Prothero on genetic distances among hominins

[nyi...@bellsouth.net]

In his 2015 book, _The Story of Life in 25 Fossils_, ungulate paleontologist
Donald Prothero gets sloppy when talking about other orders of mammals and
other classes of vertebrates. One example of sloppiness is his use, on pp.
329-331 of mere mitochondrial data to show genetic distance between various
groups (including some populations) in the clade {orangutan, human} of
hominoids.

Mitochondrial estimates of genetic distance are highly unreliable.
A notorious example is their "support" of the marsupionta hypothesis,
which claims that placental mammals and monotremes are more closely
related to each other than either is to marsupials (!)

All through the text, Prothero claims various results about distances
between humans and chimps, between chimps of different populations,
between lions and tigers, on "the DNA," even saying:

Our DNA is more similar to that of the two species of chimp
than the DNA of any two species of frog are similar to each other...

It is only in the caption of Figure 24.2 that the claims about DNA
apply only to mitochondrial DNA. The source for this is rather old:

Pascal Gagneux et. al., "Mitochondrial Sequences Show Diverse
Evolutionary Histories of African Hominoids," PNAS 93 (1999), Fig. 1B.


Does anyone reading this know of any studies of genetic distance
between some of these groups, based on genomic DNA? preferably,
a sizable chunk of it!


Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/

[JTEM is lucky in love AND money]

nyi...@bellsouth.net wrote:

> Does anyone reading this know of any studies of genetic distance
> between some of these groups, based on genomic DNA? preferably,
> a sizable chunk of it!

Why?

As many, many have pointed out, DNA and this includes
mtDNA is subject to selective pressures. Which means,
it CAN and sometimes DOES change rather rapidly and it
sometimes doesn't.

There is no molecular clock. There's lots of ways that
DNA can change rapidly -- the Founder Effect or
environmental mutagens being but two. The most likely
point within a populations life when (where) rapid
changes can be expected would be at points of speciation.

...what is a population evolving into a new species
but a rapid acquisition of genetic changes?

No, this wouldn't always mean changes to the mtDNA, and
sometimes it would. Human evolution, for example, pretty
much required new mtDNA lines BECAUSE we needed to adapt
to colder climates and BECAUSE living longer became
advantageous... both of which are helped greatly by the
right mtDNA line.

I hate to say it but our mtDNA probably developed so
many changes from Chimps only because they didn't have
to change but we did.

It's not about time since separation, it's about
selective pressure.




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http://jtem.tumblr.com/post/172524988153

[nyi...@bellsouth.net]

On Tuesday, April 3, 2018 at 11:18:15 AM UTC-4, JTEM is lucky in love AND money wrote:
> nyi...@bellsouth.net wrote:
>
> > Does anyone reading this know of any studies of genetic distance
> > between some of these groups, based on genomic DNA? preferably,
> > a sizable chunk of it!
>
> Why?

Because there are lots of influential biologists who think highly
of genetic distance, and we have to see the best they have to offer
if we are to criticize them intelligently.

> As many, many have pointed out, DNA and this includes
> mtDNA is subject to selective pressures. Which means,
> it CAN and sometimes DOES change rather rapidly and it
> sometimes doesn't.

Yes, but it would be nice to be able to distinguish between
when it DOES and when it doesn't. Any idea as to how?

> There is no molecular clock. There's lots of ways that
> DNA can change rapidly -- the Founder Effect or
> environmental mutagens being but two.

IOW, there is a distinction between genetic and chronological
distance. But the article only focuses on genetic distance
at this point. [Later on, it does talk about molecular clocks,
but Prothero makes no attempt to connect the talk with the
earlier talk about genetic distance.]

> The most likely
> point within a populations life when (where) rapid
> changes can be expected would be at points of speciation.
>
> ...what is a population evolving into a new species
> but a rapid acquisition of genetic changes?

Genetic changes don't have a simple quantitative relation to speciation.
Even something as spectacular as a diverse number of chromosomes,
like between horse and donkey, does not prevent having offspring --
with hybrid vigor in the case of mules (but not, perhaps, hinnies).

Yes, the offspring are almost always sterile, but this does illustrate
how "speciation" is not a well defined concept. "Ring species"
illustrate that too.

> No, this wouldn't always mean changes to the mtDNA, and
> sometimes it would. Human evolution, for example, pretty
> much required new mtDNA lines BECAUSE we needed to adapt
> to colder climates

But how do you explain that the mtDNA distance is bigger between
Eastern chimps and Western chimps than between humans and their
LCA? If you have access to the Prothero book, take a look at
Fig. 24.2 on page 330 of _The Story of Life in 25 Fossils_,
(Columbia University Press, 2015).

If not, but you have access to PNAS, take a look at:

Pascal Gagneux et. al., "Mitochondrial Sequences Show Diverse
Evolutionary Histories of African Hominoids," PNAS 93 (1999), Fig. 1B.

> and BECAUSE living longer became
> advantageous... both of which are helped greatly by the
> right mtDNA line.
>
> I hate to say it but our mtDNA probably developed so
> many changes from Chimps only because they didn't have
> to change but we did.

Or was it the other way around? I've been told that you
believe chimps evolved from an australopithecine. I think the
reason this idea is not taken very seriously (despite there
being no chimp fossils from more than 1mya, and the exception
is a mere tooth) is that people have a gut feeling that
australopithecines were more similar to us than they were
to chimps.

> It's not about time since separation, it's about
> selective pressure.

Btw, what is your estimate of the time chimps and ourselves
diverged from our common ancestor? how many mya?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/

nyikos "at" math.sc.edu

[JTEM is lucky in love AND money]

nyi...@bellsouth.net wrote:

> Because there are lots of influential biologists who think highly
> of genetic distance, and we have to see the best they have to offer
> if we are to criticize them intelligently.

This isn't new. This stuff wasn't new 10 years ago!
They have a rather lengthy history on mtDNA, getting
it wrong, one famous example would be their
misrepresenting the Neanderthal mtDNA data as demonstrating
no interbreeding...

> > As many, many have pointed out, DNA and this includes
> > mtDNA is subject to selective pressures. Which means,
> > it CAN and sometimes DOES change rather rapidly and it
> > sometimes doesn't.

> Yes, but it would be nice to be able to distinguish between
> when it DOES and when it doesn't. Any idea as to how?

Human evolution is a prime example of when it has
to. Modern humans required mtDNA very different from
that of Chimps if they were going to live much longer
and thrive in colder climates.

Chimps, staying put in Africa, were not under the same
kinds of selective pressure...

> > There is no molecular clock. There's lots of ways that
> > DNA can change rapidly -- the Founder Effect or
> > environmental mutagens being but two.

> IOW, there is a distinction between genetic and chronological
> distance. But the article only focuses on genetic distance
> at this point.

"Genetic Distance" is undefined here. The article claims
that humans & chimps are closer than any two frog species,
does it not? But there are frog species which can and do
interbreed. Can humans & chimps interbreed? Many have thought
so, it's long been rumored that SOMEBODY has tried, but the
overwhelming majority of sources state otherwise. So, this
would imply that, genetically, the frogs are closer to each
other than we are to Chimps... it certainly is a valid test.

> But how do you explain that the mtDNA distance is bigger between
> Eastern chimps and Western chimps than between humans and their
> LCA?

"Distance" is undefined.

Supposedly there's more variation between chimps than
between humans. But if humans required new mtDNA lines,
which we did, and breeding models were always anything
but symmetrical between human populations, which is
true, that's hardly surprising.

"Distance" implies a relationship -- or lack there --
which has never been shown.

> > I hate to say it but our mtDNA probably developed so
> > many changes from Chimps only because they didn't have
> > to change but we did.

> Or was it the other way around? I've been told that you
> believe chimps evolved from an australopithecine. I think the
> reason this idea is not taken very seriously (despite there
> being no chimp fossils from more than 1mya, and the exception
> is a mere tooth) is that people have a gut feeling that
> australopithecines were more similar to us than they were
> to chimps.

Which is odd, because why would something else be
required?

Chimps evolved from an upright walking ancestor that
probably used tools in a way that we only attribute
to the homo line.

> > It's not about time since separation, it's about
> > selective pressure.

> Btw, what is your estimate of the time chimps and ourselves
> diverged from our common ancestor? how many mya?

The problem with strict divergence estimates is
that they rely on a linear model that I can't
believe in. Ever.

See, it's not like there was [A] and then it
split into [B] and [C]. that's the linear model.

I believe that there were many populations, with
gene flow between them all, until some got so
separated from the rest -- geographically or
temporally -- that they could evolve without any
selective pressure from those groups/environments.

...sometimes it's easier to walk to a place
20 miles away than to one a mere 3 miles. Like if
there's a body of water in the way...

I believe that humans invented chimps. That, there
were lots of different populations of Austra or
their descendants, and once our line was sufficiently
different we preyed upon them as food -- just as
bush hunters had always done with chimps!

Anyhow, the forest populations were better protected
against homo hunters so the more we slaughtered
populations elsewhere, the less those forest populations
were being genetically influenced by them... the more
those forest populations were pressured they to
adapt (evolve) excursively to the forest -- those
adaptations/skills which helped them to survive there
(avoid homo).

Obviously, with my model, chimps came along quite a
spell after the split.





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http://jtem.tumblr.com/post/172524988153

[DD'eDeN aka note/nickname/alas_my_loves]

Not stupid, but requires explaining knuckle-walking in chimps & gorillas, among other things.
---

Jtem: "I believe that humans invented chimps. That, there

[JTEM is lucky in love AND money]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> Not stupid, but requires explaining knuckle-walking in chimps & gorillas, among other things.

There's nothing to explain.

Upright walking adaptations were no longer selected
for. Instead, it was only those adaptions that helped
them escape human predation... to live in the trees.



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http://jtem.tumblr.com/post/172646713128

[DD'eDeN aka note/nickname/alas_my_loves]

> Not stupid, but requires explaining knuckle-walking in chimps & gorillas, among other things.

There's nothing to explain.

Upright walking adaptations were no longer selected
for. Instead, it was only those adaptions that helped
them escape human predation... to live in the trees.
---

I agree with the point "it was...". But, knuckle-walking is unique, not ancestral, not shared with other arboreal primates (who palm-walk on the ground). It is not done in trees, where upright posture is typical. Rather it is done on the open ground, for geater locomotory speed, and differently by gorillas & chimps.

My hypothesis is that they developed it because it allowed evasion from slow-walking, spear-thrusting, shield-bearing, hominins/Homo habilis.

[DD'eDeN aka note/nickname/alas_my_loves]

Jtem: "

Anyhow, the forest populations were better protected
against homo hunters so the more we slaughtered
populations elsewhere, the less those forest populations
were being genetically influenced by them.."

---
Replace "forest" with "arboreal canopy", then it fits the evidence. Otherwise, it fails to explain how Homo habilis (rain-forest ground-dweller) dominated the tropical rainforest from West Africa to Flores, and begot Homo erectus et al. No other hypothesis does, including savanna & aquatic ones.

[JTEM is lucky in love AND money]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> Replace "forest" with "arboreal canopy"

I always meant that "They took to the trees."





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http://jtem.tumblr.com/post/172701083333

[DD'eDeN aka note/nickname/alas_my_loves]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> Replace "forest" with "arboreal canopy"

Stupid: I always meant that "They took to the trees."

They never "left" the trees, that is the arboreal canopy. Humans did, moving to the forest floor. Both retained upright bipedalism. When the forests dried due to Panama closure, both adapted, apes becoming more terrestrial via knucklewalking, humans via a more relaxed gait in armed groups.

[JTEM is lucky in love AND money]

Emotionally unstable, DD'eDeN aka note/nickname/alas_my_loves wrote:

> Stupid: I always meant that "They took to the trees."
>
> They never "left" the trees, that is th

You're clinging to a linear model.

There wasn't just one population. And there was
genetic glow between populations. It wasn't until
humans were sufficiently different/separate and
started preying on them that we created Chimps...
BY ELIMINATING THE OTHER POPULATIONS, REMOVING
THAT GENE FLOW.

Humans stopped the gene flow, allowing 100% of
the adaptation/evolutionary pressure to be on
the forest environment.





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http://jtem.tumblr.com/post/172738420518

[DD'eDeN aka note/nickname/alas_my_loves]

> They never "left" the trees,

You're clinging to a linear model.

-
No, the Principle of continuity. Apes evolved in the rainforest canopy, upright posture allowed more efficient feeding, all remain there today mostly.
-

There wasn't just one population. And there was
genetic glow between populations. It wasn't until
humans were sufficiently different/separate and
started preying on them that we created Chimps...
BY ELIMINATING THE OTHER POPULATIONS, REMOVING
THAT GENE FLOW.

-
Perhaps true.
-

Humans stopped the gene flow, allowing 100% of
the adaptation/evolutionary pressure to be on
the forest environment.
-

Australopiths were hominins too.





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http://jtem.tumblr.com/post/172738420518

[JTEM is lucky in love AND money]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> > They never "left" the trees,
>
> You're clinging to a linear model.

> No, the Principle of continuity.

i.e. "linear model."

There wasn't one population. There couldn't have
been. If there was, we wouldn't have split.

> Apes evolved in the rainforest canopy, upright posture allowed more efficient feeding, all remain there today mostly.

Again, absolutely linear.

There was more than one population, probably
lots more. There was gene flow between these
populations, pulling them all towards a common
"design," genetically. Predation eventually
isolated the forest population(s) -- or marooned
them, or left them alone with the others
extinct -- so eventually there was no more
selective pressure for anything BUT the forest.






-- --

http://jtem.tumblr.com/post/172731752518

[DD'eDeN aka note/nickname/alas_my_loves]

On Monday, April 9, 2018 at 1:33:06 PM UTC-4, JTEM is lucky in love AND money wrote:
> DD'eDeN aka note/nickname/alas_my_loves wrote:
>
> > > They never "left" the trees,
> >
> > You're clinging to a linear model.
>
>
> > No, the Principle of continuity.
>
> i.e. "linear model."

All extant organisms have continuous lineages, all extinct organisms did also.
Reality, no modelling involved.

> There wasn't one population. There couldn't have
> been. If there was, we wouldn't have split.

There was one population of numerous geographically separated groups/troops/bands/families which at various times rejoined depending upon climate, topography etc.

> > Apes evolved in the rainforest canopy, upright posture allowed more efficient feeding, all remain there today mostly.
>
> Again, absolutely linear.

No examples of non-arboreal apes. Mountain gorillas sleep in trees when young. 95% of humanity live within (formerly) forested or woodland areas, the rest use technological substitutes. Australopiths slept in trees, based on shoulder/upper limb structure, though some probably slept in cliff caves & rockshelters.

> There was more than one population, probably
> lots more. There was gene flow between these
> populations, pulling them all towards a common
> "design," genetically. Predation eventually
> isolated the forest population(s) -- or marooned
> them, or left them alone with the others
> extinct -- so eventually there was no more
> selective pressure for anything BUT the forest.

Homo-induced predation on other hominids reduced their groups undoubtedly.
Homo sapiens did the same to other Homo groups.

Again:
Homo = Forest/Woodland floor, little arboreal climbing.
Ape = Forest/Woodland canopy, little terrestrial walking.

> -- --
>
> http://jtem.tumblr.com/post/172731752518

[JTEM is lucky in love AND money]

For the record: The oldest "Chimp" fossil ever
found, and it's just a tooth, was NOT found within
what was a forest environment...

DD'eDeN aka note/nickname/alas_my_loves wrote:

> There was one population of numerous geographically separated groups/troops/bands/families which at various times rejoined depending upon climate, topography etc.

We would never have split if that was the case.

> No examples of non-arboreal apes.

Living? There's humans.

In the past? Start with Australopithecus & Ardipithecus...

Wait. That means there's never been any shortage
of non-arboreal "apes" until human emerged as
dominant....



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http://jtem.tumblr.com/post/92716599453

[DD'eDeN aka note/nickname/alas_my_loves]

Dead chimp outside the forest canopy. No surprise.

[JTEM is lucky in love AND money]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> Dead chimp outside the forest canopy. No surprise.

Strictly speaking, it may not even have been a
chimp but, rather, a close relative on the Pan
side of the divide.




-- --

http://jtem.tumblr.com/post/172747521513

[DD'eDeN aka note/nickname/alas_my_loves]

Population One: arboreal
Population Two: terrestrial
Both residing in the same rainforest, both making nightly structures of wicker & leaves, and gnawing sharp sticks to get food (gallego, ants-termites, tubers).

[JTEM is lucky in love AND money]

DD'eDeN aka note/nickname/alas_my_loves wrote:

> Population One: arboreal
> Population Two: terrestrial
> Both residing in the same rainforest, both

Rain forest. Savannah. Coastline. And, of course,
everything in between.

One of those populations evolved into what we
call "Homo," and it eventually preyed upon
the other populations. I dunno, maybe they preyed
upon each other from the start, with larger
individuals or groups feasting on the others.

..competition with one's own kind is an
easy way to drive up size, and this could
explain the later evolution/split of erectus
from the much smaller habilis.







-- --

http://jtem.tumblr.com/post/9528749746

[DD'eDeN aka note/nickname/alas_my_loves]

On Wednesday, April 11, 2018 at 3:32:56 PM UTC-4, JTEM is lucky in love AND money wrote:
> DD'eDeN aka note/nickname/alas_my_loves wrote:
>
> > Population One: arboreal
> > Population Two: terrestrial
> > Both residing in the same rainforest, both
>
> Rain forest. Savannah. Coastline. And, of course,
> everything in between.

Yes, but I'm referring to human and chimp ancestors (Y-form lineage), not to various morphological "species".

> One of those populations evolved into what we
> call "Homo," and it eventually preyed upon
> the other populations.

Apes have never been the primary food nor even significant food of rainforest people. However, agricultural Bantu people and others growing carb-rich crops around the rainforest need meat, and forest fauna was "free" for the taking as opposed to herds of cattle which were priced high for bride-price, dowries etc.

[DD'eDeN aka note/nickname/alas_my_loves]

A Megaflood-Powered Mile-High Waterfall Refilled the
Mediterranean [Video] Buried sediments near Sicily
suggest water rushed into the sea’s partially dried-out
eastern basin at speeds reaching 100 miles per hour
By Katherine Kornei, Scientific American, March 26, 2018
[www.scientificamerican.com]

The open-access paper is:

Micallef, A., Camerlenghi, A., Garcia-Castellanos,
Otero, D.C., Gutscher, M.A., Barreca, G., Spatola,
D., Facchin, L., Geletti, R., Krastel, S. and Gross, F.,
2018. Evidence of the Zanclean megaflood in the
eastern Mediterranean Basin. Scientific reports, 8(1), p.1078.
[www.nature.com]

Mile-High Waterfall Refilled the Mediterranean Sea
-
Same period as H/P split

[DD'eDeN aka note/nickname/alas_my_loves]

https://www.sciencedaily.com/releases/2018/04/180411174159.htm

15 ma changes in ape teeth

[nyi...@bellsouth.net]

A few minutes ago, I reposted the OP to this thread [preserved below] in
sci.bio.paleontology, where the subject of genomic distance came up:

https://groups.google.com/d/msg/sci.bio.paleontology/nNhyCBvm_9k/4IeW-kt_DAAJ
Date: Thu, 23 Aug 2018 11:38:44 -0700 (PDT)
Message-ID: <69b1e998-ebd5-4b9a...@googlegroups.com>
Subject: Re: Paraphyly vs. Monophyly


Some people who voiced their opinions on this thread might be
interested in voicing them too. One of the main participants is
JTEM's old nemesis, John Harshman. [Perhaps it is more accurate
to say JTEM is one of John's old nemeses.]

Peter Nyikos

On Tuesday, April 3, 2018 at 10:41:41 AM UTC-4, nyi...@bellsouth.net wrote:
> In his 2015 book, _The Story of Life in 25 Fossils_, ungulate paleontologist
> Donald Prothero gets sloppy when talking about other orders of mammals and
> other classes of vertebrates. One example of sloppiness is his use, on pp.
> 329-331 of mere mitochondrial data to show genetic distance between various
> groups (including some populations) in the clade {orangutan, human} of
> hominoids.
>
> Mitochondrial estimates of genetic distance are highly unreliable.
> A notorious example is their "support" of the marsupionta hypothesis,
> which claims that placental mammals and monotremes are more closely
> related to each other than either is to marsupials (!)
>
> All through the text, Prothero claims various results about distances
> between humans and chimps, between chimps of different populations,
> between lions and tigers, on "the DNA," even saying:
>
> Our DNA is more similar to that of the two species of chimp
> than the DNA of any two species of frog are similar to each other...
>

> It is only in the caption of Figure 24.2 that [we learn that]