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. 

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.

A 'Modern Population Bottleneck?'

NPR has a story on the (almost) disappearance of modern humans here. It is not a hypothesis that I had heard of before. Robert Krulwich writes:

Once upon a time, says Sam [Kean], around 70,000 B.C., a volcano called Toba, on Sumatra, in Indonesia went off, blowing roughly 650 miles of vaporized rock into the air. It is the largest volcanic eruption we know of, dwarfing everything else...That eruption dropped roughly six centimeters of ash — the layer can still be seen on land — over all of South Asia, the Indian Ocean, the Arabian and South China Sea. According to the Volcanic Explosivity Index, the Toba eruption scored an "8", which translates to "mega-colossal" — that's two orders of magnitude greater than the largest volcanic eruption in historic times at Mount Tambora in Indonesia, which caused the 1816 "Year Without a Summer" in the northern hemisphere.

Although this is a provative hypothesis, it does not match modern genetic studies. Dennis Venema writes:

Studies based on SNP/LD approaches have now estimated ancestral population dynamics for various human groups over time in more detail than is possible with mutation-based estimates. African groups have a higher effective population size (~7,000) than do non-African groups (~3,000) over the last 200,000 years. This approach, though based on methods and assumptions independent of previous work, nonetheless continues to support the conclusion that humans, as a species, are descended from an ancestral population of at least several thousand individuals. More importantly, the scalability of this approach reveals that there was no significant change in human population size at the time modern humans appeared in the fossil record (~200,000 years ago), or at the time of significant cultural and religious development at ~50,000 years ago.

When the first mtDNA studies began to come out in the late 1980s and early 1990s, they all supported the recent African evolution of modern humans and they all came to the same general conclusion: that modern humans had originated in sub-Saharan Africa between 140 and 280 thousand years ago. The earliest fossil evidence we have for modernity in Africa are the Herto remains at 160,000, at the site of Bouri, in the Afar Triangle. These remains bear more than a passing similarity to the modern Skhul 4 and 9 remains from the Israeli site of Skhul (dated at around 100,000) and suggest a general northern migration of these populations.

The other problem is that this does not correspond to a die-out of Neandertals either. The Neandertals didn't go away until around 30,000 and interbred with the incoming moderns anyway. Indeed, it looks as if the incoming moderns simply swamped the Neandertal genome and assimilated them. It is hard to do this if you have a very small effective population size.

I have not read this book so he may have counters for all of these arguments but I would be really curious to know what they are.

Fossil Data and Genetic Data More Concurrent Than Thought

It is now coming out that the “clocks” that are used to calculate mutation rates are badly calibrated. Ewen Callaway of Nature writes:

Geneticists have previously estimated mutation rates by comparing the human genome with the sequences of other primates. On the basis of species-divergence dates gleaned—ironically—from fossil evidence, they concluded that in human DNA, each letter mutates once every billion years. “It’s a suspiciously round number,” says Linda Vigilant, a molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The suspicion turned out to be justified.

Now it seems that the clock is off by half. This means that a bunch of divergence dates can be recalculated. One is particular is mentioned:

Take the 400,000–600,000-year-old Sima de Los Huesos site in Atapuerca, Spain, which yielded bones attributed to Homo heidelbergensis, the direct ancestors of Neanderthals. Genetic studies have suggested that earlier ancestors of Neanderthals split from the branch leading to modern humans much more recently, just 270,000–435,000 years ago. A slowed molecular clock pushes this back to a more comfortable 600,000 years ago.

It isn't a magic bullet, there are still some kinks to be worked out but it has remarkable potential for getting a handle on when the Denisova genome might have arisen.It might also give us a believable figure for the LCA of apes and humans since the current, 5 million year date is plainly not so.

More on Modern Human Origins

Scientific American is running a story on more news from the Max Planck Institute. Now, the entire genome of the hominins represented by the material from Denisova Cave has been sequenced. Here is what we find:

Unfortunately, the Denisovan genome doesn't provide many more clues about what this hominin looked like than a pinky bone does. The researchers will only conclude that Denisovans likely had dark skin. They also note that there are alleles "consistent" with those known to call for brown hair and brown eyes. Other than that, they cannot say.

Yet the new genetic analysis does support the hypothesis that Neandertals and Denisovans were more closely related to one another than either was to modern humans. The analysis suggests that the modern human line diverged from what would become the Denisovan line as long as 700,000 years ago—but possibly as recently as 170,000 years ago.

Given the amount of genetic similarity in the three groups, it makes more sense that the number is closer to 170,000, especially since there is evidence of hybridization between the three groups. What also seems to be true is the Denisova group shows some level of founder effect in the sense that the genetic variability is more restricted than that found in modern humans. Who the population split off from is anybody's guess right now.

New CFSI Post

My new CFSI post is up titled Not So Different After All. It is my take on the new data that indicates that up to nine percent of non-African modern human DNA is, in fact, Neandertal in origin. All comments are welcome there and here.

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Our Cheatin' Ancestors?

A new study suggests that modern humans are considerably less promiscuous than their forbears. In a story that appeared in the University of Oxford site, the culprit seems to be androgen levels:

Previous studies by the research team have shown that promiscuous species have low index to ring finger ratios while monogamous species have high finger ratios. High levels of androgens, such as testosterone, increase the length of the fourth finger in comparison to the second finger. It is thought that prenatal androgens affect finger length during development in the womb, which in turn is linked to adult behaviour. High levels of prenatal androgens are linked with competitiveness and promiscuity.

I would love to know what the r² on that analysis is. I am always extremely suspicious of a study that links a single process to a complex social behavior, especially something like this. Later, the article has this:

Dr Susanne Shultz, from the University of Oxford, said: ‘Social behaviours are notoriously difficult to identify in the fossil record. Developing novel approaches, such as finger ratios, can help inform the current debate surrounding the social systems of the earliest human ancestors.

They are notoriously difficult because they often leave few to no clues. This analysis also sidesteps the problems involved in trying to ascertain what other selective forces might have been at work in early hominid development. For example, in Ardipithecus, given that they exhibited incipient bipedality and were, at least in part, arboreal as well, there may have been selective pressures on metacarpal and phalanx length. Also, is finger length one trait dictated by pleiotropy? Or is it polygenic? Is there linkage disequilibrium going on? These sorts of questions could be extrapolated to other hominid species as well and need to be addressed before arriving at the conclusion that is stated in this study.

More Information about the Origin of Tetrapods

Tom Spears of the Ottawa Citizen has a story on research being done to determine the genetic link between current animals and the earliest tetrapods. He writes:

A tetrapod is something with four legs and a spine. A frog, a dinosaur, a giraffe in the high veldt. There has been life on Earth for nearly four billion years, but tetrapods for only one-tenth of that.

Before tetrapods, however, there were lots of fish. So, what's the connection?

In the zebrafish, Akimenko found a new family of genes that seemed important to how fins develop in the embryo. These genes appear in different fish species, but have disappeared from animals with legs. The genes allow fish to produce a fibrous material in fins called actinotrichia. Here's where her detective work starts.

She suggests that two mutations were necessary for the suppression of that gene which led to the earliest tetrapods. Another piece of the puzzle.

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Answers in Genesis on the Neandertal Genome

I missed this a month back. AIG weighed in on the sequencing of the Neandertal Genome here. If you will recall, it was found by Svante Paabo and colleagues that Neandertals appear to have contributed at least 4% of their DNA to modern humans, thus strongly suggesting that the speciation event in sub-Saharan Africa that gave rise to modern humans was not total, with at least some interbreeding between the two groups. The article by Layman, reads thus:

The news doesn’t surprise young-earth creationists, who predicted overlap between modern human and Neanderthal genomes. Based on Scripture, creationists consider Neanderthals to have been fully human, descendants of Adam and Eve (through Noah), and therefore they would have lived in the same time and place as other humans. But factors related to both the dispersion at Babel and environmental pressures afterward resulted in people groups with different physical characteristics, including humans with “Neanderthal” characteristics.

Liberty University cell biologist (and creationist) David DeWitt called the research an “amazing feat” of science that supports creationist expectations. “Finding Neanderthal DNA in humans was not expected by evolutionists, but it was predicted from a creation standpoint because we have said all along that Neanderthals were fully human: descendants of Adam and Eve, just like us,” he told News to Note.

There is no explanation as to why this finding would "not be expected by evolutionists." There are quite a few models that would welcome this sort of explanation. It is only unexpected if you are unfamiliar with the data or the models. As for whether Neandertals were "fully human," there is a problem with that: Neandertals aren't fully human. That is the source of the controversy in the first place. Many anthropologists regard them as a separate species of human based on their distinctness from modern humans.

The Neandertals represented a distinct European and Near Eastern variant of what has become known as "archaic Homo sapiens." This is a grade of Homo sapiens that existed after Homo erectus/ergaster but before true Homo sapiens, which are decidedly different. As biological anthropologist Dave Frayer has pointed out, there is not a single person alive that has the full suite of Neandertal characteristics. For example, in the following diagram, it is clear that there are sharp differences between these two hominid forms.



Several things are immediately apparent in this comparison. The modern human individual has much reduced ridges over the eyes, a much more vaulted forehead, a smaller nose opening, a shorter, higher cranium, smaller teeth and more forward-placed cheek bones.

There are those that argue, however, that the earliest modern humans have traits that are holdovers from the preceding Neandertals. And for those of us that hold to this perspective, this finding was perfectly expected. The last Neandertals date to around 30 thousand years ago and this overlaps with the earliest modern humans, which date to between 34 and 37 thousand years. At the point of this overlap, the earliest moderns, which are likely migrants from the Near East, either mated with the Neandertals or replaced them. While there has been evidence from the crania of the earliest moderns that some degree of interpopulational mating has occurred, the DNA evidence has largely supported the replacement idea. Svante Paabo's evidence changes that.

Anthropologist Richard Klein has stated that he doesn't see how any modern human would have found a Neandertal attractive enough to mate with. What the findings from the Neandertal genome show us is that two very different groups of people met somewhere in Europe between 30 and 40 thousand years ago and that some of the moderns did find the Neandertals suitable as mates. But modern human the Neandertals certainly were not.

P.S. Why don't sites like AIG and the Discovery Institute allow comments by readers? It would have been nice to simply point this out on the AIG site.

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Jews Found to be a Distinct Ethnic Group

Two new studies by several researchers have suggested that the children of Abraham really are related. Of the first study, the New York Post reports:

Researchers say the study, published in the American Journal of Human Genetics, puts to rest age-old questions about whether Jews are a group of unrelated people who share a religious ideology or a distinct ethnicity with common ancestry.

“The debate is over,” said Dr. Edward R. Burns, one of the lead authors of the study. “The Jewish people are one people with a common genetic thread that evolved in the second or third century BC.”

The study, “Abraham’s Children in the Genome Era,” compared the genetic analyses of 237 Jews, including Sephardic (Middle Eastern) and Ashkenazi (Eastern European) Jews — as well as an analysis of 418 non-Jews worldwide, and found that the Jews were more closely related to each other than to their fellow countrymen.

The first thing that struck me about the story is that the last time that I heard someone say "The debate is over," it was Al Gore, speaking about global warming. Such language is not often heard from a scientist, for good reason. Often, if someone says that, the debate is far from over.

The second thing is that, as Genesis reports, God promised Abraham that his descendants would be like the stars in the sky in number. 237 Jews gives new meaning to the word "sample." While it is true that other studies have largely corroborated this one (Ostrer, 2001, Nebel, 2001)¹, clearly more work needs to be done.

Since it is the New York Post, a political note needs to be interjected:

The study — and a second genetic study published Friday in the journal Nature — scientifically undermines arguments made by those who challenge Jews’ historical relationship to Israel, such as former White House correspondent Helen Thomas, who resigned last week after saying Jews in Israel should “go home” to Germany, Poland and the United States.

Turns out, the Jews in Israel are already there.

¹Ostrer, H. (2001). "A genetic profile of contemporary Jewish populations." Nature Reviews Genetics 2(11): 891-898.

Nebel, A., D. Filon, et al. (2001). "The Y chromosome pool of Jews as part of the genetic landscape of the Middle East." The American Journal of Human Genetics 69(5): 1095-1112.

Douglas Theobald and Universal Common Ancestry

Douglas Theobald has written a technical paper on a test for universal common ancestry. The text of the paper is posted at Panda's Thumb, which also gives a short synopsis. Mike Steele and David Penny have also broken down the article here. They write:

So what is the signal in sequence data that provides the evidence for common ancestry? In essence, it is site-specific correlations in the amino acids between different species. These correlations fall off as the coalescence between lineages in a tree becomes deeper in the past, but if there are sufficient data, the correlations' cumulative significance becomes statistically strong. Conversely, if two lineages have completely separate origins, correlations between amino-acid site patterns in the corresponding two extant species vanish.

This article basically suggests, if I understand it correctly, that if species were independently created (think: *poof*), they would show smaller correlations in the coalescence results. This indicates that the further back you go, the sequence data shows common descent. As you go back in the fossil record and compare that to the genetic data of different species, certain protein sequences remain in common. Hat tip to Panda's Thumb.

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The Genetics of Charles Darwin

National Geographic has a story on the ancestry of Charles Darwin. They write:

Darwin's great-great-grandson, Chris Darwin, 48, who lives in the Blue Mountains near Sydney, Australia, took a Genographic Project public participation cheek swab test analysing his "Y" chromosome.

According to Spencer Wells, project director of the Genographic Project, a research partnership between National Geographic and IBM with field support from the Waitt Family Foundation, Darwin's deep ancestry shows his ancestors left Africa around 45,000 years ago.

Eventually, the Genographic project should be able to show us the migratory trajectories of many of the genes in humans. That will help with both historic and prehistoric studies.

An interesting afterthought: There have been several of these genetic studies that have been used to trace ancestry back through time, the Cann, Stoneking and Wilson study on Mitochondrial Eve being only one. Not one of them has pointed to an origin of the modern human genome in the Middle East. Where ever modern humans originated, it was not from the Mesopotamian basin. This has always been, to me, an unanswerable question regarding the YEC model of Noah's flood: if it was universal, why doesn't the genetic information point to it? Further, why do cultures around the area not have records of it? Why don't nations across the world have a story about people that came out of the ark and moved into the area? Why are all the flood stories around the world different, with their own survivors? There seems to be this great amnesia with regard to the event, almost as if it never happened in their areas.

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Bornaviruses and Human Evolution

Wired has an article on a startling discovery in virology—that viruses other than retroviruses can attach themselves to their host DNA. Tina Hesman writes:

Bornaviruses, a type of RNA virus that causes disease in horses and sheep, can insert their genetic material into human DNA and first did so at least 40 million years ago, the study shows. The findings, published January 7 in Nature, provide the first evidence that RNA viruses other than retroviruses (such as HIV) can stably integrate genes into host DNA. The new work may help reveal more about the evolution of RNA viruses as well as their mammalian hosts.

“Our whole notion of ourselves as a species is slightly misconceived,” says Robert Gifford, a paleovirologist at the Aaron Diamond AIDS Research Center, affiliated with Rockefeller University in New York City. Human DNA includes genetic contributions from bacteria and other organisms, and humans have even come to rely on some of these genes for basic functions like fighting infections.

Retroviral segmants have been found to be involved in placental development as well and make up a sizable percentage of our DNA. I have posted about ERVs before, here and here. This just shows how "mutt"-like our DNA is and will certainly rattle some cages.

More on the ERV - Human Interaction

The Irish Times has a story on how Endogenous Retroviruses have become part of the human genome. They write:

If you think that viruses have played no part in human evolution think again. Up to 46 per cent of our DNA was actually provided some time in the past by invading viruses, Ryan says. In comparison, just 1.5 per cent of our genomes arise from the genes we inherit from our primate and animal ancestors.

Ryan argues that Human Endogenous Retroviruses, or Hervs, are a viral integration process integral to the genome of all mammals. It came about by an extensive series of retroviral epidemics that infected our ancestors over tens of millions of years. This means that the virus is something more than just a pest.

ERVs have been used extensively as evidence for evolution, since we share a large number of ERVs with the higher primates and the insertion points are always the same. But as evil as they are, they also play continuous roles in our genome:

Ryan suggests that certain viruses play vital roles in human activity. “There are eight full-length viruses in the human placenta playing different roles, such as a human virus that codes for syncytin 1, which fuses cells together to create a protective layer between mother and baby,” says Ryan. “Proof of the symbiotic inclusion of such viruses as part of our DNA is the fact they have been conserved throughout evolution.”

ID has difficulty explaining ERVs because they cause such harm to any given generation and they are clearly detrimental to health in the short term. Here is a reminder of how important ERVs are to evolutionary studies.

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Modern Human Evolution

Daily Galaxy has an article on how human evolution has proceeded in the recent past and how it might continue into the future.

A team led by University of Wisconsin-Madison anthropologist John Hawks estimates that positive selection just in the past 5,000 years alone -dating back to the Stone Age - has occurred at a rate roughly 100 times higher than any other period of human evolution. Many of the new genetic adjustments are occurring around changes in the human diet brought on by the advent of agriculture, and resistance to epidemic diseases that became major killers after the growth of human civilizations.

"In evolutionary terms, cultures that grow slowly are at a disadvantage, but the massive growth of human populations has led to far more genetic mutations," says Hawks. "And every mutation that is advantageous to people has a chance of being selected and driven toward fixation. What we are catching is an exceptional time."

While the correlation between population size and natural selection is nothing new - it was a core premise of Charles Darwin, Hawks says - the ability to bring quantifiable evidence to the table is a new and exciting outgrowth of the Human Genome Project.

This is the convergence of population genetics, comparative anatomy and palaeontology to explain how humans have evolved. About natural selection, he writes:

Another recently discovered gene, CCR5, originated about 4,000 years ago and now exists in about 10 percent of the European population. It was discovered recently because it makes people resistant to HIV/AIDS. But its original value might have come from obstructing the pathway for smallpox.

"There are many things under selection that are making it harder for pathogens to kill us," Hawks says.

Population growth is making all of this change occur much faster, Hawks says, giving a tribute to Charles Darwin. When Darwin wrote in "Origin of the Species" about challenges in animal breeding, he always emphasized that herd size "is of the highest importance for success" because large populations have more genetic variation, Hawks says.

This is contrary to popular wisdom that shows that evolution proceeds faster in smaller populations because traits are expressed more often. Typically, larger populations slow evolution down because they are much closer to Hardy-Weinberg equlibrium. I also wonder about the statement that human evolution is proceeding faster now than at any time in the past. I do not think we have the resolution to determine that, even genetically. The human "bush" has gone through some remarkable changes even in the last 200 thousand years, with the successive appearance of archaic Homo sapiens and modern Homo sapiens, with regional characteristics present in many populations. It is doubtful that any of these changes would have happened had the population been as global as it now is.


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William Reville on Religion and Science

The Irish Times has a good post by William Reville on the nature of science and what science does to answer questions. In it, he tackles a section that is persistently misinterpreted and misunderstood by modern-day creationism: historical science. After discussing what is understood to be popular science involving experimentation and replication, He writes:

However, not all aspects of the natural world are amenable to investigation by the form of the scientific method just described. For example, phenomena and processes that have developed over historical time, such as the origin and evolution of life or the origin and evolution of the universe, must be investigated in a different manner. Here you must use numerous lines of enquiry, and conclusions can only be drawn after these converge to produce an unmistakeable conclusion. Thus, the theory of evolution through natural selection rests on the converging evidence of the history of life on earth gleaned from palaeontology, geology, zoology, botany, comparative anatomy, biogeography, molecular genetics, physiology, and so on.

This is what many creationists fail to understand—it is not just the fossil record or just genetics or just anything that supports evolution. It is the whole kit 'n kaboodle. He also rightly questions whether or not the existence of God could ever be shown by using science. This is something I have argued for years. Read the whole thing.

Evolution 101

A guest post in the Winston-Salem Journal by Adam Corey, a high school biology teacher offers a clear, concise explanation about what evolution is and isn't. He writes:

This year marks the 200th anniversary of Charles Darwin's birth (1809) and the 150th anniversary of his magnum opus, On the Origin of Species by Means of Natural Selection

(1859). Our nation falls miserably behind the majority of developed countries in scientific literacy. I hope we can improve those numbers. We must continue to educate the public through solid explanations of what evolution is while correcting the misunderstandings the majority of people have.

If you have questions about evolution, ask someone. Professors and teachers would be glad to help you understand the unifying theory of biology. As Theodore Dobzhansky, a noted geneticist and evolutionary biologist, said, "Nothing in biology makes sense, except in the light of evolution." Once you understand evolution, a new door to the biological sciences opens before you.

More teachers should write like this. Oh, and its Theodosius, by the way.