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."
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.
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:
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
"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.
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.
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.
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.
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).
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.
I'm no geneticist, but isn't this "structural" number still valuable for other purposes? Also isn't the 6pp also "structural" so modulo my previous complaints we're comparing like measurements?
Yes it can help you work out how related two species are to each other, but as a means of knowing what an individual gene does in each species it can be highly misleading. Ask any pharmaceutical researcher how much the concept that sharing a gene means sharing a function can lead you astray.
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 ?
That's certainly a possibility, but you don't even need to get that complicated. Gene A in humans could have a slight difference in its DNA sequence that causes it do work differently from the chimpanzees' copy of the same gene.
It gets even more complicated than this - the gene could be identical in sequence and still have a different function because of a change somewhere else in the genome. The genome is the ultimate spaghetti code that is the result of 3.5 billions years of hacks upon hacks upon hacks.
Let's put it in git terms. Humans and chimps are derived from a common ancestor, so you can imagine them as two diverging forks of the same codebase, with their common ancestor being the last commit that they both share. Since then, either or both could have performed any sequence of additions, deletions, edits, duplications, etc., including cutting large sections out of one file and pasting them into another. However, for chimps and humans, the fork was recent enough that the vast majority of lines of code have been untouched since the fork, so for the vast majority of lines of human code, you can identify the corresponding line of chimp code, and vice versa. So when we talk about "Gene A" in humans and "Gene A" in chimps, this is presuming that the region of the genome containing Gene A is relatively unchanged between the two species. However, as you and others have pointed out, just because the gene's sequence is identical or nearly identical in the two species doesn't guarantee that it performs the same function in the two species. You could make an analogy to modifying a global variable in a completely different file that drastically changes the behavior of a function, even though that function's source code is unchanged.
So roughly speaking, a gene is a region of DNA that operates as a functional unit. The most well well-understood function is encoding a protein product and regulating its production. And when we talk about the "same" gene in different species, we're using "same" informally to refer to the genes in the two species that are derived from the same gene in their common ancestor. Usually, but not always, these genes perform the same or similar functions in the two species. Unlike a function in computer code, however, the bounds of a gene are not well-defined, and can overlap other genes or be non-contiguous.
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.
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.
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%3D...