The Ghost of an Unknown Hominin

Science Alert has a story about the Ghost of an Unknown Hominin in Africa.  Carly Cassella writes:

The gene pool of modern West Africans contains the 'ghost' of a mysterious hominin, unlike any we've detected so far. Similar to how humans and Neanderthals once mated, new research suggests this ancient long-lost species may have once mingled with our ancestors on the African continent.

Using whole-genome data from present-day West Africans, scientists have found a small portion of genetic material that appears to come from this mysterious lineage, which is thought to have split off from the human family tree even before Neanderthals.

It is not clear to me that these necessarily represent different species. This may reflect an inter-related group of populations from a very genetically diverse population. As my advisor Fred Smith once upon a time said: “If two species interbreed on a regular basis, is it reasonable to call them different species?”

BTW, the  “Unrelated” skull in the page is the Kabwe skull from What was once Rhodesia, discovered in 1925, 400 feet down, in a mine.

Genetic Data Suggests That Early Modern Humans Migrated From South to East Africa

Science Daily is running a story that supports the idea that modern humans migrated from South to East Africa before exiting the continent.  Up until recently, all of the evidence seemed to suggest that South Africa, while having evidence of modern humans at Klasies Rivers Mouth, Border Cave and other sites, did not contribute to the migration out of Africa.  That has changed.

The Huddersfield-Minho team of geneticists, led by Professor Martin Richards at Huddersfield and Dr Pedro Soares in Braga, along with the eminent Cambridge archaeologist Professor Sir Paul Mellars, have studied the maternally-inherited mitochondrial DNA from Africans in unprecedented detail, and have identified a clear signal of a small-scale migration from South Africa to East Africa that took place at just that time, around 65,000 years ago. The signal is only evident today in the mitochondrial DNA. In the rest of the genome, it seems to have been eroded away to nothing by recombination -- the reshuffling of chromosomal genes between parents every generation, which doesn't affect the mitochondrial DNA -- in the intervening millennia.

Before going further, it is worth noting that purveyors of the mtDNA evidence have been burned before by incorrectly using the programs to input the information. Originally, those results supported a hard-line Out-of-africa model of modern human origins (Stringer and Andrews 1988), a model we now know is incorrect. Onward.The paper is available through Scientific Reports, which is open-access.  What is missing from this hypothesis is good human fossil material from South Africa which is between 160 and 200 ky.  The most current remains we have are around 120k.  More work needs to be done on this.

'Swiss Army knife of prehistoric tools' Found in China

Science Daily is on a roll.  This came out a bit back during the late semester crunch and I didn't get a chance to post about it.  Stone tools have been found in south China that appear to be made using the Levallois technology, which originated during the Middle Stone Age, in Africa.  They write:

A study by an international team of researchers, including from the University of Washington, determines that carved stone tools, also known as Levallois cores, were used in Asia 80,000 to 170,000 years ago. Developed in Africa and Western Europe as far back as 300,000 years ago, the cores are a sign of more-advanced toolmaking -- the "multi-tool" of the prehistoric world -- but, until now, were not believed to have emerged in East Asia until 30,000 to 40,000 years ago.

And now the, somewhat, startling conclusion:

With the find -- and absent human fossils linking the tools to migrating populations -- researchers believe people in Asia developed the technology independently, evidence of similar sets of skills evolving throughout different parts of the ancient world.

This particular conclusion seems somewhat ignorant of the fossil record, which clearly has hominins in the area that have distinct Neandertal traits.  The authors, in fact, even mention the possibility that the appearance of the tools might be tied to these earlier migrations, then seem to dismiss this for reasons that are, in my mind, not clear. 

The site, itself, Guanyindong Cave in Guizhou Province, is not new, having been excavated in the 1960s and 1970s.What is new is the date of 80-170 kya.  Levallois tools were thought to have arrived in the area around 30-40 kya and are seen as the artifacts of a late migration.  This re-dating of the sediments of Guanyindong Cave means that these kinds of tools were in the area some 100 ky earlier than was originally thought.  I do, however, think their evidence for independent origin is sparse. 

Modern Humans Interbred with Two Groups of Denisovans

There is now more evidence that were were “one big happy family.”  Here is a short recap:

Beginning around 1.8 million years ago, a hominin form called Homo erectus left Africa for points east, eventually settling in Indonesia and China. These early humans were characterized by having heads roughly ¾ the size of modern humans with very large brow ridges and with their widest point just above the ears. They were also the first humans to conquer fire and perfect hunting.

Then, at some point, between 300 and 500 thousand years ago, a population group migrated from North Africa into Europe and, eventually into East Asia. The European branch became the Neandertals, between 200 and 250 thousand years ago, and the East Asian group eventually became the Denisovans. The Denisovans then spread east and south, eventually mixing with other populations, some of which were the precursors of the Melanesians and native Australians. The bulk of the Neandertals hunkered down in Europe and tried to outlast the bitter cold of not one but two glaciations.  Despite this, while often pilloried in cultural literature as being half-witted brutes, Neandertals were a very complex society, with advanced weaponry and hunting behavior, grave goods, habitation structures and who practiced ritual behavior. Some populations of Neandertals eventually  expanded their range into Western Asia and steppic Russia and interbred with the Denisovans.  Unfortunately, as a culture, we know next to nothing about the Denisovans. 

Roughly 100 thousand years after this, there was yet another wave of migration, between 100 and 60 thousand years ago, of early modern humans from North Africa, who moved north and East mixing with both the Neandertals in Europe and, perhaps, Western Asia and the Denisovans in East Asia.

And now we learn that the modern humans arriving from Africa interbred with not one but two groups of Denisovans.  From Gizmodo:

We know so little about the Denisovans that they don’t even have a formal scientific name, though scientists are considering Homo sp. Altai or Homo sapiens ssp. Denisova. Indeed, as these names suggest, Denisovans were a branch of humans, having diverged from Neanderthals some 200,000 years ago. We know this because the Altai fossil yielded a near-complete genome, which scientists have been poring over since it was first sequenced in 2010.

But in addition to the Neanderthal ancestry, genetic anthropologists also learned that Denisovan DNA lives on in modern humans, especially among Oceanians and East and South Asians. This means anatomically modern humans, or Homo sapiens, must’ve interbred with a population of Denisovans. But as new research published today in the science journal Cell points out, our ancestors mated with Denisovans on at least two different historical occasions. So the traces of Denisovan DNA embedded in the genomes of some people living today originated from at least two distinct Denisovan populations.

Given Palaeolithic population densities, this is not surprising.The research seems to indicate that there were early modern human/Denisovan mixes in both Asia and Oceania.  What this means is that, once the Denisovans and Neandertals split, the Denisovans migrated east and northeast (as humans will do) and established population centers in these areas.  When the modern humans came (Huh.  I wonder what is over that hill?  Oh look, humans...sort of.) it made sense to intermingle with them.  We already know that Neandertals and modern humans could, and did, mix.  It is, absent any knowledge to the contrary, reasonable to assume that the Denisovans looked mostly modern human. 

Interestingly, the research seems to indicate that the rate of interbreeding of Neandertals to early moderns was much more limited than with moderns and Denisovans.  This is at variance with other studies (and fossil material) which seems to indicate more sustained contact.  It would be nice if we could find a bit more fossil evidence to get a handle on what at least one Denisovan looked like. 

Indian Site of Attirampakkam Pushes Middle Palaeolithic of India Back to 385 Kya

Great Googlymoogly!  Fresh on the heels of the discovery of the Misliya site (upcoming BioLogos post) that the Middle Palaeolithic Levallois technology was present in Israel as early as 194 thousand years ago, we now have news from India that places the emergence of the same technology as early as 385 thousand years ago.  From Malcolm Ritter at the site PhysOrg:

Homo sapiens arose in Africa at least 300,000 years ago and left to colonize the globe. Scientists think there were several dispersals from Africa, not all equally successful. Last week's report of a human jaw showed some members of our species had reached Israel by 177,000 to 194,000 years ago.

Now comes a discovery in India of stone tools, showing a style that has been associated elsewhere with our species. They were fashioned from 385,000 years ago to 172,000 years ago, showing evidence of continuity and development over that time. That starting point is a lot earlier than scientists generally think Homo sapiens left Africa.

This tool style has also been attributed to Neanderthals and possibly other species. So it's impossible to say whether the tools were made by Homo sapiens or some evolutionary cousin, say researchers who reported the finding Wednesday in the journal Nature.

Nowhere is there any indication that modern humans are associated with the tools at Attirampakkam (ATM). In fact, there are no hominin remains whatsoever at ATM. The Indian subcontinent has always had a paucity of human remains, the most notable of which is the Narmada Homo erectus cranium.  In Europe, the Levallois technology, which also shows up at ATM, is almost exclusively associated with Neandertals and in the Levant, at the Skhul, Qafzeh, Tabun and Amud sites in the Mt. Carmel region, it is used by both Neandertals and early moderns. Consequently, while someone was using early Middle Palaeolithic tools at ATM, we don't know who.

What is incredibly striking about the ATM site is that, from 385 ky down to 172 ky, there is continuous technological evolution, beginning with what the describers call the “terminal Acheulean,” through a punch flake industry with points, to knives.  Another point made by the authors is that this Middle Palaeolithic industry appears and flourishes during a time where other sites in India are still using Acheulean technology.  This suggests “that spatial variability among Palaeolithic cultural sequences is larger than previously thought.”  From the Nature article¹:

The behavioural transformations that mark the advent of the Indian Middle Palaeolithic at ATM are summarized by the following diagnostic features: the obsolescence of Acheulian large-flake reduction sequences, with a directional shift towards smaller tool components; the adoption and continuance of Levallois recurrent and preferential strategies; a gradual intensification of blade reduction; and an increased use of finer grained quartzite during phase II than during A gradual discontinuation of biface use—which becomes definite at ATM after approximately 172 ± 41 ka—has been reported at other Middle Palaeolithic and Middle Stone Age sites worldwide (see Supplementary Information and references therein).

This is an astounding find for so many reasons. It establishes the appearance of the Levallois technology, one we know originated in Africa, outside Africa over 150 thousand years earlier than we thought. This is a technology that was considered to have originated some 400 thousand years ago. We may now have to revise this date further into the past.

It shows a clear progression of human cultural evolution, from the late Acheulean hand axes, through Middle Palaeolithic Levallois technology to a more blade-oriented technology.  Sadly, it appears as though the site began to fall into disuse and the sequence stops cold around 74 kya.  This is not surprising since it coincides with the Toba supervolcano eruption in Indonesia.  Nonetheless, as the authors point out, it suggests multiple migrations out of Africa of first archaic Homo sapiens, then modern Homo sapiens, such as those in Misliya and that these groups interacted with the Archaic hominins they encountered along the way.

¹Akhilesh, K., Pappu, S., Rajapara, H. M., Gunnell, Y., Shukla, A. D., & Singhvi, A. K. (2018). Early Middle Palaeolithic culture in India around 385–172 ka reframes Out of Africa models. Nature, 554, 97. https://doi.org/10.1038/nature25444

Why Is Homo floresiensis Still Such a Mystery?

Cosmos Magazine has an article by Debbie Argue, biological anthropologist from Australian National University, about Homo floresiensis and why it has been a struggle to accurately and adequately place this hominin within the framework of human evolution.

 Here was the initial assessment:

Peter Brown and colleagues originally proposed two competing hypotheses about the origins of H. floresiensis. One is that the species is an early hominin similar to the earliest identified in the Homo genus. The fossils for these species are known only from Africa and are between one and two million years old. This implies that the ancestors of H. floresiensis could have got to Flores Island in the vicinity of a million years ago and survived there until at least 60,000 years ago.

Their alternative hypothesis was that H. floresiensis is a dwarfed descendant of Homo erectus, which is the only known non-sapiens hominin to once have existed in Indonesia. Its remains have been found on the island of Java. According to this view, the dwarfing of H. erectus was an evolutionary response to being isolated on an island with a limited food supply. Just as the Asian elephant evolved into the dwarfed Flores stegodon after becoming marooned on the island, H. erectus could have met a similar fate.

It was also proposed that this hominin might have expressed microcephaly.  This idea failed to explain other aspects of the skeleton, however, such as its diminutive height (around 3 feet), long arms and feet and primitive skull features. Here is an image of H. floresiensis compared to a modern human, who had been running around the landscape for at least 100k years while H. floresiensis was extant.

This all saw at least some resolution with the discovery and description of some remains  on another areas of the island Flores that were very similar to the H. floresiensis remains but dated to some 600 thousand years earlier than the remains in Liang Bu.  This lent more credence to the idea that H. floresiensis was, in fact, an offshoot of Homo erectus.

So, Argue, along with Colin Groves, Bill Jungers and Mike Lee, performed statistical tests (this story does not say which kind, a peculiar omission) on a number of different hominin species, comparing them to H. floresiensis.  What did they find?

We therefore hypothesise that H. floresiensis shared a common ancestor with H. habilis. We do not know who that ancestor was or when it lived, but it would have to be older than the oldest H. habilis specimen known, so older than 1.75 million years. The implication is that the H. floresiensis ancestor evolved before that time in Africa, dispersed from that continent, and arrived on Flores earlier than 700,000 years ago, judging by the age of the jaw and teeth found at Soa Basin. This represents a hitherto unknown movement of very early hominins out of Africa.

Presently, the earliest evidence for hominins outside of Africa come from Europe, the Near East and Asia, and date to between 1.5 and 1.8 million years ago. Argue's hypothesis would suggest that H. floresiensis appearance in east Asia represents a separate migration out of African sometime either before or after the wave that saw Homo erectus show up in Trinil and Sangiran, in Indonesia.

Questions still abound as to why this species never saw the evolutionary trajectory that other hominins went through in terms of cranial expansion, increase in height and changes in brachial and crural indices. On the other hand, if evolution proceeds through what we have termed systematics, then advanced traits will show up in related species and if the ancestors of H. floresiensis were cut off, they would just go on their merry way.  We know that such a pattern holds for H. naledi, in South Africa, which coexisted with archaic Homo sapiens, in some way, shape or form. 

The article ends on a very peculiar note, in which she suggests the remote possibility that H. floresiensis is still alive out there, somewhere:

Could the Hobbit still exist in the wild mountain forests of Flores? When H. floresiensis was announced, the media picked up on the local folklore that small human-like creatures roam the forests. Descriptions of sightings are well recorded and quite detailed. The similarity to H. floresiensis is intriguing. But most researchers would say ‘show me the bones!’

This reminds one of the stories involving the Yeti/Sasquatch/Abominable Snowman, which likely derive from the finding of the bones of the Miocene ape Gigantopithecus, which was close to ten feet tall, when standing.  Is H. floresiensis still out there?  Probably not, but I am sure that the cryptozoologists haven't given up hope. 

Did Humans Become a Distinct Species 350, 000 Years Ago?

The hits just keep on coming.  On the heels of the discovery in Morocco, at Jebel Irhoud, of a skull with some modern characteristics dated to 315 thousand years ago, we now have a genetic study that proposes that our species emerged between 350 and 260 thousand years ago.  How did a genetic study reveal this?  Science News reports:

The trick was retrieving a complete version of the ancient boy’s DNA from his skeleton to compare with DNA from people today and from Stone Age Neandertals and Denisovans. Previously documented migrations of West African farmers to East Africa around 2,000 years ago, and then to southern Africa around 1,500 years ago, reshaped Africans’ genetics — and obscured ancient ancestry patterns — more than has been known, the researchers report online September 28 in Science.

The ancient boy’s DNA was not affected by those migrations. As a result, it provides the best benchmark so far for gauging when Homo sapiens originated in Africa, evolutionary geneticist Carina Schlebusch of Uppsala University in Sweden and her colleagues conclude.

In line with the new genetically derived age estimate for human origins, another team has proposed that approximately 300,000-year-old fossils found in northwestern Africa belonged to H. sapiens (SN: 7/8/17, p. 6). Some researchers suspect a skull from South Africa’s Florisbad site, dated to around 260,000 years ago, qualifies as H. sapiens. But investigators often place our species’ origins close to 200,000 years ago (SN: 2/26/05, p. 141). There is broad consensus that several fossils from that time represent H. sapiens.

What is important to understand is that we have the fossils from Herto and Omo that date to between 150 and 200 thousand but that does not mean that is the earliest time that our species may have actually showed up. The Jebel Irhoud material is only partly modern—in the face mostly—and we do not know how the genetics for this population would look. It is possible that, as some investigators are saying, the Jebel Irhoud material represents the earliest fossil representation of our clade and that over the next 100 thousand years, the modern form fully evolved.   

More Evidence of Hybrization Between Archaics and Moderns in Africa

Nature's Research Highlights points to a paper written for the journal Genome Research, in which the authors, using whole genome analyses, argue that, for the first time, conclusive evidence of admixture between archaic Homo sapiens and early modern Homo sapiens occurred in Africa.  From the Nature blurb:

Michael Hammer at the University of Arizona in Tucson and his team analysed the entire genomes of seven individuals from two contemporary Western African Pygmy groups. The researchers identified 265 regions of the Pygmy genomes that may have been acquired through ancient interbreeding with other species, events that could have happened as recently as 9,000 years ago.

The article, itself, points out the nature of introgression in hominin evolution, thus:

Introgression, the transfer of genetic material between closely related species through hybridization, is an important and ubiquitous evolutionary force in both plants and animals (Mallet 2007). Although hybrids are often nonviable or infertile, hybridization can be an important driving force for the origin of novel traits and new species (Mallet 2007; Zinner et al. 2011). Within our genus, Homo, there is strong evidence for multiple introgression events between our own species, H. sapiens, and now extinct sister taxa outside Africa (Pääbo 2014). Neanderthal whole-genome sequencing (Green et al. 2010; Prüfer et al. 2014) revealed that Neanderthals contributed an average of ∼2% of the genetic variation of present-day humans living outside of sub-Saharan Africa. This gene flow likely took place 37–86 thousand yr ago (kya), after early modern humans emigrated from Africa and before archaic forms went extinct in Eurasia (Sankararaman et al. 2012), and it may have occurred multiple times (Vernot and Akey 2014, 2015; Kim and Lohmueller 2015).

It has been found, for example, that aspects of our immune system owe themselves to Neandertal introgression. This is an often overlooked aspect of how evolution proceeds.  There is continual debate about whether or not Neandertals represent a separate species from modern humans but the evidence that they interbred and exchanged genes is pretty good at this point.  The authors suggest that introgression of archaic genes occurred continually from the period of one million years down to less than 5 thousand years ago. That says something about the depth of the hybridization as well as the persistence of archaic genes in the modern human genome. 

New Investigations at the Sima de los Huesos Cave in Atapuerca: Kind of Neandertal and Kind of Not

Science Daily is reporting on a new paper in Science, about the conclusions drawn from the largest single cache of human remains in one place in Europe, the Sima de los Huesos cave, near Atapuerca, in Spain.  They write:

“With the skulls we found," co-author Ignacio Martínez, Professor of Paleontology at the University of Alcalá, added, "it was possible to characterize the cranial morphology of a human population of the European Middle Pleistocene for the first time.”

About 400 to 500 thousand years ago, in the heart of the Pleistocene, archaic humans split off from other groups of that period living in Africa and East Asia, ultimately settling in Eurasia, where they evolved characteristics that would come to define the Neandertal lineage. Several hundred thousand years after that, modern humans -- who had evolved in Africa -- settled in Eurasia, too. They interbred with Neandertals, but even then showed signs of reproductive incompatibility. Because of this, modern humans eventually replaced Neandertals.

This is the hybrid depression that I mentioned a few posts back.  This model fits the genetics information that was summarized by Dennis Venema in his BioLogos post on palaeogenomics from a few weeks ago.  It still also fits with the idea that modern humans swamped a Neandertal genome that was already subject to selective disadvantage.  Consequently, by around 27-29 ky BP, the last populations of Neandertals are, perhaps represented by Zafarraya, a late surviving Neandertal from the very southern coast of Spain. The idea that this Neandertal represents a refugium has been kicked around for decades. Critically, the earliest moderns in Central Europe predate this “last neandertal” by between five and nine thousand years and the evidence from Lagar Velho, in Portugal, indicates that hybridization was occurring as late as this. 

The Origins of Modern Humans, The Fossil Evidence, Part II

The second of my BioLogos posts on the fossil evidence concerning the origins of modern humans is up. 

BioLogos Post: The Origins of Modern Humans, Part 1 Is Up!

The first of three posts on the origins of modern humans is up over at BioLogos.  As always, comments are welcome there and here.

Next BioLogos Post is Up

Part two of the Dispersal of the Australopithecines is up over at BioLogos. This covers the south African forms as well as the extinction/disappearance of the australopithecines as a whole. Comments welcome.

Hominids Ahoy!

It turns out that archaic Homo sapiens or perhaps even Homo erectus may have actually taken to the water in some sort of light craft. Bruce Bower of ScienceNews reports:

Human ancestors that left Africa hundreds of thousands of years ago to see the rest of the world were no landlubbers. Stone hand axes unearthed on the Mediterranean island of Crete indicate that an ancient Homo species — perhaps Homo erectus — had used rafts or other seagoing vessels to cross from northern Africa to Europe via at least some of the larger islands in between, says archaeologist Thomas Strasser of Providence College in Rhode Island.

Several hundred double-edged cutting implements discovered at nine sites in southwestern Crete date to at least 130,000 years ago and probably much earlier, Strasser reported January 7 at the annual meeting of the American Institute of Archaeology. Many of these finds closely resemble hand axes fashioned in Africa about 800,000 years ago by H. erectus, he says. It was around that time that H. erectus spread from Africa to parts of Asia and Europe.

The barrier that separates modern human intellect from that of our forebears gets fuzzier and fuzzier. This is not too much of a surprise. We know that Homo erectus harnessed fire and had somewhat sophisticated hunting tools. They obviously had a pretty clear understanding of their environment and how to maximise their intelligence to their advantage. Almost twenty years ago, Milford Wolpoff suggested that we sink the name Homo erectus and incorporate all of the hominids identified as H. erectus into the taxonomic status of Homo sapiens. He suggested this because of the lack of a definite speciation break between erectus and archaic Homo sapiens (specimens such as Kabwe, LH 18, and Omo 1, for example) in the fossil record. This information reinforces that argument from a biocultural perspective.

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New Mystery Find in South Africa

Lee Berger and Francis Thackeray have found "something" in South Africa. They just ain't sayin' what. Times Online has the story:

Why the secrecy? Simply, when a major scientific breakthrough is made, it is essential to first fully describe it to the scientific community. A peer-review process is completed and publication in an international scientific journal acts as a seal of authenticity and scientific rigour. Prior publication of any kind might diffuse both the significance of the discovery and the perceived veracity of the subject matter.

That’s why whatever has been discovered in South Africa must remain a secret.

Lee Berger has long worked in the field of australopithecine ancestry so I am guessing this is a find on the order of the importance of the Ardipithecus ramidus find publicized a few days ago. We shall see.

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Out of Europe????

Bob Holmes of the New Scientist is reporting on a spectacular find in Spain of a 12 million year old primate that seems to show characteristics of both African and European Miocene apes. While the hype level is not as high as it was with Ida, the find raises some questions about where the later hominoids came from. He writes:

The fossil, named Anoiapithecus brevirostris by Salvador Moyà-Solà of the Catalan Institute of Palaeontology in Barcelona, Spain, and his colleagues, dates from a period of human evolution for which the record is very thin. While only the animal's face, jaw and teeth survive, their shape places it within the African hominid lineage that gave rise to gorillas, chimps and humans. However, it also has features of a related group called kenyapithecins.

Moyà-Solà says that A. brevirostris and some similar-looking kenyapithecins lived in Europe shortly after the afrohominid and kenyapithecin lineages split, and so that the divergence itself may have happened there. If he is right, our hominid ancestors lived in Europe and only later migrated to Africa, where modern humans evolved.

Methinks this is a tad premature, since we have Miocene apes on all continents and the remains are not as certainly diagnostic.



It will certainly get people thinking about primate origins in a new way.