Middle Pleistocene Homo naledi

John Hawks discusses the latest news on the Rising Star Project:

Africa’s richest fossil hominin site has revealed more of its treasure. It’s been a year and a half since scientists announced that a new hominin species, which they called Homo naledi, had been discovered in the Rising Star Cave outside Johannesburg.

Now they say they have established and published the age of the original naledi fossils that garnered global headlines in 2015. Homo naledi lived sometime between 335 and 236 thousand years ago, making it relatively young.

They’ve also announced the discovery of a second chamber in the Rising Star cave system, which contained additional Homo naledi specimens. These include a child and the partial skeleton of an adult male with a well-preserved skull. They have named the skeleton “Neo” – a Sesotho word meaning “a gift”.

The Conversation Africa’s Science Editor Natasha Joseph asked Professor John Hawks, a member of the team, to explain the story behind these finds.

To an ordinary person, 236 000 years is a very long time ago. Why does the team suggest that in fact, Homo naledi is a “young” species?

The course of human evolution has taken the last seven million years since our ancestors diverged from those of chimpanzees and bonobos. The first two-thirds of that long history, called australopiths, were apelike creatures who developed the trick of walking upright on two legs.

Around two million years ago some varieties of hominins took the first real steps in a human direction. They’re the earliest clear members of our genus, Homo, and belong to species like Homo habilis, Homo erectus and Homo rudolfensis.

Homo naledi looks in many ways like these first members of Homo. It’s even more primitive than these species in many ways, and has a smaller brain than any of them. People outside our team who have studied the fossils mostly thought they should be around the same age. A few had the radical idea that H. naledi might have lived more recently, maybe around 900,000 years ago.

Nobody thought that these fossils could actually have come from the same recent time interval when modern humans were evolving, a mere 236 to 335 thousand years ago.

How do you figure out a fossil’s age?

We applied six different methods. The most valuable of these were electron spin resonance (ESR) dating, and uranium-thorium (U-Th) dating. ESR relies on the fact that teeth contain tiny crystals, and the electron energy in these crystals is affected by natural radiation in the ground over long periods of time after fossils are buried.

U-Th relies on the fact that water drips into caves and forms layers of calcite, which contain traces of uranium. The radioactive fraction of uranium decays into thorium slowly over time. So the proportion of thorium compared to uranium gives an estimate of the time since the calcite layers formed. One of these calcite deposits, called a flowstone, formed above the H. naledi fossils in the Dinaledi Chamber. That flowstone helps to establish the minimum age: the fossils must be older than the flowstone above them.

For these two methods, our team engaged two separate labs and asked them to process and analyse samples without talking to each other. Their processes produced the same results. This gives us great confidence that the results are reliable.

What does the discovery of Homo naledi’s age mean for our understanding of human history and evolution?

For at least the past 100 years, anthropologists have assumed that most of the evolution of Homo was a story of progress: brains got bigger over time, technology became more sophisticated and teeth got smaller as people relied more upon cleverness to get better food and prepare it by cooking.

We thought that once culture really got started, our evolution was driven by a feedback loop – better food allowed bigger brains, more clever adaptations, more sophisticated communication. That enabled better technology, which yielded more food, and so on like a snowball rolling downhill.

No other hominin species could compete with this human juggernaut. You would never see more than one form of human in a single part of the world, because the competition would be too intense. Other forms, like Neanderthals, existed within regions of the world apart from the mainstream leading to modern humans in Africa. But even they were basically human with large brains.

That thinking was wrong.

Africa south of the equator is the core of human evolutionary history. That’s where today’s human populations were most genetically diverse, and that diversity is just a small part of what once existed there. Different lineages of archaic humans once lived in this region. Anthropologists have found a few fossil remnants of these archaic populations. They’ve tried to connect those remnants in a straight line. But the genetic evidence suggests that they were much more complex, with deep divisions that occasionally intertwined.

H. naledi shows a lineage that existed for probably more than a million years, maybe two million years, from the time it branched from our family tree up to the last 300,000 years. During all this time, it lived in Africa with archaic lineages of humans, with the ancestors of modern humans, maybe with early modern humans themselves. It’s strikingly different from any of these other human forms, so primitive in many aspects. It represents a lost hominin community within which our species evolved.

I think we have to reexamine much of what we thought we knew about our shared evolutionary past in Africa. We know a lot of information from a few very tiny geographic areas. But the largest parts of the continent are unknown – they have no fossil record at all.

Explorers Mathabela Tsikoane, Maropeng Ramalepa, Dirk van Rooyen, Steven Tucker (seated), and Rick Hunter (seated) inside the Rising Star cave system. Wits University/Marina Elliott

We’re working to change that, and as our team and others make new discoveries, I’m pretty sure we are going to find more lineages that have been hidden to us. H. naledi will not be the last.

The first Homo naledi discoveries were made in the Dinaledi Chamber. What led researchers to the second chamber? And what did you find there?

The Dinaledi Chamber is one of the most significant fossil finds in history. After excavating only a very tiny part of this chamber, the sample of hominin specimens is already larger than any other single assemblage in Africa.

The explorers who first found these bones, Rick Hunter and Steven Tucker, saw what the team was doing when they were excavating in the chamber. The pair realised that they might have seen a similar occurrence in another part of the cave system. The Rising Star system has more than two kilometres of mapped passages underground. In another deep chamber, accessed again through very tight underground squeezes, there were hominin bones exposed on the surface.

Our team first began systematic survey of this chamber, which we named the Lesedi Chamber, in 2014. For two years Marina Elliott led excavations, joined at times by most of the team’s other experienced underground excavators. They were working in a situation where bones are jammed into a tight blind tunnel. Only one excavator can fit at a time, belly-down, feet sticking out. It is an incredibly challenging excavation circumstance.

Geologist Dr Hannah Hilbert-Wolf studying difficult to reach flowstones in a small side passage in the Dinaledi Chamber. Wits University

The most significant discovery is a partial skeleton of H. naledi, with parts of the arms, legs, a lot of the spine and many other pieces, as well as a beautifully complete skull and jaw. We named this skeleton “Neo”. We also recovered fragments of at least one other adult individual, and one child, although we suspect these bones may come from one or two more individuals.

Is there a way for people to view these discoveries in person?

On May 25 – Africa DayMaropeng at the Cradle of Humankind World Heritage Site outside Johannesburg will open a new exhibit with the discoveries from the Lesedi Chamber and the Dinaledi Chamber together for the first time.

For people outside South Africa, the data from our three-dimensional scans of the new Lesedi fossils are available online.

Anyone can download the 3D models, and people with access to a 3D printer can print their own physical copies of the new fossils, as well as the fossils from the Dinaledi Chamber. It’s a great way for people to see the evidence for themselves.

Reprint from The Conversation

Three reasons the Cerutti Mastodon was not manipulated by hominins

A team of scientists recently announced an extraordinary claim that the 130,000 Cerutti Mastodon was manipulated by hominins.

“I have read that paper and I was astonished by it,” archaeologist Donald Grayson of the University of Washington. “I was astonished not because it is so good, but because it is so bad. Cracked bones and chipped stones at a fossil site might mean anything”, said Grayson. “It is quite another thing to show that people, and people alone, could have produced those modifications. The study doesn’t take that step, he said, “making this a very easy claim to dismiss.”

Gary Haynes of the University of Nevada Reno had this to say, “The paper states that the bones were being exposed by a backhoe. These pieces of heavy equipment weigh seven to fifteen tons or more, and their weight on the sediments would have crushed bones and rocks against each other.” When asked, Holen, the study leader, said that it “was very easy to tell the difference” between fractures made by stone hammers and those seen in bones crushed by bulldozers. He did not elaborate on how the differences manifest. “He’s pretty much dead wrong — there’s no definable difference,” Haynes said. A similar fossil dispute broke out in 2015 over a 24,000 year old mammoth in Maryland, he noted, shown to be fractured by heavy equipment. Also troubling, the “hammer” and “anvil” stones described in the paper don’t unequivocally look like tools, said Michael Waters of Texas A&M’s Center for the Study of the First Americans.

Michael Waters of Texas A&M’s Center for the Study of the First Americans noted that the “hammer” and “anvil” stones described in the paper don’t unequivocally look like tools. The study also runs afoul of the mounting genetic evidence, which indicates that the first people to reach the Americas and eventually give rise to modern Native Americans arrived no earlier than 25,000 years ago.”

The First Human Epidemic: Late Pleistocene Origin?

Current models of infectious disease in the Pleistocene tell us little about the pathogens that would have infected Neanderthals (Homo neanderthalensis). High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. Independent sources of DNA-based evidence allow a re-evaluation of the nature and timing of the first epidemiologic transition. The paradigm of the first epidemiologic transmission, the hypothesis that epidemic disease did not occur until the transition to agriculture, with larger, denser and more sedentary populations, has been essentially unchallenged since the 1970s. Our views of the infectious disease environment of the Pleistocene period are heavily influenced by skeletal data and studies of contemporary hunter-gatherers. New genetic data – encompassing both hosts and pathogens – has the power to transform our view of the infectious disease landscape experienced by Neanderthals in Europe, and the anatomically modern humans (AMH) with whom they came into contact. The Pleistocene hominin environment cannot be thought of as free from infectious disease. It seems likely that the first epidemiologic transition, envisaged as part of the package of the Holocene farming lifestyle, may be fundamentally different in pace or scope than has previously been suggested. This paper demonstrates how high quality genomic data sets can be used to address questions arisingfrom the ecological context that shaped the co-evolutionary relationship we share with infectious diseases. We analyse the evidence for infectious disease in Neanderthals, beginning with that of infection-related skeletal pathologies in the archaeological record, and then consider the role of infection in hominin evolution. We have synthesised current models on the chronology of emergence of notable European disease packages and analyse what implications this evidence has for the classical model of the first epidemiologic transition. Using emerging data from Neanderthal palaeogenomics and combining this with fossil and archaeological information we re-examine the impact of infectious diseases on human populations from an evolutionary context. These palaeogeneticists argue that the first epidemiologic transition in Eurasia was not as tightly tied to the onset of the Holocene as has previously been assumed. There is clear evidence to suggest that this transition began before the appearance of agriculture and occurred over a timescale of tens of thousands of years. We suggest that the epidemiological transition was not, as has been thought since the 1970s, a phenomenon of the human shift to sedentary agriculture during the Holocene but a much older and more complex process that involved at least two species of humans. The origin of resistance to infectious disease has a much deeper timeframe and is highlighted by the ingression of Neanderthal DNA into modern human lineages. The transfer of pathogens between human species may also have played a role in the extinction of the Neanderthals. Our analysis of the genomes of archaic hominins provides evidence of pathogens acting as a population-level selection pressure, causing changes in genomes that were passed on to descendants and preserved in the genomes of modern Eurasians. the analysis of ancient genomes demonstrates that human behavioural patterns (in this case a shift to agricultural subsistence) should not be used as an ecological proxy to explain shifting trends in the co-evolutionary relationship between pathogens and human populations.

This work is available on BioRxiv: http://dx.doi.org/10.1101/017343

Acknowledgements: Rob Foley, Marta Lahr and the members of the Human Evolutionary Science Discussion Group at the University
of Cambridge. Funding for this research was provided by King’s College Cambridge and UCL.

Homo floresiensis: Extracting Ancient Deoxyribonucleic Acid (aDNA): It’s Been 4 Years, any success?

I recently came across this scientific article in the Journal of Human Evolution entitled, Ancient DNA Analysis of Dental Calculus by Weyrich et al. It reminded me of the research conducted on the Indonesian hominin, Homo floresiensis. So, here I summarise what we know thus far. Dating to between 95,000 and 17,000 years ago, the hominin was found in the cave of Liang Bua, overlooking the Wae Racang river valley, on the island of Flores. It’s most remarkable feature was the 1.06 m stature of the individual found. Begging the question, how is this hominin related to us and what led to its diminutive stature. Much of the debate was thoroughly summarised in Leslie Aiello’s paper entitled, Five Years of Homo floresiensis, back in 2010. In short, some questioned the validity of naming these individuals a new species of human. Evidence was brought forward to support the hypothesis that these people were suffering from the neurodevelopmental disorder, Microcephaly and other diseases that induce a reduced stature. As time has passed, media sensation abated and researchers had a chance to step back, the majority are now more accepting of the Australian-Indonesian team’s decision to apply the new hominin nomenclature. Much of the debate hinges on skeletal comparisons between Homo floresiensis and other hominins, like us. There is one piece of information that the individuals of Liang Bua have yet to reveal – Deoxyribonucleic Acid.

Kilimutu Crater Lakes, Flores, Indonesia
Kilimutu Crater Lakes, Flores, Indonesia

Two teams of scientists, the Australian Centre for Ancient DNA (ACAD) and the Department of Evolutionary Anthropology at the Max Planck Institute (MPI) attempted and failed to extract DNA from the individual’s teeth in 2006. This was due to the environment in which the hominins were found, which was not conducive to DNA preservation. Christina Adler of ACAD hypothesised that the reason for extraction failure could be due to extraction procedure. In 2007 the ACAD team sucessfully extracted DNA from a pig tooth unearthed at the Liang Bua Cave, which was about 6,000 years old. The team suggested that first, Cementum (calcified root covering) is the richest source of DNA and second, drilling the specimen destroys the very molecule they are after. Armed with this knowledge another attempt to extract DNA from the hominins of Liang Bua is still yet to be carried out. The year 2013, saw the successful extraction of 400,000 year old DNA in Spain, so Floresiensian DNA may still lie within the teeth. I’m hoping, despite the less than ideal high temperatures of the cave sediments, there lies within those hominin individuals such strands of the good stuff.

Cranium and mandible cast of Homo floresiensis individual, LB1
Cranium and mandible cast of Homo floresiensis individual, LB1

Returning to the paper I mentioned at the beginning, it is a summary of all we know regarding the extraction of aDNA and steps to take when extracting it from calculus on teeth. Calculus is a hardened group of micro-organisms that appear as a yellow build-up usually around the gum-tooth boundary. The first demonstration of aDNA in Calculus was documented in a paper entitled Ancient Bacterial DNA (aDNA) in dental calculus from archaeological human remains by Preus et al., in 2011. A year later, aDNA was extracted from Neolithic Argentinian and Chilean humans. In that study, five bacterial species gene sequences were amplified by targeted polymerase chain reactions (PCR). By 2014, Warinner et al., used the power of the metagenomic sequencing strategy demonstrated increased resolution, the identification of antibiotic resistence genes and though the specimens were put through an Ethylenediaminetetraacetic acid (EDTA) and bleach treatments, DNA was recoverable.

Deoxyribonucleic Acid (DNA)
Deoxyribonucleic Acid (DNA)

When analysing hominin diets, microfossils are a large component, but the strides being made in aDNA extraction will mean that the species of plant or animal will be identified or as it usually does, throws up more questions than answers.

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