of hydroxyapatite (Ca5(PO4)3(OH)). Dental enamel is the hardest material in the bodies of vertebrate animals and lies midway between fluorite and feldspar on Moh’s scale of hardness (value 5). Like the mineral apatite, teeth survive abrasion, comminution and dissolution for long periods in the surface environment. Subdivision of fossil hominin species and even among different groups of living humans relies to a marked extent on the morphology of their teeth’s biting and chewing surface. Although there are intriguing examples in Neolithic jawbones of dental cavities having been filled it is rather lack of attention to teeth that characterises hominin fossils. As well as horrifying signs of mandibular erosion due to massive root abscesses, a great many hominin remains carry large accumulations of dental plaque or calculus made of mineralised biofilm laid down by oral bacteria. Even assiduous brushing only delays the build up. Grisly as this inevitability might seem, plaque is an excellent means of preserving not only the bacteria but traces of what an individual ate. As fossil DNA is a guide to ancestry and relatedness among fossil hominins, so far going back to about 430 ka in the case of a Spanish Homo heidelburgensis, plaque potentially may reveal details of diet and to some extent social behaviour elaborating beyond the possibilities presented by carbon isotopes and dental wear patterns.

Plaque deposits have already shown that Neanderthals had a very varied vegetable diet and that they cooked their food, the sugars thereby released encouraging bacterial biofilms. There have even been hints that they used medicinal herbs, such as yarrow and chamomile. Now a large multinational team of scientists has taken this fascinating line of study a step further using short DNA fragments to identify the actual oral microbes and even plant and animal species that dominated the diets of 8 cave-dwelling Neanderthals found in Spain, Belgium and Italy (Weyrich, L.S. and 30 others 2017. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature, v. 543; online doi:10.1038/nature21674). The Spanish individuals found in El Sidrón cave seem to have been mainly vegetarian (mushrooms, pine nuts and edible moss) whereas two from the Spy cave in Belgium feasted on wooly rhinoceros and mouflon sheep. One of the El Sidrón Neanderthals had a dental abscess, and was probably in great pain, and whose calculus contained evidence of ingestion of tissue from poplar trees, known to contain salicylic acid (the active ingredient in aspirin): an example of self-medication. The unfortunate individual was also suffering from acute diarrhoea brought on by a eukaryote parasite (microsporidium). Astonishingly, DNA from several plant fungi, including Penicillium rubens (penicillin) also occurred in this individual’s calculus, from eating mouldy plant material: predating modern antibiotics by more than forty-five thousand years!

More predictable findings from the unfortunate El Sidrón individual was a spectrum of common plaque colonising bacteria. But another surprise was Methanobrevibacter oralis, an archaea common in the human mouth ecosystem, for which a complete genome was reconstructed. It is different from that in the Methanobrevibacter oralis found in living humans and the team were able to use a molecular clock approach to date the divergence between the two sub-species. This seems to have occurred between 112-143 ka ago, long after the divergence of Neanerthals and anatomically modern humans, judged to be around 450 to 750 ka ago. The authors suggest that ‘commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East’. Two alternative ‘interactions’ occurred to one commentator: kissing or exchange of chewed food (Callaway, E, 2017. Plaque DNA hints at Neanderthal lifestyle. Nature, v. 543, p. 163). Intriguingly the date, albeit imprecise, overlaps with estimates for the timing of Neanderthal – modern human interbreeding as the latter began to leave Africa: not only do living non-Africans share genes with Neanderthals, the may also share saliva and oral bacteria.

For more information on recent human evolution see here.

Denisovan(?) remains in the garden

On the edge of the small town of Lingjing near Xuchang City in Henan Province, China, local people have long practiced intensive vegetable gardening because the local soil is naturally irrigated by the water table beneath the flood plain deposits of the Yinghe River. In the mid 1960s, around a small spring, they began to find dozens of small stone tools together with animal bones. Only in 2005, after the spring had stopped flowing, did systematic excavation begin (Li, Z.-Y. et al. 2017. Late Pleistocene archaic human crania from Xuchang, China. Science, v. 355, p. 969-972; doi: 10.1126/science.aal2482) About 3.5 m below the surface tools and bone fragments, including one with a carved representation of a bird, occurred just above the base of the modern soil profile. Radiocarbon dating of charcoal from the layer clustered around 13 500 years ago, just before the start of the Younger Dryas cooling episode; probably products of modern humans, although no human remains were found in the layer. Continued excavation penetrated sediments free of fossils and tools down to a depth of 8 m, when stone tools and bone fragments began to turn up again through the lowest 2 m of sediment. Optically stimulated luminescence (OSL) dating of mineral grains, which shows the last time that sediments were exposed to sunlight, produced much older dates between 78 to 123 ka. The thousands of stone flakes and cores, and cut marks on the animal bones found through the fossil-rich layer suggests that this was a site long used for tool making and food preparation, that had begun in the last interglacial period. Among the bones were fragments of the crania of as many as five individual humans.

Who were they? Their age range is tens of thousands of years before anatomically modern humans began to migrate into east Asia, so they are likely to have been an earlier human group. Homo erectus is known to have inhabited China since as early as 1.6 Ma ago and may be a possibility. The other possible group are the Denisovans, known only from their DNA in a small finger bone from a cave in eastern Siberia. Fragments of Denisovan DNA are famously present in that of many living indigenous people from eastern Asia, Melanesia and the Americas, but hardly at all in west Asians and Europeans. They also interbred with Neanderthals and may share a common ancestor with us and them, who lived about 700 ka ago.

Map showing the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. (Credit: Sankararaman et al./Current Biology 2016;  http://dx.doi.org/10.1016/j.cub.2016.03.037)

Map showing the proportion of the genome inferred to be Denisovan in ancestry in non-Africans. The color scale ranges from black – 0, through greens – present to red – highest . (Credit: Sankararaman et al./Current Biology 2016; http://dx.doi.org/10.1016/j.cub.2016.03.037)

Unfortunately the human bones are completely fragmented and lack any teeth, jaw bones or elements of the face. However, the Chinese-US team used sophisticated computer refitting of CT-scanned fragments to reconstruct two of the crania, revealing one individual with prominent brow ridges and a flat-topped skull extended towards the back, similar to that of Neanderthals but with a much larger brain than H. erectus. The semi-circular canals associated with the ears, but used in balancing, are well preserved and also resemble those of Neanderthals. Yet east Asia has yielded not a single Neanderthal fossil. Could these be the elusive Denisovans? Even if more diagnostic bones turn up, especially teeth, such is the state of late hominin taxonomy that only DNA will provide definitive results: the Denisovans are defined entirely by DNA. The authors, perhaps wisely, do not speculate, but others may not be able to resist the temptation.

For more information on recent human evolution see here.

Gibbons, A. 2017. Close relative of Neandertals unearthed in China. Science, v. 355, p. 899; doi: 10.1126/science.355.6328.899

Earliest hydrothermal vents and evidence for life


That seawater circulates through the axial regions of rifts associated with sea-floor spreading has been known since well before the acceptance of plate tectonics. The idea stems from the discovery in 1949 of brines with a temperature of 60°C on the central floor of the Red Sea, which in the early 60s turned out to be anomalously metal-rich as well. Advanced submersibles that can withstand the high pressures at great depth a decade later produced images of swirling clouds of sediment from large sea-floor springs, first on the Galapagos rift and subsequently on many others. The first shots were of dark, turbulent clouds, prompting the term ‘black smoker’ for such hydrothermal vents and it turns out that others produce light-coloured clouds – ‘white smokers’. Sampling revealed that the sediments in black smokers were in fact fine-grained precipitates of metallic sulfides, whereas those forming white smokers were sulfates, carbonates and oxides of barium calcium and silicon also precipitated from solute-rich brines produced by partial dissolution of ocean floor through which they had passes.

A black smoker known as "the brothers".

A black smoker with associated organism. (credit: Wikipedia)

Excitement grew when hydrothermal vents were shown to have complex animal ecosystems completely new to science. A variety of chemical evidence, most importantly the common presence of proteins and other cell chemicals built around metal sulfide groups in most living organisms, prompted the idea that hydrothermal vents may have hosted the origins of life on Earth. Many fossil vent systems also contain fossils; macrofossils in the Phanerozoic and microbial ones from the Precambrian. But tangible signs of life, in the form of mats ascribed to bacteria or archaea holding together fine-grained sediments, go back no further than 3830 Ma in the Isua area of SW Greenland. Purely geochemical evidence that carbonaceous compounds may have formed in living systems  are ambiguous since quite complex hydrocarbons can be synthesised abiogenically by Fischer-Tropsch reactions between carbon monoxide and hydrogen. Signs of deep sea hydrothermal activity are common in any geological terrain containing basalt lavas with the characteristic pillows indicating extrusion beneath water. So to trace life’s origins all that is needed to trigger the interest of palaeobiologists are the oldest known pillow lavas. Until quite recently, that meant the Isua volcano-sedimentary association, but heating, high pressures and  very strong deformation affected those rocks when they were metamorphosed half a billion years after they were formed; a cause for skepticism by some geoscientists.

The primacy of Isua metavolcanic rocks has been challenged by more extensive metamorphosed basalts in the Nuvvuagittuk area in Quebec on the east side of Hudson Bay, Canada. They contain hydrothermal ironstones associated with pillowed basalts that are cut by more silica-rich intrusive igneous rocks dated between 3750 and 3775 Ma. That might place the age of basalt volcanism and the hydrothermal systems in the same ball park as those of Isua, but intriguingly the basalts’ 146Sm-142Nd systematics suggest a possible age of magma separation from the mantle of 4280 Ma (this age is currently disputed as it clashes with  U-Pb dates for zircon grains extracted from the metabasalts around the same as the age at Isua). Nonetheless, some parts of the Nuvvuagittuk sequence are barely deformed and show only low-grade metamorphism, and they contain iron- and silicon-rich hot spring deposits (Dodd, M.S. et al. 2017. Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature, v. 543, p. 60-64; doi:10.1038/nature21377). As at Isua, the ironstones contain graphite whose carbon isotope proportions have an ambiguous sign of having formed by living or abiotic processes. It is the light deformation and low metamorphism of the rocks that gives them an edge as regards being hosts to tangible signs of life. Extremely delicate rosettes and blades of calcium carbonate and phosphate, likely formed during deposition, remain intact. These signs of stasis are in direct contact with features that are almost identical to minute tubes and filaments formed in modern vents by iron-oxidising bacteria. All that is missing are clear signs of bacterial cells. Ambiguities in the dating of the basalt host rocks do not allow the authors claims that their signs of life are significantly older than those at Isua, but their biotic origins are less open to question. Neither offer definitive proof of life, despite widespread claims by media science correspondents, some of whom tend  metaphorically to ‘run amok ‘ when the phrase ‘ancient life’ appears; in this case attempting to link the paper with life on Mars …

You can find more on early life here