New Neanderthal mito genome sequence

[RonO]

I saw an article about this paper that turned out to be over hyping the
results, but the results are interesting, but not for the reason claimed
by the article. The title of the article was "New Neanderthal
mitochondrial genome suggests earlier encounter with the modern human
lineage." from a service I subscribe to.

https://www.genomeweb.com/sequencing/new-neanderthal-mitochondrial-genome-suggests-earlier-encounter-modern-human-lineage

There is basically nothing new about the genetic relationship with
Neanderthals. What the paper found was that there used to be more
Neanderthal mitochondrial lineages than Neanderthals ended up with
before they went extinct. This is pretty much a given the way maternal
lineages are expected to go extinct through just random drift.

The news is that the lineage is estimated to have diverged from the
other known Neanderthal mitochondrial lineages 270,000 years ago. All
the other mito lineages share a more recent common ancestral sequence.
In fact they are about as diverse as the current modern human lineages
and it was thought that Neanderthals may have suffered a population
bottleneck around the same time that the modern human population crashed
around 80,000 years ago. So conditions inside and outside of Africa may
not have been good for Homo around that time.

https://www.nature.com/articles/ncomms16046

The Genomeweb article made a big deal about the relationships between
modern human mitochondrial sequences and Neanderthals, but these
relationships have been known for years, and this sequence doesn't
affect the interpretation of that data.

Our mito and Neanderthal mito share a common ancestral sequence around
half a million years ago. This has been known since we had the first
mitochondrial sequence. This means that the ancestors of Neanderthal
either left Africa at that time (separating from our lineage) or a
population of Homo left Africa around that time and interbred with the
ancestors of Neanderthal and the more recent African mito sequence took
over the Neanderthal population.

The million year old Denisovan mitochondrial lineage could have come in
from interbreeding with Homo that had left Africa a million years ago or
it could have been a lineage that the original population that evolved
into Neanderthals an Denisovans took out of Africa with them. None of
this changes, so there is no evidence for an earlier encounter with the
population that stayed in Africa than we had before.

It is only evidence for a more ancient lineage and we expected such
lineages to have existed because we already knew that the Neanderthal
lineages separated from Modern Humand half a million years ago. So
finding a lineage within Neanderthals that diverged 270,000 years ago
changes nothing.

The find is interesting because it is a reflection of the genetic
diversity that has been lost over time. If we find some colder places
in Africa that better preserve DNA and find Homo fossils we could likely
find such genetic diversity in the past in Africa, but unlike the
Neanderthal lineage that nests within the Neanderthal lineage, the more
ancient African lineages of 270,000 years ago would nest with the Modern
human lineage, unless we got lucky enough to find independent African
populations that separated over half a million years ago, but stayed in
Africa. Our population supposedly got down to around 1,000 breeding
individuals, and my guess is that we were not scattered all over Africa,
but the survivors came from a specific region of Africa.

Ron Okimoto

[Swan Black]

i saw this, and it sure is mixing things up, as maybe - that's how it happened

my brain wants a much simpler explanation, for our coming into existence

marc

[eridanus]

I have the idea that humans and Neanderthals had been often, several times,
on the brink of extinction, since the previous interglacial. Not only
since 80,000 years ago or so.
We had been used too often to the idea of "absolute extinctions", and not
to the idea of some 85 or 95 % extinctions. When severe climatic collapses
occur, like during the worse part of a glacial age, the reservoir of living
creatures must survive near the equatorial belt. The more on a higher
latitude those living creatures are, the most likely is their extinction
in some regions at higher latitudes.
An explosion like that of Toba, and those living over 40 degrees latitude
or higher would had not time to flee south fast enough.

Eri

[RonO]

The fossil evidence indicates that there may have been multiple
migrations of Homo out of Africa. The first may have occurred around 1
million years ago (recent finds) and one that may have occurred around
half a million years ago (the older fossil finds). The Neanderthal mito
back up the half million year migration or at least introgression of the
half million year old African lineage into the ancestral population of
Neanderthals. The Denisovan mito is consistent with populations of Homo
diverging 1 million years ago. They think that the Denisovan mito may
have been acquired by interbreeding with the first population to leave
Africa because their nuclear DNA indicates that Denisovans separated
from Neanderthals around 300,000 years ago.

So we had multiple migrations of Homo out of Africa possibly starting
over 1 million years ago. We have evidence of the Densiovan mito
lineage separating from the African lineage around 1 million years ago
and the Neanterthal lineage separating from the African lineage 500,000
years ago. We have the modern human migration out of Africa possibly
twice. Once around 150,000 (but it didn't leave extant descendants that
we can tell) and another around 60,000 to 80,000 years ago that resulted
in the current modern human population outside of Africa. The last
migration did interbreed with both Neanderthals and Denisovans to a
limited extent. A couple percent of your DNA is Neanderthal if you are
descended from modern humans that made it out of Africa. In parts of
Asia, Indonesia and Australia the human population has some Denisovan
DNA in their genomes that they acquired by interbreeding with Denisovans.

We have no evidence that the Neanderthal or Densiovan mitochondrial
lineage survived and have not found them in the extant population.

It is complicated, but it is what it is.

Ron Okimoto

[RonO]

There is some genomic evidence of multiple bottlenecks occurring in both
modern human and Neanderthal genomes, so there may have been several
severe changes in population size in both populations within the last
half a million years. There have been multiple glacial and interglacial
periods during the last half million years. We are currently in an
interglacial period.

Ron Okimoto

[The Incredibly Lucky JTEM]

The paper is highly problematic, insisting
on interpreting all evidence strictly within
the context of a pure Out of Africa assumption.

Also: Even I have been arguing this for years!
And I've even gone further, arguing that the
later Neanderthals are probably from the
Mediterranean & middle eastern populations.

Look, Toba exploded with the force of some
280,000 nuclear weapons. We've all head of
"Nuclear Winters," we've all heard of "Volcanic
Winters," well this one would have blotted out
the sun across the entire planet. The northern
hemisphere would have been the hardest hit,
likely taking decades to return to pre eruption
norms. With no summers, the only Neanderthal
populations to survive would have been those on
the coast.

Not only does the sea moderate temperature, but
many types of sea food would have been
sustainable through such a catastrophe...

So that's the theory, what is the evidence?

The "Proto" Neanderthals found in Spain had DNA
that looked closer to Denisovan than what we
think of as Neanderthal. And then the oldest
"True" Neanderthal was found in Italy, and it's
DNA looks more like our classic idea of
Neanderthal. So we can conclude that at some
point the Denisovan-like DNA (and other lines?)
went extinct, and something looking like the
Italian line spread out, filling the vacuum
left behind.

It fits.





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http://jtem.tumblr.com/post/163152682643

[Bill]

Neanderthals were trolls. We all know that trolls only live
under bridges. Problem is, trolls never figured out to build
bridges and the Homo Sapiens, who already knew how build
them, refused to build any. Alas, that's why the
Neanderthals became extinct. All of this is well documented
by those who document these kinds of things.

Bill

[Bob Casanova]

On Wed, 19 Jul 2017 14:42:49 -0500, the following appeared
in talk.origins, posted by Bill <fre...@gmail.com>:

<snip, among other idiocies, the one, not by Bill, which
asserts/implies that nuclear weapons come in only one size:

"Toba exploded with the force of some 280,000 nuclear
weapons">

>Neanderthals were trolls.

Damn, the Internet is older than I thought.

<snip>
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[RonO]

Hey Bill. How do Neanderthals and Denisovans fit into your alternative?
Why is this type of stupid denial all that you can muster?

Ron Okimoto

[RonO]

I know that snipping and running from reality is all that someone like
you can do at this time, but you might have, at least, tried to read the
paper and determine what it was actually saying.

There were multiple migrations out of Africa. They just were not as
wide spread and numerous as you would like. African and out side of
Africa populations of Homo obviously evolved independently for long
stretches of time.

Just think of your proto Neanderthal ramblings above. Neanderthals and
Densivans shared their population genetics for hundreds of thousands of
years (this means that they were basically the same population and
shared the same genetic variation). They separated around 300,000 years
ago. Since that separation the mitochondrial lineages have changed in
both populations. Some maternal lineages may have been lost in one of
the other as expected. They do not have to retain the same
mitochondrial variation after separation. The evidence indicates that
Denisovans either retained a more ancient lineage (had deeper branch
lengths) than Neanderthal or they interbred with another population of
Homo that had the more ancient mito lineage. The Spanish fossil doesn't
tell us either way. If it is Neanderthal it could be some shared
genetic variation that Neanderthals shared with Denisovans or it could
have been due to interbreeding with the other Homo population that may
have left Africa half a million years before the population that evolved
into Neanderthals and Denisovans left Africa.

It is the Nuclear DNA of Neanderthals and Denisovans that tell us that
they separated from our lineage half a million years ago. The
Neanderthal mito lineage tells us the same thing, but the Denisovan mito
lineage has more ancient roots and was either variation that
Neanderthals and modern humans lost or that Denisovans gained by
interbreeding with the Homo that had left Africa a million years ago.

What do you not understand?

Ron Okimoto

[Bob Casanova]

On Sun, 23 Jul 2017 06:11:09 -0500, the following appeared
in talk.origins, posted by RonO <roki...@cox.net>:

Damn near everything. He also complains that complex ideas
cannot be expressed in words suitable for a first primer.

[The Incredibly Lucky JTEM]

Proving you're just an emotionally disturbed
troll...

I mean, you can't find fault with anything I
said and, desperate for negative attention,
you need to find fault... so you attack the
way I said it.

Yeah, you're "Real interested" in a mature
discussion on the topic... sure... that's
it... that's the ticket...

Bob Casanova wrote:

> <snip, among other idiocies, the one, not by Bill, which
> asserts/implies that nuclear weapons come in only one size:
> "Toba exploded with the force of some 280,000 nuclear
> weapons">

Actually it's a conservative estimate, meant as an
illustration, a means for even a simpleton like you
to grasp the issue.

The Toba eruption ejected a total mass of 2,800
cubic kilometers. What does that mean to a troll
like you? Absolutely nothing. So we have to translate
this somehow, get a mind as troubled as yours a means
to approach the issues. So, let's think in terms of
man-made sources of energy, and what would be required
to move that much material.

Nuclear weapons!

But one isn't enough. Not even close. Not to move a
cubic kilometer, and often with a great deal of force...

Now get penis augmentation surgery and move on with your
life.


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[The Incredibly Lucky JTEM]

Ron O wrote:

> I know that snipping and running from reality is all that someone like
> you can do at this time, but you might have, at least, tried to read the
> paper and determine what it was actually saying.

You're an idiot. You claim to read the paper
but you clearly never grasped it.

> There were multiple migrations out of Africa.

The paper is premised on a migration, yes. If you read
it and missed this assumption then you have no business
even discussing the matter. So, next, let's quote the
paper:

: "This scenario reconciles the discrepancy in the
: nuclear DNA and mitochondrial DNA phylogenies of
: archaic hominins and the inconsistency of the modern
: human-Neanderthal population split time estimated
: from nuclear DNA and mitochondrial DNA,"

For jackasses without reading comprehension, allow me
to explain. Then you can read the above again and hopefully
see it yourself...

They're saying that the evidence does not match their
assumptions. So they invented a new scenario that allows
them to keep their assumptions largely intact.

The "Explanation" of the evidence is purpose built to
fit inside their assumptions. The assumptions aren't
derived from this evidence, the evidence is being tailored
to the assumptions.

Now being scary crazy and living in your head you can
imagine all sorts of other evidence not present at all
in the story, and argue that they're actually basing
things on this non-existing data which you're sure
clears up everything, whatever it is.

...ah, that's oh so "Empirical" of you.

Back to reality:

The early "Proto" neanderthal DNA looks closer
to Denisovan, but it's about as far to the west
as you can get, as far away from Denisovan
territory, while still remaining in Europe. This
line clearly doesn't seem to exist later. But
what does exist later appears close to some very
old pre Toba Neanderthal DNA found in Italy. So,
unless you ate buckets of paint chips as a child,
one would have to see this as evidence that there
were other lines, and then something happened
favoring the Italian line.






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http://jtem.tumblr.com/post/163327641438

[The Incredibly Lucky JTEM]

Bob Casanova wrote:

> RonO <roki...@cox.net>:

> >It is the Nuclear DNA of Neanderthals and Denisovans that tell us that
> >they separated from our lineage half a million years ago.

No. That's now some data is interpreted.

The story is all about REINTERPRETING data, but you missed
that so your dogmatic adherence to headlines comes as no
surprise...

> >The
> >Neanderthal mito lineage tells us

It doesn't tell us anything, moron. It's INTERPRETED,
and INTERPRETATIONS change da

> Damn near everything. He also complains that complex ideas
> cannot be expressed in words suitable for a first primer.

Where? Quote me. Show me what your dementia is
misinterpreting as this.

I dare you to. Pussy.





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