Reports comparing our DNA with that of our extinct ancestors are coming in so fast and are so momentous that it is just exhausting trying to keep up! Rapid advances in DNA technology have resulted in discoveries that were thought to have improbable just ten years ago. It seems every month brings a new announcement regarding human evolution that is so persuasive that many long-festering debates are now essentially over. (Well, as “over” as they ever are in science, which means the next five years will probably overturn what we think we know today.)
When the first reports of soft tissue being isolated from a 65-million-year-old Tyrannosaurus rex thigh bone hit the press in 2005, the world’s collective jaw dropped. The researchers described finding blood vessels and collagen (the main protein in connective tissue) in otherwise fossilized bone. Who would have ever thought such a thing was possible? Then two years later, an analysis of the amino acid sequence of the collagen protein indicated that, when compared to modern animals, it was most closely related to chickens, thus providing very nice independent confirmation that birds are direct descendants of dinosaurs, a theory that was previously based solely on skeletal comparisons. It is so satisfying when independent discoveries reinforce each other—it just doesn’t get any better than that!
While we have had pretty good luck in finding these very ancient proteins, isolating ancient DNA has been much more difficult because of its susceptibility to degradation from exposure to the elements, particularly moisture and heat. Because it is so very precise, ancient DNA is the Holy Grail of on-going efforts to work out the evolutionary connections between modern humans and our ancestors. After all, if DNA can be used as conclusive proof of genetic identity in forensic science why wouldn’t it be just as powerful for establishing evolutionary relationships?
So far the oldest DNA has been found in remains of modern human ancestors. In 1997 the first DNA extractions were made from a Neanderthal skeleton estimated to be between 30,000 and 100,000 years old, based on classical fossil dating techniques. Then in 2010, a complete DNA analysis was done on the entire Neanderthal genome (that is, all of its DNA), and the results were compared to the human genome. Pretty impressive, but not so impressive as the conclusion: that 1-4% of European DNA may have been inherited from the Neanderthals.
In 2011 the same researchers analyzed DNA extractions from a 50,000-year-old skeleton from Siberia. Holy cow—turns out SHE is distinct enough to be placed in a new category separate from Neanderthal—Denisovan. So now we have three major contemporaneous humanoid groups: Neanderthals, Denisovans, and humans, all genetically very similar.
Then in 2012, it was reported that researchers had compared DNA from the Denisovan girl to DNA from modern humans and found 111,812 single-nucleotide differences. That sounds like a lot, but since the human genome has six billion nucleotides, it is actually pretty small (a difference of a little more than a thousandth of one percent). The Denisovan genome is so complete that researchers have been able to determine the color of the individual’s eyes, hair, and skin. More importantly, they have detected differences in various genes associated with speech disorders, disease, and the wiring of the nervous system. Think about it—this means that in the not-so-distant future scientists may be able to tell exactly what genetic changes would be necessary to convert a Denisovan or Neanderthal into a modern human—or the reverse!
That brings up another really interesting question, which is how much humans have in common with chimpanzees, our closest non-human “relatives”. It turns out that chimp DNA differs from human DNA, on average, by only about 90 million nucleotides (1.5%). You could say that chimpanzees are 98.5% human, but they might not take it as a compliment since by these same measures, a banana is about 60% human.
Another question, and one that has been at the root of the human evolution debates, is how long ago did humans and chimps diverge? Well, another paper published just this August pretty much nails it. First of all, based only on fossil evidence from the 400 or so skeletons that have been found so far, it has been estimated that Neanderthals lived from about 800,000 to 40,000 years ago. The same fossil evidence has placed the divergence between chimps and humans at three to five million years ago.
The problem is that fossil dating is uncertain. Fossils are found in rocks after all—they ARE rocks. Rocks move. And erode. And get contaminated. So in spite of the use of elaborate techniques based on elemental changes that are known to have occurred in rock over time, the dating of fossils remains subject to question. This has always cast doubt on the conclusions reached by anthropologists concerning the timeline for human/chimp divergence. So what we really need is another way to get at the answer to this question that avoids the problems associated with fossil dating.
It turns out that DNA changes over time at a rate that can be used to BACK CALCULATE how old skeletons are. How? By using the rate of change from one generation to the next. This means that known rates of change in DNA can be used to determine the age of Neanderthal and Denisovan skeletons as well as to estimate the time elapsed since the divergence of humans and chimps. The way this is done is by comparing the differences in DNA between parents and offspring. If you know how long a single generation lasts (25-30 years in both chimps and humans), you can calculate the spontaneous mutation rate (number of changes in nucleotides/year). And that is all you need.
An August 2012 paper reported that the application of the known mutation rate to the analysis of chimp DNA indicates that divergence between chimps and humans occurred 7-8 million years ago. These DNA-based findings place the split a bit earlier than the fossil-derived dates geologists and anthropologists have been giving us for years, but not egregiously so. The same kind of calculations for Neanderthal DNA shows a human split between the two of about 400,000 to 800,000 years ago—within the range that anthropologists have found using fossil data.
And so we have two COMPLETELY different methods of estimating the timeframe for human evolution, and they are very concordant considering the vast lengths of time involved. No longer can one dispute the estimates by arguments against “old fossils” and their presumed inaccuracy in dating. (Well, I guess you could, but that argument is now very much weakened, at least in my mind.)
There are many more questions remaining to be answered. First, it is important to stress that even though there is a smooth continuum in terms of genetic differences between Neanderthals and humans, and between Denisovans and humans, that does not mean humans descended from these ancient “cousins.” In fact, the skeletal information says they did not. Neanderthals and humans probably shared a common ancestor—perhaps the well-known Homo erectus, who lived from about 1.8 million to 300,000 years ago. Exactly where Homo erectus and the far older Homo habilis (2.3 million to 1.4 million years ago) fit into this ever-more-branching and complicated picture remains to be seen. Then there is the genus Australopithecus, which may have given rise to the genus Homo, and lived 4 million to 2 million years ago. Australopithecus itself has 3-4 species, depending on one’s taxonomic orientation. Closely related to Australopithecus is the genus Paranthropus, who appeared on the scene 2.7 million years ago. And then there is Ardipithecus, which may have predated the split between chimpanzees and humans.
And so we have a virtual bestiary of bi-pedal ancestors, a thorny bush of complex relationships, many competing to be Homo’s ancestor. But you can rest assured that if researchers are able to isolate proteins from a 65-million-year-old T. rex and DNA from 100,000-year-old skeletons, there are scientists out there somewhere who are trying to isolate proteins and possibly even DNA from Homo erectus, and maybe even from Australopithecus and Paranthropus fossils. And maybe proteins will be found to be just as diagnostic for fossil age as DNA is turning out to be.
These complex taxonomic and evolutionary relationships will be sorted out in time. As the cost of molecular investigation continues to fall and more and more people learn the laboratory techniques involved, the Homo family tree will probably be simplified. The time is ripe for collaborations between anthropologists and geneticists to answer questions that have been around for 150 years.
But, as with all science, there will be huge surprises. New skeletons will be found and theories will be overturned. But with enough research funding, good science moves inexorably forward.
When the first reports of soft tissue being isolated from a 65-million-year-old Tyrannosaurus rex thigh bone hit the press in 2005, the world’s collective jaw dropped. The researchers described finding blood vessels and collagen (the main protein in connective tissue) in otherwise fossilized bone. Who would have ever thought such a thing was possible? Then two years later, an analysis of the amino acid sequence of the collagen protein indicated that, when compared to modern animals, it was most closely related to chickens, thus providing very nice independent confirmation that birds are direct descendants of dinosaurs, a theory that was previously based solely on skeletal comparisons. It is so satisfying when independent discoveries reinforce each other—it just doesn’t get any better than that!
While we have had pretty good luck in finding these very ancient proteins, isolating ancient DNA has been much more difficult because of its susceptibility to degradation from exposure to the elements, particularly moisture and heat. Because it is so very precise, ancient DNA is the Holy Grail of on-going efforts to work out the evolutionary connections between modern humans and our ancestors. After all, if DNA can be used as conclusive proof of genetic identity in forensic science why wouldn’t it be just as powerful for establishing evolutionary relationships?
So far the oldest DNA has been found in remains of modern human ancestors. In 1997 the first DNA extractions were made from a Neanderthal skeleton estimated to be between 30,000 and 100,000 years old, based on classical fossil dating techniques. Then in 2010, a complete DNA analysis was done on the entire Neanderthal genome (that is, all of its DNA), and the results were compared to the human genome. Pretty impressive, but not so impressive as the conclusion: that 1-4% of European DNA may have been inherited from the Neanderthals.
In 2011 the same researchers analyzed DNA extractions from a 50,000-year-old skeleton from Siberia. Holy cow—turns out SHE is distinct enough to be placed in a new category separate from Neanderthal—Denisovan. So now we have three major contemporaneous humanoid groups: Neanderthals, Denisovans, and humans, all genetically very similar.
Then in 2012, it was reported that researchers had compared DNA from the Denisovan girl to DNA from modern humans and found 111,812 single-nucleotide differences. That sounds like a lot, but since the human genome has six billion nucleotides, it is actually pretty small (a difference of a little more than a thousandth of one percent). The Denisovan genome is so complete that researchers have been able to determine the color of the individual’s eyes, hair, and skin. More importantly, they have detected differences in various genes associated with speech disorders, disease, and the wiring of the nervous system. Think about it—this means that in the not-so-distant future scientists may be able to tell exactly what genetic changes would be necessary to convert a Denisovan or Neanderthal into a modern human—or the reverse!
That brings up another really interesting question, which is how much humans have in common with chimpanzees, our closest non-human “relatives”. It turns out that chimp DNA differs from human DNA, on average, by only about 90 million nucleotides (1.5%). You could say that chimpanzees are 98.5% human, but they might not take it as a compliment since by these same measures, a banana is about 60% human.
Another question, and one that has been at the root of the human evolution debates, is how long ago did humans and chimps diverge? Well, another paper published just this August pretty much nails it. First of all, based only on fossil evidence from the 400 or so skeletons that have been found so far, it has been estimated that Neanderthals lived from about 800,000 to 40,000 years ago. The same fossil evidence has placed the divergence between chimps and humans at three to five million years ago.
The problem is that fossil dating is uncertain. Fossils are found in rocks after all—they ARE rocks. Rocks move. And erode. And get contaminated. So in spite of the use of elaborate techniques based on elemental changes that are known to have occurred in rock over time, the dating of fossils remains subject to question. This has always cast doubt on the conclusions reached by anthropologists concerning the timeline for human/chimp divergence. So what we really need is another way to get at the answer to this question that avoids the problems associated with fossil dating.
It turns out that DNA changes over time at a rate that can be used to BACK CALCULATE how old skeletons are. How? By using the rate of change from one generation to the next. This means that known rates of change in DNA can be used to determine the age of Neanderthal and Denisovan skeletons as well as to estimate the time elapsed since the divergence of humans and chimps. The way this is done is by comparing the differences in DNA between parents and offspring. If you know how long a single generation lasts (25-30 years in both chimps and humans), you can calculate the spontaneous mutation rate (number of changes in nucleotides/year). And that is all you need.
An August 2012 paper reported that the application of the known mutation rate to the analysis of chimp DNA indicates that divergence between chimps and humans occurred 7-8 million years ago. These DNA-based findings place the split a bit earlier than the fossil-derived dates geologists and anthropologists have been giving us for years, but not egregiously so. The same kind of calculations for Neanderthal DNA shows a human split between the two of about 400,000 to 800,000 years ago—within the range that anthropologists have found using fossil data.
And so we have two COMPLETELY different methods of estimating the timeframe for human evolution, and they are very concordant considering the vast lengths of time involved. No longer can one dispute the estimates by arguments against “old fossils” and their presumed inaccuracy in dating. (Well, I guess you could, but that argument is now very much weakened, at least in my mind.)
There are many more questions remaining to be answered. First, it is important to stress that even though there is a smooth continuum in terms of genetic differences between Neanderthals and humans, and between Denisovans and humans, that does not mean humans descended from these ancient “cousins.” In fact, the skeletal information says they did not. Neanderthals and humans probably shared a common ancestor—perhaps the well-known Homo erectus, who lived from about 1.8 million to 300,000 years ago. Exactly where Homo erectus and the far older Homo habilis (2.3 million to 1.4 million years ago) fit into this ever-more-branching and complicated picture remains to be seen. Then there is the genus Australopithecus, which may have given rise to the genus Homo, and lived 4 million to 2 million years ago. Australopithecus itself has 3-4 species, depending on one’s taxonomic orientation. Closely related to Australopithecus is the genus Paranthropus, who appeared on the scene 2.7 million years ago. And then there is Ardipithecus, which may have predated the split between chimpanzees and humans.
And so we have a virtual bestiary of bi-pedal ancestors, a thorny bush of complex relationships, many competing to be Homo’s ancestor. But you can rest assured that if researchers are able to isolate proteins from a 65-million-year-old T. rex and DNA from 100,000-year-old skeletons, there are scientists out there somewhere who are trying to isolate proteins and possibly even DNA from Homo erectus, and maybe even from Australopithecus and Paranthropus fossils. And maybe proteins will be found to be just as diagnostic for fossil age as DNA is turning out to be.
These complex taxonomic and evolutionary relationships will be sorted out in time. As the cost of molecular investigation continues to fall and more and more people learn the laboratory techniques involved, the Homo family tree will probably be simplified. The time is ripe for collaborations between anthropologists and geneticists to answer questions that have been around for 150 years.
But, as with all science, there will be huge surprises. New skeletons will be found and theories will be overturned. But with enough research funding, good science moves inexorably forward.
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