

New DNA Analysis Shows Ancient Humans Interbred with Denisovans - daegloe
http://www.scientificamerican.com/article.cfm?id=denisovan-genome

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tokenadult
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....](https://gustavus.edu/events/nobelconference/2008/presenters.php)

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%...](http://people.virginia.edu/~ent3c/papers2/Turkheimer%20GWAS%20EWAS%20Final.pdf)

"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-...](http://www.arts.cornell.edu/econ/dbenjamin/IQ-SNPs-
PsychSci-20111205-accepted.pdf)

Johnson, Penke, and Spinath (2011) "Understanding Heritability: What it is and
What it is Not"

[http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_He...](http://www.larspenke.eu/pdfs/Johnson_Penke_Spinath_2011_-_Heritability_rejoinder.pdf)

"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>

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.

~~~
lifeisstillgood
Thank you for a detailed overview.

I am still confused over the mechanism used to identify a "species" via mtDNA.
I understand that the meaning of species as it stems from Linnaeus is unlikely
to be useful in the DNA age, and I grasp the impossibility of defining when
one species stops being another, but I would like to understand the science
first, then the more political side of how to apply a loaded word like species
to a DNA result.

~~~
fghh45sdfhr3
_I understand that the meaning of species as it stems from Linnaeus is
unlikely to be useful in the DNA age_

Actually it is more useful than ever.

Genetically there is no line in the sand between one species and all others.
That's how everything evolves.

Only practically do you have a chance to draw a line in the sand between two
groups of animals. And keep in mind it is possible for A + B to have fertile
offspring, and B + C too, but not A + C. Freaky, but that's biology for you.

That's why a practical kludge like "fertile with itself, but not with others"
is the best definition to use.

~~~
lifeisstillgood
I see, everything smoothes out.

But that makes my question more relevant

the article, and the scientists behind it seem to be saying there _is_ a line
to draw, between Denisovia and Humans and Neanderthal. And they can draw that
line with mtDNA

* how can we distinguish between three species 41000 years ago

* what are the metrics in DNA used (% of gene sequences different?)

* if we are saying that xmillion yrs ago there was a common ancestor and they diverged into three species who evovled down till 40k yrs ago, then how can we call them different species if we were still interbreeding 40k ago? If we were interbreeding then we were same species, so again what is the DNA based reason for saying seperate species?

One last thing - if the A+B scenarios imply that say humans bred with
Neanderthal and their offspring had to breed with denisovians whose offspring
then could bring DNA back to human line, (while human/denisovians could never
produce fertile offspring) then I still see the same issue

if we interbreed we are same species, so what is the DNA based rationale for
saying no we weren't

if we were not interbreeding ... It makes more sense but presumably the
mutations in different trees got shared after common ancestor ?

Edit: tokenadult kindly re-edited and I did not spot it I time but makes the
point that DNA definition of different species in Pre history is weak at best,
and relies on other Indixators of breeding success. I shall assume that the
"DNA shows a different species" to be poor science journalism rather than poor
science and bookmark this for further Reading later apologies for any iPhone
based typos.

Edit again:

Just checking: If we find two skeletons 250k yrs old, definitetly Neanderthal
and human, sequence their genomes. Then find two skeletons at 150k one has
acquired a random mtDNA mutation and then find the same mutation on both at
50k years ago - then can we estimate the odds of that being mutally independnt
mutations? And is that what this branch of science is trying to do?

(I remember Leakey being quoted as saying we have only found enough ancient
skeleton bones to fit in the back of his car, so the above convenient pairs of
skeletons are understandably hypothetical)

pps HN and iPhones do not get on so if this editlooksawful I am justleaving it
- thank you for the comments - always nice to have questions treated seriously
- and thanks to tokenadult again for living upto your handle

~~~
fghh45sdfhr3
_the article, and the scientists behind it seem to be saying there is a line
to draw, between Denisovia and Humans and Neanderthal._

There is a line because you can differentiate between almost any two groups of
people using DNA. Ashkenazim Jews versus other Jews for example. That
obviously does not make them different species, it just means you can separate
the two groups with enough math, like principal component analysis.

That's why the quoted scientist in the article says:

 _"It was the first time a new group of distinct humans was discovered"_

A new group of humans.

 _what are the metrics in DNA used_

That information is hopefully in their paper. Usually it's some fairly
straightforward statistics.

 _how can we call them different species if we were still interbreeding 40k
ago?_

I think we call them different species because the status quo used to be that
we never interbred with them. We couldn't find any Neanderthal mtDNA in
humans, despite the strong archeology evidence that we had contact with them.

As DNA technology kept improving, we were able to recover more DNA from
ancient samples, and looked at the Y chromosome, and surprise you might have
enough Neanderthal DNA to count as full grand, grand father!

So I think at this point, we can't call them a separate species any more. But
inertia being what it is, we keep doing it. Also it makes for more eye
catching article headlines.

 _while human/denisovians could never produce fertile offsprin_

That was just my example about how we define species. According to the
article:

 _"...but the evidence also suggests that Denisovans and humans interbred."_

 _can we estimate the odds of that being mutally independnt mutation_

Yeah, that's kind of what they are doing. It is heavily based on statistical
estimation and that's why when then guess the age of a sample it is between A
LOT of years. They know their error margin is large.

~~~
lifeisstillgood
Thank you, some reading to do, starting with the actual paper. Cheers

------
lifeisstillgood
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?

~~~
fghh45sdfhr3
_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
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
_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.

