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.

New Jebel Irhoud Date Causes Rethink of Chinese Dali Skull

Newsweek (Yes, that Newsweek) has a story on the reexamination of the Chinese Dali cranium, in light of the revised dates for the Jebel Irhoud skulls.  Kastalia Medrano writes:

Known as the Dali skull, it was discovered nearly 40 years ago in China’s Shaanxi province. It belonged to a member of the early hominin species Homo erectus. Its facial structure and brain case are intact, despite being dated to around 260,000 years ago. The Dali skull is so old that archaeologists initially didn’t believe it could share features with the modern Homo sapiens.

But Xinzhi Wu of the Chinese Academy of Sciences in Beijing believed that due to the overwhelming physical similarities, Homo erectus must have shared DNA with Homo sapiens. After decades of this idea being dismissed by mainstream academia, Wu and a colleague, Sheela Athreya of Texas A&M University, recently reanalyzed the Dali skull and found it may force us to rewrite our evolutionary history after all. It’s incredibly similar to two separate Homo sapiens skulls previously found in Morocco. “I really wasn’t expecting that,” Athreya told New Scientist.

If we’d found only the Moroccan skulls, and not the Dali skull, it would make sense to keep believing all modern humans evolved in Africa. But the similarities show that early modern humans may not have been genetically isolated from other parts of the world, like what we know today as China.

“I think gene flow could have been multidirectional, so some of the traits seen in Europe or Africa could have originated in Asia,” Athreya told New Scientist.

Okay, now the nuts and bolts.Dali has always been thought to occupy that rarified space between Homo erectus  and early modern Homo sapiens.  It was always thought to be between 200 and 250 kya, and optically-stimulated luminescence dating (a variant of thermoluminescence) places it between 258 and 267 kya.  My analyses of the skull suggested that it was, in no way, shape or form, a modern human but it did not tend to cluster with the Neandertals in terms of head shape.  Athreya and Wu have done an extensive multivariate analysis and conclude (from the article, likely behind a paywall:

When just the facial skeleton is considered, Dali aligns with Middle Paleolithic H. sapiens and is clearly more derived than African or Eurasian Middle Pleistocene Homo. When just the neurocranium is considered, Dali is most similar to African and Eastern Eurasian but not Western European Middle Pleistocene Homo. When both sets of variables are considered together, Dali exhibits a unique morphology that is most closely aligned with the earliest H. sapiens from North Africa and the Levant.

These results add perspective to our previous view of as Dali a “transitional” form between Chinese H. erectus and H. sapiens. Athough no taxonomic allocation is appropriate at this time for Dali, it appears to represent a population that played a more central role in the origin of Chinese H. sapiens. Dali's affinities can be understood in the context of Wu's Continuity with Hybridization scenario and a braided-stream network model of gene flow. Specifically, we propose that Pleistocene populations in China were shaped by periods of isolated evolutionary change within local lineages at certain times, and gene flow between local lineages or between Eastern and Western Eurasia, and Africa at other times, resulting in contributions being made in different capacities to different regions at different times.

In combination with the Xuchang remains, the reanalysis of this skull suggests that, indeed, there is a long and complex interrelationship between different hominin groups that dates back some 400 thousand years. From the paper:

In the braided-stream network model, evolutionary change in China was the result of a shifting network of gene flow among distinct regional Chinese populations, as well as between Chinese and Western Eurasian populations. These were not isolated evolutionary lineages; gene flow both within China and between Eastern Eurasia, Western Eurasia and Africa was intermittent and could explain the similarities in aspects of the neurocranium found here between Dali and Western Eurasian Middle Pleistocene humans. Gene flow would best be described as a braided stream network with periods of isolated evolutionary change within a local lineage at times, and periods of gene flow between local lineages or paleo-demes at other times, resulting in contributions being made in different capacities to different regions at different times.

It is pretty clear that our simplistic models of Recent African Replacement and Multiregional Evolution need to be reworked. It is becoming more apparent that what we are looking at either a polytypic species with a huge geographical range or a syngamion of related species that intermixed regularly. The Xuchang skulls were, apparently, not unique.

Neandertal to Modern Transition Full of Fits and Spurts

New evidence suggests that Neandertals survived longer on the Iberian peninsula than elsewhere in Europe.  The redating of the Zafarraya Neandertal from the late 20k's to between 38 and 40 ky saw a revision of theories about Neandertal extinction. Now more evidence has been unearthed suggesting that this window is more secure.   From The Statesman:

Neanderthals may have survived at least 3,000 years longer than thought in what is now Spain – much after the species had died out everywhere else, a study has found.

The findings suggest that the process of modern human populations absorbing Neanderthal populations through interbreeding was not a regular, gradual wave-of-advance but a “stop-and-go, punctuated, geographically uneven history.”

Over more than ten years of fieldwork, researchers excavated three new sites in southern Spain, where they discovered evidence of distinctly Neanderthal materials dating until 37,000 years ago.

“Technology from the Middle Paleolithic in Europe is exclusively associated with the Neanderthals,” said Joao Zilhao, from the University of Barcelona in Spain.

“In three new excavation sites, we found Neanderthal artefacts dated to thousands of years later than anywhere else in Western Europe,” said Zilhao, lead author of the study published in the journal Heliyon.

It seems pretty clear now that the model of rapid replacement of Neandertals does not hold. This kind of evidence, along with sites such as Lagar Velho, suggest that the transition, at least in this region was long-term, with much hybridization.  We still do not know exactly how long Neandertals persisted in this region.  It makes perfect sense that they would have been the last ones to undergo the transition (however that happened) because the earliest Aurignacian sites, associated with modern humans, occur in far eastern Europe as the wave of moderns came through during the Würm I/Würm II interglacial.

The question that I have is why didn't the earliest modern humans, represented by the Jebel Irhoud remains, come through the Strait of Gibraltar?  North of that, all you find are archaic, all the way down to the Zafarraya remains.  I wonder why this is.

Neandertals and Modern Humans Had Longer Period of "Intimate" Contact

New research suggests that the earliest time that Neandertals and moderns humans got jiggy with it was around 100,000 years ago.  This is a break from the conventional (if you can call an argument five years old “conventional”) argument that most of these interactions occurred between 50 and 60 thousand years ago.  According to Jennifer Viegas, in Discovery News:

Remains of a Neanderthal woman who lived around 100,000 years ago in the Altai Mountains of Siberia reveal that human and Neanderthals mated much earlier than previously thought.

One or more of her relatives were actually humans, a new study shows.

It has been known that Neanderthals contributed DNA to modern humans, so people today of European and Asian descent retain Neanderthal DNA in their genomes, but the Neanderthal woman offers the first evidence that gene flow from interbreeding went from modern humans into Neanderthals as well.

The study, published in the journal Nature¹, "is also the first to provide genetic evidence of modern humans outside Africa as early as 100,000 years ago," Sergi Castellano, who co-led the study and is a researcher at the Max Planck Institute for Evolutionary Anthropology, told Discovery News.

Given the now closely intertwined histories of Neanderthals and Homo sapiens, Castellano added that "it is better to refer to Neanderthals and modern humans as two different human groups, one archaic and one modern, and not different species."

This last point is hotly contested. The prevailing wisdom is that they were two different species that could interbreed when they came into contact but had their own stable genomes. If the time of contact can be stretched from 100 kya to 50 kya, though, it lends more credence to the ideas that their lifestyles were largely compatible, especially given the new information from Schöningen, which seems to indicate complex patterns of subsistence emerging as early as 300 kya. Oddly, missing from the story is that the researchers suggest that these hybridizations may have occurred in the ancestors of the Neandertals in Southwest Asia, not northern Europe.  This would one of the natural corridors for people coming out of Africa, although recent research has focused on the Arabian peninsula for that migration.

¹Kuhlwilm, Martin, Gronau, Ilan, Hubisz, Melissa J., de Filippo, Cesare, Prado-Martinez, Javier, Kircher, Martin, Fu, Qiaomei, Burbano, Hernán A., Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajkovic, Dejana, Kucan, Željko, Gušic, Ivan, Marques-Bonet, Tomas, Andrés, Aida M., Viola, Bence, Pääbo, Svante, Meyer, Matthias, Siepel, Adam, & Castellano, Sergi. (2016). Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530(7591), 429-433.
http://dx.doi.org/10.1038/nature16544

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. 

Todd Wood on the Neandertal Interbreeding Question

Todd Wood has weighed in on the Neandertal hybridization results in ArXiv with some of his own thoughts and he raised the spectre of incomplete lineage sorting...something that entirely escaped my thought process when I was waxing about the ArXiv paper yesterday. But as he, himself, points out, there are problems with this explanation. He writes:

Since incomplete lineage sorting is a random process, I would not expect to see any modern human population significantly more similar to Neandertals than any other modern human population. Modern human populations diverged well after the Neandertal divergence, so whatever genes were still very similar to Neandertals should have been evenly divided. Even more interesting is the geography: the ancestors of the modern humans with Neandertal-like genes come from the same geographic region as the Neandertals. If incomplete lineage sorting is to blame for Neandertal-like genes in modern humans, that geographic pattern would just be a weird coincidence. That's not to say that one couldn't make a case for incomplete lineage sorting, but we would need some new evidence to really seal the deal (such as new samples of Eurasians that don't have Neandertal-like genes or Africans that do).

He is right. If modern humans and Neandertals diverged as much as 250 ky BP as many people think, then drift would ensure that the two genomes would be more highly divergent than they appear to be. He is also correct about the geographical coincidence. As I wrote yesterday, the interbreeding conclusion would tend to be supported by the appearance of Neandertal-reminiscent traits in the earliest moderns from the area.

The authors argue that linkage dis-equilibrium, which is when you have allele combinations that are present in two related populations in higher percentages than can be accounted for by chance, supports the recent interbreeding model, a conclusion that Wood agrees with (although how a young-earth creationist can agree with that kind of model, I will never know).

Archaeological Evidence: Neandertals and Modern Humans Interacted and Interbred

The Newsroom at the University of Colorado has released news of a study that links the archaeological evidence in Europe with Neandertal/early modern human interaction and, probably, interbreeding. They write:

Anthropologists using computer modeling to determine how early hominins adapted to climate change during the last Ice Age, have gained new insights into why Neanderthals disappeared as a distinct population some 30,000 years ago.

The scientists believe Neanderthals interbred with more numerous modern humans until they ceased to exist as their own population.

This is called "gene swamping" and is not uncommon. The authors further argue:

“Neanderthal genes make up between one and four percent of today’s human genome, especially in those of European descent. Their legacy lives on in our genome and possibly in our cultural knowledge.”

Modern humans begin to show up in Europe during the Early Würm/Late Würm glaciation, between 35 and 40 thousand years B.P. A good representation of these hominins are those from the cave of Mladeč, which, while being classified as modern humans, have characteristics reminiscent of Neandertals. Even the later hominins such as those from the central European site of Dolní Vĕstonice, show archaic characteristics such as expanded occipital buns (a bulge at the rear of the vault). This all makes sense within the context of hybridization between the two groups of people. Fred Smith was right.

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Dear Svante, I am a Neandertal

The Guardian's Notes and Theories has a column on the mail that Svante Pääbo received after delivering the revelation that Neandertals and Early modern humans interbred. They write:

In the months after the paper was published, Pääbo began to receive letters and emails from people who had read about the work. He decided to keep track of the correspondence, at least until September that year, to see if any trends appeared. He wasn't disappointed.

Some 45 men wrote in to declare themselves fully or partially Neanderthal and several asked if they should provide saliva samples for Pääbo to analyse. Over the same few months, only two women wrote in to declare themselves of Neanderthal stock.

I think that it was Dave Frayer who once said that, on an individual trait basis, you could see the remnants of Neandertals in the modern European populations but that if you took the whole suite of Neandertal traits, there wasn't a person alive who had them. I wonder what led the women to think they were Neandertals? “Evening vear. Svimvear. Very nice!”

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More on the Neandertal/Modern Link

The Independent has an article on the Neandertal/modern human link, called Making Woopee with Neandertals. Steve Connor writes:

The latest study aimed at answering this question suggests the latter – when Neanderthal man met Homo sapiens woman it resulted in what scientists euphemistically call "gene flow". It seems that this interbreeding, which probably took place somewhere in the Middle East when the first modern humans migrated out of Africa, has resulted in a little bit of Neanderthal in all of us today with a non-African ancestry.

The story also shows how hard it can be do science:

This enabled them to compare the Neanderthal genome with that of five modern-day people from around the world, and, to Paabo's astonishment, Neanderthal DNA sequences were found in the genomes of the three people who lived outside Africa. Paabo freely admits that he was biased against such a finding. His earlier work on mitochondrial DNA suggested no such interbreeding between Neanderthals and modern humans, so his initial reaction was that the data had to be a statistical fluke, or erroneous.

But it is a measure of greatness in science if you can accept something that you had previously rejected, when faced with new and convincing evidence.

Comparisons between the genomes of modern humans and the Neanderthals clearly indicated that there was a small but significant amount of interbreeding early in the evolutionary history of Homo sapiens, most probably after our species had first emerged from Africa between about 80,000 and 50,000 years ago. Other scientists, such as Professor Joao Zilhao of Bristol University, who has long argued that there was close cultural and biological interaction between Neanderthals and modern humans, can rightly feel vindicated for their somewhat unfashionable stance.

This shows two things:

1. it shows how science can and should be done. New information should always be incorporated into the existing framework of a particular discipline. On one side of the fence, there is the perspective that Neandertals were replaced by early modern humans that came from North Africa. On the other side is the idea that Neandertals interbred with the incoming moderns and that the modern Europeans are a result of this hybridization. Maybe the answer lies somewhere in between. As Jan Simek once put it, maybe there was hybridization here in this valley but replacement two valleys over. It is becoming increasingly clear that the transition to modern humans was neither simple nor quick.

2. it shows how stark the contrast between conventional science and young earth creationism really is. For YECs, there are no new ideas or hypothetical constructs to be tested. Data that does not fit the model must be shoehorned, twisted or distorted to fit or else be ignored, as much data is. The ability to take a favored concept or theory and rethink it based on new ideas or new information is the hallmark of science, not creationism.

This new finding shows how science progresses and how only by adding the new information to the mix will we ever be able to understand the transition to modern humans. As such, it enriches our understanding of modern human ancestry in particular and the universe in general.

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Neandertal, Early Modern Hybridization

The Telegraph has a story about research indicating a shared history between Neandertals and early modern humans. This story appeared a few days ago in the New York Times. I did not link to this. Richard Alleyne, the Telegraph science correspondent writes:

Human-Neanderthal relations occurred as the first pioneering bands of homo sapiens ventured out of Africa, scientists believe.

When they reached the Middle East they ran into groups of Neanderthals who preceded them and it is now thought that they mated.

The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree.

Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

This is support for the contention of Erik Trinkaus that the Lagar Velho burial in Portugal reflects hybridization, as well as the findings of Dave Frayer and Fred Smith, who have long argued that the early modern humans in Europe from Mladec, Stetten, Predmosti and several other sites have traits present in their Neandertal antecedents from the area. This will certainly add fuel to the fire in the continuity/replacement debate concerning the appearance of modern humans.

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