6 ms·

How Neanderthal DNA Helps Humanity

57 points by Geojim 10y ago

tokenadult 10y ago
The article is very interesting and informative, and comes from a good source. But I have to quibble about describing Denisovan and Neandertal hominins who were ancestors of current human beings as coming from a "different species," because by one of the main concepts of speciation, if two organisms can mate and have viable offspring, and then the offspring can further reproduce, you say the two organisms are part of the SAME species. There are, of course, full-length books about the details of defining species among the common descendants of the earliest living things, and about the mechanisms that bring about speciation among the descendants of a common ancestor species,[1] but right now we don't always know for sure when we dig up old hominin bones which belong to relatives of direct ancestors of living human beings and which do not--that is part of what the studies of ancient DNA are intended to find out. To make the point I am bringing up here, I would rewrite the second sentence of the helpful article kindly submitted here to read, "As the individuals who provided the main genetic contribution to modern humans began to spread out of Africa roughly 50,000 years ago, they encountered other hominin clades that looked remarkably like them — the Neanderthals and Denisovans, two groups of archaic humans that shared an ancestor with us roughly 600,000 years earlier." [1] http://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Daps&field-keywords=Speciation http://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3D...
- danieltillett 10y ago
  Lions and tigers can mate and have fertile offspring yet no one would consider them the same species [1]. Actually there is evidence that the offspring of ancient African and Neanderthal matings [2] followed Haldan's rule [3]. If this discussion was about anything other than humans there would be no question that Ancient Africans, Neanderthals and Denosovians were anything other than different species. 1. https://en.m.wikipedia.org/wiki/Liger https://en.m.wikipedia.org/wiki/Liger 2. http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7 http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7 3. https://en.m.wikipedia.org/wiki/Haldane%27s_rule https://en.m.wikipedia.org/wiki/Haldane%27s_rule
- grondilu 10y ago
  That conception of what a species is has been my understanding as well for a long time. It's a very simple and clear concept but apparently biologists have given up on it for various reasons. There's actually a whole wikipedia article about it: https://en.wikipedia.org/wiki/Species_problem https://en.wikipedia.org/wiki/Species_problem
  - mikeash 10y ago
    That's because the ability to mate and have viable offspring is not anything like a simple and clear concept in some cases. For example: https://en.m.wikipedia.org/wiki/Ring_species https://en.m.wikipedia.org/wiki/Ring_species
  - Steko 10y ago
    Nothing in your link suggests they've all given up on the concept.
    - grondilu 10y ago
      Not the concept itself, but the aforementioned simple and clear definition.
- falsestprophet 10y ago
  "If two organisms can mate and have viable offspring, and then the offspring can further reproduce, you say the two organisms are part of the SAME species." Firstly, that's not true. Even if that were true, there is no evidence of reproductive success between human males and Neanderthal females.
danieltillett 10y ago
The world map for Denosovian DNA is wrong. The Australian/Papua population is around 6% not the 0.8% which the figure shows. It is a shame that Africa is so ignored in these studies. We know that there were many interbreeding events that occurred in Africa (the African pygmies are one example), but we know almost nothing more.
- riffraff 10y ago
  > the African pygmies are one example can you expand on this?
  - danieltillett 10y ago
    Sure. Have a look at this post [1]. 1. http://dienekes.blogspot.com.au/2016/02/archaic-introgression-in-pygmies.html http://dienekes.blogspot.com.au/2016/02/archaic-introgressio...
Ericson2314 10y ago
The genome percentages in the article are a bit confusing. It is oft-quoted that we are "99% Chimpanzee", so how could we also be no more than "6% Denisovan"? Answer: they really mean 6 percentage points "realigned" vs the African reference populations. I've read many other articles repeating the "6%" and it would be nice if they (and this) were clearer (and used the correct units--but maybe that's too much to ask). Some cool charts for reference: http://www.scientificamerican.com/article/tiny-genetic-differences-between-humans-and-other-primates-pervade-the-genome/ http://www.scientificamerican.com/article/tiny-genetic-diffe...
- danieltillett 10y ago
  The 99% is basically wrong. What it is referring to is that for 99% of genes you can find in humans you can find an ortholog in chimps. It tells you nothing about the function of the genes in the two species and is basically meaningless from a functional perspective.
  - agumonkey 10y ago
    Does this means that if there are 3 genes a,b,c in mammal 1 and a,b in mammal 2, the lack of c can lead to a significant difference in the role/interpretation/function of a and b ?
    - Ericson2314 10y ago
      I think so. That + epigenetics, and the "one gene one protein" slogan one learns in grade school aggregiously plays down the complexity, even if it's not false per se.
      - agumonkey 10y ago
        I didn't study biology so my 'knowledge' is limited to the approximations fed before. But as a programmer, I can imagine that a change at lower layers can impacts upper layers tremendously. I'd like to read more about gene interrelation / dynamics.
jrapdx3 10y ago
Based on prior discussions I've had the impression that the BNC2 and other skin-related Neanderthal genes were associated with less melanin pigmentation. Melanin reduces penetration of UVB into skin cells, important in an equatorial environment to protect skin integrity. However in northerly latitudes, heavily pigmented skin is a disadvantage due to the role of UVB exposure in producing vitamin D, essential to survival. Indeed the most pigmented skin requires 5 times the UVB exposure to produce equivalent amount of vitamin D vs. least pigmented. A possible tradeoff for adaptating to an environment with less available sunlight is greater susceptibility to developing conditions like melanoma, but that's admittedly an oversimplification of a very complex subject.
JoeAltmaier 10y ago
The colored map is informative - color reflects percent of archaic genes inherited by modern populations. But the placement of the colored dots looks suspiciously like a heatmap. I know the data is sparse. But maybe there'd be a better way to represent it.

57 points by Geojim 10y ago

The article is very interesting and informative, and comes from a good source. But I have to quibble about describing Denisovan and Neandertal hominins who were ancestors of current human beings as coming from a "different species," because by one of the main concepts of speciation, if two organisms can mate and have viable offspring, and then the offspring can further reproduce, you say the two organisms are part of the SAME species. There are, of course, full-length books about the details of defining species among the common descendants of the earliest living things, and about the mechanisms that bring about speciation among the descendants of a common ancestor species,[1] but right now we don't always know for sure when we dig up old hominin bones which belong to relatives of direct ancestors of living human beings and which do not--that is part of what the studies of ancient DNA are intended to find out. To make the point I am bringing up here, I would rewrite the second sentence of the helpful article kindly submitted here to read, "As the individuals who provided the main genetic contribution to modern humans began to spread out of Africa roughly 50,000 years ago, they encountered other hominin clades that looked remarkably like them — the Neanderthals and Denisovans, two groups of archaic humans that shared an ancestor with us roughly 600,000 years earlier." [1] http://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Daps&field-keywords=Speciation http://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3D...

danieltillett 10y ago
Lions and tigers can mate and have fertile offspring yet no one would consider them the same species [1]. Actually there is evidence that the offspring of ancient African and Neanderthal matings [2] followed Haldan's rule [3]. If this discussion was about anything other than humans there would be no question that Ancient Africans, Neanderthals and Denosovians were anything other than different species. 1. https://en.m.wikipedia.org/wiki/Liger https://en.m.wikipedia.org/wiki/Liger 2. http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7 http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7 3. https://en.m.wikipedia.org/wiki/Haldane%27s_rule https://en.m.wikipedia.org/wiki/Haldane%27s_rule
grondilu 10y ago
That conception of what a species is has been my understanding as well for a long time. It's a very simple and clear concept but apparently biologists have given up on it for various reasons. There's actually a whole wikipedia article about it: https://en.wikipedia.org/wiki/Species_problem https://en.wikipedia.org/wiki/Species_problem
- mikeash 10y ago
  That's because the ability to mate and have viable offspring is not anything like a simple and clear concept in some cases. For example: https://en.m.wikipedia.org/wiki/Ring_species https://en.m.wikipedia.org/wiki/Ring_species
- Steko 10y ago
  Nothing in your link suggests they've all given up on the concept.
  - grondilu 10y ago
    Not the concept itself, but the aforementioned simple and clear definition.
falsestprophet 10y ago
"If two organisms can mate and have viable offspring, and then the offspring can further reproduce, you say the two organisms are part of the SAME species." Firstly, that's not true. Even if that were true, there is no evidence of reproductive success between human males and Neanderthal females.

danieltillett 10y ago

The world map for Denosovian DNA is wrong. The Australian/Papua population is around 6% not the 0.8% which the figure shows. It is a shame that Africa is so ignored in these studies. We know that there were many interbreeding events that occurred in Africa (the African pygmies are one example), but we know almost nothing more.

riffraff 10y ago
> the African pygmies are one example can you expand on this?
- danieltillett 10y ago
  Sure. Have a look at this post [1]. 1. http://dienekes.blogspot.com.au/2016/02/archaic-introgression-in-pygmies.html http://dienekes.blogspot.com.au/2016/02/archaic-introgressio...

Ericson2314 10y ago

The genome percentages in the article are a bit confusing. It is oft-quoted that we are "99% Chimpanzee", so how could we also be no more than "6% Denisovan"? Answer: they really mean 6 percentage points "realigned" vs the African reference populations. I've read many other articles repeating the "6%" and it would be nice if they (and this) were clearer (and used the correct units--but maybe that's too much to ask). Some cool charts for reference: http://www.scientificamerican.com/article/tiny-genetic-differences-between-humans-and-other-primates-pervade-the-genome/ http://www.scientificamerican.com/article/tiny-genetic-diffe...

danieltillett 10y ago
The 99% is basically wrong. What it is referring to is that for 99% of genes you can find in humans you can find an ortholog in chimps. It tells you nothing about the function of the genes in the two species and is basically meaningless from a functional perspective.
- agumonkey 10y ago
  Does this means that if there are 3 genes a,b,c in mammal 1 and a,b in mammal 2, the lack of c can lead to a significant difference in the role/interpretation/function of a and b ?
  - Ericson2314 10y ago
    I think so. That + epigenetics, and the "one gene one protein" slogan one learns in grade school aggregiously plays down the complexity, even if it's not false per se.
    - agumonkey 10y ago
      I didn't study biology so my 'knowledge' is limited to the approximations fed before. But as a programmer, I can imagine that a change at lower layers can impacts upper layers tremendously. I'd like to read more about gene interrelation / dynamics.

jrapdx3 10y ago

Based on prior discussions I've had the impression that the BNC2 and other skin-related Neanderthal genes were associated with less melanin pigmentation. Melanin reduces penetration of UVB into skin cells, important in an equatorial environment to protect skin integrity. However in northerly latitudes, heavily pigmented skin is a disadvantage due to the role of UVB exposure in producing vitamin D, essential to survival. Indeed the most pigmented skin requires 5 times the UVB exposure to produce equivalent amount of vitamin D vs. least pigmented. A possible tradeoff for adaptating to an environment with less available sunlight is greater susceptibility to developing conditions like melanoma, but that's admittedly an oversimplification of a very complex subject.

JoeAltmaier 10y ago

The colored map is informative - color reflects percent of archaic genes inherited by modern populations. But the placement of the colored dots looks suspiciously like a heatmap. I know the data is sparse. But maybe there'd be a better way to represent it.