Evolution: The Scientific Evidence

[ewmayer]

A few posts above there was discussion (based on the significant fraction of human DNA that appears to be retroviral in origin) of the potential evolutionary usefulness of such exogenous genetic material derived from "lower" species to the "higher" species. Now, closer to home, an interesting twist on the long-running "did humans and Neandertals interbreed?" question, courtesy of the New York Times:

Neanderthals in Gene Pool, Study Suggests

By http://topics.nytimes.com/top/refere... NOBLE WILFORD
Published: November 9, 2006

Scientists have found new genetic evidence that they say may answer the longstanding question of whether modern humans and Neanderthals interbred when they co-existed thousands of years ago. The answer is: probably yes, though not often.

In research being published online this week by the Proceedings of the National Academy of Sciences, the scientists reported that matings between Neanderthals and modern humans presumably accounted for the presence of a variant of the gene that regulates brain size.

Bruce T. Lahn of the University of Chicago, the report's senior author, said the findings demonstrated that such interbreeding with relative species, those on the brink of extinction, contributed to the evolutionary success of modern humans.

Other researchers in evolutionary biology said the new study offered strong support for the long-disputed idea that archaic species like Neanderthals contributed to the modern human gene pool.

Two other reports of DNA studies of possible mixing of human and related genes are expected to be published in the next few weeks.

Both genetic and fossil studies show that anatomically modern humans emerged 200,000 years ago in Africa and migrated into Europe 40,000 years ago. In about 10,000 years, Europe’s longtime inhabitants, Neanderthals, became extinct. The mainstream interpretation is that modern humans somehow replaced them without interbreeding.

In previous research, Dr. Lahn and associates discovered that a gene for brain size called microcephalin underwent a significant change 37,000 years ago. Its modified variant, or allele, appeared to confer a fitness advantage on those who possessed it. It is now present in about 70 percent of the world’s population.

The new research focused on the two classes of alleles of the brain gene. One appeared to have emerged 1.1 million years ago in an archaic Homo lineage that led to Neanderthals and was separate from the immediate predecessors of modern humans. The 37,000-year date for the other variant immediately suggested a connection with Neanderthals.

Dr. Lahn said it did not necessarily show that interbreeding was widespread. It could have been a rare, perhaps even single, event.

[Xyzzy]

Originally Posted by ewmayer

...Neanderthals in Gene Pool...

I think there was a Gary Larson cartoon about this.

[ewmayer]

Originally Posted by Xyzzy

I think there was a Gary Larson cartoon about this.

Maybe something about them swimming "in the shallow end" of the gene pool? (Or maybe they got kicked out for peeing...)

Or perhaps a Neandertal version of Larson's classic "The real reason the dinosaurs went extinct" cartoon? (I love that one, especially the furtive looks on the dinos' faces.)

Seriously, I've always thought the Neandertals were unfairly maligned (and not just by the Geico car-insurance "so simple, a caveman could do it!" TV ads). It seems a pervasive bias, even among paleontologists (i.e. people who might be expected to know better) to confuse absence of evidence for evidence of absence. So little of a vanished culture survives in the fossil record ... we have no tape recordings of the Neandertals and their hyoid bones are differently-shaped than ours ... so we assume they spoke only in grunts and shouts. We weren't around to witness their personal interactions and burial rituals, so we assume they were a brutish, survival-mode-only species. And so on...

On a lighter note, NFL scouts are probably hoping science will someday find a Neandertal "linebacker" gene - as a species they were physically tough as nails - a typical Neandertal skeleton has bones twice as strong as a humans, and much of that is not just genetic, but simply from a lifetime of extreme physical rigor.

[ewmayer]

More on the suddenly white-hot field of Neandertal Genomics:

New DNA Test Is Yielding Clues to Neanderthals -- New York Times

New DNA Test Is Yielding Clues to Neanderthals

By NICHOLAS WADE
Published: November 16, 2006

The archaic human species that dominated Europe until 30,000 years ago is about to emerge from the shadows. With the help of a new DNA sequencing machine that operates with firefly light, the bones of the Neanderthals have begun to tell their story to geneticists.

One million units of Neanderthal DNA have already been analyzed, and a draft version of the entire genome, 3.2 billion units in length, should be ready in two years, said Dr. Svante Paabo, the leader of the research project at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Biologists expect knowledge of the Neanderthal genome to reveal, by its differences with the human genome, many distinctive qualities of what it means to be human. Researchers also hope to resolve such questions as whether the Neanderthals spoke, their hair and skin color, and whether they interbred at all with the modern humans who first arrived on their doorstep 45,000 years ago, or were driven to extinction without leaving any genetic legacy.

Dr. Paabo has shared some of his precious sample of Neanderthal DNA with Edward M. Rubin of the Joint Genome Institute in Walnut Creek, Calif., whose team has identified 62,250 units of Neanderthal DNA by a different method. The two teams report their results in this week’s issues of the journals Nature and Science respectively, saying they have independently demonstrated that recovery of the Neanderthal genome is now possible.

From the data so far, Dr. Rubin’s team reports that the Neanderthal and human genomes are at least 99.5 percent identical. Dr. Paabo’s team has calculated that the “effective” size of the founding Neanderthal population was about 3,000, corresponding to a census size of fewer than 10,000 individuals. Both teams say it now seems much more unlikely that modern humans and Neanderthals interbred, though the possibility cannot yet be excluded.

“I think these results are monumental,” said Richard G. Klein, a paleoanthropologist at Stanford University who was not involved in the studies. The full Neanderthal genome will resolve many longstanding issues about Neanderthals and their relationship to modern humans, including their physical and perhaps behavioral differences, he said.

The Neanderthals, who flourished for some 400,000 years before their extinction about 30,000 years ago, physically resembled modern humans, but the middle of their face jutted forward and their large brain case had a distinctive bulge or bun at the back. They were heavily muscled and presumably well adapted to the cold conditions of the last ice age. They may well have been terrifying to the lighter-boned modern humans who first encountered them, except that their weapons were considerably less advanced. The Neanderthals still used a million-year-old stone tool kit that modern humans abandoned 5,000 years before they encountered the Neanderthals.

Archaeologists have shown that as the first modern humans, known as the Aurignacian culture, moved westward across Europe, the Neanderthals receded in parallel. By 30,000 years ago or even earlier, the Aurignacian conquest of Europe was complete and the Neanderthals had disappeared from their last refuges in what are now Spain and Portugal.

Dr. Paabo began his quest for Neanderthal DNA more than a decade ago, and has had to overcome a daunting array of obstacles. Many extravagant claims were then being made about DNA in old bones, with some scientists claiming to have recovered DNA from dinosaur bones millions of years old. But such bones were often contaminated by the DNA of the people who handled them, and Dr. Paabo saved the field from disrepute by demonstrating the extreme precautions necessary to avoid analyzing human DNA by mistake.

In 1997 he succeeded in analyzing part of the Neanderthal mitochondrial DNA, showing that it differed profoundly from modern human DNA. Mitochondria, the small organelles that provide the cell’s energy, are separate from the main genome in the cell’s nucleus. Since the nuclear DNA in old bones is degraded into millions of short fragments, 50 or so units in length, it seemed beyond hope of retrieval.

But recently a new kind of DNA sequencing machine was invented. Made by 454 Life Sciences of Branford, Conn., it prompts each DNA unit to generate a flash of light by stimulating the firefly enzyme luciferase. The flashes are captured by the same sort of image-sensing plate used in telescopes to capture starlight. From the timing and position of the flashes, a computer reconstructs the sequence of the DNA units. The kind of DNA the 454 machine works best with are tiny fragments the size of those found in old bones.

Dr. Paabo then scoured the museums of Europe for Neanderthal bones that might still retain DNA. Most of the 70 he tested had none, since DNA quickly degrades after the death of the organism. Many others were heavily contaminated with DNA from the curators and scientists who had handled them. Since human DNA is almost identical to Neanderthal DNA, the contamination posed serious problems.

Just one bone, retrieved from the Vindija cave in Croatia, turned out to retain DNA and be fairly free of human contamination. Asked at a news conference what made it so special, Dr. Paabo said that because it was small and uninteresting it had been “thrown in a big box of uninformative bones in the museum in Zagreb and wasn’t handled very much.”

The owner of the Vindija bone was a male Neanderthal who died about 38,000 years ago. As with other ancient bones, most of the surviving DNA belongs to the bacteria that consumed it when fresh. Less than 6 percent is Neanderthal DNA, and this has suffered a chemical degradation of the four DNA bases, referred to as A, T, G and C, whereby some of the C’s are converted to T’s and some G’s to A’s. Dr. Paabo has developed methods for distinguishing the real Neanderthal DNA and addressing the chemical conversion problem.

Dr. Paabo hopes to find other Neanderthal bones with retrievable DNA. But even if no more turn up, he believes there is enough DNA in the Vindija bone alone to complete a draft of the full Neanderthal genome.

He and his team still have many more problems to overcome, but other researchers are impressed with the progress so far. “He’s superbright and superthoughtful, and if anyone’s ever going to do it, it’s him,” Dr. Klein said.

If the full Neanderthal genome is retrieved, biologists may be able to ask if the Neanderthals had language by looking at their version of the human gene known as FOXP2, thought to be one of the last components to evolve in mediating the modern human language faculty. FOXP2 has changed significantly since the human lineage split apart from that of chimps some six million years ago. If the Neanderthal version resembles the chimp version, that would make it less likely they had modern, syntactical language.

The Neanderthal genome should also enable biologists to calculate which aspects of human evolution took place between 6 million and 500,000 years ago, and which are more recent. The latter is the approximate date at which the Neanderthal and human lineages split apart. Dr. Paabo also believes the Neanderthal genome will help geneticists identify which human genes have been subject to the pressures of natural selection in the last 500,000 years. This would be of great interest in identifying the distinctive genetic attributes of modern humans.

From the data already obtained, Dr. Paabo and his colleagues estimate that the ancestral Neanderthal population was very small, perhaps fewer than 10,000 individuals. Since the ancestral population of modern humans was much the same size, it seems that all populations of early humans were tiny, expanding only after the ice age ended.

From the data gathered so far by Dr. Paabo’s and Dr. Rubin’s teams, there is no evidence of interbreeding between Neanderthals and modern humans. But the possibility of a small amount of genetic interchange cannot yet be ruled out. Dr. Bruce T. Lahn, a geneticist at the University of Chicago, published a report earlier this month suggesting that one of the two principal versions of the human gene for microcephalin, which helps determine brain size, came from an archaic population, presumably the Neanderthals.

So far neither team has analyzed enough Neanderthal DNA to test Dr. Lahn’s proposal.

[brunoparga]

Thanks for the posting, Ernst. I read something else about these exciting new discoveries today. It seems Dr. Rubin's results show Neanderthals and us diverging at a later date, about 370 000 years ago. There was a comment that this was not much of a controversy; since the portion sequenced so far isn't large, these dates still have overlapping error margins.

Bruno

[xilman]

Originally Posted by Jwb52z

As scientifically fascinating as it is, these kinds of ideas take away from humanity's specialness, as I see it. If we just happened to come in contact with something that made us the way we are, we end up no better than the various uncivilized creatures/animals on the planet. Yes, we may find out that some mutation effect protects us from a disease, but the fact of how it got there, in my opinion, lessens humanity from what I think it's rightful place is when that idea becomes widely known or accepted.

Whether you like it or not, the evidence strongly suggests that such events happen all the time and in many species.

Look up the word "transposon" in Wikipedia.

Almost all wild Drosophila melanogaster individuals have been infected with these things over the last century or so. I believe a few lab stocks are still uncontaminated but I'm not entirely sure of that claim.

(Statement of interest: I'm presently employed by FlyBase. Transposons and their aoosicated molecular bits and pieces are both a source of great complexity and a powerful mechanism for exploring the Drosophila genome.)

Paul

[mfgoode]

In this post I am not advocating Creationism or backing evolution.
I'm sending this URL so that it will make us think. Please click on the other links (Top stories at the end) to get a better perspective.

http://www.space.com/scienceastronom...ds_020327.html

Mally

[Xyzzy]

http://www.nytimes.com/2006/12/10/sc...d3383d&ei=5088

[Uncwilly]

Originally Posted by Xyzzy

http://www.nytimes.com/2006/12/10/sc...d3383d&ei=5088

That is not 'Evolution'.

[jinydu]

Originally Posted by Uncwilly

That is not 'Evolution'.

And why not? It is a systematic change in a population's distribution of genotypes brought about by natural selection.

[Uncwilly]

Originally Posted by jinydu

And why not? It is a systematic change in a population's distribution of genotypes brought about by natural selection.

The natural variation within a species can drift around with out it being 'Evoultion' (note the capital and quotes). This is the same thing that has happened with the peppered moth. Movement within the bounds of a species is normal and not the same as the branching out of a species into a different one. Just because the Sweedes tend to look different than Nigerians, does not make them a different subspecies.