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New DNA Analysis Shows Ancient Humans Interbred with Denisovans

35 points by daegloe 14y ago

lifeisstillgood 14y ago
The most obvious worry about the "new" science of defining species by DNA analysis, is that we will eventually "prove" humans are no longer one species. I know its all just definitions, but fairly big wars get fought over less. (But only by those non-humans. We humans are peaceful) A quick goolge does not tell me what are the actual differences in mtDNA genome that says "yes" this lot are not Homo sapiens, nor how much of a difference counts. Anyone?
- CreRecombinase 14y ago
  I really don't see any way you could possible come to such a conclusion. By really any definition of a species, humans are one species. Not only that, but as a consequence of the youth of our species, the amount of genetic variation amongst humans really pales in comparison to the variation found in other species. If anything, I think the lesson of genomics is that the concept of a "species" is less useful than it has ever been.
  - lifeisstillgood 14y ago
    Someone has come to a definition of a species that is a) definable through DNA sequencing of a finger bone b) excludes from being Human, a girl 40,000 years old whom the articvle claims we mated with and had offspring as her DNA is also found in modern day humans. So, unless I got some facts wrong, quite possible, it is possible to mate with humans and have viable offspring and still be defined as non human by DNA testing. That has implications. I would like to understand the science.
- ktizo 14y ago
  A quick goolge does not tell me what are the actual differences in mtDNA genome that says "yes" this lot are not Homo sapiens, nor how much of a difference counts. Anyone? That's not how it works. The only "measurement" that really defines species is ability to have viable offspring. And even that border is wide and very fuzzy. Ligers and Tigons are good examples of this.
- fghh45sdfhr3 14y ago
  The most obvious worry about the "new" science of defining species by DNA analysis, is that we will eventually "prove" humans are no longer one species. The official scientific definition of species is old and very well known and very well defined. A species breeds successfully with itself. If you can't produce fertile offspring then you are two species. Horses and Donkeys are two species because mules can not reproduce. Even if A + B = C, and C + C = D, if D + D = nothing, then A and B are separate species. So no matter who or what we interbred with, or how large our genetic differences are, we are obviously one species. And or "large" genetic differences are actually tiny compared to what you can find in say chimpanzees.
  - lifeisstillgood 14y ago
    Edit: Trying to be clearer The official definition of species seems to be shifting. The article claims that humans interbred with Denisovans, implying that the offspring were viable and lead to us, and that they could distinguish between ancient humans and Denisovians via DNA testing. That implies to me, that Denisovians and Humans are distinct species, and can be told apart by some DNA testing. I am interested in the process of defining of species via DNA - the implications for that seem reasonable to infer given our unpleasant history. What did they measure - which part of the genome did they say is human and which Denisovans. Are those sequences ever found in modern humans? Could they be? What would that human who had more Denisovian DNA than typical be called? Why? There are two things here - the scientific metrics used, and the political decision to turn metrics into loaded words like species. I can argue all day over the second but I have no infomration on the first.
    - fghh45sdfhr3 14y ago
      That implies to me, that Denisovians and Humans are distinct species, and can be told apart by some DNA testing. You can tell apart almost any two groups of modern humans with DNA testing. You can tell apart paternal twins with DNA testing, that doesn't make them two different species. Are those sequences ever found in modern humans? Yes. Could they be? Yes. What would that human who had more Denisovian DNA than typical be called? Well today Neanderthal DNA in humans can range from almost nothing to as much as if your great grand father was pure Neanderthal. What do we call either extreme? Human.
tokenadult 14y ago
Here's the key sentence in the article: "'We're looking at a very interesting population scenario'—one that does not jibe entirely with what we thought we knew about how waves modern human populations migrated into and through Asia and out to Oceania's islands." Svante Pääbo was the pioneer of doing DNA sequencing on samples of old human tissues (he started with Egyptian mummies when he was an Egyptologist). I heard a lecture by Pääbo at the 2008 Nobel Conference https://gustavus.edu/events/nobelconference/2008/presenters.php https://gustavus.edu/events/nobelconference/2008/presenters.... and heard there from some of the other researchers who use DNA analysis to trace human origins. One of the problems in the discipline so far, as you can well figure out for yourself by thinking about it, is that the sample sizes for defining what genome pattern is "modern human" are still remarkably small, especially when we get to full genome sequences of individuals with well determined geographic origin, and smaller still for Neanderthal sequences and smallest of all for Denisovan sequences. So much work still needs to be done to figure out what the usual range of free variation of genes that are not under strong selection pressure is in the hominin genome line. Figuring out what genes actually do at the individual level in a genome as complicated as the human genome has turned out to be much harder than was first supposed (as mentioned in the submitted article), so while tracing lineages with gene markers that are not under strong selection pressure helps define geographical population groups with common founder populations, knowing even an individual's complete genome does little to show the traits of the individual. (The first human genome sequenced didn't even reveal that the sequenced individual has blue eyes, for example.) Turkheimer, E. (2012). Genome wide association studies of behavior are social science. In K. S. Plaisance & T.A.C. Reydon (Eds.) Philosophy of Behavioral Biology (pp. 43-64). New York, NY: Springer. http://people.virginia.edu/~ent3c/papers2/Turkheimer%20GWAS%20EWAS%20Final.pdf http://people.virginia.edu/~ent3c/papers2/Turkheimer%20GWAS%... "If the history of empirical psychology has taught researchers anything, it is that correlations between causally distant variables cannot be counted on to lead to coherent etiological models." "Most Genetic Associations with General Intelligence Probably False Positives" http://www.arts.cornell.edu/econ/dbenjamin/IQ-SNPs-PsychSci-20111205-accepted.pdf http://www.arts.cornell.edu/econ/dbenjamin/IQ-SNPs-PsychSci-... Johnson, Penke, and Spinath (2011) "Understanding Heritability: What it is and What it is Not" http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_Heritability_rejoinder.pdf http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_He... "Presuming this is correct and, as Visscher and Keller appear to have implied, applicable to most behavioural traits, this indicates that literally thousands of genes are likely involved in each trait, with no single polymorphism having substantial effect, which is the quasi-in?nite model to which Munafo and Flint refer. Whatever would we as psychologists do with such information?" AFTER EDIT: The interesting question raised by the top-level comment that was posted before this comment has received some good replies. The question, and the issue of defining a "species," reminds me of what Richard Dawkins points out about common descent. If you lined up in a line by order of descent with ALL of your ancestors, including the ancestors no longer living, as you looked at each individual in the line you could say "He is the son of the father standing next to him," going back as far as you want, even hundreds of millions of years, and yet at some point in the deep past the ancestors would not look anything at all like "humans," or indeed even like mammals or like tetrapods. At the individual level, OF COURSE you are part of the same species as your parents (by definition of "species"). Life on Earth today has a common ancestor, or at the very least a common set of one-celled ancestors, by general agreement of biologists, so all the species that have differentiated from one another over time can be traced to common ancestors of multiple species. You are undoubtedly related to your parents, who belong to the same species you do, but you have remote ancestors whom no one would call individuals of the species Homo sapiens. There simply isn't any definite line to draw between one species and the next, historically, and that was what was shocking about Darwin's idea of branching speciation from common ancestors, the only idea he presented visually in his book The Origin of Species. For a book-length treatment of speciation as a scientific issue for the thoroughly curious, see Speciation by Jerry A. Coyne and H. Allen Orr, http://www.amazon.com/Speciation-Jerry-A-Coyne/dp/0878930892 http://www.amazon.com/Speciation-Jerry-A-Coyne/dp/0878930892 which discusses mechanisms of speciation and how theories about those mechanisms are tested by biologists. ONE MORE EDIT: The questioner in the other top-level comment is coming back with follow-up questions, which is good. The simple answer to the basic question is that biologists properly do NOT define a "species" by looking at DNA sequences, but by looking at reproductive behavior. For individuals who are dead and long gone, out inferences about reproductive behavior, and thus species definitions, are weak, and we shouldn't rely on a single DNA sequence to say a sample of old bones belongs to a different "species" from another sample of old bones until we gather other forms of evidence about the possibility of the individuals mating and having offspring with each other.

35 points by daegloe 14y ago

The most obvious worry about the "new" science of defining species by DNA analysis, is that we will eventually "prove" humans are no longer one species. I know its all just definitions, but fairly big wars get fought over less. (But only by those non-humans. We humans are peaceful) A quick goolge does not tell me what are the actual differences in mtDNA genome that says "yes" this lot are not Homo sapiens, nor how much of a difference counts. Anyone?

CreRecombinase 14y ago
I really don't see any way you could possible come to such a conclusion. By really any definition of a species, humans are one species. Not only that, but as a consequence of the youth of our species, the amount of genetic variation amongst humans really pales in comparison to the variation found in other species. If anything, I think the lesson of genomics is that the concept of a "species" is less useful than it has ever been.
- lifeisstillgood 14y ago
  Someone has come to a definition of a species that is a) definable through DNA sequencing of a finger bone b) excludes from being Human, a girl 40,000 years old whom the articvle claims we mated with and had offspring as her DNA is also found in modern day humans. So, unless I got some facts wrong, quite possible, it is possible to mate with humans and have viable offspring and still be defined as non human by DNA testing. That has implications. I would like to understand the science.
ktizo 14y ago
A quick goolge does not tell me what are the actual differences in mtDNA genome that says "yes" this lot are not Homo sapiens, nor how much of a difference counts. Anyone? That's not how it works. The only "measurement" that really defines species is ability to have viable offspring. And even that border is wide and very fuzzy. Ligers and Tigons are good examples of this.
fghh45sdfhr3 14y ago
The most obvious worry about the "new" science of defining species by DNA analysis, is that we will eventually "prove" humans are no longer one species. The official scientific definition of species is old and very well known and very well defined. A species breeds successfully with itself. If you can't produce fertile offspring then you are two species. Horses and Donkeys are two species because mules can not reproduce. Even if A + B = C, and C + C = D, if D + D = nothing, then A and B are separate species. So no matter who or what we interbred with, or how large our genetic differences are, we are obviously one species. And or "large" genetic differences are actually tiny compared to what you can find in say chimpanzees.
- lifeisstillgood 14y ago
  Edit: Trying to be clearer The official definition of species seems to be shifting. The article claims that humans interbred with Denisovans, implying that the offspring were viable and lead to us, and that they could distinguish between ancient humans and Denisovians via DNA testing. That implies to me, that Denisovians and Humans are distinct species, and can be told apart by some DNA testing. I am interested in the process of defining of species via DNA - the implications for that seem reasonable to infer given our unpleasant history. What did they measure - which part of the genome did they say is human and which Denisovans. Are those sequences ever found in modern humans? Could they be? What would that human who had more Denisovian DNA than typical be called? Why? There are two things here - the scientific metrics used, and the political decision to turn metrics into loaded words like species. I can argue all day over the second but I have no infomration on the first.
  - fghh45sdfhr3 14y ago
    That implies to me, that Denisovians and Humans are distinct species, and can be told apart by some DNA testing. You can tell apart almost any two groups of modern humans with DNA testing. You can tell apart paternal twins with DNA testing, that doesn't make them two different species. Are those sequences ever found in modern humans? Yes. Could they be? Yes. What would that human who had more Denisovian DNA than typical be called? Well today Neanderthal DNA in humans can range from almost nothing to as much as if your great grand father was pure Neanderthal. What do we call either extreme? Human.

tokenadult 14y ago

Here's the key sentence in the article: "'We're looking at a very interesting population scenario'—one that does not jibe entirely with what we thought we knew about how waves modern human populations migrated into and through Asia and out to Oceania's islands." Svante Pääbo was the pioneer of doing DNA sequencing on samples of old human tissues (he started with Egyptian mummies when he was an Egyptologist). I heard a lecture by Pääbo at the 2008 Nobel Conference https://gustavus.edu/events/nobelconference/2008/presenters.php https://gustavus.edu/events/nobelconference/2008/presenters.... and heard there from some of the other researchers who use DNA analysis to trace human origins. One of the problems in the discipline so far, as you can well figure out for yourself by thinking about it, is that the sample sizes for defining what genome pattern is "modern human" are still remarkably small, especially when we get to full genome sequences of individuals with well determined geographic origin, and smaller still for Neanderthal sequences and smallest of all for Denisovan sequences. So much work still needs to be done to figure out what the usual range of free variation of genes that are not under strong selection pressure is in the hominin genome line. Figuring out what genes actually do at the individual level in a genome as complicated as the human genome has turned out to be much harder than was first supposed (as mentioned in the submitted article), so while tracing lineages with gene markers that are not under strong selection pressure helps define geographical population groups with common founder populations, knowing even an individual's complete genome does little to show the traits of the individual. (The first human genome sequenced didn't even reveal that the sequenced individual has blue eyes, for example.) Turkheimer, E. (2012). Genome wide association studies of behavior are social science. In K. S. Plaisance & T.A.C. Reydon (Eds.) Philosophy of Behavioral Biology (pp. 43-64). New York, NY: Springer. http://people.virginia.edu/~ent3c/papers2/Turkheimer%20GWAS%20EWAS%20Final.pdf http://people.virginia.edu/~ent3c/papers2/Turkheimer%20GWAS%... "If the history of empirical psychology has taught researchers anything, it is that correlations between causally distant variables cannot be counted on to lead to coherent etiological models." "Most Genetic Associations with General Intelligence Probably False Positives" http://www.arts.cornell.edu/econ/dbenjamin/IQ-SNPs-PsychSci-20111205-accepted.pdf http://www.arts.cornell.edu/econ/dbenjamin/IQ-SNPs-PsychSci-... Johnson, Penke, and Spinath (2011) "Understanding Heritability: What it is and What it is Not" http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_Heritability_rejoinder.pdf http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_He... "Presuming this is correct and, as Visscher and Keller appear to have implied, applicable to most behavioural traits, this indicates that literally thousands of genes are likely involved in each trait, with no single polymorphism having substantial effect, which is the quasi-in?nite model to which Munafo and Flint refer. Whatever would we as psychologists do with such information?" AFTER EDIT: The interesting question raised by the top-level comment that was posted before this comment has received some good replies. The question, and the issue of defining a "species," reminds me of what Richard Dawkins points out about common descent. If you lined up in a line by order of descent with ALL of your ancestors, including the ancestors no longer living, as you looked at each individual in the line you could say "He is the son of the father standing next to him," going back as far as you want, even hundreds of millions of years, and yet at some point in the deep past the ancestors would not look anything at all like "humans," or indeed even like mammals or like tetrapods. At the individual level, OF COURSE you are part of the same species as your parents (by definition of "species"). Life on Earth today has a common ancestor, or at the very least a common set of one-celled ancestors, by general agreement of biologists, so all the species that have differentiated from one another over time can be traced to common ancestors of multiple species. You are undoubtedly related to your parents, who belong to the same species you do, but you have remote ancestors whom no one would call individuals of the species Homo sapiens. There simply isn't any definite line to draw between one species and the next, historically, and that was what was shocking about Darwin's idea of branching speciation from common ancestors, the only idea he presented visually in his book The Origin of Species. For a book-length treatment of speciation as a scientific issue for the thoroughly curious, see Speciation by Jerry A. Coyne and H. Allen Orr, http://www.amazon.com/Speciation-Jerry-A-Coyne/dp/0878930892 http://www.amazon.com/Speciation-Jerry-A-Coyne/dp/0878930892 which discusses mechanisms of speciation and how theories about those mechanisms are tested by biologists. ONE MORE EDIT: The questioner in the other top-level comment is coming back with follow-up questions, which is good. The simple answer to the basic question is that biologists properly do NOT define a "species" by looking at DNA sequences, but by looking at reproductive behavior. For individuals who are dead and long gone, out inferences about reproductive behavior, and thus species definitions, are weak, and we shouldn't rely on a single DNA sequence to say a sample of old bones belongs to a different "species" from another sample of old bones until we gather other forms of evidence about the possibility of the individuals mating and having offspring with each other.