Another Mystery Ancestor Joins The Group

Science Daily has a story on genetic work done by researchers at Cornell University and Cold Spring Harbor Laboratory that suggests that there is, as yet, another unnamed ancestor to the modern human line. They write:

In the new paper, the researchers developed an algorithm for analyzing genomes that can identify segments of DNA that came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source. They used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans. The researchers found evidence that 3 percent of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago. Furthermore, 1 percent of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these "super-archaic" regions may have been passed down to modern humans who are alive today.

The paper is available in PLoS Genetics, which means that it is free to the public.  The above-description makes it sound like bootstrapping on stilts.  Here is a paragraph from the paper, itself, that describes the process:

In this paper, we describe a powerful and highly general new method, called ARGweaver-D, that samples ancestral recombination graphs (ARGs) [18–20] conditional on a generic demographic model, including population divergence times, size changes, and migration events. After introducing ARGweaver-D, we present simulation studies showing it can successfully detect Nea→Hum introgression, even when using a limited number of genomes, and that it also has power for older migration events, including Hum→Nea, Sup→Den, and Sup→Afr events. Finally, we apply this method to modern-day Africans and ancient hominins, and characterize both new and previously reported cases of introgression between humans and archaic hominins.

Okay, it still sounds like bootstrapping on stilts.  I am not sure how you can do a simulation to detect older migration events when that is what you are looking for in the first place.  What exactly is an ancestral recombination graph, you ask?  From a previous paper on this subject:

It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences.

The best data we have suggests that Neandertals and African archaics split some 600 ky ago when a group of Homo ergaster migrated out of Africa and took up residence in western Europe, leading to branching events that eventually included H. antecessor and the Neandertals.  This is supported by this research, which found about 7% introgression into the Neandertal genome of archaic H. sapiens.  The surprise was that 1% of the Denisovan genome likely came from an, as yet, undiscovered hominin.  

Increasingly, there is evidence that considerable interbreeding occurred throughout the middle to late Pleistocene, continuing through the interbreeding that occurred in China and Europe.  As I wrote about the 105-130 ky old Chinese Xuchang skulls:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

This likely represents only a small part of the vast scope of population mixing. I will be curious to see where the ARG research leads.

Denisovans More Closely Related to Modern Humans than Neandertals

Science Daily has a post relating recent research on the genetic studies involving the Denisovan material from Siberia.  The research, done by CNRS in France has this to report:

Now a team of scientists from the Institut Jacques Monod (CNRS / Université de Paris) has measured and photographed another fragment found in Denisova Cave. Genomic analysis reveals it is the missing piece of the same phalanx whose proximal fragment enabled initial sequencing of the Denisovan genome.

Together with colleagues from the PACEA laboratory (CNRS / University of Bordeaux / French Ministry of Culture) and the University of Toronto (Canada), the scientists compared the new fragment to the phalanges of Neanderthals and anatomically modern humans. Their analysis indicates it is very close to the latter, and less like the former..

This research suggests that there was considerable population mixing and genetic variability in this population, given the news that came out last year detailing the finding of a child skeleton that was, as nearly as the researchers could tell, the offspring of a Neandertal and a modern human.This just continues to solidify the idea that these groups interbred routinely throughout the late Pleistocene. 

More Information About the Denisovans

Discover Magazine has an article on new finds at Denisova and their context in early modern human evolution.  Bridget Alex writes:

Nestled in foothills of Russia’s Altai Mountains, Denisova Cave has been a research mecca since 2010, when fossil DNA from the site revealed a previously unknown human lineage, now called the Denisovans. Scientists have been working hard to reconstruct the cave’s history, through ongoing excavations as well as new analyses of materials recovered years ago.

First, what everyone wants to know: Yes, they found more human remains. In addition to the four Denisovan specimens (one pinky finger, two adult molars and a baby tooth), the cave has yielded 12 fossils from ancient humans, including teeth, toes, fingers and unclassifiable fragments.

Based on their genomes, proteins and physical appearance, the collection contains four Denisovans, three Neanderthals and one hybrid cross between the two human types. Excavators have also found four more fossils that belong to the Homo genus, but haven’t yet been assigned to a particular human species. Additional DNA sequences, recovered directly from the dirt, suggest the presence of even more individuals.

As reported last year, Denisova 11 has been determined to be the offspring between a Neandertal mother and Denisovan father. As with other finds in Asia, we are finding that there appears to have been considerable population mixing over the course of at least 100 thousand years. Although the article indicates that the Neandertals were “sandwiched” in between two modern human occupations, that is difficult to square with any hybridization model. I suspect that the habitation patterns were more complex.

DNA Proteins Revealing Information About Human Evolution

Since the advent of population genetics and modern techniques to examine DNA, research has focused on, first, Mitochondrial DNA and then nuclear DNA.  Now we have another weapon in our arsenal.  Matthew Warren of Nature News relates new research done on palaeoproteomics.  This is the study of proteins found in fossilized human ancestors.  How is this possible, you ask?

Some time in the past 160,000 years or so, the remains of an ancient human ended up in a cave high on the Tibetan Plateau in China. Perhaps the individual died there, or parts were taken there by its kin or an animal scavenger. In just a few years, the flesh disappeared and the bones started to deteriorate. Then millennia dripped by. Glaciers retreated and then returned and retreated again, and all that was left behind was a bit of jawbone with some teeth. The bone gradually became coated in a mineral crust, and the DNA from this ancient ancestor was lost to time and weather. But some signal from the past persisted.

Deep in the hominin’s teeth, proteins lingered, degraded but still identifiable. When scientists analysed them earlier this year, they detected collagen, a structural support protein found in bone and other tissues. And in its chemical signature was a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals — instead, it flagged the jawbone as belonging to a member of the mysterious hominin group called Denisovans. The discovery of a Denisovan in China was a major landmark. It was the first individual found outside Denisova Cave in Siberia, where all other remains of its kind had previously been identified. And the site’s location on the Tibetan Plateau — more than 3,000 metres above sea level — suggested that Denisovans had been able to live in very cold, low-oxygen environments.

As the author notes, this kind of research has opened many other doors that, up until now, have been shut to researchers. The realization that proteins have much longer staying power than DNA could radically reshape our understanding of human evolution:

Previously, scientists had recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. Now, they hope that palaeoproteomics could be used to provide insights about other ancient hominin fossils that have lost all traces of DNA — from Homo erectus, which roamed parts of the world from about 1.9 million to 140,000 years ago, to Homo floresiensis, the diminutive ‘hobbit’ species that lived in Indonesia as recently as 60,000 years ago. By looking at variations in these proteins, scientists hope to answer long-standing questions about the evolution of ancient human groups, such as which lineages were direct ancestors of Homo sapiens.

Whether that level of resolution will ever be possible remains to be seen, especially given that the modus operandi of modern palaeontology is focused on clade relationships. It will be interesting to see.

More Information From Denisova

Nature News is reporting about some more evidence from Denisova, following up on the bombshell news last year that bones discovered there belonged to a person (who they named “Denny”) who's father was a Denisovan and mother a Neandertal. From the story:

In the years that followed the discovery of Denisovans, scientists used DNA sequencing to attribute a few molar teeth from the cave to the same group4. They have also found other remains that harboured Neanderthal DNA. The analysis of Denny fills in some important details about the two groups. “We knew that Denisovans and Neanderthals had been there. We just didn’t think they interacted this intimately,” says [Svante] Pääbo. “It was so amazing to find direct proof — to find these people in the act, almost, of mixing.”

Denny’s discovery has also convinced Pääbo and other scientists that the remains of similar individuals, with recent ancestry from two groups of hominin, will be found — perhaps also in Denisova Cave. Researchers who analysed Denny’s genome found signs that the chromosome set that was contributed by her father, although clearly Denisovan, harboured some Neanderthal ancestry, which hints at earlier encounters between the groups2. “We should be able to pick up these individuals,” says [Katerina] Douka.

The Denisova cave appears to have been occupied for several hundred thousand years, being originally settled by either Denisovans or Neandertals, no one is sure which. Subsequent to this, it is unclear how much interbreeding actually occurred. 

“It’s still a head scratcher,” adds Tom Higham, an archaeological scientist at the University of Oxford, UK, who works with Douka and Brown. “It’s either an incredible piece of luck, or interbreeding happens so frequently that we might expect to find these types of occurrence in the archaeological record.”

One thing becomes increasingly clear with each new discovery, however: the complete replacement model of modern human origins, as espoused by Stringer and Andrews, is dead.

Neandertal/Denisovan Hybrid?

As J. Lawrence Angel once said: “When two groups of people meet, they may fight, but they will always mate.”  A story is now coming out of Russia describing more research at the Denisova Cave, in the Altai Mountain region that recounts exactly what Angel was talking about.  From Richard Coniff, at Scientific American:

In a remarkable twist in the story line of early human evolution, scientists have announced the discovery of “Denisova 11”—a female who was at least 13 years old, lived more than 50,000 years ago and was a child of mixed parentage. Her parents were not just of different races, but two different and now-extinct early human types. Their exact taxonomic designations—whether they were separate species or subspecies—is still a matter of scientific debate. But the bottom line for Denisova 11 is that mom was a Neandertal and dad a Denisovan.

This is a remarkable claim, similar to the one that Erik Trinkaus made about the Lagar Velho child discovered in Portugal that is thought to be a Neandertal/modern human offspring. What evidence has been marshalled to support this claim?  In a word: genetics.  The evidence is taken from another bone fragment from the site.  From the abstract:

The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave. The mother came from a population more closely related to Neanderthals who lived later in Europe than to an earlier Neanderthal found in Denisova Cave, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

So, if they interbred regularly (or regularly enough, anyway), why aren't they just one species?  Svante Paabo argues that it is because they simply did not come together very often.  To this, I would argue that they probably also had fairly distinct cultures. 

If this kind of information had come out a few decades back, there would have been quite a few squawks and naysayers but as the evidence piles up for hybridization between many different groups throughout the Pleistocene, researchers have become more accepting of it.  It is pretty clear that the evolutionary picture was a whole lot more complex than we thought. 

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.   

Scientists Use Revolutionary Technological Advance to Locate Human DNA

The Telegraph (and other outlets) are reporting on an incredible breakthrough that allows the recovery of human DNA from sediment where no actual human fossil remains exist:

The researchers collected 85 sediment samples from seven caves in Europe and Russia that humans are known to have entered or even lived during the Pleistocene, between 14,000 and 550,000 years ago.

By refining a method previously used to find plant and animal DNA, they were able to search specifically for genetic material belonging to ancient humans and other mammals.

"This work represents an enormous scientific breakthrough," said Antonio Rosas, scientist at Spain's Natural Science Museum in Madrid.

"We can now tell which species of hominid occupied a cave and on which particular stratigraphic level, even when no bone or skeletal remains are present."

Scientists focused on mitochondrial DNA, which is passed down the maternal line, because it is particularly suited to telling apart closely related species. By analysing damaged molecules they were able to separate ancient genetic material from any contamination left behind by modern visitors.

It is difficult to overestimate the importance and impact this will have on the anthropological world. This technique will allow us to reconstruct migration routes, occupational histories, times of first appearance in an area and many other aspects of Neandertal, Denisovan and modern human demography.This will open doors to research that we can only begin to imagine.

Another Human Species in China?

The Christian Science Monitor and other outlets are reporting on a new find from Xuchang, China, that seems to possess intermediate traits between archaic and modern Homo sapiens:

In an article published Friday in the journal Science, the researchers note that the skull fragments date to the Late Pleistocene epoch, a time marked by the expansion of H. sapiens and the extinction of other species in the genus Homo. During the early part of that epoch, Neanderthals roamed Europe and western Asia while humans began to journey out of Africa. But fossil records of human species in Eastern Asia from that time period are thin, muddying the picture of that era for a substantial region of the planet.

The skulls found in China were found to bear very close resemblances to those of Neanderthals, including a very similar inner ear bone and a prominent brow ridge. But the brow ridge was much less pronounced than one would expect from Neanderthals, with a considerably less dense cranium, as one might expect in an early H. sapiens. Researchers also found that the skulls were large by both modern and Neanderthal standards, with a whopping 1800 cubic centimeters of brain capacity.

So where do they fit in the grand scheme of things?

"The overall cranial shape, especially the wide cranial base, and low neurocranial vault, indicate a pattern of continuity with the earlier, Middle Pleistocene eastern Eurasian humans. Yet the presence of two distinctive Neanderthal features ... argue for populational interactions across Eurasia during the late Middle and early Late Pleistocene," said Dr. Trinkaus in a statement.

This kind of population mixing makes sense. We already know that modern humans and Neandertals interbred in Europe and that the geographic range of Neandertals stretched from Portugal to Teshik Tash, in Russia and Shanidar Cave, in Iraq.

The remains are dated to Marine Oxygen Isotope Stage 5d or 5e, making them between 105 and 125 ky in age.  Here is a description of the neurocranium from the paper:

The large Xuchang 1 neurocranium closely approximates the shapes of those of Middle Pleistocene humans, especially eastern Eurasians (Fig. 2 and fig. S17). The vault height is low, similar to those of the Neandertals and the higher Middle Pleistocene vaults, and the low vault height is reflected in a low temporal squamous portion (figs. S27 and S28). It is also produced by the very flat midsagittal parietal arc. In contrast, the maximum cranial breadth is the largest known in the later Pleistocene (fig. S15), and it is securely based on an undistorted posterior cranium. Moreover, the widest point is low, on the temporal bones (fig. S17), as in most earlier crania, rather than on the parietal bones, as among Neandertals and most modern humans. In addition, the one complete mastoid process is short and slopes inward (fig. S17), rather than being longer and more vertical, as in modern humans and some Neandertals. These features combine to provide the cranium with an occipital profile similar to those of earlier human crania, contrasting with the rounded profiles of Neandertals and the laterally vertical ones of modern humans.

There are a few things that are immediately interesting about this. First, this skull is YUGE.  1800 cc is monstrous.  The average cranial capacity of modern humans is around 1450 cc and that of Neandertals, around 1550 cc.  Second, the low, flat cranium with the widest point on the temporal bones (just above your ears) are traits of Homo erectus, not modern humans or Neandertals, suggesting strongly that there was some sort of continuity from this group through to modern humans in this region.  Neandertals simply don't have those traits.  Nonetheless, the cranium clearly shows some Neandertal traits in the ear and rear of the vault.  This continuity is characterized by the authors thus: "This morphological combination, and particularly the presence of a mosaic not known among early Late Pleistocene humans in the western Old World, suggests a complex interaction of directional paleobiological changes and intra- and interregional population dynamics."  As more information becomes available, we will have a better idea of how this find fits in the east Asian evolutionary picture.  This is exciting.  Up until this point, we have had very few finds in China that fall within this general time frame, most notably the Dali and Mapa remains.  I will have to rework my section on human origins for the BioLogos site for this region. 

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. 

Nuclear DNA From the Simo de los Huesos Fossil Material

Nature has a paper that focuses on DNA that has been extracted from the Sima de los Huesos fossil material from the site of Atapuerca, in northern Spain.  The letter does not appear to be behind the pay wall, at the moment.  In 2014, researchers completed a mitochondrial genome sequence for a hominin and the results were interesting, to say the least.  Here is the abstract from the 2014 paper:

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene¹. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils^{2, 3}, consisting of at least 28 individuals⁴ dated to over 300,000 years ago⁵. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits^{6, 7, 8}. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans^{9, 10}, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

The authors argued at the time that Denisovans and the population from Sima de los Huesos shared a common ancestor, with a split of about 700 kya, and that both are more closely related to each other than either is to Neandertals.  This strongly suggests that Neandertals are a later derivation from a common crown group that represented the progenitors of all three groups.  The authors suggest that these findings are unexpected because of the incipient Neandertal traits found in the Sima collection, including occipital bunning in the back of the head and some mid-facial prognathism (it looks like the maxilla is puffed out).  Arsuaga and others have stated previously that they thought all of the Sima de los Huesos material belonged to the Neandertal lineage. That, apparently, is not the case.  As these authors point out, there may have been more than one evolutionary lineage roaming the valleys and forests of Europe.

Now the nuclear DNA has been  sequenced and these results strongly suggest that the people represented by the SH population were, in fact, early Neandertals.  From the paper by Meyer et al:

The nuclear DNA sequences of femur AT-5431 and the incisor show that they belonged to the Neanderthal evolutionary lineage, and the limited data available for the molar suggest that the same is true for this specimen. Thus, the results show that the SH hominins were early Neanderthals or closely related to the ancestors of Neanderthals after the divergence from a common ancestor shared with Denisovans. Although it is difficult to determine the age of Middle Pleistocene sites with certainty, geological dating methods¹, as well as the length of the branches in trees relating the mtDNAs from femur XIII and an SH cave bear to other mtDNAs^{2, 12}, suggest an age of around 400,000 years for the SH fossils. This age is compatible with the population split time of 381,000–473,000 years ago estimated for Neanderthals and Denisovans on the basis of their nuclear genome sequences and using the human mutation rate of 0.5 × 10⁻⁹ per base pair per year⁷

These authors now suggest that, in combination with the MtDNA results from last year, that the SH hominins are ancestral to Neandertals and that the MtDNA found in later Neandertals is derived relative to that in the SH hominins and that the SH hominins may have had several different MtDNA strands. 

It appears that the evidence supports a model in which the classic Neandertals from France and Germany, which are dated to between 50 and 70 kya, represent a more stabilized, homogenous genome relative to that of earlier hominins.  I have always been struck by the similarities between the Atapuerca 4 cranium and Petralona, from Greece, and this suggests that there may have been extensive migration between regions and considerable gene flow between groups (J. Lawrence Angel, again).  We know that the range of Neandertals extended from the lower Iberian peninsula to Teshik-Tash, north of the Taurus Mountains and Okladnikov, in Siberia.  It does not seem like a stretch that their precursors did the same thing. 

Hat tip to Todd Wood.

40,000 Year-Old Bracelet Found at Denisova Cave

A bracelet has been discovered at the site of Denisova Cave that excavators have dated to c. 40,000 years BP.  Archaeology Hub has the story:

In what is quite an amazing discovery, scientists have confirmed that a bracelet found in Siberia is 40,000 years old. This makes it the oldest piece of jewelry ever discovered, and archeologists have been taken aback by the level of its sophistication.

The bracelet was discovered in a site called the Denisova Cave in Siberia, close to Russia’s border with China and Mongolia. It was found next to the bones of extinct animals, such as the wooly mammoth, and other artifacts dating back 125,000 years.

The cave is named after the Denisovan people — a mysterious species of hominins from the Homo genus, who are genetically different from both Homo sapiens and Neanderthals.

Here is the image of the bracelet from this site:

We know very little about the Denisovans, except that they coexisted with Neandertals and early modern humans and that their genetic fingerprint is present in modern-day Melanesian populations.  Here is a link to the National Geographic special that was done a few years back that covers the basics behind these mysterious hominins.  This find gives us a window into their culture. 

New DNA Information From Denisova Teeth

Many news outlets are reporting on new findings from the Denisova teeth that were discovered a few years ago.  Here is what the Chicago Tribune has to write:

According to a new analysis of a huge, recently-discovered fossilized molar, published Monday in the journal Proceedings of the National Academy of Sciences, the Denisovans lived for roughly 60,000 years in Asia alongside both Neanderthals, their close cousins, and more distantly related Homo sapiens - us. Their complicated genetic legacy suggests that they interbred with both species, and, possibly, with another hominid group that has yet to be discovered.

"The world at that time must have been far more complex than previously thought," Susanna Sawyer, an author of the study, told National Geographic. "Who knows what other hominids lived and what effects they had on us?"

It is taking us a bit long to wrap our brains around the fact that we are the only version of Homo on the planet now and have been for probably fifty thousand years. Prior to our ascendancy, there may well have been three or four related species—part of a syngameon—that occupied the landscape at approximately the same time and, as the researchers point out, likely interbred.  We know that archaic Homo sapiens in Africa interbred with the moderns there and that the moderns that left Africa interbred with the Neandertals and the Denisovans that they encountered.  One big happy family until we ruined the party.  More to come I am sure.

Elizabeth Mitchell, Homo naledi and the Straw Man

Elizabeth Mitchell, of Answers in Genesis, has written the rebuttal to the eLife Science paper on the new hominin find from South Africa, Homo naledi.  Sadly, her opening premise suffers from a fatal logical error, and all that follows proceeds from this premise. She writes:

Berger’s team believes the bones paint a mosaic picture of a species mixing human-like “Homo” and australopithecine ape features. Composites constructed from four partial skulls in the assemblage have small brain capacities—560 cc and 465 cc—that overlap the usual brain capacities of australopithecines. Such braincases are much smaller than those seen in most archaic humans1 and less than half the average for modern humans.

Hidden in this paragraph is a theme which runs throughout the post: that australopithecines were apes.  Compare, for example, these passages.  First, what Berger et al. write about the shoulder girdle:

The shoulders are configured largely like those of australopiths. The vertebrae are most similar to Pleistocene members of the genus Homo, whereas the ribcage is wide distally like Au. afarensis.

Now, what Mitchell writes:

Homo naledi’s shoulder joints and curved finger bones are typical of tree-swinging apes. Its flared hips are typical of australopithecine apes. The lower ribcage widens just like the ribcage of australopithecine apes.

When Raymond Dart discovered the first australopithecine specimen, in 1924, the first thing he noticed was that

it was not an ape.

As I wrote in more detailed fashion here, the find had several characteristics simply not found on any ape. First, the foramen magnum, the hole through which the spinal cord exits the head, was not at the back of the head, as in apes, but was on the bottom of the skull. Second, the teeth were not those of an ape, but had the dimensions of human teeth. In apes, even infant apes, the canines extend beyond the tooth row. In this skull, they did not. Third, the skull was simply too large to be that of an infant ape, based on the development. Fourth, there had never been found any apes in South Africa. Dart was a good anatomist and knew that what he had was not quite human—the skull was too small for that and the front of the face was too ape-like, but he also knew he did not have an ape.  That is why Dart gave it the name he did: Australopithecus africanus, “Southern Ape-Man from Africa.”   

Since this discovery some ninety one years ago,  the validity of this genus has only been reinforced, with the additional discoveries of more than ten different species of Australopithecus, all with variations on the same theme, and all with the following non-ape characteristics:

• human-like teeth (although quite large in some species)
• modern double-s shaped vertebral column
• short, wide hips that resemble humans and not apes
• a valgus knee, with the femoral-tibial articulation at an angle, instead of straight up, as in apes
• a laterally-bending proximal femur to accomodate the wide hips and the connexion to the tibia and
• a modern gait (reflected in preserved 3.6 million year old footprints at Laetoli)

There are countless other small anatomical characteristics that separate apes from these early hominins but the ones outlined above are enough to demonstrate that the initial premise of Dr. Mitchell is, simply, incorrect.

But there is something deeper at work here.  Pick up a paper on australopithecines, any paper, written in the last sixty years and you will find discussions of how these forms differed from each other and, more importantly, how they differ from apes.  Are they human?  Manifestly not.  In some early species, there are characteristics that are, indeed, intermediate between apes and early humans. But even that gives rise to the concept of transitional traits and forms in the fossil record.  That is where the problem lies.  If australopithecines can be painted as apes from the outset, then the task of showing that the new Homo naledi specimen is not different from australopithecines, and therefore, apes, becomes easier.

Then she writes something startling:

The question then is what is Homo naledi? Even the evolutionary anthropologists are not in agreement on that point, though most seem to have jumped on the Homo bandwagon. Yet while the fossil record contains many legitimate examples of extinct varieties of humans, such as Homo erectus and Homo neanderthalensis, after assessing the published reports, we beg to differ with Berger’s assessment of Homo naledi. We do not believe Homo naledi deserves its Homo designation. [Emphasis Mine]

When did they these fossil forms go extinct? There is no evidence of extinction in the accounts in the Bible. Other writers do not seem to think they went extinct during the flood.  David Menton is firm in his conviction that Homo erectus represents a post-Babel population:

Neanderthals buried their dead and may have worn jewelry. Homo erectus seems to have divvied up jobs to prepare food and sailed the high seas. Even with little to go on, we can be fairly certain the Denisovans wore jewelry, and the much-maligned “hobbits” left tools useful for dicing up lunch. All uniquely human traits—traits that show creatures made in the image of God.

Which one of the biblical patriarchs had an angular torus, large brow ridges, thick cranial bones and a cranial capacity of 900 cubic centimeters? All of these traits would have stood out in any population. The variation present that Menton squeezes into one happy family vastly exceeds that present in any other naturally-occurring genus on the planet, let alone species. 

She finishes her post with the same, time and time again rebutted argument that the reason that Homo naledi is not a human is similar to australopithecines and, therefore, is nothing more than an ape.  This is the vacuum chamber/wind tunnel that AiG operates within.  Despite clear, decisive anatomical evidence to the contrary, the writers keep telling themselves that australopithecines were nothing more than apes.  The argument still has no credibility.

The Origins of Modern Humans, Part III: The Fossil Evidence

My third BioLogos post on the fossil evidence concerning the origins of modern humans is up over at BioLogos.  This is the part that will, likely, rattle a few cages.  Comments welcome.

Science Daily: Neanderthal Genome Shows Early Human Interbreeding, Inbreeding

More clarity.  A new study coming out of the University of California at Berzerkeley posits that not only did early modern humans and Neandertals interbreed, but Neandertals inbred, as well.  From the story:

Population geneticist Montgomery Slatkin, graduate student Fernando Racimo and post-doctoral student Flora Jay were part of an international team of anthropologists and geneticists who generated a high-quality sequence of the Neanderthal genome and compared it with the genomes of modern humans and a recently recognized group of early humans called Denisovans.

The comparison shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago. Neanderthals and Denisovans split about 300,000 years ago.

It is not clear to me when you make the species break but for two species to interbreed several hundred thousand years after they split is unusual.  Dogs and wolves, for example, don't have nearly that time depth.  The split must have been a very subtle one, then.  As to how they know that Neandertals interbred without having two related Neandertals on hand, here is the explanation:

In another analysis, Jay discovered that the Neanderthal woman whose toe bone provided the DNA was highly inbred. The woman's genome indicates that she was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins (the offspring of two siblings who married siblings).

Depending on how large the population was, this may have been a necessity. it may also be an artifact of sampling. This happens in modern human populations as well but is not common.  As the authors note, there are quite a few unanswered questions.  For example, they really have no idea how much interbreeding between Neandertals, Denisovans and modern humans took place.

Oldest Human DNA Recovered

Using the fossil material from the Sima de Los Huesos cave, at the Spanish site of Atapuerca, geneticists have recovered DNA.   From the National Geographic story by Karl Gruber:

Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans. Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.

Although the report argues that the Atapuerca remains show a greater similarity to Denisovans than Neandertals, we already know that modern Europeans and East Asians have Neandertal genes in them, indicating that admixture was occurring.  Milford Wolpoff has been arguing for decades that archaic Homo sapiens represents a polytypic species that has genetic ties to modern human groups in different parts of the Old World.  While it certainly appears that Neandertals were distinctive, this information, in conjunction with various studies (here and here) of the Denisovans and African archaics indicates that this model may be the more correct one. 

Lost in the shuffle, however, is that the ability to recover this DNA is an astounding feat of science and portends for great advances in human palaeontology in the future. 

Science Daily: Neanderthal Viruses Found in Modern Humans

A year a half ago, I was sitting in a discussion group in the anthropology department at the University of Tennessee discussing the importance of the Denisova fossil and DNA that was extracted from it.  At that point, it had already been established that Neandertal DNA had been found in modern humans to the tune of between 3 and 9 % depending on the population.  I then publicly wondered when a study of endogenous retroviruses in the Neandertal genome would be forthcoming and whether that would also link them to modern humans.

It has.  Science Daily is reporting on genetic studies that have discovered Neandertal retroviral DNA in modern humans.  From the story:

The researchers compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients. They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.

Lets back up.  What are endogenous retroviruses, or ERVs? These are RNA-based viruses that write themselves into the DNA of an individual.  They are thought by some to be directly involved in causing things such as MS and a host of different cancers.  It is not quite clear what kind of role they play in this, however.  It has also been found that some ERV DNA has been co-opted by the reproductive system, and are involved in the creation and stability of the placenta.  They are highly conspicuous and easily recognizable.  ERVs also makes up around eight percent of modern human DNA.

If they get written into the sex chromosome, since they are part of the DNA, they get passed on and, usually over time, lose their virus-causing capabilities, ending up as non-coding parts of the genome.  Sometimes, they don't insert correctly and end up not causing trouble at all.   One of the most interesting things, though is that they insert themselves into the genome in random places.  Therefore, if they show up across related species, it is a marker of evolutionary similarity.  They have, understandably, figured into human evolutionary studies.  ERVs have been found in all of the higher apes that are also found in humans and, broadly, provide evidence of common ancestry with the higher apes.  Here is a paper in Comparative Functional Genomics by Khudosovich et al., explaining the role in detail¹.

Now it seems that ERVs that are specific to Neandertals have been found in modern humans.   As with the results of the Neandertal genome, this can only mean one thing: Neandertals directly contributed, in some way, to the ancestry of modern humans.  This has broad implications not just for human evolutionary response but also for theological models involving Adam and Eve.  Conventional science posits that Neandertals appeared around 130 000 years ago in Europe and that, as modern humans moved out of Africa, they met and mated with the resident Neandertals.  The evidence further suggests that, over time, the modern human genome swamped the Neandertal genome and that, in combination with changing climatic conditions and the selective advantage of the modern human genome, Neandertals died out. 

But we know that the last Neandertal died out around 32 000 years ago.  If modern humans carry Neandertal genes (and by extension ERVs), then there must have been modern humans around at least that long.  Further, given that most of these DNA elements are non-coding and insert themselves randomly in the genome, in order to postulate a separate, non-evolutionary, special recent ancestry for modern humans, one must argue that these ERVs were separately inserted into the DNA of Neandertals and modern humans (unintelligent design).

I'm going out into left field now.

Further, if one is to argue that there were only two humans at the beginning of human history, one has to account for how the Neandertal genes got into their descendants.  One could, I suppose, argue that, in the time period between Adam and Eve to Noah, one of Adam's descendants mixed it up with the Neandertals (although one has to account for why they aren't mentioned) and that is how the Neandertal ERVs got there.  There were Neandertals in the Levant, so that is, at least within that framework, possible (Neandertals as Nephilim?).  I will be curious to see if that explanation appears in creationist' writings.

The most parsimonious explanation is that modern humans carry some Neandertal ancestry in them and that this process occurred through evolutionary means. 

¹Khodosevich, Konstantin, Lebedev, Yuri and Sverdlov, Eugene (2002) Endogenous Retroviruses and Human Evolution Comparative and Functional Genomics 3(6),494-498
http://dx.doi.org/10.1002/cfg.216

National Geographic Special on Denisova

National Geographic is running a special report on the importance of the Denisova hominin for later human evolution.  The timing is curious since this was big news two years ago, but “The Case of the Missing Human Ancestor” goes into the depths of the discovery, the tests done, the complex stratigraphy of the cave, and the significance of what the Max Planck Institute found.  Further, it is written by Jamie Shreeve, and he is always a good read.  He writes:

In the summer of 2010 a human toe bone had emerged, along with the enormous tooth, from Layer 11. In Leipzig a graduate student named Susanna Sawyer analyzed its DNA. At the symposium in 2011 she presented her results for the first time. To everyone’s shock, the toe bone had turned out to be Neanderthal, deepening the mystery of the place.

The green stone bracelet found earlier in Layer 11 had almost surely been made by modern humans. The toe bone was Neanderthal. And the finger bone was something else entirely. One cave, three kinds of human being. “Denisova is magical,” said Pääbo. “It’s the one spot on Earth that we know of where Neanderthals, Denisovans, and modern humans all lived.” All week, during breaks in the conference, he kept returning alone to the cave. It was as if he thought he might find clues by standing where the little girl may have stood and touching the cool stone walls she too may have touched.

Look for this site to continue to influence models of later human evolution. There seem to have been several locations at which there were both, at various times, Neandertals and modern humans.

Study: Neandertal Speech and Language Abilities Like Modern Humans

Science Daily has a story on Neandertal speech.  Work by Dan Didiu and Stephen Levinson suggests that Neandertals and modern humans share a common ancestry with regard to the use of language.  Science Daily writes:

Dediu and Levinson review all these strands of literature and argue that essentially modern language and speech are an ancient feature of our lineage dating back at least to the most recent ancestor we shared with the Neandertals and the Denisovans (another form of humanity known mostly from their genome). Their interpretation of the intrinsically ambiguous and scant evidence goes against the scenario usually assumed by most language scientists, namely that of a sudden and recent emergence of modernity, presumably due to a single -- or very few -- genetic mutations. This pushes back the origins of modern language by a factor of 10 from the often-cited 50 or so thousand years, to around a million years ago -- somewhere between the origins of our genus, Homo, some 1.8 million years ago, and the emergence of Homo heidelbergensis. This reassessment of the evidence goes against a saltationist scenario where a single catastrophic mutation in a single individual would suddenly give rise to language, and suggests that a gradual accumulation of biological and cultural innovations is much more plausible..

I am still a bit “iffy” on the whole “common ancestor of modern humans and Neandertals” thing since some are trying to argue for a common ancestor based on the material from the Gran Dolina, in Spain, and it sure as all get out looks like modern humans originated in Northeast Africa at, or near, Herto. I have a tendency to think that there was a good deal of panmixia throughout Europe and north Africa.  Otherwise, we are required to believe that there was a species split at H. antecessor into what became modern humans (how'd they get to north Africa?) on one side and Neandertals on the other and that, some 700 to 720 thousand years later, emerging moderns and Neandertals encountered one another and interbred.  That is overly simplistic, I am sure but it seems far-fetched.  It seems easier to argue that the H. antecessor material represents an archaic Homo sapiens population that was the precursor (or something like it was) to later archaics, such as Petralona and Atapuerca, out of which Neandertals came.  Then the Neandertals interbred with the north-moving moderns and somewhere in there, the Denisova population split off.  The panmixia in Europe, western Asia and Russia explains why moderns have both Neandertal and Denisovan genes, along with the modern genes that originated in North Africa.  Subsequent swamping of the archaic genome led to the demise of both the Neandertals and Denisovans.