Monday, 27 February 2017

A Twist in the Tale of Human Evolution

This article first appeared in New Dawn Special Issue volume 10, Number 6, December 2016. © Brett Lothian.
A Twist in the Tale of Human Evolution

New DNA research reveals our 'Lord of the Rings' antiquity

What are we and where did we come from? Eternal questions, we may finally be on the verge of answering. Thanks to the recent remarkable discoveries in the field of DNA research, we are starting to get a much clearer, if not stranger picture than we ever could have imagined. For decades there were two main competing theories, the “Out of Africa” theory and the “Multi-regional” hypothesis. The study of DNA has shown us that both of these models are at the same time correct and incorrect. Or more correctly, not exactly the entire picture. Whilst we still do not have the entire picture yet, the picture that is emerging is a far more Tolkienesque ancient history, filled with many different types of weird and wonderful humans, reaching out all over the planet, who were by no means isolated from each other in time and space, but instead co-existed and even interbred, creating the new hybrid species that would go on to claim the Earth for itself. Homo sapien sapien, Humanity.

The Out of Africa theory is the most widely accepted model of the geographic origin and early migration of anatomically modern humans. The theory argues for the recent East African origins of modern humans, who left Africa in one, possibly two waves of migration which populated the world, replacing the older human species. A first dispersal took place between 130,000–115,000 years ago via northern Africa, but died out or retreated (although Chinese and some Australian researchers question this extinction and claim the presence of modern humans in Australia up to 120,000 years ago and in China at least 80,000 years ago). According to the theory a second dispersal took place via the so-called Southern Route, which followed the southern coastline of Asia, and colonized Australia by around 50,000 years ago. Europe and Asia were populated by an early offshoot which settled the Middle East and India around 40,000 years ago. Finally the Americas were beginning to be populated possibly as far back as 30,000 years ago.

It was widely believed that in the relative vacuum after the Mount Toba mega volcano explosion around 60,000 years ago which nearly wiped all forms of humans from the planet completely, the modern Homo sapiens that remained, out competed all of the many other forms of archaic humans that also remained. Largely by being more intelligent, garnering us the ability to be better able to acquire and defend resources. Other theories postulated that we murdered them all being more war like (which is a tempting theory considering our modern tendencies), we were better adapted to climate change and possibly that we had natural immunities to diseases that they did not.  

The Multi regional hypothesis holds that the human species first arose around two to three million years ago and subsequent human evolution has been within a single, continuous human species. This species encompasses all archaic human forms such as Homo erectus and Neanderthals as well as modern forms, and evolved worldwide to the diverse populations of modern Homo sapiens sapiens. 

Now thanks to the recent breakthroughs in the study of DNA, we have to form a new type of synthesis between the two and add an entirely new element that until recently was not proven, hybridization. The Victorian era arrogance of our intellectual superiority leading us to take over the world from the likes of the supposedly less intelligent Neanderthal cave man, has proven to be false, we simply did not just out compete or wipe out all the archaic species of human leaving only us, they are in fact still alive today, inside of us all. We are them, at least partially. The fact that we were able to interbreed with the other species of human and have fertile offspring leads us to ask, were we really different species after all? Or just isolated pockets of the same species that recombined over time, until we have the truly global society we have today? This brings us to what is known as the species problem, which basically means that the definitions of exactly what meets a species requirements, do not fit all species and are constantly changing, making species definitions areas of grey, rather than hard and fast lines. 

But let’s start at the beginning, we start out around two to three million years before present, in the species known as Homo erectus or Upright Man. Homo erectus was the first in our line to harness fire and develop the stone tool technology we used right up until the Bronze Age, which did not begin until 4,500 and 2,000 BC and is still used today in some regions. It is where we can truly say we became human, operating as intelligent hunter gatherers, largely as we always have right up until modern times and as some small pockets of the world still do. 

Until recently it was believed that the species known as Homo habilis and Homo rudolfensis preceded Homo erectus in the evolutionary scale. That is until the findings at the Dmanisi site in Georgia, Eastern Europe. An analysis of the five 1.8 million year old hominid skulls found at Dmanisi, suggests that the earliest Homo species, Homo habilis, Homo rudolfensis and Homo ergaster and so forth actually belonged to the same species. “The differences between these Dmanisi fossils are no more pronounced than those between five modern humans or five chimpanzees,” said Dr David Lordkipanidze from the Georgian National Museum in Tbilisi, a lead author of a paper in the journal Science and co-author of a paper published in the Proceedings of the National Academy of Sciences. Traditionally, researchers have used variation among Homo fossils to define different species. But in light of these new findings, Dr Lordkipanidze and his colleagues suggest that early, diverse Homo fossils, with their origins in Africa, actually represent variation among members of a single, evolving lineage – most appropriately, Homo erectus.

“Had the braincase and the face of Skull five been found as separate fossils at different sites in Africa, they might have been attributed to different species,” said Dr Christoph Zollikofer from the Anthropological Institute and Museum in Zurich, Switzerland, a co-author of the Science paper. That’s because Skull five unites some key features, like the tiny braincase and large face, which had not been observed together in an early Homo fossil until now. Given their diverse physical traits, the fossils associated with Skull five at Dmanisi can be compared to various Homo fossils, including those found in Africa, dating back to about 2.4 million years ago, as well as others unearthed in Asia and Europe, which are dated between 1.8 and 1.2 million years ago. “The Dmanisi finds look quite different from one another, so it’s tempting to publish them as different species,” Dr Zollikofer said. “Yet we know that these individuals came from the same location and the same geological time, so they could, in principle, represent a single population of a single species.” This seems the most likely scenario.

Homo erectus is generally thought to have originated in Africa two to three million years ago and spread from there, migrating throughout Eurasia as far as Southern Europe, Georgia, India, Sri Lanka, China and Indonesia, were it survived right up until possibly only 30,000 years ago. On the Indonesian island of Flores in 2003, archaeologists discovered what has become known as the Flores hobbits or more correctly Homo floresiensis. The remains of an individual that would have stood about one metre in height was discovered in a cave at Liang Bua on the island. Partial skeletons of nine individuals have been recovered from the site, including one complete skull. This hominin had originally been considered to be remarkable for its survival until relatively recent times, only 12,000 years ago. 

However, more extensive stratigraphic and chronological work has pushed the dating of the most recent evidence of their existence back to 50,000 years ago. Their skeletal material is now dated to from 100,000 to 60,000 years ago. Stone tools recovered alongside the skeletal remains were from archaeological horizons ranging from 190,000 to 50,000 years ago. Fossil teeth and a partial jaw from hominins believed ancestral to H. floresiensis were discovered in 2014 and described in 2016. These remains are from a site on Flores called Mata Menge, about 74 km from Liang Bua. They date to about 700,000 years ago and are even smaller than the later fossils. The form of the fossils has been interpreted as suggesting that they are derived from a population of Homo erectus that arrived on Flores about a million years ago, as indicated by the oldest artefacts excavated on the island and rapidly there after became dwarfed through the phenomenon known as insular dwarfism. 

It’s worth noting that the Indonesian island of Flores is on the Australian side of what is known as the Wallace line.  The Wallace Line or Wallace's Line is a faunal boundary line drawn in 1859 by the British naturalist Alfred Russel Wallace that separates the ecozones of Asia and Wallacea, a transitional zone between Asia and Australia. West of the line are found organisms related to Asiatic species; to the east, a mixture of species of Asian and Australian origin is present. Understanding the biogeography of the region centres on the relationship of ancient sea levels to the continental shelves. Wallace's Line is visible geographically when the continental shelf contours are examined; it can be seen as a deep-water channel that marks the south-eastern edge of the Sunda Shelf which links Borneo, Bali, Java, and Sumatra underwater to the mainland of south-eastern Asia. Australia is likewise connected by the Sahul Shelf to New Guinea. The biogeographic boundary known as Lydekker's Line, which separates the eastern edge of Wallacea from the Australian region, has a similar origin to the Wallace line. Which means, if the ancestors of the Flores Hobbits, Homo erectus, could cross one ocean boundary, why not another and make it further to New Guinea and therefore Australia? 

Unfortunately we do not yet have a sample of Homo erectus or Homo floresiensis DNA but hopefully with the improvements in analysis techniques and technology, in the near future we will. From Homo erectus onwards, things start to get really interesting and at the same time, quite confusing. After spreading out of Africa, Homo erectus managed to colonize Europe, and Asia where it seems to have persisted the longest, perhaps being more isolated for a longer period of time. Somewhere around one million to 800,000 years ago the Asian Homo erectus populations seems to have split through isolation and genetic drift from their African forebears, remaining relatively unchanged, except of course for the Flores Hobbits. However back in Africa things were beginning to change, in ways that would reshape the world. A new line emerged, having the mixed features of both Homo erectus and modern humans, most notably a larger brain. 

The new line again pushed out of Africa once more, spanning Europe and Asia, evolving into what is known as the Denisovan hominid in the east and in west evolving into the Neanderthal Man. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. Three teeth belonging to different members of the same population have since been reported. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known. Little is known of the precise anatomical features of the Denisovans, since the only physical remains discovered thus far are the finger bone, two teeth from which genetic material has been gathered and a toe bone. The single finger bone is unusually broad and robust, well outside the variation seen in modern people. Surprisingly, it belonged to a female, indicating that the Denisovans were extremely robust, perhaps similar in build to the Neanderthals. The tooth that has been characterized shares no derived morphological features with Neanderthal or modern humans. 

The mitochondrial DNA from the finger bone differs from that of modern humans by 385 bases (nucleotides) in the mitochondrial DNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mitochondrial DNA base pairs. This suggested a divergence time around one million years ago. The mitochondrial DNA from a tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population. From a second tooth, a mitochondrial DNA sequence was recovered that showed an unexpectedly large number of genetic differences compared to that found in the other tooth and the finger, suggesting a high degree of mitochondrial DNA diversity. These two individuals from the same cave showed more diversity than seen among sampled Neanderthals from all of Eurasia, and were as different as modern-day humans from different continents today.

Neanderthals and the Denisovans made advanced tools, apparently kindled fire on demand, most likely had languages and lived in complex social groups. The Molodova I archaeological site in eastern Ukraine suggests some Neanderthals built dwellings using animal bones. A building was made of mammoth skulls, jaws, tusks and leg bones, and had twenty five hearths inside. Circumstantial evidence suggests Neanderthals may have been building some form of watercraft since the Palaeolithic. Scientists have speculated that these watercraft may have been similar to dugout canoes, which are among the oldest known boats in the archaeological record. Stone tools discovered on the southern Ionian Islands suggests that Neanderthals were sailing the Mediterranean Sea as early as 110,000 years ago. Quartz hand-axes, three-sided picks, and stone cleavers from Crete have also been recovered that date back about 170,000 years ago.

It was once thought that Neanderthals lacked the sophistication for hunting, perhaps scavenging meat from carcasses, but increasing evidence suggests they were apex predators like us, capable of bringing down a wide range of prey from red deer, reindeer, ibex and wild boar, to larger animals such as aurochs and even, on occasion, mammoth, straight tusked elephant and rhinoceros. However, while they were largely carnivorous, new studies indicate Neanderthals also had cooked vegetables in their diet. In 2010, an isotope analysis of Neanderthal teeth found traces of cooked vegetable matter, and more recently a 2014 study of Neanderthal coprolites (fossilized faeces) found substantial amounts of plant matter, contradicting the earlier belief they were exclusively (or almost exclusively) carnivorous. The size and distribution of Neanderthal sites, along with genetic evidence, suggests Neanderthals lived in much smaller and more sparsely distributed groups than their Homo sapiens contemporaries. Some experts suggest that this disparity alone was a major contributing factor to their ultimate replacement by Homo sapiens, which may have outnumbered them by as much as 9 to 1 according to some estimates. Their lower population density may have also increased Neanderthal susceptibility to mutations caused by inbreeding.

Neanderthals differed from modern humans in that they had a more robust build and distinctive morphological features, these include shorter limb proportions, a wider, barrel-shaped rib cage, a reduced chin and, perhaps most notably, a large nose, which was much larger in both length and width, and started somewhat higher on the face, than in modern humans. Neanderthals are known for their sloped forehead and large cranial capacity, which at 1600 cm3 is larger on average than that of modern humans. One study has found that Neanderthal brains were more asymmetric than other hominid brains. A 2013 study of Neanderthal skulls suggests that their eyesight may have been better than that of modern humans, owing to larger eye sockets and larger areas of the brain devoted to vision. Evidence suggests they were much stronger than modern humans, with particularly strong arms and hands, while they were comparable in height. Neanderthal males averaged 164–168 cm and females 152–156 cm tall. Samples of 26 specimens in 2010 found an average weight of 77.6 kg for males and 66.4 kg for females. A 2007 genetic study suggested some Neanderthals may have had red hair and blond hair, along with a light skin tone. The Denisovans were most likely similar in build, with their scant remains also being very robust. 

Back home in Africa the remaining late Homo erectus or Homo heildelbergensis was on the way to becoming us, Homo sapiens. By around 200,000 years ago we emerge in the Great Rift Valley as anatomically modern humans after breaking off from the Denisovan populations around 800,000 years before and the Neanderthal populations by around 350,000 years ago. According to the old theories anatomically modern humans then eventually go on to colonize the world, out smarting, or killing the previous inhabitants. But is that really true? Or merely a reflection of our Darwinist philosophy of survival of the fittest and our Abrahamic philosophy of the world being created for us to dominate? Since it has been shown that we in fact interbred with archaic forms of Homo, it may be that we simply out bred them. 

Some researchers have postulated that the interbreeding was forced as in the case of Neanderthal DNA which is present in everyone outside of sub-Saharan Africa being from female Neanderthals only. Simply assuming that early humans were brutish cave men who raped everything they could, I think comes back to our modern attitudes more than any actual evidence. More likely we interbred both ways in cultural exchange, with the Neanderthal’s offspring being infertile or less fertile, as is often the case with interbreeding. This over time would decimate an already endangered population such as the Neanderthal.
This is where the “Multi-regional” model comes back in. Whilst it is accepted that Homo erectus first evolved in Africa, once it had evolved into different species in different parts of the world, evolving new genes, and the fact that we interbred with these different homo species outside of Africa shows that a large proportion of our genetic make-up evolved multi-regionally. So in essence, both the “Out of Africa” and “Multi-regional” models are to a certain extent correct. 

Initial analysis of genomes of modern humans showed that we mated with at least two groups of ancient humans, the Neanderthals and Denisovans. Approximately 4% of the DNA of everyone outside of Sub-Saharan Africa, is shared with Neanderthals. Tests comparing the Denisovan hominin genome with those of six modern humans – a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese showed that between 4% and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. This DNA was possibly introduced during the early migration to Melanesia. These findings are in concordance with the results of other comparison tests which show a relative increase in allele sharing between the Denisovan and the Aboriginal Australian genome, compared to other Eurasians and African populations; however, it has been observed that Papuans, the population of Papua New Guinea, have more allele sharing than Aboriginal Australians.

Melanesians and Aboriginal Australians are not the only modern day descendants of the Denisovans. David Reich of Harvard University, in collaboration with Mark Stoneking of the Planck Institute team, found genetic evidence that Denisovan ancestry is shared by Melanesians, Australian Aborigines, and smaller scattered groups of people in South-East Asia, such as the Mamanwa, a Negrito people in the Philippines. A paper by Kay Prüfer in 2013 said that mainland Asians and Native Americans had around 0.2% Denisovan ancestry. Tibetans have a region of DNA, haplotype, around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude. According to a study published in Nature in July 2014, this region is also found in the Denisovan genome. However, not all Negritos were found to possess Denisovan genes, Onge Andaman Islanders and Malaysian Jehai, for example, were found to have no significant Denisovan inheritance. These data place the interbreeding event in mainland South-East Asia, and suggest that Denisovans once ranged widely over eastern Asia. Based on the modern distribution of Denisovan DNA, Denisovans may have crossed the Wallace Line, with Wallacea serving as their last refugium. How this would have affected the resident Flores Hobbits is unknown. Perhaps they interbred? 

In 2016 researchers reported that they had found modern human DNA in the genome of a female Neanderthal from the Altai Mountains region near the border between Mongolia and Russia, further backing up that the interbreeding was both ways. They calculated that the mating must have taken place about 100,000 years ago. Studies published in March 2016 suggest that modern humans bred with hominins, including Neanderthals, on multiple occasions. Another study in April 2016 found differences between Homo sapiens and Neanderthal Y chromosomes that, they postulated, could cause female Homo Sapiens to miscarry male babies that had Neanderthal fathers. This would explain why no modern man had to date been found with a Neanderthal Y chromosome. 

Melanesians and Australoid populations show evidence of only one interbreeding event, possibly 100,000 years ago, occurring in the Middle East, Europeans show a second event, which may also be of Middle Eastern origin, occurring possibly 50,000 years ago, while East Asians show an additional third interbreeding event possibly 30,000 years ago occurring in Siberia. Evidence that Neanderthal genomic material is often found amongst genes of the immune system suggests that some of the interbreeding may have secured resistance to diseases that Neanderthal populations had bred resistance to.

A detailed comparison of the Denisovan, Neanderthal, and human genomes has revealed evidence for a complex web of interbreeding among the lineages. Through such interbreeding, 17% of the Denisovan genome represents DNA from the local Neanderthal population, while evidence was also found of a contribution to the nuclear genome from an ancient hominin lineage yet to be identified, 8% of the Denisovan genome is derived from interbreeding with mysterious unknown species from Asia one million years ago, which was neither homo heildelbergensis nor Neanderthal. Most likely Asian Homo erectus.

New research has discovered populations from South and Southeast Asia including the Australian Aboriginal and Melanesian populations contain a small amount of ancestral DNA, not present in East Asians or Europeans, suggesting some modern humans have another, mystery ancestor. The research undertaken by Professor Jaume Bertranpetit from Pompeu Fabra University in Spain along with a team of researchers published in Nature Genetics, involved whole-genome sequence analysis. The genome sequences of 60 individuals of different ethnicities from India’s mainland were compared with those of 10 Andamanese individuals as well as publicly available data for other populations. The study found a small proportion of the genome sequence in populations from South and South East Asia contained DNA from an unknown, extinct, hominid ancestor. Dr Alan Cooper, from the University of Adelaide and Australian Centre for Ancient DNA said, “We already knew there was another species or group of hominids in Southeast Asia who had contributed to the Denisovan genome. This paper further confirms that one other group, maybe the same one, has contributed to modern humans.”

In Africa in 2011, researchers found yet another example of interbreeding with an unknown hominid, likely to be late African Homo erectus or Homo heildelbergensis, after finding three candidate regions with introgression by searching for unusual patterns of variations—indicating a different origin—in 61 non coding regions from two hunter gatherers (Biaka Pygmies and San, shown significant for admixture in the data) and one West African agricultural group (Mandinka, shown not significant for admixture in the data), researchers concluded that roughly 2% of the genetic material found in some Sub-Saharan African populations was inserted into the human genome approximately 35,000 years ago from archaic hominins that broke away from the modern human lineage around 700,000 years ago. After a survey for the introgressive haplotypes across Sub-Saharan populations, it was suggested that the admixture event happened with archaic hominins that possibly once inhabited Central Africa.

In 2012, researchers studied high-coverage whole-genome sequences of fifteen Sub-Saharan hunter-gatherer males from three groups, five Pygmies (three Baka, a Bedzan, and a Bakola) from Cameroon, five Hadza from Tanzania, and five Sandawe from Tanzania. Finding signs that the ancestors of the hunter gatherers interbred with one or more archaic human populations, probably over 40,000 years ago. They also found that the median time of the most recent common ancestor of the fifteen test subjects with the putative introgressive haplotypes was 1.2–1.3 million years ago.

It may turn out in the near future, with further and better testing that there were even more “other” humans in our lineage, who knows? We are still just scratching the surface. The more we look, the stranger our DNA and the ancient world seem to become. Unfortunately today’s world is preoccupied with wars and consumerism, so there is very little funding for research into one of the most important aspects of our existence, human history and evolution. Perhaps the powers that be (who happen to write and control the history books) like keeping us obfuscated to our true origins and history, therefore more easily controlling the culture. Too often the true depth of our history is passed off as “pre-history,” obscure and unimportant. The history we are presented as important starts with the dominator form of culture, as if that is all there has ever been. Wars, conquests and tyrants mark our greatest achievements. If only people knew there was so much more.

So where does this leave us today? Continuing to hold on to outdated notions born out of largely old fashioned racial bias, or dropping all that nonsense and accepting that all of us are simply hybrids. Mutts, mongrels, half casts and Alley Apes. Can we really hold to notions of “racial purity” when every single one of us are hybrids, mixed breeds? Seems rather silly doesn’t it. Maybe the problem is in how we classify things? The DNA evidence is showing us that in reality, all the way back to Homo erectus, we are one sputtering and spurting, cross mingling surge of humanity. In us, anatomically modern humans, Homo sapien sapien, we today contain the genetic material of two different unknown homonids (that we know of so far), most likely in the Asian and Australian case, late Asian Homo erectus or potentially Homo floresiensis. In the African case late Homo erectus, otherwise known as Homo heildelbergensis who we ourselves are evolved from. We have Neanderthal and Denisovan DNA inside us. That leaves us genetically covering pretty much the entire spectrum of the Homo/human experience, all the way back to two to three million years ago and are currently now undergoing the greatest global melting pot society, social experiment in human history. In reality, all of humanity, right from the very start until today, are one people. It’s just sometimes we lose touch with each other for a while, before getting back together. 

Perhaps even still today, the “other” humans exist out there in the some of the hidden, unexplored corners of our beautiful blue planet. Ancient legends from all around the world that continue right up until this day of the Yeti, Sasquatch, Yowie, Alma, Orang pendek, Ebu gogo, and other such strange wild men of the forest come to mind. It turns out, our ancestor’s tales of meeting “other” types of humans, the hairy men wasn’t just tall tales and silly superstitions after all. Our DNA is now showing us that our forebears did in fact meet “other” species of humans all over the world, and even more than that, they got it on in the bedroom, or cave, or where ever it was. That’s not important, what’s important is they were telling the truth, that the ancient legends are true. Whether the hairy men of legend still exist today is disputed, but many still have close encounters and sightings all around the world every year. Where there is smoke, there is usually fire. Man make fire.

Where we all go in the future is anyone’s guess. The fact is we cannot continue the way we currently are, it is quite simply unsustainable. We need to look back at what brought us here, we need to learn from our mistakes. Perhaps we should reconsider the only way of life that has been successful and stable over millions of years, the way of life that allows other ways of life to also share the planet, the way of life that allows us to live on the Earth without destroying it? Hunter gathering and sustainable food forest permaculture has shown to be able to sustain people at relatively stable levels for millions of years, invented by Homo erectus and still used successfully by many people today. In the very near future we may have no choice. A society based on the premise of its ability to grow until infinity (only truly benefiting the elite), on very finite recourses… Sounds like a mix for disaster.

About the author: Brett Lothian is an Australian author, professional arborist, market gardener and ethnobotanist. He is the author of the Tricho Serious Ethnobotany blog and creator of the Trichocereus Cacti Appreciation group, the Peyote Appreciation group and the Ethnobotany Appreciation Society group on facebook.


Recent African origin of modern humans

Multiregional origin of modern humans


Timeline of human evolution

Homo erectus

Homo floresiensis

Wallace Line

Homo heidelbergensis



Neanderthal extinction

Archaic human admixture with modern humans

Mystery genes – do we have an unknown ancestor? By Shannon Verhagen

Homo sapiens interbred with THIRD species of hominin on way to Australia: DNA study finds mystery new ancestor. By Mark Prigg

Pre-modern humans may have picked up genes from Homo erectus. By John Timmer

Archaic admixture in Africans. By Peter Frost

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