Kissing cousins
HOW Neanderthal are you? That question sounds vaguely insulting. But unless you are African, or of recent African ancestry, the answer is likely to be 1-3%.
Though Homo sapiens is the only type of human around at the moment, that was not true until recently. Sixty thousand years ago, when modern humans first left Africa, they encountered other species of humanity, such as Neanderthals (imagined above, in an artist’s interpretation), in Europe and Asia. In some cases, they interbred with them. The genetic traces of those encounters remain in modern human genomes. And two studies, one just published in Nature, and one in Science, have now looked in detail at this miscegenation, and tried to understand its consequences.
The Nature study, conducted by Sriram Sankararaman of Harvard Medical School and his colleagues, looked at the genomes of 1,004 living people of European and Asian descent and compared them with Neanderthal DNA from a 50,000-year-old toe bone found in a Siberian cave, and also with the genomes of 176 west Africans. This latter group, Dr Sankararaman assumed, could have little Neanderthal DNA in them because Neanderthals, as far as can be determined from the fossil record, lived only in Europe and western Asia.
Dr Sankararaman and his colleagues certainly did find plenty of DNA which seems to have come from Neanderthals in their Eurasians. Tellingly, it was not sprinkled evenly throughout the modern human genome. That let them make educated guesses about the effects it is having on those who carry it. For instance, genes affecting the production of keratin—an important component of hair and skin—showed more Neanderthal influence than most. Neanderthals, whose homeland was much colder then than it is now because of the ice age, were hairier (and thus better insulated) than Homo sapiens. Retaining Neanderthal traits of this sort, in an African species that was trying to make good in sub-Arctic conditions, would thus be encouraged by natural selection.
More surprisingly, Dr Sankararaman also found Neanderthal DNA in genes associated with diabetes, Crohn’s disease, lupus and even the propensity to smoke. This does not necessarily mean such DNA was bad for those who inherited it. A gene which increases the risk of diabetes in modern circumstances of abundant food might, for example, have had benefits in a more austere environment.
Indeed, truly deleterious DNA would be expected to be noticeable by its absence, because natural selection would have worked to eliminate it in the 30,000 years since Neanderthals died out. And Dr Sankararaman found evidence for exactly that, as well.
There is, for example, little Neanderthal DNA on the X chromosome (which, along with the Y chromosome, determines an individual’s sex). Nor is there much in genes that are expressed in the testicles. Studies from other hybrid animals, which are frequently sterile, suggest genes which reduce male fertility are often found on the X chromosome. Since few things are a bigger evolutionary no-no than being unable to produce children, tremendous selective pressure would have existed to remove the offending DNA from the hybrid descendants of Neanderthals and Homo sapiens.
The study published in Science, by Benjamin Vernot and Joshua Akey of the University of Washington, in Seattle, reaches similar conclusions to Dr Sankararaman’s. Dr Vernot and Dr Akey hunted down Neanderthal DNA in the genomes of 665 Europeans and East Asians. They, too, found evidence of its having inserted itself into genes associated with the skin, and that not all of the newly arrived genetic material is helpful to its current bearers.
They made other discoveries, too. With the help of computer models, they concluded that there were probably several pulses of interbreeding over the millennia, rather than a steady stream of it. Both they and Dr Sankararaman also found that, on average, East Asians have more Neanderthal DNA than Europeans do—which is odd, because Neanderthals are not known to have lived in East Asia.
The ghost in the machine
Dr Vernot and Dr Akey also used their data to try to improve understanding of the Neanderthal genome itself, by combining the bits and bobs scattered among modern humans. Though both their study and Dr Sankararaman’s depended on being able to identify what was Neanderthal by comparing modern human genomes with fossil DNA, the fossil material available is imperfect. Looking at the exact sequence of DNA “letters” (the chemical bases which carry the genetic message) in areas identified as Neanderthal in modern genomes can therefore improve understanding of the Neanderthal original.
Crucially, though the amount of Neanderthal DNA in any individual is small, the exact bits vary a lot from person to person. Look at enough people, then, and it becomes possible to rebuild quite large swathes of the Neanderthal genome. Dr Vernot and Dr Akey reckon that from their sample of 665 they have recovered around 20% of it.
This is an impressive figure for an extinct species. It shows just how much the concept of a “species” is a construct of human thinking rather than a truly natural category. Technically, Neanderthals may be gone. But their DNA ghosts linger on.
From the print edition: Science and technology
ORIGINAL: The Economist
HOW Neanderthal are you? That question sounds vaguely insulting. But unless you are African, or of recent African ancestry, the answer is likely to be 1-3%.
Though Homo sapiens is the only type of human around at the moment, that was not true until recently. Sixty thousand years ago, when modern humans first left Africa, they encountered other species of humanity, such as Neanderthals (imagined above, in an artist’s interpretation), in Europe and Asia. In some cases, they interbred with them. The genetic traces of those encounters remain in modern human genomes. And two studies, one just published in Nature, and one in Science, have now looked in detail at this miscegenation, and tried to understand its consequences.
The Nature study, conducted by Sriram Sankararaman of Harvard Medical School and his colleagues, looked at the genomes of 1,004 living people of European and Asian descent and compared them with Neanderthal DNA from a 50,000-year-old toe bone found in a Siberian cave, and also with the genomes of 176 west Africans. This latter group, Dr Sankararaman assumed, could have little Neanderthal DNA in them because Neanderthals, as far as can be determined from the fossil record, lived only in Europe and western Asia.
Dr Sankararaman and his colleagues certainly did find plenty of DNA which seems to have come from Neanderthals in their Eurasians. Tellingly, it was not sprinkled evenly throughout the modern human genome. That let them make educated guesses about the effects it is having on those who carry it. For instance, genes affecting the production of keratin—an important component of hair and skin—showed more Neanderthal influence than most. Neanderthals, whose homeland was much colder then than it is now because of the ice age, were hairier (and thus better insulated) than Homo sapiens. Retaining Neanderthal traits of this sort, in an African species that was trying to make good in sub-Arctic conditions, would thus be encouraged by natural selection.
More surprisingly, Dr Sankararaman also found Neanderthal DNA in genes associated with diabetes, Crohn’s disease, lupus and even the propensity to smoke. This does not necessarily mean such DNA was bad for those who inherited it. A gene which increases the risk of diabetes in modern circumstances of abundant food might, for example, have had benefits in a more austere environment.
Indeed, truly deleterious DNA would be expected to be noticeable by its absence, because natural selection would have worked to eliminate it in the 30,000 years since Neanderthals died out. And Dr Sankararaman found evidence for exactly that, as well.
There is, for example, little Neanderthal DNA on the X chromosome (which, along with the Y chromosome, determines an individual’s sex). Nor is there much in genes that are expressed in the testicles. Studies from other hybrid animals, which are frequently sterile, suggest genes which reduce male fertility are often found on the X chromosome. Since few things are a bigger evolutionary no-no than being unable to produce children, tremendous selective pressure would have existed to remove the offending DNA from the hybrid descendants of Neanderthals and Homo sapiens.
The study published in Science, by Benjamin Vernot and Joshua Akey of the University of Washington, in Seattle, reaches similar conclusions to Dr Sankararaman’s. Dr Vernot and Dr Akey hunted down Neanderthal DNA in the genomes of 665 Europeans and East Asians. They, too, found evidence of its having inserted itself into genes associated with the skin, and that not all of the newly arrived genetic material is helpful to its current bearers.
They made other discoveries, too. With the help of computer models, they concluded that there were probably several pulses of interbreeding over the millennia, rather than a steady stream of it. Both they and Dr Sankararaman also found that, on average, East Asians have more Neanderthal DNA than Europeans do—which is odd, because Neanderthals are not known to have lived in East Asia.
The ghost in the machine
Dr Vernot and Dr Akey also used their data to try to improve understanding of the Neanderthal genome itself, by combining the bits and bobs scattered among modern humans. Though both their study and Dr Sankararaman’s depended on being able to identify what was Neanderthal by comparing modern human genomes with fossil DNA, the fossil material available is imperfect. Looking at the exact sequence of DNA “letters” (the chemical bases which carry the genetic message) in areas identified as Neanderthal in modern genomes can therefore improve understanding of the Neanderthal original.
Crucially, though the amount of Neanderthal DNA in any individual is small, the exact bits vary a lot from person to person. Look at enough people, then, and it becomes possible to rebuild quite large swathes of the Neanderthal genome. Dr Vernot and Dr Akey reckon that from their sample of 665 they have recovered around 20% of it.
This is an impressive figure for an extinct species. It shows just how much the concept of a “species” is a construct of human thinking rather than a truly natural category. Technically, Neanderthals may be gone. But their DNA ghosts linger on.
From the print edition: Science and technology
ORIGINAL: The Economist
Feb 1st 2014
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