Assimilation

[J.LyonLayden]

"From this diverse population emerged most of the genetic ancestors of present-day humans. Sometime after 150,000 years ago, Africans began to move into West Asia where they could interact with the Neanderthals. This interaction resulted in the disappearance of Neanderthal, Denisovan, and other archaic human populations. These archaic people were in part assimilated into the succeeding population of modern humans, evident from DNA."

http://johnhawks.net/research/human-evolution-and-genetics-encyclopedia-race.html

Assimilation:

The description above is an extreme simplification of what happened. If you watch John Hawks latest BBC film, a four part series on human evolution, you will get more details.

Homo Sapiens Sapiens existed in many different genomic populations or "ethnic groups" before 150,000 years ago in Africa. By 120,000 years ago, they had spread into the Middle East and even into southern China.
http://johnhawks.net/weblog/fossils/china/zhirendong-2010-liu-chin.html

They may have lived in the Narmada Valley of India, but didn't get into most of South Asia at this time. John Hawks thinks another hominid kept them out until after the Toba event.

The first Anbatomically Modern Humans appeared at this time, in what Hawks says is a hybridization event between several different "ethnic groups."

Around 100,000 years Neanderthal territory extended into the Middle East and Levant and drove homo sapiens out of the region.

Neanderthals in the area begin to exhibit chins and other human features.

Between 70,000 and 45,000 years ago there are no Homo Sapiens fossils in the Middle east or Europe.

But Neanderthal took Toba hard, and around 45,000 years ago there's high volcanic activity in their homebase of Europe.

And Homo Sapiens Sapiens developed the atlatl around 45,000 years ago. This enabled them to launch spears at neanderthal and run away.

The last Neanderthal fossils in "West Asia" exhibit large projectile point wounds, such as in Shanidar.

I posted this to establish a definition of the word "assimilation."
I do not know if paleontologists accept assimilation as a driving force in the evolution of other creatures, but if they don't I would like to know why they don't.

There are hybrid zones for birds and mammals, and hybrid vigor is known to science, so I am unaware of a problem with the concept.

We know close species and subspecies can indeed mate, and even chromosome number is no indication two subspecies cannot do so. The proof is in the chromosome numbers in subspecies of zebra.




My two cents, totally speculative:

Because the only group on the planet who do not have neanderthal introggression are San Bushman, Hadza, and a few other groups dominated by Y Haplogroup A and A00, we can say that Neanderthal hybrids assimilated the planet. Because the original introggressing neanderthal groups were fewer than the genomic population they assimilated, the introgression is diluted to 2-4%.

(A "hundred" alpha male neanderthals bred into Hss, and the offspring of those neanderthals hybrids assimilated many "thousands" of homo sapiens sapiens).

Th number of people living today with Neanderthal genes is many times the number of Neanderthals living at any given time in prehistory.

That is why isolated populations in the Medit. and W. Asia, including Brian Sykes 'Xana," possess extremely ancient African DNA.

Y Hap A and other ancient haplogroups once stretched all the way to S. China, and then came Toba. Afterward, the spread of Neanderthal hybrids.


Hunter gatherers of group A survived by entering the dense jungle where Neanderthal hybrids couldn't go (at least at the time).

African hunter gatherers have resistances to Malaria and other diseases that the rest of the world has no defense against.

They inherited genes and immunities from yet more archaic peoples. Both San and Hadza have a 700,000 year old introgression and Hadza also have a 1.3 million year old introgression.

Two more hominids which lived into the Upper Paleolithic and probably the Holocene.

An aside:


If Climate Change brought about a jungle or rain forest planet, everyone but the Hadza and San might go extinct. They could survive to repopulate the world, because they have the genes and they already know how to live without modern comforts.

[J.LyonLayden]

I would like to add a definition of "mutation deletion" to this post for the sake of future conversations.

Deletion Mutation and DNA
A deletion mutation occurs when part of a DNA molecule is not copied during DNA replication. This uncopied part can be as small as a single nucleotide or as much as an entire chromosome. The loss of this DNA during replication can lead to a genetic disease.

http://study.com/academy/lesson/deletion-mutation-definition-examples-diseases.html

My observation was that

1. If geneticists link Afrotheria and Xenarthra, it is via shared genes or mutations.

2, If geneticists say "Xenarthra cannot be ruled out as basal to all" it means that the two "Laurasian" groups and Afrotheres could have evolved directly from Xenarthra. The three groups are Xenarthra + a suite of new mutations.

3. But Afrotheres and Xenarthra share genes, as is shown in "1."

4. Therefore, they must be saying that the two "Laurasian" groups "deleted" the genes or mutations that unite Afrotheres and Xenarthra.

You may not agree, but at least we can talk without needless arguing now.

[J.LyonLayden]

The alternative is that all 4 groups possess the genes that define Atlantogenata, and that Atlantogenata (Afrothere and Xenarthra) are defined by lack of genes/mutations which unite the two "Laurasian" groups.

[John Harshman]

On 11/11/17 9:56 AM, J.LyonLayden wrote:

Please stop with the logorrhea.

I don't like this word "assimilation", as it implies much more than the
evidence shows or Hawks claims. All we have is a small amount of
introgression. That tells us that some number of Neandertals mated with
some number of modern humans, and a small number of Neandertal genes
were introduced into the modern population. But "assimilation" implies
that the entire Neandertal population was absorbed by the modern human
population, which is unlikely and for which we have no evidence, as
Hawks acknowledges by "in part".

Still, thanks for the reference.

> "From this diverse population emerged most of the genetic ancestors of present-day humans. Sometime after 150,000 years ago, Africans began to move into West Asia where they could interact with the Neanderthals. This interaction resulted in the disappearance of Neanderthal, Denisovan, and other archaic human populations. These archaic people were in part assimilated into the succeeding population of modern humans, evident from DNA."
>
> http://johnhawks.net/research/human-evolution-and-genetics-encyclopedia-race.html
>
> Assimilation:
>
> The description above is an extreme simplification of what happened. If you watch John Hawks latest BBC film, a four part series on human evolution, you will get more details.
>
> Homo Sapiens Sapiens existed in many different genomic populations or "ethnic groups" before 150,000 years ago in Africa. By 120,000 years ago, they had spread into the Middle East and even into southern China.
> http://johnhawks.net/weblog/fossils/china/zhirendong-2010-liu-chin.html
>
> They may have lived in the Narmada Valley of India, but didn't get into most of South Asia at this time. John Hawks thinks another hominid kept them out until after the Toba event.
>
> The first Anbatomically Modern Humans appeared at this time, in what Hawks says is a hybridization event between several different "ethnic groups."
>
> Around 100,000 years Neanderthal territory extended into the Middle East and Levant and drove homo sapiens out of the region.
>
> Neanderthals in the area begin to exhibit chins and other human features.
>
> Between 70,000 and 45,000 years ago there are no Homo Sapiens fossils in the Middle east or Europe.
>
> But Neanderthal took Toba hard, and around 45,000 years ago there's high volcanic activity in their homebase of Europe.
>
> And Homo Sapiens Sapiens developed the atlatl around 45,000 years ago. This enabled them to launch spears at neanderthal and run away.
>
> The last Neanderthal fossils in "West Asia" exhibit large projectile point wounds, such as in Shanidar.
>
> I posted this to establish a definition of the word "assimilation."
> I do not know if paleontologists accept assimilation as a driving force in the evolution of other creatures, but if they don't I would like to know why they don't.

Well, it doesn't appear to have been much of a driving force in the
evolution of Homo sapiens, a minor element at best, so why should anyone?

> There are hybrid zones for birds and mammals, and hybrid vigor is known to science, so I am unaware of a problem with the concept.

Yes. You are unaware. There is no problem with the concept, especially,
but it seems not to be important in evolution. Hybrid zones don't
generally move much, and one species seldom assimilates another. It does
happen occasionally; it may be true that American black ducks are
disappearing into mallards, for example. But the effect on evolution
seems minimal, since only very close relatives do that sort of thing,
very seldom, and they even more seldom differ in ways that cause the
assimilating species to change significantly.

> We know close species and subspecies can indeed mate, and even
> chromosome number is no indication two subspecies cannot do so. The
> proof is in the chromosome numbers in subspecies of zebra.

All true, but so what? This is a rare phenomenon of generally trivial
effect when it does happen.

> My two cents, totally speculative:
>
> Because the only group on the planet who do not have neanderthal
> introggression are San Bushman, Hadza, and a few other groups
> dominated by Y Haplogroup A and A00, we can say that Neanderthal
> hybrids assimilated the planet. Because the original introggressing
> neanderthal groups were fewer than the genomic population they
> assimilated, the introgression is diluted to 2-4%.
> (A "hundred" alpha male neanderthals bred into Hss, and the offspring
> of those neanderthals hybrids assimilated many "thousands" of homo
> sapiens sapiens).

Wait: "alpha male"?

> Th number of people living today with Neanderthal genes is many times
> the number of Neanderthals living at any given time in prehistory.
> That is why isolated populations in the Medit. and W. Asia, including Brian Sykes 'Xana," possess extremely ancient African DNA.
>
> Y Hap A and other ancient haplogroups once stretched all the way to
> S. China, and then came Toba. Afterward, the spread of Neanderthal
> hybrids.

> Hunter gatherers of group A survived by entering the dense jungle where Neanderthal hybrids couldn't go (at least at the time).
>
> African hunter gatherers have resistances to Malaria and other diseases that the rest of the world has no defense against.
>
> They inherited genes and immunities from yet more archaic peoples.
> Both San and Hadza have a 700,000 year old introgression and Hadza
> also have a 1.3 million year old introgression.

> Two more hominids which lived into the Upper Paleolithic and probably the Holocene.

You will have to be more coherent and complete in your argument before
anyone but you will be able to make sense of it. Also, might I suggest
that organization into paragraphs, each with more than a single
sentence, might be a useful tool for clear expression?

> An aside:
>
> If Climate Change brought about a jungle or rain forest planet,
> everyone but the Hadza and San might go extinct. They could survive
> to repopulate the world, because they have the genes and they already
> know how to live without modern comforts.

That is an extremely silly aside on so many levels.

[John Harshman]

On 11/11/17 10:48 AM, J.LyonLayden wrote:
> I would like to add a definition of "mutation deletion" to this post for the sake of future conversations.
>
> Deletion Mutation and DNA
> A deletion mutation occurs when part of a DNA molecule is not copied
> during DNA replication. This uncopied part can be as small as a
> single nucleotide or as much as an entire chromosome. The loss of
> this DNA during replication can lead to a genetic disease.

Yes, that's an oddly stated but essentially correct definition of
"deletion" as used in molecular genetics. But it doesn't seem to have
anything to do with your past usage.

> http://study.com/academy/lesson/deletion-mutation-definition-examples-diseases.html
>
> My observation was that
>
> 1. If geneticists link Afrotheria and Xenarthra, it is via shared genes or mutations.
>
> 2, If geneticists say "Xenarthra cannot be ruled out as basal to all"
> it means that the two "Laurasian" groups and Afrotheres could have
> evolved directly from Xenarthra. The three groups are Xenarthra + a
> suite of new mutations.

No, that's not what it means. It means that the first divergence within
Placentalia would be between Xenarthra and everything else. Neither
group would be necessarily primitive in any particular character,
neither group would be necessarily derived in any particular character,
and both groups would be primitive in some characters and derived in
others. Of course 1 and 2 are mutually incompatible.

> 3. But Afrotheres and Xenarthra share genes, as is shown in "1."
>
> 4. Therefore, they must be saying that the two "Laurasian" groups "deleted" the genes or mutations that unite Afrotheres and Xenarthra.

No, they are saying nothing of the sort. I would have to explain
phylogenetic analysis in detail to really get at the nub of your
misunderstanding, but I'll try the short version. First, you are using
"deleted" differently than the definition you began with. Second, it's
not that they share genes, but that they share various features; what
those features are would require looking at the methods section of
whatever paper you're relying on. Third, there are multiple explanations
for shared features shared between Xenarthra and Afrotheria exclusive of
Boreoeutheria, but they all fall into three categories: synapomophory,
shared derived characters (in a common ancestor of Atlantogenata),
homoplasy (between Xenarthra and Afrotheria), independently derived
features or autapomorphy (in Boreoeutheria), in which one taxon
transforms, leaving other taxa with shared primitive features. Some
autapomorphies of Boreoeutheria might be deletions, but others would be
other sorts of transformations: insertions, point mutations, etc.

[J.LyonLayden]

I do not agree. This is exactly what they are saying happened after Toba with HSS.

Just as many populations of HSS went extinct as neanderthal populations. If you read the literature, there are a plethora of ghost lineages of modern human to explain there are multiple ghost lineages.

There is ghost lineage of Hss that was absorbed only by certain Amazon tribes, the Ainu, and PNGers, for instance.

Some mtDNA lineages in Europe and China are up to 30 thousand years older than Y Haplogroups there. this implies a ghost lineage of males.

The list goes on and on and on.

HSS is thought to have done better after Toba because Africa was least affected by Toba. It has been claimed many times that Africans repopulated the world and assimilated Eurasian survivors in Toba's aftermath.

John Hawks is saying that Anatomically Modern Humans arose from assimilation of several different "subspecies" of Homo Sapiens Sapiens.
Yes he uses the word "sub-species" in the documentary.

He is also saying that Anatomically Modern Human assimilated denisovans, neanderthals, and at least 4 other archaic groups.

There is a significant change between Homo Sapiens Sapiens of 150 thousand years ago and those of today.

Imagine what 6 million years of the same damn thing happening and you get the difference between Austrolepiths and modern humans.

It is almost assuredly a driving force in evolution, but so subtle that we have not been able to discern it's effect on human evolution until now.

And we spend a lot more money and research on human evolution than we do plaeontology.

And yes of course it only happens between closely related groups.

I already told you I'm not Dr. McCarthy.

[J.LyonLayden]

Since when did geneticists start caring about "features" instead of genes?\

And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.

[John Harshman]

On 11/11/17 11:31 AM, J.LyonLayden wrote:
> Since when did geneticists start caring about "features" instead of genes?\

Genes are features, but that doesn't exhaust the category of genomic
features. Yes, they care about "features": genes, point mutations,
insertions, deletions, inversions, translocations, chromosomal fusions
and fissions, and various subcategories thereof. I don't know what your
source or sources is/are talking about, though if you provide a citation
to the scientific literature we could find out.

> And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
>

I can't be held responsible for what you prefer or why you prefer it.
But the proper term is "primitive", meaning "present in the common
ancestor".

[John Harshman]

Please stop with the single-sentence paragraphs and the vague allusions
to unstated and unreferenced facts. Make a coherent argument, and I
might be able to discuss it.

Also, "ghost lineage" is another term taken from paleontology that you
seem to be using in a quite different sense, one unknown to me.

[J.LyonLayden]

On Saturday, November 11, 2017 at 2:38:21 PM UTC-5, John Harshman wrote:
> On 11/11/17 11:31 AM, J.LyonLayden wrote:
> > Since when did geneticists start caring about "features" instead of genes?\
>
> Genes are features, but that doesn't exhaust the category of genomic
> features. Yes, they care about "features": genes, point mutations,
> insertions, deletions, inversions, translocations, chromosomal fusions
> and fissions, and various subcategories thereof. I don't know what your
> source or sources is/are talking about, though if you provide a citation
> to the scientific literature we could find out.

https://pdfs.semanticscholar.org/dbc3/a416c3c24eea1d2455b65eb479c20a6b3ea5.pdf

In figure 1 you will see an unbroken blue line from Placentalia to armadillos. This means there are few "features" separating basal Xenarthra from all other Placentalia groups.

It isn't saying Placentalia evolved from an armadillo. It is saying the earliest member of Xenarthra could have been the earliest member of Placentalia as well. There are fewer "features" in Armadillos separating them from hypothetical "basal placental" than in any other group.

Therefore, the Armadillo has gone through the least amount of "specialization" since the "basal placental." No that does not necessarily mean "basal Placental" still possessed scutes.
But it could.
We would need to know what "features" create scutes to find out. We would need to know whether this "primitive feature" is also present in Afrotheres and "Laurasians" to make an educated guess.

Are the "features" which distinguish hair from scutes in other mammals the same across all clades?

Are pangolin scales more "advanced" than armadillo scutes?

These questions might be a good place to start.

>
> > And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
> >
> I can't be held responsible for what you prefer or why you prefer it.
> But the proper term is "primitive", meaning "present in the common
> ancestor".

In human paleoanthropology, the term is no longer accepted. I guess I'll have to live with "primitive" and you'll have to live with "assimilate."


From the paper's conclusion:

The diversification
of placental orders began in the Late Cretaceous
(∼75.2 Ma), continued without apparent interruption across the
KPg boundary, and ended in the early Cenozoic (∼55.3 Ma)

Do you know what the "~" stands for?

"For example, the dating estimates
for the divergence between northern tree shrews and Chinese
tree shrews and for the base of Cetacea penetrated beyond
the minimum bounds suggested by fossils, thereby resulting in
younger molecular clock divergences, a potential issue of “zombie
lineages” (53). Whether these outcomes are due to errors in clock
methodology or the unreliability surrounding the fossil record is a
topic for further study (54)."

If so, I think after this we will be able to talk without all of the unnecessary nit-picking.

[J.LyonLayden]

It can either mean we don't have any fossils or that we don't have any extant DNA old enough to match another DNA lineage.

For instance, the oldest mt DNA extracted from Tibetans supposedly entered the plateau 20,000 years ago. Theoldest Y DNA entered around 10,000 years ago.

The old mtDNA had to be reproducing during with someone during the 10,000 year span, so it implies a "ghost lineage" of males that went extinct (or were exterminated, assimilated, etc.).

The Microcephalin D hominid is another "ghost lineage," since we don't know if fossils like "homo erectus soloensis" or "Narmada Man" represent it or not.

[John Harshman]

On 11/11/17 12:20 PM, J.LyonLayden wrote:
> On Saturday, November 11, 2017 at 2:38:21 PM UTC-5, John Harshman wrote:
>> On 11/11/17 11:31 AM, J.LyonLayden wrote:
>>> Since when did geneticists start caring about "features" instead of genes?\
>>
>> Genes are features, but that doesn't exhaust the category of genomic
>> features. Yes, they care about "features": genes, point mutations,
>> insertions, deletions, inversions, translocations, chromosomal fusions
>> and fissions, and various subcategories thereof. I don't know what your
>> source or sources is/are talking about, though if you provide a citation
>> to the scientific literature we could find out.
>
> https://pdfs.semanticscholar.org/dbc3/a416c3c24eea1d2455b65eb479c20a6b3ea5.pdf
>
> In figure 1 you will see an unbroken blue line from Placentalia to
> armadillos. This means there are few "features" separating basal
> Xenarthra from all other Placentalia groups.

Perhaps that's what you see, but in my copy the line from Placentalia to
basal Xenarthra is pink. But the colors don't represent anything about
changes or lack thereof. Nor is that line any longer than the line from
Placentalia to basal Afrotheria, and in fact it's longer than the line
from basal Placentalia to basal Euarchontoglires or basal
Laurasiatheria. Hmmm...I think I can see what you did. You are
interpreting the vertical lines as meaningful. They aren't; they just
allow for graphical separation of the taxa, and are exactly as long as
that separation requires. It's the horizontal lines that are meaningful
and the horizontal axis that represents time. Or if that's not what
you're doing, then I have no idea where you got your notion. But it's wrong.

> It isn't saying Placentalia evolved from an armadillo. It is saying
> the earliest member of Xenarthra could have been the earliest member
> of Placentalia as well. There are fewer "features" in Armadillos
> separating them from hypothetical "basal placental" than in any other
> group.

No, it isn't saying anything of the sort.

> Therefore, the Armadillo has gone through the least amount of
> "specialization" since the "basal placental." No that does not
> necessarily mean "basal Placental" still possessed scutes.

> But it could.

No, it couldn't. That would be a highly unparsimonious reconstruction,
for which there is no evidence.

> We would need to know what "features" create scutes to find out. We
> would need to know whether this "primitive feature" is also present
> in Afrotheres and "Laurasians" to make an educated guess.

Sigh. I don't think you know what "features" means; still.

> Are the "features" which distinguish hair from scutes in other mammals the same across all clades?
>
> Are pangolin scales more "advanced" than armadillo scutes?
>
> These questions might be a good place to start.

Those questions are nonsensical, I'm afraid.

>>> And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
>>>
>> I can't be held responsible for what you prefer or why you prefer it.
>> But the proper term is "primitive", meaning "present in the common
>> ancestor".
>
> In human paleoanthropology, the term is no longer accepted. I guess
> I'll have to live with "primitive" and you'll have to live with
> "assimilate."

That would be fine if we could agree on the definitions.

> From the paper's conclusion:
>
> The diversification
> of placental orders began in the Late Cretaceous
> (∼75.2 Ma), continued without apparent interruption across the
> KPg boundary, and ended in the early Cenozoic (∼55.3 Ma)
>
> Do you know what the "~" stands for?

I do. Thanks for asking.

> "For example, the dating estimates
> for the divergence between northern tree shrews and Chinese
> tree shrews and for the base of Cetacea penetrated beyond
> the minimum bounds suggested by fossils, thereby resulting in
> younger molecular clock divergences, a potential issue of “zombie
> lineages” (53). Whether these outcomes are due to errors in clock
> methodology or the unreliability surrounding the fossil record is a
> topic for further study (54)."

I'm unclear on what point you want to derive from this quote.

> If so, I think after this we will be able to talk without all of the unnecessary nit-picking.

You call it unnecessary nit-picking, I call it a combination of your
inability to communicate and your fundamental misconceptions.

[John Harshman]

On 11/11/17 12:30 PM, J.LyonLayden wrote:

>> Also, "ghost lineage" is another term taken from paleontology that you
>> seem to be using in a quite different sense, one unknown to me.
>
> It can either mean we don't have any fossils or that we don't have any extant DNA old enough to match another DNA lineage.

I am not acquainted with the second usage. It seems an unwarranted
extrapolation from the paleontological term and its meaning is unclear,
made less clear by your attempted example.

> For instance, the oldest mt DNA extracted from Tibetans supposedly
> entered the plateau 20,000 years ago. Theoldest Y DNA entered around
> 10,000 years ago.

I would presume that all DNA extracted from Tibetans would be equally
recent, i.e. within the last few years. You are being very unclear.

> The old mtDNA had to be reproducing during with someone during the
> 10,000 year span, so it implies a "ghost lineage" of males that went
> extinct (or were exterminated, assimilated, etc.).

> The Microcephalin D hominid is another "ghost lineage," since we
> don't know if fossils like "homo erectus soloensis" or "Narmada Man"
> represent it or not.

Once more you allude to facts and references not in evidence and persist
in these one-sentence paragraphs. Please stop. It prevents communication.

[J.LyonLayden]

That was just one instance and one study.
I have read 5 papers in the past week and at least two of them contained this comment about their specifally genetic stdy.

We cannot rule out Xenarthra as basal to all placental mammals.

If that does not mean "There are fewer features between the LCA of all extant placentals and Xenarthra than any other group" then it means ABSOLUTELY NOTHING.

And it has to friggin' mean something.

Do you want to pretend you have never read that sentence in a paper and make me read all 5 damn papers over again?

I'll wait until I really need it in a citation for an article.

>
> > It isn't saying Placentalia evolved from an armadillo. It is saying
> > the earliest member of Xenarthra could have been the earliest member
> > of Placentalia as well. There are fewer "features" in Armadillos
> > separating them from hypothetical "basal placental" than in any other
> > group.
> No, it isn't saying anything of the sort.

Then what does the sentence above, which I know you've read, indicate?

>
> > Therefore, the Armadillo has gone through the least amount of
> > "specialization" since the "basal placental." No that does not
> > necessarily mean "basal Placental" still possessed scutes.
>
> > But it could.
>
> No, it couldn't. That would be a highly unparsimonious reconstruction,
> for which there is no evidence.

Explain.

>
> > We would need to know what "features" create scutes to find out. We
> > would need to know whether this "primitive feature" is also present
> > in Afrotheres and "Laurasians" to make an educated guess.
> Sigh. I don't think you know what "features" means; still.
>
> > Are the "features" which distinguish hair from scutes in other mammals the same across all clades?
> >
> > Are pangolin scales more "advanced" than armadillo scutes?
> >
> > These questions might be a good place to start.
>
> Those questions are nonsensical, I'm afraid.

Why? Please explain in minute detail how pangolin scales arose and list your citations.

>
> >>> And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
> >>>
> >> I can't be held responsible for what you prefer or why you prefer it.
> >> But the proper term is "primitive", meaning "present in the common
> >> ancestor".
> >
> > In human paleoanthropology, the term is no longer accepted. I guess
> > I'll have to live with "primitive" and you'll have to live with
> > "assimilate."
>
> That would be fine if we could agree on the definitions.
>
> > From the paper's conclusion:
> >
> > The diversification
> > of placental orders began in the Late Cretaceous
> > (∼75.2 Ma), continued without apparent interruption across the
> > KPg boundary, and ended in the early Cenozoic (∼55.3 Ma)
> >
> > Do you know what the "~" stands for?
>
> I do. Thanks for asking.
>
> > "For example, the dating estimates
> > for the divergence between northern tree shrews and Chinese
> > tree shrews and for the base of Cetacea penetrated beyond
> > the minimum bounds suggested by fossils, thereby resulting in
> > younger molecular clock divergences, a potential issue of “zombie
> > lineages” (53). Whether these outcomes are due to errors in clock
> > methodology or the unreliability surrounding the fossil record is a
> > topic for further study (54)."
>
> I'm unclear on what point you want to derive from this quote.

It means there a margin of error. Duh.

>
> > If so, I think after this we will be able to talk without all of the unnecessary nit-picking.
>
> You call it unnecessary nit-picking, I call it a combination of your
> inability to communicate and your fundamental misconceptions.

Since you want to use vague insults, I'll comply. Let's get kindergarten playground.
You're old, close-minded, and probably ugly. Nanny-nanny-boo-boo.

[J.LyonLayden]

John,
I think you know EXACTLY what I meant when I told you that the oldest DNA in Tibet entered THE PLATEAU 20,000 years ago.

Nit-picking like you did proves, beyond shadow of a doubt, that you are a vicious troll.

You are no longer worthy of reply. The peanut gallery should not be taken seriously.

From now on, I will reply each time you comment, but it will not be in response to your trolling. You seek to win by having the last word, no matter how stupid and close-minded your words are. So we'll fix it.

[John Harshman]

Again, what you think it means is unclear due to your unfortunate
inability to write. But what it means is we can't rule out the
possibility that Xenarthra is the sister group of all other placentals.
I'm not sure whether the definition of Xenarthra is as a crown group,
but if it is, there is no necessary connection between the age of
Xenarthra and the age of its divergence from other placental groups
(except that the latter must not precede the former).

> And it has to friggin' mean something.
>
> Do you want to pretend you have never read that sentence in a paper and make me read all 5 damn papers over again?
>
> I'll wait until I really need it in a citation for an article.

The problem isn't in the statement but in your misinterpretation of it.

>>> It isn't saying Placentalia evolved from an armadillo. It is saying
>>> the earliest member of Xenarthra could have been the earliest member
>>> of Placentalia as well. There are fewer "features" in Armadillos
>>> separating them from hypothetical "basal placental" than in any other
>>> group.
>> No, it isn't saying anything of the sort.
>
> Then what does the sentence above, which I know you've read, indicate?

See the explanation above.

>>> Therefore, the Armadillo has gone through the least amount of
>>> "specialization" since the "basal placental." No that does not
>>> necessarily mean "basal Placental" still possessed scutes.
>>
>>> But it could.
>>
>> No, it couldn't. That would be a highly unparsimonious reconstruction,
>> for which there is no evidence.
>
> Explain.

All we know is that armadillos have scutes (is that really the proper
term?); glyptodonts too. But is that even an ancestral chracter in
Xenarthra? Doubtful. What you need to do is look at the known
distribution of scutes in mammals, both extant and extinct. If you map
that onto a tree, I'm pretty sure you would find that assuming the
presence of scutes to be primitive in placentals would take more
independent losses of scutes than assuming their absence to be primitive
would require independent gains.

>>> We would need to know what "features" create scutes to find out. We
>>> would need to know whether this "primitive feature" is also present
>>> in Afrotheres and "Laurasians" to make an educated guess.
>> Sigh. I don't think you know what "features" means; still.
>>
>>> Are the "features" which distinguish hair from scutes in other mammals the same across all clades?
>>>
>>> Are pangolin scales more "advanced" than armadillo scutes?
>>>
>>> These questions might be a good place to start.
>>
>> Those questions are nonsensical, I'm afraid.
>
> Why? Please explain in minute detail how pangolin scales arose and list your citations.

That's another nonsensical requirement. What does "more advanced" mean?

When was that a matter of contention?

>>> If so, I think after this we will be able to talk without all of the unnecessary nit-picking.
>>
>> You call it unnecessary nit-picking, I call it a combination of your
>> inability to communicate and your fundamental misconceptions.
>
> Since you want to use vague insults, I'll comply. Let's get kindergarten playground.
> You're old, close-minded, and probably ugly. Nanny-nanny-boo-boo.

I wouldn't have called those insults vague.

[John Harshman]

On 11/11/17 1:25 PM, J.LyonLayden wrote:
> John,
> I think you know EXACTLY what I meant when I told you that the oldest DNA in Tibet entered THE PLATEAU 20,000 years ago.

Nope.

> Nit-picking like you did proves, beyond shadow of a doubt, that you are a viscious troll.

>
> You are no longer worthy of reply. The peanut gallery should not be taken seriously.
>
> From now on, I will reply each time you comment, but it will not be
> in response to your trolling. You seek to win by having the last
> word, no matter how stupid and close-minded your words are. So we'll
> fix it.

?

[erik simpson]

Just curious: have you been privately communicating with Peter Nyikos?

[J.LyonLayden]

Last week I shared my real evolutionary model with him, my findings and several of the obscure facts that I've uncovered.

Things it's useless to share here.

He doesn't have any problem understanding the word "assimilate" or the phrase "20,000 year old" Tibetan mtDNA.

For you I will explain what I mean, Erik. Some Tibetans have mtDNA haplogroups which split off from the rest of the human genome 20,000 years ago. Only Tibetans have it, and it's diversified within their genome enough that we know it's been there since 20,000 years ago.

That means women entered Tibet 20,000 years ago and reproduced until 10,000 years ago with men whose Y DNA line is now extinct.

We know this because the oldest Y DNA found there is a type of Y Hap D that only split from the rest in Asia 10,000 years ago.

That means there is a 10,000 year old ghost lineage of extinct men in Tibet.

They existed for 10,000 years but left no record of their existence in the "Tibetan genome."

As Anthony Hopkins would say "We ate them."

[J.LyonLayden]

Egyptian hounds paintings decorate walls in Egypt, painted hundreds of years before the DNA says the mtDNA and Y DNA of those hounds got to Egypt.

Know why? The mtDNA and YDNA comes from war dogs brought by invaders.
Just a few war dogs eliminated the old Y and mtDNA, but the dogs kept the morphology, color, and most of the nuclear genome.

I learned that from the paleoanthropology forum, and the citations were good.

That's what happens in nature, though. Subspecies assimilate other subspecies.

Niches get filled, adaptations are made. If an adaptation causes dominance it will sometimes create population growth. Especially if the niche itself grows. Population growth brings the subspecies into contact with other subspecies, hence more assimilation. If you get two subspecies with two excellent adaptations expanding into each other's genome you may get a subspecies with both excellent adaptations. Inside an expanding niche, that subspecies becomes dominant, spreads out, and assimilates still more subspecies.

Until the subspecies are separated from each other by terrestrial barriers for several million years, they will remain the same species. And if they don't stay separated for more than 7 million years, they can still hybridize or assimilate each other again.

As with us and neanderthals, recombination may be difficult. It may follow mammalian pattern infertility, where only the female hybrids are fertile. This creates even more "ghost lineages" in our genome.

So when sea levels rise or lower, when ice sheets melt, or right after natural global distasters you're going to get a few new "hybrid species" in the aftermath.

And it starts all over again.

Nothing like lions and tigers of course.

More like Hss and neanderthal. Grisly bears and polar bears. Ergaster and erectus. Separate species of large bodied new world monkeys:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950642/


This is why, in human evolution, 5 or 6 different subspecies of HSS had 5 or 6 different features that would make up Anatomically Modern Homo Sapiens. The five tribes mixed, and sexually selected the 5 traits over time.

We think we're pretty because we picked what we thought was pretty.

A big problem for about 50 thousand years was that neanderthal thought we were pretty too.

John is breathing hamburger meat out of his nose right now while he's reading this, but if you don't believe me please watch First Peoples where Hawks and several other top scientists explain this in detail.

[J.LyonLayden]

- show quoted text -
All of sudden you are showing a semblance of being a civilized hominid.
I don't know why you couldn't do that before.
You still had to slip an insult in there but at least you also made a coherent objection.

I'll give it one more shot because now there's a ray of hope for actual discussion.

Let me ask you this.

But if Xenarthra is the sister group of all placental animals, and Xenarthra is a placental animal, it means the last common ancestor of Xenarthra and all other placental mammals are one in the same. And it means that ancestor was a placental mammal.

IF basal armadillos do not have a significant amount of unique "features" compared to other groups of placental animals, then we can surmise that basal Xenarthra is closest to basal placental.

If that is not so, please provide your definition of "sister group."
My understanding is that a sister group splits of at the time the main group's origin, or directly before.

I didn't say Xenarthra was older. I am implying that basal members of Xenarthra are the "least adapted" and "least changed" since the KT or Cretaceous.

I should be able to prove this by showing that basal armadillos have the least amount of genetic features. But I'm pretty sure I'll find that already stated in one of these papers.

>
> > And it has to friggin' mean something.
> >
> > Do you want to pretend you have never read that sentence in a paper and make me read all 5 damn papers over again?
> >
> > I'll wait until I really need it in a citation for an article.
>
> The problem isn't in the statement but in your misinterpretation of it.
>
> >>> It isn't saying Placentalia evolved from an armadillo. It is saying
> >>> the earliest member of Xenarthra could have been the earliest member
> >>> of Placentalia as well. There are fewer "features" in Armadillos
> >>> separating them from hypothetical "basal placental" than in any other
> >>> group.
> >> No, it isn't saying anything of the sort.

Then what do you mean by sister group?

Sister groups split off from a common ancestor.
If Xenarthra is a placental and also the sister group of all other placentals, what separates the first member of the sister group from the first ancestor of both?

One measly generation? One measly mutation? A couple of measly features?

> >
> > Then what does the sentence above, which I know you've read, indicate?
>
> See the explanation above.
>
> >>> Therefore, the Armadillo has gone through the least amount of
> >>> "specialization" since the "basal placental." No that does not
> >>> necessarily mean "basal Placental" still possessed scutes.
> >>
> >>> But it could.
> >>
> >> No, it couldn't. That would be a highly unparsimonious reconstruction,
> >> for which there is no evidence.

What is unparsimonious about Xenarthra undergoing less adaptations than all the other niche placentals?

What is wrong with Xenarthra remaining a "generalist?"
Are you saying that all placentals adapted to niches at the exact same rate? Are you saying all placentals deviate equally from the first placental mammal?

> >
> > Explain.
>
> All we know is that armadillos have scutes (is that really the proper
> term?);

That's the term used in those articles and papers I provided. I am assuming that's the correct term.

>glyptodonts too. But is that even an ancestral chracter in
> Xenarthra? Doubtful. What you need to do is look at the known
> distribution of scutes in mammals, both extant and extinct. If you map
> that onto a tree, I'm pretty sure you would find that assuming the
> presence of scutes to be primitive in placentals would take more
> independent losses of scutes than assuming their absence to be primitive
> would require independent gains.

Thank you. That makes sense.

>
> >>> We would need to know what "features" create scutes to find out. We
> >>> would need to know whether this "primitive feature" is also present
> >>> in Afrotheres and "Laurasians" to make an educated guess.
> >> Sigh. I don't think you know what "features" means; still.
> >>
> >>> Are the "features" which distinguish hair from scutes in other mammals the same across all clades?
> >>>
> >>> Are pangolin scales more "advanced" than armadillo scutes?
> >>>
> >>> These questions might be a good place to start.
> >>
> >> Those questions are nonsensical, I'm afraid.
> >
> > Why? Please explain in minute detail how pangolin scales arose and list your citations.
>
> That's another nonsensical requirement. What does "more advanced" mean?

More mutations, more features.

Hair, plates, horns, and feathers are all adapted scutes. They are scutes that have evolved into structures more complex than scutes, with more "features" or "mutations" than basal scutes.

>
> >>>>> And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
> >>>>>
> >>>> I can't be held responsible for what you prefer or why you prefer it.
> >>>> But the proper term is "primitive", meaning "present in the common
> >>>> ancestor".
> >>>
> >>> In human paleoanthropology, the term is no longer accepted. I guess
> >>> I'll have to live with "primitive" and you'll have to live with
> >>> "assimilate."
> >>
> >> That would be fine if we could agree on the definitions.

I hope that we have agreed now and I can at least get to a point without you stopping me for a long discourse on the definition of words like "assimilation."

I hope that you will stop trying to pretend you don't know what I mean by attacking the terms I use.

I will try to be more technical with my terms, but I hope that we can one day use "shorthand" like we do in other scientific forums.

> >>
> >>> From the paper's conclusion:
> >>>
> >>> The diversification
> >>> of placental orders began in the Late Cretaceous
> >>> (∼75.2 Ma), continued without apparent interruption across the
> >>> KPg boundary, and ended in the early Cenozoic (∼55.3 Ma)
> >>>
> >>> Do you know what the "~" stands for?
> >>
> >> I do. Thanks for asking.
> >>
> >>> "For example, the dating estimates
> >>> for the divergence between northern tree shrews and Chinese
> >>> tree shrews and for the base of Cetacea penetrated beyond
> >>> the minimum bounds suggested by fossils, thereby resulting in
> >>> younger molecular clock divergences, a potential issue of “zombie
> >>> lineages” (53). Whether these outcomes are due to errors in clock
> >>> methodology or the unreliability surrounding the fossil record is a
> >>> topic for further study (54)."
> >>
> >> I'm unclear on what point you want to derive from this quote.
> >
> > It means there a margin of error. Duh.
>
> When was that a matter of contention?

When I first encountered you, it surely seemed that you could not budge from 66 million.

I would like to have a discussion with people who acknowledge that the most accepted date is 75 million, but that the date could be 130 million or could be 66 million at the two extremes.

That is what the scientist mean by "molecular data can't rule out a divergence origin deep in the Cretaceous."

If you are absolutely closed to the idea, there's no use discussing it with you.

I do not accept a post-KT origin of major clades for placentals. I think it is impossible. I think there's much less impetus for genomic isolation of subspecies directly after the KT.

In fact, post-KT should have been a time when subspecies were re-aquainting themselves with each other, not isolating themselves from one another.

On the other hand, the Aptian Age and the two following marine extinctions were the perfect impetus for genomic separation. Sea level rise, tectonic activity, increased continental drift.
And these extinction events match up perfectly with the date the molecular clock continues to give for placental clade divergence - 75 to 114 mya.

The "strict" date before fossil calibration and certain controls was 93 million. That's the date first reported before the controversy began. It is exactly the age of the second extinction event 9actually two extinction events via volcanic activity).

The only objection to a date that coincides with the further separation of continents and the sea level rise is the lack of fossils.

But most clades lack fossils for 10 -15 million years after the KT anyway.

And if you'll let me make a point or two without needless interruption, I may be able to present the missing fossils to you.

>
> >>> If so, I think after this we will be able to talk without all of the unnecessary nit-picking.
> >>
> >> You call it unnecessary nit-picking, I call it a combination of your
> >> inability to communicate and your fundamental misconceptions.
> >
> > Since you want to use vague insults, I'll comply. Let's get kindergarten playground.
> > You're old, close-minded, and probably ugly. Nanny-nanny-boo-boo.
>
> I wouldn't have called those insults vague.

You really haven't corrected much that I've said. You've just complained about my terminology. In almosty every case what I stated was exactly what you later stated, we just stated it in different terms. Perhaps yours are more correct for paleoanthropology.


What flaws exactly do you think you've found?

Assimilation is still a thing. Deletion is still a thing. Xenarthra is still the most basal placental.

All you've done was to force me to change some of my language.

Proving someone used the wrong language in a specific field they are not used to is not proving them wrong.

I hope that we can discuss these topics civilly in the future, but if you troll me again I already have my "Cut and Paste" thread bump message ready for you.

[John Harshman]

On 11/12/17 7:58 AM, J.LyonLayden wrote:

> All of sudden you are showing a semblance of being a civilized hominid.
> I don't know why you couldn't do that before.
> You still had to slip an insult in there but at least you also made a coherent objection.

Please stop with the single-sentence paragraphs. Please devote a little
more effort into composing your posts. That would make it easier to read
and understand what you're trying to say.

> I'll give it one more shot because now there's a ray of hope for actual discussion.
>
> Let me ask you this.
>

> But if Xenarthra is the sister group of all plavental animals, and

> Xenarthra is a placental animal, it means the last common ancestor

> between Xenarthra and all other placental mammals are one in the
> same.
I have no idea whatsoever what you intended to say. Is there some
important part of that sentence that's just plain missing?

> IF basal armadillos do not have a significant amount of unique
> "features" compared to other groups of placental animals, then we can
> surmise that basal Xenarthra is closest to basal placental.

Are you using "armadillo" as a proxy for Xenarthra, or do you really
mean armadillos? This makes no sense.

> If that is not so, please provide your definition of "sister group."

> My understanding is that a sister group splits of at the time the main group's origin.

There is no main group, just two groups that split from each other. The
two groups that split from each other are called sister groups. Fairly
often, "living sister group" is implied. Humans are the sister group of
chimpanzees. Peccaries are the sister group of pigs. Tapirs are the
sister group of horses. And so on.

> I didn't say it was older. I am implying thatbasal members of

> Xenarthra are the "least adapted" and "least changed" since the KT or
> Cretaceous.

Why would you imply that? And what "basal members" do you refer to, and
how would you determine them to be basal members?

> I should be able to prove this by showing that basal armadillos have the least amout of genetic features.

"Least amount of genetic features" is a nonsense term.

>>> And it has to friggin' mean something.
>>>
>>> Do you want to pretend you have never read that sentence in a paper and make me read all 5 damn papers over again?
>>>
>>> I'll wait until I really need it in a citation for an article.
>>
>> The problem isn't in the statement but in your misinterpretation of it.
>>
>>>>> It isn't saying Placentalia evolved from an armadillo. It is saying
>>>>> the earliest member of Xenarthra could have been the earliest member
>>>>> of Placentalia as well. There are fewer "features" in Armadillos
>>>>> separating them from hypothetical "basal placental" than in any other
>>>>> group.
>>>> No, it isn't saying anything of the sort.
>

> Then what do you mean by sister group?
>
> Sister groups split off from a common ancestor.

> If Xenarthra is a placental and also the sister group of all other
> placentals, what separates the sister group from the first ancestor

> of both?

> One measly generation? One measly mutation? A couple of measly features?

You must understand that sister groups are symmetrical. If A is the
sister group of B, B is the sister group of A. What separates Xenarthra
from the first ancestor of both is that same distance that separates
other placentals from the sister group of both. One is not more basal
than the other. Now, if you're talking about a branch-based group, the
distinction between the common ancestor and the first member of the
group is very small. But if you're talking about a crown group, it's
considerably bigger.

>>> Then what does the sentence above, which I know you've read, indicate?
>>
>> See the explanation above.
>>
>>>>> Therefore, the Armadillo has gone through the least amount of
>>>>> "specialization" since the "basal placental." No that does not
>>>>> necessarily mean "basal Placental" still possessed scutes.
>>>>
>>>>> But it could.
>>>>
>>>> No, it couldn't. That would be a highly unparsimonious reconstruction,
>>>> for which there is no evidence.
>

> What is unparsimonious about Xenarthra undergoing less adaptations than all the other niche placentals?
>
> What is wrong with Xenarthra remaining a "generalist?"

It just isn't true. The range of adaptation within Xenarthra is huge,
and most if not all of them are highly specialized in myriad ways.

>>> Explain.
>>
>> All we know is that armadillos have scutes (is that really the proper
>> term?);
>

> That's the term used in those articles and paers I provided.

Could you define "scute"? Generally it's used to refer to a reptilian
scale that's much wider than it is long. What is a scute in an armadillo?

>> glyptodonts too. But is that even an ancestral chracter in
>> Xenarthra? Doubtful. What you need to do is look at the known
>> distribution of scutes in mammals, both extant and extinct. If you map
>> that onto a tree, I'm pretty sure you would find that assuming the
>> presence of scutes to be primitive in placentals would take more
>> independent losses of scutes than assuming their absence to be primitive
>> would require independent gains.
>
>

> Thank you. That makes sense.
>
>
>>

>>>>> We would need to know what "features" create scutes to find out. We
>>>>> would need to know whether this "primitive feature" is also present
>>>>> in Afrotheres and "Laurasians" to make an educated guess.
>>>> Sigh. I don't think you know what "features" means; still.
>>>>
>>>>> Are the "features" which distinguish hair from scutes in other mammals the same across all clades?
>>>>>
>>>>> Are pangolin scales more "advanced" than armadillo scutes?
>>>>>
>>>>> These questions might be a good place to start.
>>>>
>>>> Those questions are nonsensical, I'm afraid.
>>>
>>> Why? Please explain in minute detail how pangolin scales arose and list your citations.
>>
>> That's another nonsensical requirement. What does "more advanced" mean?
>

> More mutations, more features.
>
> Hair, plates,horns, and feathers are all adapted scutes. Scutes that
> have evolved in to structures more complex than scutes, with more
> "features" or "mutation" than basal scutes.

That seems a highly subjective determination. Good luck with it, but I
don't see a good way to proceed.

>>>>>>> And I prefer the word "generalized" to "primitive," although I still use it on occasion as well.
>>>>>>>
>>>>>> I can't be held responsible for what you prefer or why you prefer it.
>>>>>> But the proper term is "primitive", meaning "present in the common
>>>>>> ancestor".
>>>>>
>>>>> In human paleoanthropology, the term is no longer accepted. I guess
>>>>> I'll have to live with "primitive" and you'll have to live with
>>>>> "assimilate."
>>>>
>>>> That would be fine if we could agree on the definitions.
>

> I hope that we have agreed now and I can at least get to a point
> without you stopping me for a long discourse on the definition of
> words like "assimilation."

In order to have a discussion, I must know what you mean by the words
you use. "Assimilation" seems at the moment to be nothing more than a
synonym of "introgression".

>>>>
>>>>> From the paper's conclusion:
>>>>>
>>>>> The diversification
>>>>> of placental orders began in the Late Cretaceous
>>>>> (∼75.2 Ma), continued without apparent interruption across the
>>>>> KPg boundary, and ended in the early Cenozoic (∼55.3 Ma)
>>>>>
>>>>> Do you know what the "~" stands for?
>>>>
>>>> I do. Thanks for asking.
>>>>
>>>>> "For example, the dating estimates
>>>>> for the divergence between northern tree shrews and Chinese
>>>>> tree shrews and for the base of Cetacea penetrated beyond
>>>>> the minimum bounds suggested by fossils, thereby resulting in
>>>>> younger molecular clock divergences, a potential issue of “zombie
>>>>> lineages” (53). Whether these outcomes are due to errors in clock
>>>>> methodology or the unreliability surrounding the fossil record is a
>>>>> topic for further study (54)."
>>>>
>>>> I'm unclear on what point you want to derive from this quote.
>>>
>>> It means there a margin of error. Duh.
>>
>> When was that a matter of contention?
>>
>>>>> If so, I think after this we will be able to talk without all of the unnecessary nit-picking.
>>>>
>>>> You call it unnecessary nit-picking, I call it a combination of your
>>>> inability to communicate and your fundamental misconceptions.
>>>
>>> Since you want to use vague insults, I'll comply. Let's get kindergarten playground.
>>> You're old, close-minded, and probably ugly. Nanny-nanny-boo-boo.
>>
>> I wouldn't have called those insults vague.
>

> You really haven't corrected much that I've said. You've just

> complained about my terminolgy. In almosty every case what I stated
> was exactly what you later sated, we just stated it in different

> terms. Perhaps yours are more correct for paleoanthropology.

I would disagree with your characterization.

> What flaws exactly do you think you've found?
>
> Assimilation is still a thing. Deletion is still a thing. Xenarthra is still the most basal placental.

Assimilation is apparently a synonym of introgression. You are using
deletion in at least two contradictory senses. "The most basal
placental" is a complete misunderstanding on your part of how
phylogenetic trees work.

> All you've done was to force me to change some of my language.
>
> Proving someone used the wrong language in a specific field they are not used to is not proving them wrong.

I hope you will be able to see that your problems go way beyond language.

> I hope that we can discuss these topics civilly in the future, but if
> you troll me again I already have my "Cut and Paste" thread bump
> message ready for you.

I'm not sure you know what "troll" means.

[J.LyonLayden]

Sigh. Just tell me what you mean by sister group.
I mean the actual fucking and birthing of children. Don't use any vagueries.

Explain two generations before the birth of the "Last Common Ancestor of All Extant Placental Mammals" and then summarize the generations and fucking patterns between that LCAAEPM and the very first Xenarthra.

If you can't do that, it may be suspect. I can explain my model of how it happened to an 8 year old, and it does not break any evolutionary or genetic rules.

>
> > IF basal armadillos do not have a significant amount of unique
> > "features" compared to other groups of placental animals, then we can
> > surmise that basal Xenarthra is closest to basal placental.
> Are you using "armadillo" as a proxy for Xenarthra, or do you really
> mean armadillos? This makes no sense.

The most basal member of Xenarthra is a genus of armadillo. So yes, as a proxy.
Of all extant Xenarthra, the earliest most basal member of Xenartha should be most genetically similar to the most basal extant Xenarthra.

>
> > If that is not so, please provide your definition of "sister group."
> > My understanding is that a sister group splits of at the time the main group's origin.
>
> There is no main group, just two groups that split from each other. The
> two groups that split from each other are called sister groups. Fairly
> often, "living sister group" is implied. Humans are the sister group of
> chimpanzees. Peccaries are the sister group of pigs. Tapirs are the
> sister group of horses. And so on.

OK now we're getting somewhere. Chimps and humans split off around 4 mya (or between 2 and 8 for the extremes).

However, we kept on fucking and birthing for 1 million years.

Can you explain in a similar way how Xenarthra and the aforementioned sister group came to diverge from one another?

Or do you have an educated guess?

>
> > I didn't say it was older. I am implying thatbasal members of
> > Xenarthra are the "least adapted" and "least changed" since the KT or
> > Cretaceous.
> Why would you imply that? And what "basal members" do you refer to, and
> how would you determine them to be basal members?
>
> > I should be able to prove this by showing that basal armadillos have the least amout of genetic features.
>
> "Least amount of genetic features" is a nonsense term.

Least amount of divergent genetic features.
Least amount of adaptations
Most amount of generalized features.
Most amount of basal attributes.
Most amount of primitive features.
The one that's changed the least, and experienced the least sweeps and bottlenecks.
Please pick a term and I will use it.

Scutes are basal to fur. Y Haplogroup P is "basal" to Y haplogroup R and Q. Microcephalin is "basal" to "Microcephalin D". D is the divergent form, the one that split off from our direct ancestor and evolved in isolation for a while, and then suffered a severe bottleneck.

Let's clarify this. We need to agree on a generalized term for all of the above in order to have a casual conversation.

"The one that has experienced the least genetic sweeps and bottlenecks since a common ancestor."

I would prefer the term not to contain more than one word.

>
> >>> And it has to friggin' mean something.
> >>>
> >>> Do you want to pretend you have never read that sentence in a paper and make me read all 5 damn papers over again?
> >>>
> >>> I'll wait until I really need it in a citation for an article.
> >>
> >> The problem isn't in the statement but in your misinterpretation of it.
> >>
> >>>>> It isn't saying Placentalia evolved from an armadillo. It is saying
> >>>>> the earliest member of Xenarthra could have been the earliest member
> >>>>> of Placentalia as well. There are fewer "features" in Armadillos
> >>>>> separating them from hypothetical "basal placental" than in any other
> >>>>> group.
> >>>> No, it isn't saying anything of the sort.
> >
> > Then what do you mean by sister group?
> >
> > Sister groups split off from a common ancestor.
> > If Xenarthra is a placental and also the sister group of all other
> > placentals, what separates the sister group from the first ancestor
> > of both?
>
> > One measly generation? One measly mutation? A couple of measly features?
>
> You must understand that sister groups are symmetrical. If A is the
> sister group of B, B is the sister group of A. What separates Xenarthra
> from the first ancestor of both is that same distance that separates
> other placentals from the sister group of both.

I know that. That doesn't change what I'm asking. It's not about time it's about genetic sweeps. Which friggin animal experienced the least amount of genetic sweeps over that time period?

The answer is almost certainly Xenarthra, and Xenartha most likely has the least amount of genetic sweeps marked by "features" or "mutations."

I will find out for sure, but not today. i wanna do something else than debate on my day off.


Given no sweep, diversity is maintained in a genome. Only sweeps and bottlenecks(founder effect) cause a mutation to become ubiquitous across a genetic population. All of the 107 mutations which define Y Haplogroup R are separate evidences of genetic sweeps. The refugia population which contained Y Hap R "extincted" or "deleted" all of the diversity.

Basal does not mean "primitive" in this sense. It just means R is most divergent, and has lost many more lineages of diversity in the same amount of time.

If you disagree, let's compare the mutations that define Xenarthra with the mutations that define each order of placental mammals. I'm predicting the mutations which define "Xenarthra" will be fewer by far.

One is not more basal
> than the other. Now, if you're talking about a branch-based group, the
> distinction between the common ancestor and the first member of the
> group is very small. But if you're talking about a crown group, it's
> considerably bigger.

I'll concede on that point.

>
> >>> Then what does the sentence above, which I know you've read, indicate?
> >>
> >> See the explanation above.
> >>
> >>>>> Therefore, the Armadillo has gone through the least amount of
> >>>>> "specialization" since the "basal placental." No that does not
> >>>>> necessarily mean "basal Placental" still possessed scutes.
> >>>>
> >>>>> But it could.
> >>>>
> >>>> No, it couldn't. That would be a highly unparsimonious reconstruction,
> >>>> for which there is no evidence.
> >
> > What is unparsimonious about Xenarthra undergoing less adaptations than all the other niche placentals?
> >
> > What is wrong with Xenarthra remaining a "generalist?"
>
> It just isn't true. The range of adaptation within Xenarthra is huge,
> and most if not all of them are highly specialized in myriad ways.

Can you prove this? On what evidence is this based?

>
> >>> Explain.
> >>
> >> All we know is that armadillos have scutes (is that really the proper
> >> term?);
> >
> > That's the term used in those articles and paers I provided.
>
> Could you define "scute"? Generally it's used to refer to a reptilian
> scale that's much wider than it is long. What is a scute in an armadillo?

The definition from wikipedia

https://en.wikipedia.org/wiki/Scute

I am not saying that fish scutes and mammal scutes are the same, but several studies point to the fact we can't really tell the difference between reptile and mammal scutes yet. We only know that mammal scutes and mammal hair evolved from reptile scutes at some point before (or early among) mammals.

http://www.sciencemag.org/news/2016/06/human-hair-bird-feathers-came-reptile-scales

https://pterosaurheresies.wordpress.com/2015/03/16/the-origin-of-feathers-and-hair-part-1-skin-and-scales/

http://indianapublicmedia.org/amomentofscience/scales-feathers-fur/


https://books.google.com/books?
id=gSzXAwAAQBAJ&pg=PT353&lpg=PT353&dq=feathers+and+fur+evolved+from+scutes&source=bl&ots=dQqnD9ayf_&sig=Yg4B554aszaHEjTvmByBh7vrUOw&hl=en&sa=X&ved=0ahUKEwimquDiy7nXAhVDMSYKHR6JCasQ6AEIZTAM#v=onepage&q=feathers%20and%20fur%20evolved%20from%20scutes&f=false

We are discussing this above civilly. We may soon have some clarification between the differences in our viewpoints.

>
> > All you've done was to force me to change some of my language.
> >
> > Proving someone used the wrong language in a specific field they are not used to is not proving them wrong.
>
> I hope you will be able to see that your problems go way beyond language.
>
> > I hope that we can discuss these topics civilly in the future, but if
> > you troll me again I already have my "Cut and Paste" thread bump
> > message ready for you.
>
> I'm not sure you know what "troll" means.

I think a troll is someone who objects to a hypothesis belligerently without fully explaining himself, and without bothering to wait for the full presentation. Instead, a troll nit-picks small minutiae that may not even have a large bearing on the overall theory.
A troll seeks to discredit by confusing the point, and disrupting the presentation of the "model." It's also someone who objects only for the sake of objecting or to "get the last word."

[J.LyonLayden]

Introgression and assimilation are not the same thing. Introgression is part of assimilation, and it requires no sexual or natural selection.

The Tibetans have negatively selected most of their Denisovan genes, so most of their introgressed Denisovan genes are gone. The oxygen gene is one of only a few Denisovan genes that remain in their genome, and the only one that's made a genetic "sweep" across the genome in the past.

It was useful, so they kept it. Having it got you laid, and helped you to survive. That's assimilation.

[J.LyonLayden]

"and it requires no sexual or natural selection."

To clarify, introgression requires no sexual or natural selection within the genome into which the introgression has occurred.

[John Harshman]

On 11/12/17 8:26 AM, J.LyonLayden wrote:

Please stop with the multiple redundant responses. Think before you
post. Write in paragraphs. Write clearly.

> I didn't say Xenarthra was older. I am implying that basal members of
> Xenarthra are the "least adapted" and "least changed" since the KT or
> Cretaceous.

> I should be able to prove this by showing that basal armadillos have
> the least amount of genetic features. But I'm pretty sure I'll find
> that already stated in one of these papers.

Bet you won't.

> When I first encountered you, it surely seemed that you could not budge from 66 million.
>
> I would like to have a discussion with people who acknowledge that
> the most accepted date is 75 million, but that the date could be 130
> million or could be 66 million at the two extremes.

Most accepted date of what?

> That is what the scientist mean by "molecular data can't rule out a divergence origin deep in the Cretaceous."
>
> If you are absolutely closed to the idea, there's no use discussing it with you.
>
> I do not accept a post-KT origin of major clades for placentals. I
> think it is impossible. I think there's much less impetus for genomic
> isolation of subspecies directly after the KT.

Why is it impossible? What do you mean by "genomic isolation"?

> In fact, post-KT should have been a time when subspecies were
> re-aquainting themselves with each other, not isolating themselves
> from one another.

Why?

> On the other hand, the Aptian Age and the two following marine
> extinctions were the perfect impetus for genomic separation. Sea
> level rise, tectonic activity, increased continental drift. And these
> extinction events match up perfectly with the date the molecular
> clock continues to give for placental clade divergence - 75 to 114
> mya.

It seems to me that no vague and in the last case imperceptibly slow
event can match up perfectly with even a date itself so vague as
75-114ma. Or at least if it did that would be no evidence of anything.

> The "strict" date before fossil calibration and certain controls was
> 93 million. That's the date first reported before the controversy
> began. It is exactly the age of the second extinction event 9actually
> two extinction events via volcanic activity).
> The only objection to a date that coincides with the further
> separation of continents and the sea level rise is the lack of
> fossils.

> But most clades lack fossils for 10 -15 million years after the KT
> anyway.

What do you mean "most clades"? There are plenty of Paleocene fossils.
Perhaps they aren't members of "most clades", but a great many of them
are placentals. How does this fit your ideas?

> And if you'll let me make a point or two without needless
> interruption, I may be able to present the missing fossils to you.

Sure. But they would have to be placentals, and they would have to
clearly fit into whatever clades you're talking about. You would
probably need a phylogenetic analysis based on many characters.

[erik simpson]

Two clades A and B are "sister" clades if any member of A is more closely to
ANY member of B than any member of other clades, and vice versa.

The last common ancestor (LCA) of A and the LCA of B are generally NOT the same
organism. Can you see why?

When you pick armadillos as representative of Xenarthra (which is fine), why
armadillos instead of sloths or anteaters? They're equally related to you, or
dogs or elephants, after all. Use your imagination to visualize the LCA of
sloths and armadillos, for a start. Do the same for chimps and whales. As
an advanced visualization problem, what was the LCA of all four like?

[John Harshman]

"Two generations" is way too fine a level on which to consider
speciation. But here's the standard story. At one point, there was a
single species, the last common ancestral species of all placentals. At
some point two populations of that species became geographically
isolated from each other (allopatric speciation is generally supposed to
be the most common form). They diverged over time, to the point where if
they encountered each other in sympatry they would not recognize each
other as potential mates. At this point they were different species. One
of those species was ancestral to Xenarthra and the other was ancestral
to all other living placentals. At some point something similar happened
to a species descended from the xenarthran ancestor. That species was
the last common ancestor of Xenarthra, and it split into two species
that form the basal divergence within Xenarthra.

I wish the 8 year old good luck.

>>> IF basal armadillos do not have a significant amount of unique
>>> "features" compared to other groups of placental animals, then we can
>>> surmise that basal Xenarthra is closest to basal placental.
>> Are you using "armadillo" as a proxy for Xenarthra, or do you really
>> mean armadillos? This makes no sense.
>
> The most basal member of Xenarthra is a genus of armadillo. So yes,
> as a proxy. Of all extant Xenarthra, the earliest most basal member
> of Xenartha should be most genetically similar to the most basal
> extant Xenarthra.

What is this genus, how do you know it's "the most basal member"? Why
should the "earliest most basal member" be most genetically similar to

"the most basal extant Xenarthra".

Let me recommend a book for you, one you are sorely in need of:

Tree Thinking, by David A Baum and Stacey D. Smith.

https://www.amazon.com/Tree-Thinking-Introduction-Phylogenetic-Biology/dp/1936221160

It's an introduction to phylogenetic trees and how to understand them.

>>> If that is not so, please provide your definition of "sister group."
>>> My understanding is that a sister group splits of at the time the main group's origin.
>>
>> There is no main group, just two groups that split from each other. The
>> two groups that split from each other are called sister groups. Fairly
>> often, "living sister group" is implied. Humans are the sister group of
>> chimpanzees. Peccaries are the sister group of pigs. Tapirs are the
>> sister group of horses. And so on.
>
> OK now we're getting somewhere. Chimps and humans split off around 4
> mya (or between 2 and 8 for the extremes). However, we kept on
> fucking and birthing for 1 million years. Can you explain in a
> similar way how Xenarthra and the aforementioned sister group came to
> diverge from one another? Or do you have an educated guess?

There can be introgression between species, but there is generally very
little because, even in sympatry, hybrids are generally selected
against. And hybridization decreases as time goes by. We have no
evidence of introgression at the base of Placentalia.

>>> I didn't say it was older. I am implying thatbasal members of
>>> Xenarthra are the "least adapted" and "least changed" since the KT or
>>> Cretaceous.
>> Why would you imply that? And what "basal members" do you refer to, and
>> how would you determine them to be basal members?
>>
>>> I should be able to prove this by showing that basal armadillos have the least amout of genetic features.
>>
>> "Least amount of genetic features" is a nonsense term.
>
> Least amount of divergent genetic features.
> Least amount of adaptations
> Most amount of generalized features.
> Most amount of basal attributes.
> Most amount of primitive features.
> The one that's changed the least, and experienced the least sweeps and bottlenecks.
> Please pick a term and I will use it.

I wouldn't like any of them, because I think you would misunderstand the
significance of all of that.

> Scutes are basal to fur. Y Haplogroup P is "basal" to Y haplogroup R
> and Q. Microcephalin is "basal" to "Microcephalin D". D is the
> divergent form, the one that split off from our direct ancestor and
> evolved in isolation for a while, and then suffered a severe
> bottleneck.

I don't think any of that is true, largely because you are implying that
evolution has a main line and side branches, and that just isn't the case.

> Let's clarify this. We need to agree on a generalized term for all of the above in order to have a casual conversation.
>
> "The one that has experienced the least genetic sweeps and bottlenecks since a common ancestor."
>
> I would prefer the term not to contain more than one word.

There is no word for that, and you are making unwarranted assumptions of
the process. Also, I doubt you know what "genetic sweep" (more correctly
"selective sweep") means. But the problem is less with your terminology
than with your unstated assumptions of the processes.

I don't think you know that, or you wouldn't be talking the way you do.
Most genetic change is not due to selective sweeps or bottlenecks.

> Given no sweep, diversity is maintained in a genome. Only sweeps and
> bottlenecks(founder effect) cause a mutation to become ubiquitous
> across a genetic population. All of the 107 mutations which define Y
> Haplogroup R are separate evidences of genetic sweeps. The refugia
> population which contained Y Hap R "extincted" or "deleted" all of
> the diversity.

Not true. Mutations can become ubiquitous ("fixed" is the term) through
drift in a population of constant size or through selection that doesn't
carry any other loci along. Of course it's true that selection in a
non-recombining sequence, like most of the Y-chromosome or the
mitochondrial genome, will carry along the rest of that linkage group.
But that isn't what happens in most of the genome, because of recombination.

> Basal does not mean "primitive" in this sense. It just means R is
> most divergent, and has lost many more lineages of diversity in the
> same amount of time.

> If you disagree, let's compare the mutations that define Xenarthra
> with the mutations that define each order of placental mammals. I'm
> predicting the mutations which define "Xenarthra" will be fewer by
> far.

Go for it. But first you will need a clearly defined hypothesis, which
you don't have so far.

>> One is not more basal
>> than the other. Now, if you're talking about a branch-based group, the
>> distinction between the common ancestor and the first member of the
>> group is very small. But if you're talking about a crown group, it's
>> considerably bigger.
>
> I'll concede on that point.

>>>>> Then what does the sentence above, which I know you've read, indicate?
>>>>
>>>> See the explanation above.
>>>>
>>>>>>> Therefore, the Armadillo has gone through the least amount of
>>>>>>> "specialization" since the "basal placental." No that does not
>>>>>>> necessarily mean "basal Placental" still possessed scutes.
>>>>>>
>>>>>>> But it could.
>>>>>>
>>>>>> No, it couldn't. That would be a highly unparsimonious reconstruction,
>>>>>> for which there is no evidence.
>>>
>>> What is unparsimonious about Xenarthra undergoing less adaptations than all the other niche placentals?
>>>
>>> What is wrong with Xenarthra remaining a "generalist?"
>>
>> It just isn't true. The range of adaptation within Xenarthra is huge,
>> and most if not all of them are highly specialized in myriad ways.
>
> Can you prove this? On what evidence is this based?

Have you ever seen a xenarthran? Tree sloths, ground sloths, armadillos,
anteaters, glyptodonts? How similar is a two-toed sloth to a giant anteater?

>>>>> Explain.
>>>>
>>>> All we know is that armadillos have scutes (is that really the proper
>>>> term?);
>>>
>>> That's the term used in those articles and paers I provided.
>>
>> Could you define "scute"? Generally it's used to refer to a reptilian
>> scale that's much wider than it is long. What is a scute in an armadillo?
>
> The definition from wikipedia
>
> https://en.wikipedia.org/wiki/Scute

That was confused. Bird scutes are not underlain by bone, nor are lizard
scales.

> I am not saying that fish scutes and mammal scutes are the same,

Good, because they're unrelated.

> but
> several studies point to the fact we can't really tell the difference
> between reptile and mammal scutes yet. We only know that mammal
> scutes and mammal hair evolved from reptile scutes at some point
> before (or early among) mammals.

I expect you would find that armadillo scutes are evolved separately and
many millions of generations of its ancestors didn't have them.

> http://www.sciencemag.org/news/2016/06/human-hair-bird-feathers-came-reptile-scales
>
> https://pterosaurheresies.wordpress.com/2015/03/16/the-origin-of-feathers-and-hair-part-1-skin-and-scales/

Please don't cite that web site; that guy is a well known nutcase.

No, that isn't what a troll is. A troll is a person who posts things
without regard to whether he believes them, purely to incite a reaction.

[John Harshman]

I think you have just changed your definition of assimilation.

[J.LyonLayden]

Yes. However the two LCAs should be closer to one another than the most derived descendent of B is to the LCA of B, given that more time has passed between the derived ancestor and its LCA.

In other words if placental mammal LCA is 66 mya, and the Xenarthra LCA is 64 mya, and the derived species of Xenarthra arose diverged 20 thousand years ago....the two LCAs will be more similar.

>
> When you pick armadillos as representative of Xenarthra (which is fine), why
> armadillos instead of sloths or anteaters?

Mainly because Cingulata shows lest diversity of morphology than Pilosa. The Cingulata genus Dasypodidae is the most basal form of Xenarthra. Cingulata is made up of animals with armadillo morphology. Also because the earliest members of Pilosa had exoskeletons or scutes, some still do, and some still hold an armadillo-like morphology themselves:

https://en.wikipedia.org/wiki/Cyclopedidae



because

> dogs or elephants, after all. Use your imagination to visualize the LCA of
> sloths and armadillos, for a start. Do the same for chimps and whales. As
> an advanced visualization problem, what was the LCA of all four like?

All the giant sloth needed to do was to economize the shell (it beacame a lighter exoskeleton) and grow it's body a little longer to reach for leaves. It still had the same "cheek flanges" as Gondwanatheres, Glyptodonts, and Vintana and the same basic body structure of most early Xenarthrans.

Further economization of those extraneous body parts led to the vestiges of cheek flanges on Dasypodidae and extant sloths.

[John Harshman]

On 11/12/17 2:18 PM, J.LyonLayden wrote:
> Mainly because Cingulata shows lest diversity of morphology than
> Pilosa. The Cingulata genus Dasypodidae is the most basal form of
> Xenarthra. Cingulata is made up of animals with armadillo morphology.
> Also because the earliest members of Pilosa had exoskeletons or
> scutes, some still do, and some still hold an armadillo-like
> morphology themselves

I would dearly love to see the evidence for each of these claims.

[J.LyonLayden]

I would basically describe it to the 8 year old the same way you did.

But I would not assume that they ever would have seen each other again before further speciation.

I know you didn't assume that, but the distinction is important.

If they were separated by tectonic activity, and the moving away of continents, one or both may have stayed similar to their LCA for 7 million years or more. I mean that one population may have retained all diversity of the LCA group and developed no mutations that became beneficial enough to make a genetic sweep.

But if one of the two 'niches" changed drastically, the species occupying that niche would experience more change and hence more genetic sweeps.

[J.LyonLayden]

Just look at Cingulata in wikipedia. It's all armadillos. Look at Dasypodidae in wikipedia, it says it's most basal. Just look at the Cyclopedidae in wikipedia, it's a Pilosa with scutes with an armadillo morphology.

And I'd be willing to bet it's the most basal form of extant Pilosa.

[John Harshman]

On 11/12/17 2:34 PM, J.LyonLayden wrote:
> I would basically describe it to the 8 year old the same way you did.
>
> But I would not assume that they ever would have seen each other again before further speciation.
>
> I know you didn't assume that, but the distinction is important.
>
> If they were separated by tectonic activity, and the moving away of
> continents, one or both may have stayed similar to their LCA for 7
> million years or more. I mean that one population may have retained
> all diversity of the LCA group and developed no mutations that became
> beneficial enough to make a genetic sweep.

You are leaning on this "genetic sweep" thing, but I don't think you
know what it means or how often it actually happens. I think you have a
false view of evolution at the genetic level. I also doubt that two
species that have been separate for as much as 7 million years would be
likely to exchange genes.

> But if one of the two 'niches" changed drastically, the species
> occupying that niche would experience more change and hence more
> genetic sweeps.

Stripped of the "genetic sweeps" language, there is some truth to that.
Not more genetic change in general, but more selective change. Still,
this would not be likely to have the results you imagine.

[John Harshman]

I don't see any scutes. Are you sure? Now, if what you mean by "scutes"
is nothing more than "scales", then there are a great many mammals with
scaled tails, and that might be primitive for placentals. But that isn't
just Xenarthra.

> And I'd be willing to bet it's the most basal form of extant Pilosa.

Again, there is no such thing as "the most basal form". What "basal"
means in terms of extant taxa is just "the less speciose of two basal
branches".

I would still like to see the evidence for each of your claims.

[J.LyonLayden]

On Sunday, November 12, 2017 at 5:38:40 PM UTC-5, John Harshman wrote:
> On 11/12/17 2:34 PM, J.LyonLayden wrote:
> > I would basically describe it to the 8 year old the same way you did.
> >
> > But I would not assume that they ever would have seen each other again before further speciation.
> >
> > I know you didn't assume that, but the distinction is important.
> >
> > If they were separated by tectonic activity, and the moving away of
> > continents, one or both may have stayed similar to their LCA for 7
> > million years or more. I mean that one population may have retained
> > all diversity of the LCA group and developed no mutations that became
> > beneficial enough to make a genetic sweep.
>
> You are leaning on this "genetic sweep" thing, but I don't think you
> know what it means or how often it actually happens. I think you have a
> false view of evolution at the genetic level. I also doubt that two
> species that have been separate for as much as 7 million years would be
> likely to exchange genes.

I only know for a fact it's happened in primate evolution one hell of a lot. At least among the lineage that led to chimps and humans.

Chimps have a 3 mya LCM with many lineage deletions.
Mystery Hominids split off 3 mya.
Denisovans split off 800k ago.
neanderthals 500,000.

Our lineage made sweeps over all of those subspecies I just named, beginning when we were little more than animals.

We assimilated every single one of them, from the ancestor of chimps to Denisovans to neanderthals, and about 5 others.

That's what happens. It's the best way to explain speciation.

And we are true hybrids mind you. Our immune systems, unless you're a bushman , are 90% neanderthal and Denisovan.

In a sense, animals cannot expand into new territories without assimilating what's already there. They need the immunities to thrive in the new environment.

A heat map of neanderthal immunity genes over the globe gives you a great map of where neanderthals used to be. Same with Denisovans.

>
> > But if one of the two 'niches" changed drastically, the species
> > occupying that niche would experience more change and hence more
> > genetic sweeps.
>
> Stripped of the "genetic sweeps" language, there is some truth to that.
> Not more genetic change in general, but more selective change. Still,
> this would not be likely to have the results you imagine.

What results do you think I imagine?

[J.LyonLayden]

On Sunday, November 12, 2017 at 8:13:10 PM UTC-5, John Harshman wrote:
> On 11/12/17 2:38 PM, J.LyonLayden wrote:
> > On Sunday, November 12, 2017 at 5:22:13 PM UTC-5, John Harshman wrote:
> >> On 11/12/17 2:18 PM, J.LyonLayden wrote:
> >>> Mainly because Cingulata shows lest diversity of morphology than
> >>> Pilosa. The Cingulata genus Dasypodidae is the most basal form of
> >>> Xenarthra. Cingulata is made up of animals with armadillo morphology.
> >>> Also because the earliest members of Pilosa had exoskeletons or
> >>> scutes, some still do, and some still hold an armadillo-like
> >>> morphology themselves
> >>
> >> I would dearly love to see the evidence for each of these claims.
> >
> > Just look at Cingulata in wikipedia. It's all armadillos. Look at
> > Dasypodidae in wikipedia, it says it's most basal. Just look at the
> > Cyclopedidae in wikipedia, it's a Pilosa with scutes with an
> > armadillo morphology.
>
> I don't see any scutes. Are you sure? Now, if what you mean by "scutes"
> is nothing more than "scales", then there are a great many mammals with
> scaled tails, and that might be primitive for placentals. But that isn't
> just Xenarthra.

I was wrong about that. Thinking of the wrong animal. The earliest members of the Pilosa clade had osteoderms. Giant sloth and ground sloth.

Osteoderm is a scute with bone- Xenartha is the only mammal group with osteoderms, but pangolins and maybe others have scutes.

Before DNA when they had pangolins and armadillos in the same group, they used to think the ancestral Xenarthran had scutes or even an osteoderm exoskeleton.

The thinking was because of the idea that scutes evolve into hair or scales or fur or osteoderms, but not vice versa. Or at least it's one step back and one step forward, and more evolutionary effort.

I don't know what they think now, but the recent steady I shared says hair and fur and feathers came from scutes.

I don't think they used to think the LCA of Xenarthra was hairless, just that it also had scutes.

But while looking for the info i did find another study that says the ancestral Eutherian mammal Karyotype is contained within Xenarthra:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020109

>
> > And I'd be willing to bet it's the most basal form of extant Pilosa.
>
> Again, there is no such thing as "the most basal form". What "basal"
> means in terms of extant taxa is just "the less speciose of two basal
> branches".

Well that's what I mean. Least changed.

>
> I would still like to see the evidence for each of your claims.

Which ones?

[J.LyonLayden]

Oh! I might have been wrong about New World Monkeys. I still don't think they rafted but I no longer see the problem. We've got monkeys in N. America way before 20 mya; they could have island hopped by then.

They used to think monkeys rafted all the way from Africa, I hadn't gotten the memo.

[J.LyonLayden]

On Sunday, November 12, 2017 at 8:13:10 PM UTC-5, John Harshman wrote:
> On 11/12/17 2:38 PM, J.LyonLayden wrote:
> > On Sunday, November 12, 2017 at 5:22:13 PM UTC-5, John Harshman wrote:
> >> On 11/12/17 2:18 PM, J.LyonLayden wrote:
> >>> Mainly because Cingulata shows lest diversity of morphology than
> >>> Pilosa. The Cingulata genus Dasypodidae is the most basal form of
> >>> Xenarthra. Cingulata is made up of animals with armadillo morphology.
> >>> Also because the earliest members of Pilosa had exoskeletons or
> >>> scutes, some still do, and some still hold an armadillo-like
> >>> morphology themselves
> >>
> >> I would dearly love to see the evidence for each of these claims.
> >
> > Just look at Cingulata in wikipedia. It's all armadillos. Look at
> > Dasypodidae in wikipedia, it says it's most basal. Just look at the
> > Cyclopedidae in wikipedia, it's a Pilosa with scutes with an
> > armadillo morphology.
>
> I don't see any scutes. Are you sure? Now, if what you mean by "scutes"
> is nothing more than "scales", then there are a great many mammals with
> scaled tails, and that might be primitive for placentals. But that isn't
> just Xenarthra.

Ok now that makes sense. I didn't know those were scales on the rodent tails.
So scutes beget scales or might even be synonymous, and they evolve into hair, fur, etc. like those studies say. They may be primitive for placentals. Osteoderms are present in placental mammals only among Xenarthrans, and they're made up of unattached bone and scutes.

So which came first, the bone or the scute/scale?

Just trying to use Occam's razor here.

[John Harshman]

On 11/12/17 8:29 PM, J.LyonLayden wrote:
> On Sunday, November 12, 2017 at 5:38:40 PM UTC-5, John Harshman wrote:
>> On 11/12/17 2:34 PM, J.LyonLayden wrote:
>>> I would basically describe it to the 8 year old the same way you did.
>>>
>>> But I would not assume that they ever would have seen each other again before further speciation.
>>>
>>> I know you didn't assume that, but the distinction is important.
>>>
>>> If they were separated by tectonic activity, and the moving away of
>>> continents, one or both may have stayed similar to their LCA for 7
>>> million years or more. I mean that one population may have retained
>>> all diversity of the LCA group and developed no mutations that became
>>> beneficial enough to make a genetic sweep.
>>
>> You are leaning on this "genetic sweep" thing, but I don't think you
>> know what it means or how often it actually happens. I think you have a
>> false view of evolution at the genetic level. I also doubt that two
>> species that have been separate for as much as 7 million years would be
>> likely to exchange genes.
>
>
> I only know for a fact it's happened in primate evolution one hell of a lot. At least among the lineage that led to chimps and humans.
>
> Chimps have a 3 mya LCM with many lineage deletions.
> Mystery Hominids split off 3 mya.
> Denisovans split off 800k ago.
> neanderthals 500,000.

What is a LCM and what do you mean by lineage deletions? You appear to
be using "deletion" in yet another sense.

> Our lineage made sweeps over all of those subspecies I just named, beginning when we were little more than animals.

You seem to be using "sweep" in yet another sense. And "subspecies".

> We assimilated every single one of them, from the ancestor of chimps to Denisovans to neanderthals, and about 5 others.

And "assimilate".

> That's what happens. It's the best way to explain speciation.

What's the best way to explain speciation?

> And we are true hybrids mind you. Our immune systems, unless you're a bushman , are 90% neanderthal and Denisovan.

I would be interested in support for that assertion.

> In a sense, animals cannot expand into new territories without
> assimilating what's already there. They need the immunities to thrive
> in the new environment.

In what sense is that true?

> A heat map of neanderthal immunity genes over the globe gives you a great map of where neanderthals used to be. Same with Denisovans.

I presume that by "genes" you mean "alleles". Where is this heat map?

>>> But if one of the two 'niches" changed drastically, the species
>>> occupying that niche would experience more change and hence more
>>> genetic sweeps.
>>
>> Stripped of the "genetic sweeps" language, there is some truth to that.
>> Not more genetic change in general, but more selective change. Still,
>> this would not be likely to have the results you imagine.
>
> What results do you think I imagine?

The main driving engine of speciation and evolutionary change, apparently.

[John Harshman]

The scute came first. Osteoderms have evolved several times,
independently, in tetrapods. Osteoderms are not evidence that
xenarthrans are "basal".

[John Harshman]

On 11/12/17 9:13 PM, J.LyonLayden wrote:
> On Sunday, November 12, 2017 at 8:13:10 PM UTC-5, John Harshman wrote:
>> On 11/12/17 2:38 PM, J.LyonLayden wrote:
>>> On Sunday, November 12, 2017 at 5:22:13 PM UTC-5, John Harshman wrote:
>>>> On 11/12/17 2:18 PM, J.LyonLayden wrote:
>>>>> Mainly because Cingulata shows lest diversity of morphology than
>>>>> Pilosa. The Cingulata genus Dasypodidae is the most basal form of
>>>>> Xenarthra. Cingulata is made up of animals with armadillo morphology.
>>>>> Also because the earliest members of Pilosa had exoskeletons or
>>>>> scutes, some still do, and some still hold an armadillo-like
>>>>> morphology themselves
>>>>
>>>> I would dearly love to see the evidence for each of these claims.
>>>
>>> Just look at Cingulata in wikipedia. It's all armadillos. Look at
>>> Dasypodidae in wikipedia, it says it's most basal. Just look at the
>>> Cyclopedidae in wikipedia, it's a Pilosa with scutes with an
>>> armadillo morphology.
>>
>> I don't see any scutes. Are you sure? Now, if what you mean by "scutes"
>> is nothing more than "scales", then there are a great many mammals with
>> scaled tails, and that might be primitive for placentals. But that isn't
>> just Xenarthra.
>
>
> I was wrong about that. Thinking of the wrong animal. The earliest
> members of the Pilosa clade had osteoderms. Giant sloth and ground
> sloth.

Did they? And why do you say they're the earliest members of the clade?

> Osteoderm is a scute with bone- Xenartha is the only mammal group
> with osteoderms, but pangolins and maybe others have scutes.
>
> Before DNA when they had pangolins and armadillos in the same group,
> they used to think the ancestral Xenarthran had scutes or even an
> osteoderm exoskeleton.

Who are "they"?

> The thinking was because of the idea that scutes evolve into hair or
> scales or fur or osteoderms, but not vice versa. Or at least it's one
> step back and one step forward, and more evolutionary effort.

Whose thinking was that?

> I don't know what they think now, but the recent steady I shared says
> hair and fur and feathers came from scutes. I don't think they used
> to think the LCA of Xenarthra was hairless, just that it also had
> scutes.

Who are "they"?

> But while looking for the info i did find another study that says the
> ancestral Eutherian mammal Karyotype is contained within Xenarthra:
> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020109

So do chimpanzees. What does that show?

>>> And I'd be willing to bet it's the most basal form of extant Pilosa.
>>
>> Again, there is no such thing as "the most basal form". What "basal"
>> means in terms of extant taxa is just "the less speciose of two basal
>> branches".
>
> Well that's what I mean. Least changed.

That isn't what I just said. You perhaps don't know what "speciose"
means. It means "having lots of species". "Less speciose" means "having
fewer species.

>> I would still like to see the evidence for each of your claims.
>
> Which ones?

All the ones you made in the paragraph at the top of this post, for a
start, at least the ones you haven't abandoned.

[J.LyonLayden]

On Monday, November 13, 2017 at 10:07:09 AM UTC-5, John Harshman wrote:
> On 11/12/17 8:29 PM, J.LyonLayden wrote:
> > On Sunday, November 12, 2017 at 5:38:40 PM UTC-5, John Harshman wrote:
> >> On 11/12/17 2:34 PM, J.LyonLayden wrote:
> >>> I would basically describe it to the 8 year old the same way you did.
> >>>
> >>> But I would not assume that they ever would have seen each other again before further speciation.
> >>>
> >>> I know you didn't assume that, but the distinction is important.
> >>>
> >>> If they were separated by tectonic activity, and the moving away of
> >>> continents, one or both may have stayed similar to their LCA for 7
> >>> million years or more. I mean that one population may have retained
> >>> all diversity of the LCA group and developed no mutations that became
> >>> beneficial enough to make a genetic sweep.
> >>
> >> You are leaning on this "genetic sweep" thing, but I don't think you
> >> know what it means or how often it actually happens. I think you have a
> >> false view of evolution at the genetic level. I also doubt that two
> >> species that have been separate for as much as 7 million years would be
> >> likely to exchange genes.
> >
> >
> > I only know for a fact it's happened in primate evolution one hell of a lot. At least among the lineage that led to chimps and humans.
> >
> > Chimps have a 3 mya LCM with many lineage deletions.
> > Mystery Hominids split off 3 mya.
> > Denisovans split off 800k ago.
> > neanderthals 500,000.
>
> What is a LCM and what do you mean by lineage deletions? You appear to
> be using "deletion" in yet another sense.

I meant LCA.
Yes. When we speak of all the lineages missing between Y Haplogroup P and Y Haplogoup R, and between Y Haplogroup R and Y haplogroup R1b, we call them deletions too.

Each mutation which defines y haplogroup R is evidence of natural and sexual dselection of men with those mutations. So each mutation represents all diversity within T hap R EXCEPT each mutation being driven to extinction.

Nobody survived one generation except those Y Hap Rs with the M207 muation. Then no one survived the next generation except the family with M207 and Page37. Then nobody survived the next generation but people with M207, Page37, and UTY2.

For many generations, only one man arose each generation from the uber-violence, cannabilism, headhunting, and neanderhtal predation to reproduce.

We call all of the diversity driven to extinction "deletions."

>
> > Our lineage made sweeps over all of those subspecies I just named, beginning when we were little more than animals.
>
> You seem to be using "sweep" in yet another sense. And "subspecies".

Subspecies is a tricky term. In anthropology, some people think Neanderthals are a subspecies of homo sapiens. Others think it's a different species than homo sapines.

Some think the different genetic populations which came together to make Anatomically Modern Humans were ethnic groups, other think the were subspecies, others think they were totally different species.

There's no consensus.

Some scientists think there's only one species - homo sapiens sapiens from Homo Habilis right up until until now.


As far as sweeps I was not using a scientific term in this sense.

"The armies of the Khan swept over the barbarians."

And McArthur's troops swept over the invading forces.

It was a poor choice of words but I meant the assimilated the populations.\

But there is a difference between assimilating a whole population and assimilating a single gene.

I noticed you called me out on the distinction elsewhere.

Would you like me to use the word "absorb" instead of "assimilate" when I am speaking of whole genomic populations? I could make an attempt to remember.

A genomic population is an isolated breeding population. It is defined by its DNA makeup and diversity.

A separate genomic population of the same species of animals may have a different DNA makeup and different diversity.

For instance, Europe is 70% y Hap R1b.

East Asia is 70% Y Hap O.

They are two genomic populations made up of different defineable "genomes," but they are still the same species.

>
> > We assimilated every single one of them, from the ancestor of chimps to Denisovans to neanderthals, and about 5 others.
>
> And "assimilate".

Would you like "absorb?"

Is that how you want it? "Absorb" for absorbing whole genomic populations and "assimilate" for the act of reducing a genomic population to a single set of valuable genes? Both involve absorbing the population and sexually selecting what we want out of it.

>
> > That's what happens. It's the best way to explain speciation.
>
> What's the best way to explain speciation?

Animals find niches. Animals adapt to those niches. Animals expand into niches. the absorb subspecies and assimilate those subspecies adaptations. After several million years, the species becomes a new species. Any subspecies that have been left out of the fucking and assimilating for more than 3 to 7 million years do not become another species.

3 to 7 million years is the current estimate. yes like you said, 7 million years is hard to believe.

But the zebras seem to have done it. That's part of the reason they say "7 million."
Most subspecies, including ours, had problems after only one or two million. But we could still reproduce.

>
> > And we are true hybrids mind you. Our immune systems, unless you're a bushman , are 90% neanderthal and Denisovan.
>
> I would be interested in support for that assertion.

I just googled "neanderthal immunity heat map" and look what I found! Wasn't hard to do at all.

https://www.google.com/search?q=distribution+of+denisovan+and+neanderthal+immune+genes&rlz=1C1GGRV_en___US751&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjS6P75jbzXAhVDJiYKHboACOIQ_AUICigB&biw=1097&bih=476

>
> > In a sense, animals cannot expand into new territories without
> > assimilating what's already there. They need the immunities to thrive
> > in the new environment.
> In what sense is that true?
>
> > A heat map of neanderthal immunity genes over the globe gives you a great map of where neanderthals used to be. Same with Denisovans.
>
> I presume that by "genes" you mean "alleles". Where is this heat map?

Several pages of them here.

https://www.google.com/search?q=distribution+of+denisovan+and+neanderthal+immune+genes&rlz=1C1GGRV_en___US751&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjS6P75jbzXAhVDJiYKHboACOIQ_AUICigB&biw=1097&bih=476

>
> >>> But if one of the two 'niches" changed drastically, the species
> >>> occupying that niche would experience more change and hence more
> >>> genetic sweeps.
> >>
> >> Stripped of the "genetic sweeps" language, there is some truth to that.
> >> Not more genetic change in general, but more selective change. Still,
> >> this would not be likely to have the results you imagine.
> >
> > What results do you think I imagine?
>
> The main driving engine of speciation and evolutionary change, apparently.

Well that's what John Hawks thinks happened to humans, and pretty much all the other credible researchers too. If we haven't realized it happens elsewhere, it's a state of special pleading.

Yoy saw the results I provided for the amount of hybridization in wild New World Monkeys, right?

Do the same test anywhere else in the mammal kingdom and I bet you'll get a similar phenomenon.

Hybridization and assimilation is going on all the time.

[J.LyonLayden]

They are the oldest fossil we have of the clade. They're might be earlier members without osteoderms, but we don't know.

>
> > Osteoderm is a scute with bone- Xenartha is the only mammal group
> > with osteoderms, but pangolins and maybe others have scutes.
> >
> > Before DNA when they had pangolins and armadillos in the same group,
> > they used to think the ancestral Xenarthran had scutes or even an
> > osteoderm exoskeleton.
>
> Who are "they"?

The classification system of the consensus?

You realize that Xenarthra, Carnivora, and Philedota have been altered dramatically since DNA testing, right? I think "Philedota" was actually invented, because it used to be in Xenarthra.

>
> > The thinking was because of the idea that scutes evolve into hair or
> > scales or fur or osteoderms, but not vice versa. Or at least it's one
> > step back and one step forward, and more evolutionary effort.
>
> Whose thinking was that?

The thinking I heard and read in highschool and college in the late 80s and 90s.

What is your interpretation of what the thinking was then?

What is your interpretation of what the thinking is now on this subject?

>
> > I don't know what they think now, but the recent steady I shared says
> > hair and fur and feathers came from scutes. I don't think they used
> > to think the LCA of Xenarthra was hairless, just that it also had
> > scutes.
>
> Who are "they"?

Consensus. Mainstream. the people who write college textbooks.

>
> > But while looking for the info i did find another study that says the
> > ancestral Eutherian mammal Karyotype is contained within Xenarthra:
> > http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020109
>
> So do chimpanzees. What does that show?

Do they? Do all mammal groups? Then why did someone write a paper on this? Busy work?

Can you show me proof that it's contained in primates?

>
> >>> And I'd be willing to bet it's the most basal form of extant Pilosa.
> >>
> >> Again, there is no such thing as "the most basal form". What "basal"
> >> means in terms of extant taxa is just "the less speciose of two basal
> >> branches".
> >
> > Well that's what I mean. Least changed.
>
> That isn't what I just said. You perhaps don't know what "speciose"
> means. It means "having lots of species". "Less speciose" means "having
> fewer species.

OK. Some species have more mutations separating them from the clades "LCA" than other species in even given group.

The one with the least mutations between the LCA and that species is what we call "basal" in when describing primate evolution.

What mother fucking word do you want me to use for "the species with the least mutations separating it from the LCA of it's clade?"

Wikipedia uses the mother fucking word basal when describing it.
If you do not believe me read the entry on the most primitive/basal genus of armadillo which I provided.

Every sentence takes a novel with you because you have no ability to use context clues and you seek find fault with words that NO ONE has problems understanding except you.

I can provide you with many post on reddit where I use these terms all the time, others use these terms all the time, and no one has a fucking problem.

You are either trying to seem smart, aor you are being an ass-hat.

>
> >> I would still like to see the evidence for each of your claims.
> >
> > Which ones?
>
> All the ones you made in the paragraph at the top of this post, for a
> start, at least the ones you haven't abandoned.

At the top of this post? What fucking claims are you talking about? Speak up, son. I'm not going over each sentence and rewriting it to try and figure out what you mean unless I get .07 cents a word.

[J.LyonLayden]

Xenarthrans are basal. You can't read, and I can't stop the explanation to define words for the dumb kids who never learned to read context clues.

I was never trying to prove Xenarthrans were basal via their osteoderms. I was trying to find out whether the first Xenarthran had an odteoderm or possessed scutes. You were absolutely no help, I still haven't found out, and will keep searching.

Just because osteoderms arose more than once does not mean scutes came first in those species.

It may well mean that, but we must have more data to know for sure.

And we must apply Occam's Razor on everything, or our predictions for the future scientific findings will likely be wrong.

That's how I work.

Don't like it? then fuck off and be surprised when they find the next whale that's older than even Himalayacetus. I won't be, I'll be expecting it. And predicting it.

[erik simpson]

I think you have a problem in perception of "mainstream", "consensus", and
similar terms. Date of publication matters a lot, particularly when it comes
to genetic data and methods. Enormous progress has been made in just the last
decade or so. What you learned in 80s and 90s isn't current, and any
conclusions drawn then need to be (and have been) subjected to scrutiny in the
light of what we know now. You're still running too fast, and your language is
sloppy. It's obvious you're frustrated when somebody demands clear definitions,
but if you want to talk science (rather than science fiction) you have to be
more careful.

For one (of many examples), "basal" is a perfectly good term to use as an
adjective referring to a clade or subclade, but is problematic to use as
describing a particular species or genus, particularly when that species or
genus is extant. All of them are separated from the "base" by 60-70 My.
Genomes evolve and change even if certain morphological characteristics may be
highly conserved.

[J.LyonLayden]

Man I feel ya.
But here's the deal; I can't find updates on those old ideas.

I know what they thought about armadillos and pangolins. Then they found out alot of it isn't true. So...how has that changed the other things they used to think? How does that change what they think about scutes, osteoderms, and scales? If no one has done a study, I must make an educated guess myself with all data available.

All I can find is a recent study that hair,fur,and feathers evolved from scutes.

> sloppy. It's obvious you're frustrated when somebody demands clear definitions,
> but if you want to talk science (rather than science fiction) you have to be
> more careful.
>
> For one (of many examples), "basal" is a perfectly good term to use as an
> adjective referring to a clade or subclade, but is problematic to use as
> describing a particular species or genus, particularly when that species or
> genus is extant. All of them are separated from the "base" by 60-70 My.
> Genomes evolve and change even if certain morphological characteristics may be
> highly conserved.

So what should we use for "the least changed" extant member of a species?
Is "primitive" more correct?

A definition for the genus or species with the most conserved morphological characteristics and least genomic sweeps?

"Dasypus are primitive mammals known for their hard armor like shell, called a carapace..." wikipedia, Dasypus

[J.LyonLayden]

Correction:

So what should we use for "the least changed" extant member of a clade or group?

[J.LyonLayden]

I want to totally divulge to you guys what I am doing. I am using Occam's Razor to predict exactly what animals were walking around on this planet 64 million years ago and what they looked like. I plan to use all available data, and I plan to be 95% correct.
I've done it before in human evolution, and I believe it was more difficult.
My methods included matching folklore with archeology and paleoanthropology, so you may object to my considering all possibilities when I go into "investigative journalist" mode. All data is subject to the razor.
I don't mean that to sound arrogant, it's just what I spend all of my time on.
I am assessing he KT evidence just like I assessed the Toba evidence 10 years ago.

[erik simpson]

A lot has changed, indeed. It's a active field of study, and unless you're a
pro, or have lots of time, i's difficult to keep up with all of it. Even most
of the practitioners don't keep up with all of it. But if you want better
understanding, you have to invest time studying it.

Occam's razor is sharp, and it often isn't as easy as you seem to think to
determine what the least unlikely explanation really is. Figuratively speaking,
you can cut yourself. A lot of what's out there to read is pretty wrong, some
is very wrong. It's hard to develope your own personal BS detectors. Talking
to pros is very good, if you have the chance. The internet by itself (blogs,
talk groups, etc) is highly unreliable. Anybody can say anything. Refereed
journals and professional monographs are best, but journal articles are usually
too technical for most people who aren't really into it, and most of the
scientists waorking in a field don't have time to write books.

A couple of rules of thumb that seem to work for me:
If it's about genetics, it ought to be pretty recent, ~10y back is a long
time.

If it's morphological, good paleontology was done a long time ago, but the
contruction of evolutionary trees, cladograms, phylogenetic systematics
also changed in big ways since the 80s. See "cladistics", or "the cladistics
wars". The war is over, and the "cladophiles" as Peter would call them won,
but there remain some stubborn holdouts. My take: try to stick with 21st
century perspective.

[J.LyonLayden]

Fascinating material on the cladistics wars looks like I've got some reading to do.

What I'm looking for is something like the relationship between homo sapiens and homo floresiensis.

150,000 years ago, both had been evolving from a 3 million year old ancestor for the same amount of time.

Yet homo floresiensis is "basal" and has "primitive" features.

This is because its skull, wrist, shoulder blades, and several other traits harken back to australopithecines, homo georgicus, and homo habilis.

These traits aren't seen anywhere else in the fossil record since 2 million years ago. Therefore we can say, at least where these traits are concerned, that homo floresiensis is the most basal form of hominoid around 150 thousand years ago. How can I apply the same terminology to Xenarthra without invoking ire from commenters?

When speaking of a genome, we would say that Denisovan is more basal than Neanderthal or HSS because of several reasons:
1. The Denisovan mito DNA "Eve" is far older
2. The Denisovan genome is part of a larger genome which also existed in europe 400,000 years ago before Neanderthal arose
3. It contains more of The Mystery Hominid introgression, containing genetic material which diverged 3 million years ago and experienced no sweeps until recombination.
4. It can be said that Hss, Neanderthals, and Denisovans share a common ancestor who lived 1.1 million years ago. Therefore the 3 are subspecies of "Homo Sapiens." The Denisovan genome contains more of the original diversity because it has experienced less genetic sweeps and bottlenecks. Therefore it is more "basal."
It was more basal even 30 million years ago when all three genomes existed separately and simultaneously. But it was not necessarily more primitive.

Is this incorrect terminology when discussing paleoanthropology in the same manner?

[John Harshman]

Who is "we"? And what do you mean by "lineages missing"?

> Each mutation which defines y haplogroup R is evidence of natural and
> sexual dselection of men with those mutations. So each mutation
> represents all diversity within T hap R EXCEPT each mutation being
> driven to extinction.

> Nobody survived one generation except those Y Hap Rs with the M207
> muation. Then no one survived the next generation except the family
> with M207 and Page37. Then nobody survived the next generation but
> people with M207, Page37, and UTY2.

> For many generations, only one man arose each generation from the
> uber-violence, cannabilism, headhunting, and neanderhtal predation to
> reproduce.

I don't know what you're trying to say there, but it seems nonsensical.
Much of molecular evolution is neutral, and coalescence doesn't require
bottlenecks, much less the series of extreme bottlenecks you seem to be
claiming here.

> We call all of the diversity driven to extinction "deletions."

Again, who is "we"?

>>> Our lineage made sweeps over all of those subspecies I just named, beginning when we were little more than animals.
>>
>> You seem to be using "sweep" in yet another sense. And "subspecies".
>
> Subspecies is a tricky term. In anthropology, some people think
> Neanderthals are a subspecies of homo sapiens. Others think it's a
> different species than homo sapines.

> Some think the different genetic populations which came together to
> make Anatomically Modern Humans were ethnic groups, other think the
> were subspecies, others think they were totally different species.

> There's no consensus. >
> Some scientists think there's only one species - homo sapiens sapiens from Homo Habilis right up until until now.

> As far as sweeps I was not using a scientific term in this sense.
>
> "The armies of the Khan swept over the barbarians."
>
> And McArthur's troops swept over the invading forces.
>
> It was a poor choice of words but I meant the assimilated the populations.\
>
> But there is a difference between assimilating a whole population and assimilating a single gene.
>
> I noticed you called me out on the distinction elsewhere.
>
> Would you like me to use the word "absorb" instead of "assimilate"
> when I am speaking of whole genomic populations? I could make an
> attempt to remember.

I would like you to concentrate on writing clearly. Whatever it takes to
say what you mean so that another person can understand what you meant,
do that. Certainly using the same word with two different meanings and
with no clues in the text as to when or even whether you are using the
different meanings is not conducive to clarity.

> A genomic population is an isolated breeding population. It is defined by its DNA makeup and diversity.

Is this a term you made up? It's an ugly term.

> A separate genomic population of the same species of animals may have a different DNA makeup and different diversity.

Let's add "diversity" to the list of words I suspect you have have
multiple, private definitions for.

> For instance, Europe is 70% y Hap R1b.
>
> East Asia is 70% Y Hap O.
>
> They are two genomic populations made up of different defineable "genomes," but they are still the same species.

These aren't isolated breeding populations, they aren't made up of
different definable genomes, just different frequencies of the same
haplotypes. There you are again, using the same words to mean different
things within the space of a few lines. Please help.

>>> We assimilated every single one of them, from the ancestor of chimps to Denisovans to neanderthals, and about 5 others.
>>
>> And "assimilate".
>
> Would you like "absorb?"
>
> Is that how you want it? "Absorb" for absorbing whole genomic
> populations and "assimilate" for the act of reducing a genomic
> population to a single set of valuable genes? Both involve absorbing
> the population and sexually selecting what we want out of it.

This is hopelessly confused. Are you even trying to communicate?

>>> That's what happens. It's the best way to explain speciation.
>>
>> What's the best way to explain speciation?
>
> Animals find niches. Animals adapt to those niches. Animals expand
> into niches. the absorb subspecies and assimilate those subspecies
> adaptations. After several million years, the species becomes a new
> species. Any subspecies that have been left out of the fucking and
> assimilating for more than 3 to 7 million years do not become another
> species.
> 3 to 7 million years is the current estimate. yes like you said, 7 million years is hard to believe.

Current estimate of what?

> But the zebras seem to have done it. That's part of the reason they say "7 million."
> Most subspecies, including ours, had problems after only one or two million. But we could still reproduce.

Seem to have done what? Who says "7 million", and why do they?

>>> And we are true hybrids mind you. Our immune systems, unless you're a bushman , are 90% neanderthal and Denisovan.
>>
>> I would be interested in support for that assertion.
>
> I just googled "neanderthal immunity heat map" and look what I found! Wasn't hard to do at all.
>
> https://www.google.com/search?q=distribution+of+denisovan+and+neanderthal+immune+genes&rlz=1C1GGRV_en___US751&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjS6P75jbzXAhVDJiYKHboACOIQ_AUICigB&biw=1097&bih=476

That isn't a search for "neanderthal immunity heat map"; it's a search
for "distribution of denisovan and neanderthal immune genes". Please
don't give me your searches; give me the references you found in
searches. Show me the heat map. I'm not going to click on random links
until I find the one you intend.

>>> In a sense, animals cannot expand into new territories without
>>> assimilating what's already there. They need the immunities to thrive
>>> in the new environment.
>> In what sense is that true?
>>
>>> A heat map of neanderthal immunity genes over the globe gives you a great map of where neanderthals used to be. Same with Denisovans.
>>
>> I presume that by "genes" you mean "alleles". Where is this heat map?
>
> Several pages of them here.
>
> https://www.google.com/search?q=distribution+of+denisovan+and+neanderthal+immune+genes&rlz=1C1GGRV_en___US751&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjS6P75jbzXAhVDJiYKHboACOIQ_AUICigB&biw=1097&bih=476

I found one map in the first page of references. Could I ask you to do a
little more work than that when answering a question? Of course even
that map doesn't tell you where Denisovans (in that case) used to be.
All it tells you is where humans with Denisovan ancestry live now, quite
a different thing.

>>>>> But if one of the two 'niches" changed drastically, the species
>>>>> occupying that niche would experience more change and hence more
>>>>> genetic sweeps.
>>>>
>>>> Stripped of the "genetic sweeps" language, there is some truth to that.
>>>> Not more genetic change in general, but more selective change. Still,
>>>> this would not be likely to have the results you imagine.
>>>
>>> What results do you think I imagine?
>>
>> The main driving engine of speciation and evolutionary change, apparently.
>
> Well that's what John Hawks thinks happened to humans, and pretty
> much all the other credible researchers too. If we haven't realized
> it happens elsewhere, it's a state of special pleading.

I would like to see the evidence that John Hawks (and all the other
creidible experts) think that hybridization is the main driving engine
of speciation and evolutionary change.

> Yoy saw the results I provided for the amount of hybridization in
> wild New World Monkeys, right?

I didn't.

> Do the same test anywhere else in the mammal kingdom and I bet you'll
> get a similar phenomenon.
>
> Hybridization and assimilation is going on all the time.

If that were true, wouldn't we be seeing more hybrids than we do?

[J.LyonLayden]

We see plenty of hybridization. You might call it introgression. It's not like 50/50 all the time if that's what you imagine I'm saying.

Introgressed genetic material is sometimes useful and therefore makes a sweep across the genome.

Especially immunity genes in areas where those immunities are needed.

Other times, subspecies are assimilated by another subspecies.

This would only show up as 4% to 30% introgression in any given individual.

But as you should know, most Europeans in the Eurasian paleolithic have more introgression than anyone living today.

Could that be because they were closer to the time of the source of the introgression? Could that be because we've negatively selected what we didn't need of the introgressed DNA?

This isn't hard to figure out, man.

Scroll up for the paper with the monkey introgression. I can keep providing instances of introgression in the wild all day.

What, do you think we're gonna see hybrid dominated take-overs every year or something? This is a process that takes longer than we've been recording DNA.

I told you about the egyptian hounds. Did you not understand? I provided a paper on monkeys. Did you not understand? You told me about several more species in a reply. Did you not understand what's happeneing to those species? How many more evidences of hybrid zones, introgression, and genetic sweeps do you need?

I can start finding them and posting them here, it will fill up many pages for you.

[J.LyonLayden]

This is what I mean by "basal" and "least changed"


Extinct glyptodonts really were gigantic armadillos, ancient DNA shows:

https://phys.org/news/2016-02-extinct-glyptodonts-gigantic-armadillos-ancient.html

[erik simpson]

I still don't like the use of "basal" in this context. And "least changed" is
also ambiguous. Least changed in what respect? Physical appearance (morphology) is only one aspect. There are brachiopods living now that are
extremely similar to brachiopods that lived in the Cambrian over 500 Mya, at least as far as their shells are concerned. This doesn't mean that modern
brachiopods are "basal", or that the modern brachiopods are the same as their
distant ancestors.

[John Harshman]

So when convenient, you assume that the earliest fossils can be
considered near the ancestor of the clade, and when convenient, you
assume they aren't. Convenience to your pet theories is not a good guide
to reality.

Still, there is some literature claiming that osteoderms are the
primitive state in Xenarthra. On the other hand, that says nothing about
the primitive state in Placentalia.

>>> Osteoderm is a scute with bone- Xenartha is the only mammal group
>>> with osteoderms, but pangolins and maybe others have scutes.
>>>
>>> Before DNA when they had pangolins and armadillos in the same group,
>>> they used to think the ancestral Xenarthran had scutes or even an
>>> osteoderm exoskeleton.
>>
>> Who are "they"?
>
> The classification system of the consensus?

> You realize that Xenarthra, Carnivora, and Philedota have been
> altered dramatically since DNA testing, right? I think "Philedota"
> was actually invented, because it used to be in Xenarthra.

First off, it's Pholidota. Consistent misspellings also get in the way
of communication. Of course Pholidota was invented; all names are
invented. However, Pholidota was removed from Xenarthra long before
there were any molecular studies. Again, who are "they"?

>>> The thinking was because of the idea that scutes evolve into hair or
>>> scales or fur or osteoderms, but not vice versa. Or at least it's one
>>> step back and one step forward, and more evolutionary effort.
>>
>> Whose thinking was that?
>
> The thinking I heard and read in highschool and college in the late
> 80s and 90s. What is your interpretation of what the thinking was
> then? What is your interpretation of what the thinking is now on this
> subject?

I can't imagine that anyone was thinking this, ever. Can you cite any
actual publication? My interpretation is that osteoderms are a new
feature evolved in Xenarthra, though possibly primitive within the
order, and having nothing to do with osteoderms in other taxa.

>>> I don't know what they think now, but the recent steady I shared says
>>> hair and fur and feathers came from scutes. I don't think they used
>>> to think the LCA of Xenarthra was hairless, just that it also had
>>> scutes.
>>
>> Who are "they"?
>
> Consensus. Mainstream. the people who write college textbooks.

Name one. Of course the ancestor of Xenarthra wasn't hairless, but why
bring that up?

>>> But while looking for the info i did find another study that says the
>>> ancestral Eutherian mammal Karyotype is contained within Xenarthra:
>>> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020109
>>
>> So do chimpanzees. What does that show?
>
> Do they? Do all mammal groups? Then why did someone write a paper on this? Busy work?
>
> Can you show me proof that it's contained in primates?
>

According to the paper, the ancestral karyotype in placentals is 2N=48.
That's also the karyotype in chimpanzees. Surely an expert on human
evolution such as yourself is aware of that simple fact. The point of
the paper was that the karyotype of the xenarthrans studied helps to
resolve the ancestral placental karyotype, just as all the other
karyotypes previously studied do.

>>>>> And I'd be willing to bet it's the most basal form of extant Pilosa.
>>>>
>>>> Again, there is no such thing as "the most basal form". What "basal"
>>>> means in terms of extant taxa is just "the less speciose of two basal
>>>> branches".
>>>
>>> Well that's what I mean. Least changed.
>>
>> That isn't what I just said. You perhaps don't know what "speciose"
>> means. It means "having lots of species". "Less speciose" means "having
>> fewer species.
>
> OK. Some species have more mutations separating them from the clades
> "LCA" than other species in even given group.

True, though the main reason for that is random variance, and you can't
draw any serious conclusions from it.

> The one with the least mutations between the LCA and that species is
> what we call "basal" in when describing primate evolution.

It may be what you call basal, but "we" seems unlikely. Still, who is "we"?

> What mother fucking word do you want me to use for "the species with
> the least mutations separating it from the LCA of it's clade?"

There is no reason to have a word for such an uninteresting and
non-useful concept.

> Wikipedia uses the mother fucking word basal when describing it. If
> you do not believe me read the entry on the most primitive/basal
> genus of armadillo which I provided.

Wikipedia is not a reliable guide to science. Why, even some scientific
papers are not reliable guides. You should ask an evolutionary biologist
if you're unsure.

> Every sentence takes a novel with you because you have no ability to
> use context clues and you seek find fault with words that NO ONE has
> problems understanding except you.

Or perhaps other people you talk to just think they understand what
you're saying.

> I can provide you with many post on reddit where I use these terms
> all the time, others use these terms all the time, and no one has a
> fucking problem.

> You are either trying to seem smart, aor you are being an ass-hat.

Please stop with all the single-sentence paragraphs. That's poor and
lazy writing. I don't care what happens on reddit.

>>
>>>> I would still like to see the evidence for each of your claims.
>>>
>>> Which ones?
>>
>> All the ones you made in the paragraph at the top of this post, for a
>> start, at least the ones you haven't abandoned.
>
> At the top of this post? What fucking claims are you talking about?
> Speak up, son. I'm not going over each sentence and rewriting it to
> try and figure out what you mean unless I get .07 cents a word.

Is it too much trouble to look for yourself? Here, let me cut and paste
from the top:

[John Harshman]

How can you possibly be 95% correct, given the paucity of data? How are
you applying Occam's Razor? How can folkoore, archaeology, or
paleoanthropology possible help determine anything that happened 64
million years ago?

It isn't that I mind you considering all possibilities; it's the
impossibilities and absurdities I'm mostly concerned with. Now, there is
a way to apply Occam's Razor to the questions you're interested in here.
It's referred to in the trade as "parsimony", and it enjoins us to
provisionally accept the phylogenetic tree that minimizes the number of
independent evolutionary steps. And given the tree it's possible to run
the method in reverse to extrapolate the appearances of ancestral nodes.
Perhaps that's what you're trying to do, but you need to make that
process much more formal than you have been, because now it seems that
you're just fastening on hypotheses you think would be nice and looking
for evidence that lets you believe them.

[John Harshman]

On 11/13/17 6:52 PM, J.LyonLayden wrote:
> On Monday, November 13, 2017 at 9:08:25 PM UTC-5, John Harshman wrote:
>> On 11/13/17 9:51 AM, J.LyonLayden wrote:

>>> Hybridization and assimilation is going on all the time.
>> If that were true, wouldn't we be seeing more hybrids than we do?
>
>
> We see plenty of hybridization. You might call it introgression. It's
> not like 50/50 all the time if that's what you imagine I'm saying.

Hybridization and introgression are not the same thing. Most
hybridization doesn't involve introgression.

> Introgressed genetic material is sometimes useful and therefore makes
> a sweep across the genome.

Again, I think you may be using "sweep" incorectly, but it isn't clear
what you mean by it or by "across the genome".

> Especially immunity genes in areas where those immunities are
> needed.
>
> Other times, subspecies are assimilated by another subspecies.

I'm sure this happens on occasion, but we have little evidence of it and
it seems rare.

> This would only show up as 4% to 30% introgression in any given
> individual.
>
> But as you should know, most Europeans in the Eurasian paleolithic
> have more introgression than anyone living today.

I don't know that. What is your source?

> Could that be because they were closer to the time of the source of
> the introgression? Could that be because we've negatively selected
> what we didn't need of the introgressed DNA?

Perhaps, but why would it rise to a high frequency and then decline?

> This isn't hard to figure out, man.
>
> Scroll up for the paper with the monkey introgression. I can keep
> providing instances of introgression in the wild all day.

Scroll up where? I saw no reference to such a paper.

> What, do you think we're gonna see hybrid dominated take-overs every
> year or something? This is a process that takes longer than we've
> been recording DNA.
>
> I told you about the egyptian hounds. Did you not understand? I
> provided a paper on monkeys. Did you not understand? You told me
> about several more species in a reply. Did you not understand what's
> happeneing to those species? How many more evidences of hybrid zones,
> introgression, and genetic sweeps do you need?

If it's the major engine of speciation and evolutionary change, I would
expect it to be abundant. A few examples don't demonstrate this. Most
species in the world do not commonly hybridize with other species. Of
the hundreds of bird species in the U.S., for example, there is evidence
for introgression or a hybrid zone for at most a couple of dozen.

> I can start finding them and posting them here, it will fill up many
> pages for you.

Will those many pages ever reach a significant fraction of all the taxa
there are?

[Peter Nyikos]

That seems like an artificial, ad hoc use of the word "basal" having
nothing to do with "being close to the LCA" which is what I have
always thought it meant.

To make it worse, your definition of "basal" has the word "basal"
as an indispensable part of it.

If I put a command in my math program to define X by using a term
with X in it, the computer would go into a potentially infinite loop
which only built-in safeguards would keep the computer from continuing
indefinitely.

> > Well that's what I mean. Least changed.
>
> That isn't what I just said. You perhaps don't know what "speciose"
> means. It means "having lots of species". "Less speciose" means "having
> fewer species.

Yes, and that seems to make for a totally arbitrary choice. For instance,
what happens if a lot of species discovered in a remote New Guinea valley
make the formerly less speciose clade more speciose?

> >> I would still like to see the evidence for each of your claims.
> >
> > Which ones?
>
> All the ones you made in the paragraph at the top of this post, for a
> start, at least the ones you haven't abandoned.

Abandonment seems to be a common occurrence with JLL, but that's
not necessarily a bad thing.

Peter Nyikos

[Peter Nyikos]

It is only the dictatorial restriction of systematics to mean
"phylogenetic systematics," specifically phylogenetic classification,
through the complete banishing of evolutionary systematics,
to which I object. BOTH use the information
used in the construction of evolutionary trees, and both use
cladograms although they serve up the information in a different way.

> See "cladistics", or "the cladistics
> wars". The war is over, and the "cladophiles" as Peter would call them won,

So did the Bolsheviks in 1917 - 1921. And what they ushered in wasn't
either all good or all bad. But they put a lot of unnecessary restrictions
into place, analogously to the dictatorial restriction I refer to above.

> but there remain some stubborn holdouts. My take: try to stick with 21st
> century perspective.

Communism was long touted by its adherents as being the correct
20th century perspective. Those who don't pay attention to history
are doomed to repeat its mistakes.


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

[John Harshman]

It might sometimes mean that in a paleontological setting, but here
we're discussing trees made from molecular data, composed entirely of
living species. Clearly all the species in the tree are equally close to
the LCA. And "basal" is sometimes used unconsciously in the way I
mention and with a false impression of what it implies, as Mr. L does here.

> To make it worse, your definition of "basal" has the word "basal"
> as an indispensable part of it.

Not a problem, since it wasn't a definition of "basal"; it was a
definition of "basal taxon".

> If I put a command in my math program to define X by using a term
> with X in it, the computer would go into a potentially infinite loop
> which only built-in safeguards would keep the computer from continuing
> indefinitely.

This is an advantage humans have over computers. Some humans, at least.

>>> Well that's what I mean. Least changed.
>>
>> That isn't what I just said. You perhaps don't know what "speciose"
>> means. It means "having lots of species". "Less speciose" means "having
>> fewer species.
>
> Yes, and that seems to make for a totally arbitrary choice. For instance,
> what happens if a lot of species discovered in a remote New Guinea valley
> make the formerly less speciose clade more speciose?

That would switch the application. It should be apparent that I don't
like the term, as to many people misunderstand its implications.

>>>> I would still like to see the evidence for each of your claims.
>>>
>>> Which ones?
>>
>> All the ones you made in the paragraph at the top of this post, for a
>> start, at least the ones you haven't abandoned.
>
> Abandonment seems to be a common occurrence with JLL, but that's
> not necessarily a bad thing.

Agreed.

[erik simpson]

Nobody's dictating anaything, but there aren't many Mensheviks left.

[J.LyonLayden]

The thing is, John...you are so sure of yourself but most of what I read contradicts what you say. You have an extremely different view of what basal means than the scientists who write these papers. You can try to twist words and be a spin doctor if you want, but I'm not stupid.

I know what this report means when it says

"This observation, besides reinforcing the hypothesized karyotype, suggests that Xenarthra may be at the root of the Eutherian tree."

Nobody says that about mother-fuckin' monkeys.

Spin it all you want, but I have plenty of papers saying the same thing in many ways - every damn placental mammal could have evolved from basal Xenartha. Every placental mammal can not have evolved from monkeys. I'm sorry but you are wrong. And no one who reads my article with have a problem with what I say about Xenarthra being basal.

I also have papers from 2016 saying glyptodonts are the same thing as extant armadillos, just bigger. And that the osteoderm was there from the start.

I do not know what scares your little bitty mind so much about the first placental mammal possibly having an osteoderm, but I don't care to fight you anymore. You can read the citations in my article.

Complain all you want when I post my article. Thumbs down my post, write nasty comments. No one but you will understand what you are talking about. I'm checking everything and citing everything and you're wrong most of the time.

If I can show it's more plausible for the mother of all placentals to have had a shell and provide citations, none of this bullshit you're pulling will matter.

You're the only person shitting themselves about the idea that Xenartha might be very much like the first placental. I'm just trying to find out, I am not saying it was....yet. I still have work to do.

Spend all you're time bitching if you want, I have to get back to work.

[J.LyonLayden]

To answer your question, I will be 95% correct because I will only use animals I know for a fact were there. You can tell which animals were definitely there with Occam's razor.

That's how I knew neanderthal DNA would be found in us despite the mtDNA. That's how I knew we'd find a whale older than Rhodocetus. That's how I knew we'd find evidence of a Plaeolithic and Neolithic exodus from SE Asia in our genome. That's how I knew Basquaes, native Americans, Ainu, and Irish would have the most Neanderthal DNA. That's how I knew they'd find Neanderthal DNA everywhere but Subsahara. that's how I knew they'd find archaics in the Holocene.

The way I use it serves me well to make predictions about future archeological and fossil studies.

And you don't read very well.
Folklore will not help me with this project—I said it helped me in the last project.

But what you don't seem to be using is geology or knowledge of how the continents drifted and reformed. You're not applying the new knowledge of speciation to ancient species. If I were to judge by you, I'd think paleontology was far behind the times.

Thankfully you are far from exemplary.

And you are dismissing coincidences.
When scientists dismiss coincidences, they are producing assumptions. Occam loves the theory with NO ASSUMPTIONS

[John Harshman]

I don't think "evolutionary" systematics is likely to return.

>> See "cladistics", or "the cladistics
>> wars". The war is over, and the "cladophiles" as Peter would call them won,
>
> So did the Bolsheviks in 1917 - 1921. And what they ushered in wasn't
> either all good or all bad. But they put a lot of unnecessary restrictions
> into place, analogously to the dictatorial restriction I refer to above.
>
>
>> but there remain some stubborn holdouts. My take: try to stick with 21st
>> century perspective.
>
> Communism was long touted by its adherents as being the correct
> 20th century perspective. Those who don't pay attention to history
> are doomed to repeat its mistakes.

I do not find the analogy between communism and phylogenetic systematics
to be a useful one. But if you would like to make arguments in favor of
"evolutionary" systematics, that might be better. Of course you already
have, but they have not been convincing. Still, better.

[J.LyonLayden]

On Tuesday, November 14, 2017 at 3:03:31 PM UTC-5, John Harshman wrote:
> On 11/13/17 6:52 PM, J.LyonLayden wrote:
> > On Monday, November 13, 2017 at 9:08:25 PM UTC-5, John Harshman wrote:
> >> On 11/13/17 9:51 AM, J.LyonLayden wrote:
>
> >>> Hybridization and assimilation is going on all the time.
> >> If that were true, wouldn't we be seeing more hybrids than we do?
> >
> >
> > We see plenty of hybridization. You might call it introgression. It's
> > not like 50/50 all the time if that's what you imagine I'm saying.
>
> Hybridization and introgression are not the same thing. Most
> hybridization doesn't involve introgression.

I think you need to ask your mommy to tell you about the birds and the bees.

>
> > Introgressed genetic material is sometimes useful and therefore makes
> > a sweep across the genome.
>
> Again, I think you may be using "sweep" incorectly, but it isn't clear
> what you mean by it or by "across the genome".
>
> > Especially immunity genes in areas where those immunities are
> > needed.
> >
> > Other times, subspecies are assimilated by another subspecies.
>
> I'm sure this happens on occasion, but we have little evidence of it and
> it seems rare.
>
> > This would only show up as 4% to 30% introgression in any given
> > individual.
> >
> > But as you should know, most Europeans in the Eurasian paleolithic
> > have more introgression than anyone living today.
>
> I don't know that. What is your source?
>
> > Could that be because they were closer to the time of the source of
> > the introgression? Could that be because we've negatively selected
> > what we didn't need of the introgressed DNA?
>
> Perhaps, but why would it rise to a high frequency and then decline?

Because people who had it fucked a lot of people who didn't have it.

[John Harshman]

On 11/14/17 8:30 PM, J.LyonLayden wrote:
> The thing is, John...you are so sure of yourself but most of what I
> read contradicts what you say. You have an extremely different view
> of what basal means than the scientists who write these papers. You
> can try to twist words and be a spin doctor if you want, but I'm not
> stupid.

First, that was a reply to Eric, not me. Second, what papers are you
referring to? Third, we have yet to establish that.

> I know what this report means when it says
>
> "This observation, besides reinforcing the hypothesized karyotype, suggests that Xenarthra may be at the root of the Eutherian tree."
>
> Nobody says that about mother-fuckin' monkeys.

People can say silly things even in peer-reviewed papers. No, nothing
suggests that Xenarthra is at the root of the Eutherian tree. That's
wrong for many reasons: confusion of Eutheria with Placentalia,
confusion of root with sister group, confusion of karyotype with taxon.

> Spin it all you want, but I have plenty of papers saying the same
> thing in many ways - every damn placental mammal could have evolved
> from basal Xenartha. Every placental mammal can not have evolved from
> monkeys. I'm sorry but you are wrong. And no one who reads my article
> with have a problem with what I say about Xenarthra being basal.

I'd like to see some of those papers.

> I also have papers from 2016 saying glyptodonts are the same thing as
> extant armadillos, just bigger. And that the osteoderm was there from
> the start.

I'd like to see those papers too. And what do you refer to by "the start"?

> I do not know what scares your little bitty mind so much about the
> first placental mammal possibly having an osteoderm, but I don't care
> to fight you anymore. You can read the citations in my article.

I'd just like to see some justification for that claim. Do you have any?

> Complain all you want when I post my article. Thumbs down my post,
> write nasty comments. No one but you will understand what you are
> talking about. I'm checking everything and citing everything and
> you're wrong most of the time.

Or perhaps a systematist is likely to understand these questions better
than a sf writer. That could be.

> If I can show it's more plausible for the mother of all placentals to
> have had a shell and provide citations, none of this bullshit you're
> pulling will matter.

Agreed. Go for it.

> You're the only person shitting themselves about the idea that
> Xenartha might be very much like the first placental. I'm just trying
> to find out, I am not saying it was....yet. I still have work to do.

> Spend all you're time bitching if you want, I have to get back to work.

Still, why all this in a reply to Eric that has nothing to do with the
subject of your rant?

[J.LyonLayden]

I'll let you read the paper. All those papers you asked for are cited. I have a couple more dafts to go. Sorry I didn't mean to reply to Eric I meant to reply to you.
Do you get these in an email or something?

I just reply on the site, the format is kind of strange.

[John Harshman]

On 11/14/17 8:49 PM, J.LyonLayden wrote:
> To answer your question, I will be 95% correct because I will only
> use animals I know for a fact were there. You can tell which animals
> were definitely there with Occam's razor.

Again, this appears as a reply to your reply to Eric. Are you
unacquainted with threading?

How does Occam's Razor tell you which animals were definitely there?

> That's how I knew neanderthal DNA would be found in us despite the
> mtDNA. That's how I knew we'd find a whale older than Rhodocetus.
> That's how I knew we'd find evidence of a Plaeolithic and Neolithic
> exodus from SE Asia in our genome. That's how I knew Basquaes, native
> Americans, Ainu, and Irish would have the most Neanderthal DNA.
> That's how I knew they'd find Neanderthal DNA everywhere but
> Subsahara. that's how I knew they'd find archaics in the Holocene.

How, exactly?

> The way I use it serves me well to make predictions about future
> archeological and fossil studies.
>
> And you don't read very well. Folklore will not help me with this
> project—I said it helped me in the last project.
>
> But what you don't seem to be using is geology or knowledge of how
> the continents drifted and reformed. You're not applying the new
> knowledge of speciation to ancient species. If I were to judge by
> you, I'd think paleontology was far behind the times.

Yeah, I don't think your "new knowledge of speciation" is real.

> Thankfully you are far from exemplary.
>
> And you are dismissing coincidences.
> When scientists dismiss coincidences, they are producing assumptions. Occam loves the theory with NO ASSUMPTIONS

I have no idea what this refers to.

[John Harshman]

On 11/14/17 9:05 PM, J.LyonLayden wrote:
> On Tuesday, November 14, 2017 at 3:03:31 PM UTC-5, John Harshman wrote:
>> On 11/13/17 6:52 PM, J.LyonLayden wrote:
>>> On Monday, November 13, 2017 at 9:08:25 PM UTC-5, John Harshman wrote:
>>>> On 11/13/17 9:51 AM, J.LyonLayden wrote:
>>
>>>>> Hybridization and assimilation is going on all the time.
>>>> If that were true, wouldn't we be seeing more hybrids than we do?
>>>
>>>
>>> We see plenty of hybridization. You might call it introgression. It's
>>> not like 50/50 all the time if that's what you imagine I'm saying.
>>
>> Hybridization and introgression are not the same thing. Most
>> hybridization doesn't involve introgression.
>
> I think you need to ask your mommy to tell you about the birds and the bees.

Stripped of the insult, did that mean anything?

>>> Introgressed genetic material is sometimes useful and therefore makes
>>> a sweep across the genome.
>>
>> Again, I think you may be using "sweep" incorectly, but it isn't clear
>> what you mean by it or by "across the genome".
>>
>>> Especially immunity genes in areas where those immunities are
>>> needed.
>>>
>>> Other times, subspecies are assimilated by another subspecies.
>>
>> I'm sure this happens on occasion, but we have little evidence of it and
>> it seems rare.
>>
>>> This would only show up as 4% to 30% introgression in any given
>>> individual.
>>>
>>> But as you should know, most Europeans in the Eurasian paleolithic
>>> have more introgression than anyone living today.
>>
>> I don't know that. What is your source?
>>
>>> Could that be because they were closer to the time of the source of
>>> the introgression? Could that be because we've negatively selected
>>> what we didn't need of the introgressed DNA?
>>
>> Perhaps, but why would it rise to a high frequency and then decline?
>
> Because people who had it fucked a lot of people who didn't have it.

I don't think you have thought out this scenario very well.

[John Harshman]

On 11/14/17 9:11 PM, J.LyonLayden wrote:

> I'll let you read the paper. All those papers you asked for are
> cited. I have a couple more dafts to go. Sorry I didn't mean to reply
> to Eric I meant to reply to you.

> Do you get these in an email or something?

No, I get them on usenet, with a usenet reader, specifically
Thunderbird. That's the way they're intended to be read.

> I just reply on the site, the format is kind of strange.

There is no "site". I believe you're referring to Google Groups, which
parasitizes usenet and has a lot of problems, formatting not least among
them.

[J.LyonLayden]

On Wednesday, November 15, 2017 at 12:11:41 AM UTC-5, John Harshman wrote:
> On 11/14/17 8:49 PM, J.LyonLayden wrote:
> > To answer your question, I will be 95% correct because I will only
> > use animals I know for a fact were there. You can tell which animals
> > were definitely there with Occam's razor.
>
> Again, this appears as a reply to your reply to Eric. Are you
> unacquainted with threading?
>
> How does Occam's Razor tell you which animals were definitely there?
>
> > That's how I knew neanderthal DNA would be found in us despite the
> > mtDNA. That's how I knew we'd find a whale older than Rhodocetus.
> > That's how I knew we'd find evidence of a Plaeolithic and Neolithic
> > exodus from SE Asia in our genome. That's how I knew Basquaes, native
> > Americans, Ainu, and Irish would have the most Neanderthal DNA.
> > That's how I knew they'd find Neanderthal DNA everywhere but
> > Subsahara. that's how I knew they'd find archaics in the Holocene.
>
> How, exactly?

Look at all the data from all possible sources. If any contradict, rule the least likely out. If neither is less likely, consider that they may not contradict and your perspective is wrong.

Create theoretic models. Compare models, see which has the most assumptions and coincidences. Rule the ones with more assumptions and coincidences out.

Etc.

With neanderthals, there was no way so many neanderthal traits showed up in Cro-Magnons without introgression, no way certain modern ethnic groups exhibited neanderthal features, no way certain traditions and folk memories could coincide.

No way basques could be dominated so heavily by O negative without introgression. The list went on and on. The only contradictory data was the mtDNA, and science let it dictate our perception for 40 years.

I figured all data had to be correct, but we weren't looking at it correctly.

My conclusion: Of course we don't have neanderthal DNA. Neanderthal men were doing the raping and kidnapping. I theorized they shipped human women all the way to Siberia clan to clan. But the hybrid men must have been sterile, as is the pattern in mammalian sterility.

Then I wrote my story.

Sure enough, we found Hss female introgression in Siberian neanderthals a couple of years ago. The only genes from Neanderthal we don't have in our genome are those to do with sight and sex.

If a hybrid got the neanderthal sex genes and was a male, he couldn't reproduce. If a child got the neanderthal sight genes, its occipital bun complicated pregnancy.

[John Harshman]

Ah, Bjorn Kurten's theory in reverse. Have you ever read his two novels
on the subject?

> Then I wrote my story.
>
> Sure enough, we found Hss female introgression in Siberian
> neanderthals a couple of years ago. The only genes from Neanderthal
> we don't have in our genome are those to do with sight and sex.

> If a hybrid got the neanderthal sex genes and was a male, he couldn't
> reproduce. If a child got the neanderthal sight genes, its occipital
> bun complicated pregnancy.

I hesitate to encourage you to tell me more of this.

[J.LyonLayden]

No but I will check him out.
Stan Gooch also said it was human men and neanderthal women, but that wasn't possible with the mtDNA results, so I ruled it out.

>
> > Then I wrote my story.
> >
> > Sure enough, we found Hss female introgression in Siberian
> > neanderthals a couple of years ago. The only genes from Neanderthal
> > we don't have in our genome are those to do with sight and sex.
>
> > If a hybrid got the neanderthal sex genes and was a male, he couldn't
> > reproduce. If a child got the neanderthal sight genes, its occipital
> > bun complicated pregnancy.
> I hesitate to encourage you to tell me more of this.

That last part's just my theory, and I didn't come up with it before the DNA results or the story.

Supposedly we could "virtually" reconstruct a neanderthal with just the neanderthal introgression in our current genome. But we'd be missing the testes and certain special genes thought to govern parts of the "occipital bun," which is for enhanced vision. Some northern East Asian men have prior selection for a neanderthal gene which allows them so see low levels of ultraviolet light. So we know neanderthals possessed better sight- they had even more special genes for it that we DIDN'T get.

It's not my theory alone that the reason we're missing the testes is because of "mammalian hybrid infertility." I doubt I'm the only one saying the reason we didn't get the vision genes was because of labor complications, but have you seen a neanderthal occipital bun? It's the least assumptive reason I've found so far.

[J.LyonLayden]

I like this—I think there are two major assumptions early thinkers made in the late 1800s which have not been scrutinized in over a hundred years.

Both assumptions have been proven wrong, but no one has gone back to look at what that means for the entire model.

And no one will, because every expert is a specialist. One specialist will send you to the other on a wild goose chase.

The only way to make someone see the problem is to display all of the coincidences in the model, and then propose a model that makes less assumptions.

[John Harshman]

Kurten wrote long before there was any DNA sequence, living or ancient.

>>> Then I wrote my story.
>>>
>>> Sure enough, we found Hss female introgression in Siberian
>>> neanderthals a couple of years ago. The only genes from Neanderthal
>>> we don't have in our genome are those to do with sight and sex.
>>
>>> If a hybrid got the neanderthal sex genes and was a male, he couldn't
>>> reproduce. If a child got the neanderthal sight genes, its occipital
>>> bun complicated pregnancy.
>> I hesitate to encourage you to tell me more of this.
>
> That last part's just my theory, and I didn't come up with it before the DNA results or the story.
>
> Supposedly we could "virtually" reconstruct a neanderthal with just
> the neanderthal introgression in our current genome. But we'd be
> missing the testes and certain special genes thought to govern parts
> of the "occipital bun," which is for enhanced vision. Some northern
> East Asian men have prior selection for a neanderthal gene which
> allows them so see low levels of ultraviolet light. So we know
> neanderthals possessed better sight- they had even more special genes
> for it that we DIDN'T get.

> It's not my theory alone that the reason we're missing the testes is
> because of "mammalian hybrid infertility." I doubt I'm the only one
> saying the reason we didn't get the vision genes was because of labor
> complications, but have you seen a neanderthal occipital bun? It's
> the least assumptive reason I've found so far.

I applaud you for moving to multi-sentence paragraphs. But I would also
encourage you to check your posts for coherence, clarity, and support
for claims.

[J.LyonLayden]

Was just using this for a citation in my article, and since you asked for it and it was convenient, here you go:

[John Harshman]

Would it be too much trouble to make your replies attached to the posts
to which they are replies. So far I haven't been able to locate your
claim for which this is support.

[J.LyonLayden]

I couldn't find it either. I just remember saying that I had a paper which said Glyptodonts were just big armadillos and I thought you'd replied that you'd like to see it.

Sorry if I misread, can't take time to look through all of that useless arguing.

[John Harshman]

I found it. You said "I also have papers from 2016 saying glyptodonts

are the same thing as extant armadillos, just bigger."

Now if what you meant by that is that glyptodonts are nested within the
armadillo crown group, that's not controversial. You really should be
more careful about clarity. Also, you should learn how to deal with
threading.

[J.LyonLayden]

What I'd like to know is the date of megatherium and armadillo common ancestor, because it must have had an osteoderm.

The split of Pilosa and Cingulata is more than 55 million years, since Cingulata begins 55 mya and Pilosa begins 58.5 mya. So the osteoderm had to have formed before then, barring coincidence or extremely complicated and unnecessary pseudo-explanations. In other words, if this is convergent evolution within the same clade, there needs to be a good explanation of why convergent evolution occurred. Otherwise, Occam's Razor will choose the more likely, simpler explanation: their common ancestor had an osteoderm.

[John Harshman]

Where are you getting the above dates? But congratulations: your
reasoning in this particular case is sound, and you have independently
discovered parsimony analysis. The common ancestor of Xenarthra is
likely to have possessed osteoderms.

Congratulations also on your new-found ability to write in paragraphs.

[J.LyonLayden]

On Wednesday, November 15, 2017 at 2:47:12 PM UTC-5, J.LyonLayden wrote:I

I apologize for the formatting I did write those sentences in paragraphs, not sure what happens with google. I need to switch over.

[J.LyonLayden]

Thanks.


Those dates are from wikipedia, but they are cited from:

O'Leary, M. A.; Bloch, J. I.; Flynn, J. J.; Gaudin, T. J.; Giallombardo, A.; Giannini, N. P.; Cirranello, A. L. (2013). "The placental mammal ancestor and the post–K-Pg radiation of placentals". Science. 339 (6120): 662–667. doi:10.1126/science.1229237. PMID 23393258.

and

Gardner, A.L. (2005). "Order Pilosa". In Wilson, D.E.; Reeder, D.M. Mammal Species of the World: A Taxonomic and Geographic Reference (3rd ed.). Johns Hopkins University Press. pp. 100–103. ISBN 978-0-8018-8221-0. OCLC 62265494.




Now the way I see it, despite the "basal placental" nature of early "basal" Xenarthra, this does not necessarily confirm that the LCA of placental mammals had an osteoderm. However, it suggests the possibility of an ancestral osteoderm.

When researching the origins of true horn bosses, which are only present in Artiodactyla among placentals, I could find no explanation of how pairs of horns in the supraorbital region evolved in mammals.


However, it would explain two things.

1. The scutes in other placentals (the osteoderm bones became an expense).
2. The horns in fossil Xenarthra and the Artiodactyls

I've not been able to find a theory of why shorn pairs in the suprorbital position evolved in Artiodactyls. Only theories as to why they diversified. But some Xenarthrans have them in the same position as Artiodactyls. And I have found an explanation as to why they evolved in Ceratopsid dinosaurs, so it may be a similar process:

"The horns may have originally been osteoderms (armor plates) that fused to the skull."

https://en.wikipedia.org/wiki/Ankylosaurus

This means nothing on its own. But if other paths of study also point to Xenarthra as the placental ancestor, the facts begin to build up. If Xenarthra answers more questions than the current model while maintaining the same plausibility in all other respects, it emerges as most likely. Once seven or eight totally separate paths lead me to "it must have been Xenarthra" a model will begin to take shape. Or they will lead me elsewhere and it won't. I just have to keep digging and applying Occam's to the possible models.

That's why I disregard models so quickly—I'm driving for the most probable one.

[J.LyonLayden]

Now I've found the only other placental mammals with pairs of horns in the supraorbital region are basal Xenarthrans, so I have another connection. I wonder if there are vestigal horns in other placentals, especially "basal" and early species? if so it could point to horns in the basal ancestor of placentals.

I would then need to look at early Monotremes and Metatherians, to see if any early species possessed horn bosses. If some do, we can imagine that the basal state of mammal itself had them.

I hesitate to except offhand that osteoderms led to horn pairs in the same position, so if these groups had horn pairs too I would consider the possibility in the stem or root group.

Unless, of course...I could find another explanation for horn boss evolution than ancestral osteoderms.

[John Harshman]

On 11/15/17 11:47 AM, J.LyonLayden wrote:

> Thanks.
>
>
> Those dates are from wikipedia, but they are cited from:

Where? What page?

> O'Leary, M. A.; Bloch, J. I.; Flynn, J. J.; Gaudin, T. J.;
> Giallombardo, A.; Giannini, N. P.; Cirranello, A. L. (2013). "The
> placental mammal ancestor and the post–K-Pg radiation of placentals".
> Science. 339 (6120): 662–667. doi:10.1126/science.1229237. PMID
> 23393258.
> and
>
> Gardner, A.L. (2005). "Order Pilosa". In Wilson, D.E.; Reeder, D.M.
> Mammal Species of the World: A Taxonomic and Geographic Reference
> (3rd ed.). Johns Hopkins University Press. pp. 100–103. ISBN
> 978-0-8018-8221-0. OCLC 62265494.

Note that the first paper is the one that puts the placental radiation
as entirely Cenozoic. Now, what do you mean by Cingulata and Pilosa
beginning: are you referring to the age of the crown group or a
particular fossil?

> Now the way I see it, despite the "basal placental" nature of early
> "basal" Xenarthra, this does not necessarily confirm that the LCA of
> placental mammals had an osteoderm. However, it suggests the
> possibility of an ancestral osteoderm.

It's certainly possible, but it may or may not be parsimonious depending
on tree topology. If there is Atlantogenata, it's clearly unparsimonious
based on the ingroup only. And as far as I know, none of the
non-placental eutherians found so far has osteoderms.

> When researching the origins of true horn bosses, which are only
> present in Artiodactyla among placentals, I could find no explanation

> of how pairs of horns in the supraorbital region evolved in mammals.
> However, I did find an explanation of how they formed in ceratopsid
> dinosaurs:

> However, it would explain two things.
>
> 1. The scutes in other placentals (the osteoderm bones became an expense).
> 2. The horns in fossil Xenarthra and the Artiodactyls

You will have to explain what you mean by that.

> I've not been able to find a theory of why shorn pairs in the
> suprorbital position evolved in Artiodactyls. Only theories as to why
> they diversified. But some Xenarthrans have them in the same position
> as Artiodactyls. And I have found an explanation as to why they
> evolved in Ceratopsid dinosaurs, so it may be a similar process:
> "The horns may have originally been osteoderms (armor plates) that fused to the skull."
>
> https://en.wikipedia.org/wiki/Ankylosaurus

Those aren't ceratopsians, though it may be that the ancestral
thyreophoran had osteoderms. Still, though no ceratopsian did that I
know of, pachycephalosaurs did. But this doesn't have anything to do
with mammal evolution.

> This means nothing on its own. But if other paths of study also point
> to Xenarthra as the placental ancestor, the facts begin to build up.
> If Xenarthra answers more questions than the current model while
> maintaining the same plausibility in all other respects, it emerges
> as most likely.

What do you mean by "Xenarthra as the placental ancestor"?

> Once seven or eight totally separate paths lead me to "it must have
> been Xenarthra" a model will begin to take shape. Or they will lead
> me elsewhere and it won't. I just have to keep digging and applying
> Occam's to the possible models.

> That's why I disregard models so quickly—I'm driving for the most probable one.

You need to develop an objective criterion for "most probable". I
suggest that optimization on a tree is the best currently available.

[John Harshman]

On 11/15/17 11:48 AM, J.LyonLayden wrote:
> On Wednesday, November 15, 2017 at 2:47:12 PM UTC-5, J.LyonLayden wrote:I
>
> I apologize for the formatting I did write those sentences in paragraphs, not sure what happens with google. I need to switch over.
>

Agreed. Google Groups is the worst of all ways to do usenet.

[J.LyonLayden]

https://en.wikipedia.org/wiki/Xenarthra
https://en.wikipedia.org/wiki/Cingulata
https://en.wikipedia.org/wiki/Pilosa
Both citations are the first footnotes from dates in the Xenarthra and Pilosa entries. The date for Cingulata bears no citation, but it's only... what ...3 million years different? that's less than the margin of error for most dating techniques.

>
> > O'Leary, M. A.; Bloch, J. I.; Flynn, J. J.; Gaudin, T. J.;
> > Giallombardo, A.; Giannini, N. P.; Cirranello, A. L. (2013). "The
> > placental mammal ancestor and the post–K-Pg radiation of placentals".
> > Science. 339 (6120): 662–667. doi:10.1126/science.1229237. PMID
> > 23393258.
> > and
> >
> > Gardner, A.L. (2005). "Order Pilosa". In Wilson, D.E.; Reeder, D.M.
> > Mammal Species of the World: A Taxonomic and Geographic Reference
> > (3rd ed.). Johns Hopkins University Press. pp. 100–103. ISBN
> > 978-0-8018-8221-0. OCLC 62265494.
>
> Note that the first paper is the one that puts the placental radiation
> as entirely Cenozoic. Now, what do you mean by Cingulata and Pilosa
> beginning: are you referring to the age of the crown group or a
> particular fossil?

Crown Group

>
> > Now the way I see it, despite the "basal placental" nature of early
> > "basal" Xenarthra, this does not necessarily confirm that the LCA of
> > placental mammals had an osteoderm. However, it suggests the
> > possibility of an ancestral osteoderm.
>
> It's certainly possible, but it may or may not be parsimonious depending
> on tree topology. If there is Atlantogenata, it's clearly unparsimonious
> based on the ingroup only. And as far as I know, none of the
> non-placental eutherians found so far has osteoderms.

How many are there now? I can only find a few that aren't heavily disputed.
Just curious.

>
> > When researching the origins of true horn bosses, which are only
> > present in Artiodactyla among placentals, I could find no explanation
> > of how pairs of horns in the supraorbital region evolved in mammals.
> > However, I did find an explanation of how they formed in ceratopsid
> > dinosaurs:
> > However, it would explain two things.
> >
> > 1. The scutes in other placentals (the osteoderm bones became an expense).
> > 2. The horns in fossil Xenarthra and the Artiodactyls
>
> You will have to explain what you mean by that.

Which is more likely? That scutes formed independently in Pangolins, rodents, and Xenarthra or that they come from a common ancestor?
Which is more likley, that scutes form without osteoderms or that scutes remain when bones disappear from osteoderms?

I don't know yet.

>
> > I've not been able to find a theory of why shorn pairs in the
> > suprorbital position evolved in Artiodactyls. Only theories as to why
> > they diversified. But some Xenarthrans have them in the same position
> > as Artiodactyls. And I have found an explanation as to why they
> > evolved in Ceratopsid dinosaurs, so it may be a similar process:
> > "The horns may have originally been osteoderms (armor plates) that fused to the skull."
> >
> > https://en.wikipedia.org/wiki/Ankylosaurus
>
> Those aren't ceratopsians, though it may be that the ancestral
> thyreophoran had osteoderms. Still, though no ceratopsian did that I
> know of, pachycephalosaurs did. But this doesn't have anything to do
> with mammal evolution.

Yes but there's no explanation in mammal evolution, so I must find an explanation as to why only Xenarthrans and Artiodactyla have horn bosses in the supraorbital region. I am not satisfied with "they just grew there." If scientists won't find out I will have a go at it using Occam's razor on all available information.

>
> > This means nothing on its own. But if other paths of study also point
> > to Xenarthra as the placental ancestor, the facts begin to build up.
> > If Xenarthra answers more questions than the current model while
> > maintaining the same plausibility in all other respects, it emerges
> > as most likely.
> What do you mean by "Xenarthra as the placental ancestor"?

That the very first Xenarthran was the same species as the very first placental.
And whether or not the species had an osteoderm.

>
> > Once seven or eight totally separate paths lead me to "it must have
> > been Xenarthra" a model will begin to take shape. Or they will lead
> > me elsewhere and it won't. I just have to keep digging and applying
> > Occam's to the possible models.
>
> > That's why I disregard models so quickly—I'm driving for the most probable one.
>
> You need to develop an objective criterion for "most probable". I
> suggest that optimization on a tree is the best currently available.

Thank you.

[J.LyonLayden]

Right now it looks like Artiodactyls and Xenarthra got their horn bosses from the same ancestor. Not confirmed, just looking that way. Since the explanation for horns in dinosaurs is "osteoderms" and early Xenarthrans had an osteoderm, it may have happened in the same way.

Only more data and more slicing will tell.

If osteoderms provide the best explanation for horns, several different mammal groups had scutes, and the first Xenarthra had an osteoderm I will be getting closer to the most probable answer to the question:

Did the first placental have an osteoderm?

Will my time traveling scientist see something that looks like an armadillo and be surprised or not?

[John Harshman]

I don't have a list on me, but one may add non-eutherian fossil mammals
to the list. And lots of older therapsids. How far down the tree to you
have to go to find osteoderms?

>>> When researching the origins of true horn bosses, which are only
>>> present in Artiodactyla among placentals, I could find no explanation
>>> of how pairs of horns in the supraorbital region evolved in mammals.
>>> However, I did find an explanation of how they formed in ceratopsid
>>> dinosaurs:
>>> However, it would explain two things.
>>>
>>> 1. The scutes in other placentals (the osteoderm bones became an expense).
>>> 2. The horns in fossil Xenarthra and the Artiodactyls
>>
>> You will have to explain what you mean by that.
>
> Which is more likely? That scutes formed independently in Pangolins, rodents, and Xenarthra or that they come from a common ancestor?
> Which is more likley, that scutes form without osteoderms or that scutes remain when bones disappear from osteoderms?
>
> I don't know yet.

I know. It's more likely that scutes (=keratinous scales) came from a
common ancestor and that they form without osteoderms, as in most living
reptiles.

>>> I've not been able to find a theory of why shorn pairs in the
>>> suprorbital position evolved in Artiodactyls. Only theories as to why
>>> they diversified. But some Xenarthrans have them in the same position
>>> as Artiodactyls. And I have found an explanation as to why they
>>> evolved in Ceratopsid dinosaurs, so it may be a similar process:
>>> "The horns may have originally been osteoderms (armor plates) that fused to the skull."
>>>
>>> https://en.wikipedia.org/wiki/Ankylosaurus
>>
>> Those aren't ceratopsians, though it may be that the ancestral
>> thyreophoran had osteoderms. Still, though no ceratopsian did that I
>> know of, pachycephalosaurs did. But this doesn't have anything to do
>> with mammal evolution.
>
> Yes but there's no explanation in mammal evolution, so I must find
> an explanation as to why only Xenarthrans and Artiodactyla have horn bosses
> in the supraorbital region. I am not satisfied with "they just grew
> there." If scientists won't find out I will have a go at it using
> Occam's razor on all available information.

Sometimes the answer is "we don't know". I am not confident in your
mastery of Occam's razor.

>>> This means nothing on its own. But if other paths of study also point
>>> to Xenarthra as the placental ancestor, the facts begin to build up.
>>> If Xenarthra answers more questions than the current model while
>>> maintaining the same plausibility in all other respects, it emerges
>>> as most likely.
>> What do you mean by "Xenarthra as the placental ancestor"?
>
> That the very first Xenarthran was the same species as the very first placental.
> And whether or not the species had an osteoderm.

You will have to redefine Xenarthra. At the moment the first placental
doesn't belong to Xenarthra, by definition. If the first placental
belongs to Xenarthra, then Xenarthra becomes a synonym of Placentalia.

>>> Once seven or eight totally separate paths lead me to "it must have
>>> been Xenarthra" a model will begin to take shape. Or they will lead
>>> me elsewhere and it won't. I just have to keep digging and applying
>>> Occam's to the possible models.
>>
>>> That's why I disregard models so quickly—I'm driving for the most probable one.
>>
>> You need to develop an objective criterion for "most probable". I
>> suggest that optimization on a tree is the best currently available.
>
> Thank you.

Are you acquainted with cladistic parsimony?

[John Harshman]

On 11/15/17 1:04 PM, J.LyonLayden wrote:
> Right now it looks like Artiodactyls and Xenarthra got their horn
> bosses from the same ancestor. Not confirmed, just looking that way.
> Since the explanation for horns in dinosaurs is "osteoderms" and
> early Xenarthrans had an osteoderm, it may have happened in the same
> way.

What make it look that way? And why should dinosaurs be relevant?

> Only more data and more slicing will tell.
>
> If osteoderms provide the best explanation for horns, several
> different mammal groups had scutes, and the first Xenarthra had an
> osteoderm I will be getting closer to the most probable answer to the
> question:

How are "scutes" (=keratinous scales) relevant?

> Did the first placental have an osteoderm?
>
> Will my time traveling scientist see something that looks like an armadillo and be surprised or not?

I see no reason not to invent such an animal. It's fiction, after all.

[J.LyonLayden]

On Wednesday, November 15, 2017 at 4:26:24 PM UTC-5, John Harshman wrote:
> On 11/15/17 1:04 PM, J.LyonLayden wrote:
> > Right now it looks like Artiodactyls and Xenarthra got their horn
> > bosses from the same ancestor. Not confirmed, just looking that way.
> > Since the explanation for horns in dinosaurs is "osteoderms" and
> > early Xenarthrans had an osteoderm, it may have happened in the same
> > way.
> What make it look that way? And why should dinosaurs be relevant?

Because early xenarthra is "near the root of the placental family tree," and artiodactyles had to get a pair of head horns from somewhere in order to have diverse head horns. Xenartha are the only other placental mammal group who have horns in the same place as Artiodactyls. Unless you count Cutaneous horns on humans, which I don't.
A shared trait among two groups with a shared ancestor opens the possibility of the trait being found in the ancestor. Otherwise you have to claim "convergent evolution." Convergent evolution is an assumption of coincidence. Unless you have a reason for the development of the same trait evolving in both groups, it's another assumption.

And so far I've found nothing as to how it could have arisen in mammals, or by what processes. Dinosaurs are only relavent because I need to know how horns can develop in amniotes. By what process do they form? Is bone from an osteoderm more likely than an extension of bone or something else?

[John Harshman]

On 11/15/17 2:23 PM, J.LyonLayden wrote:
> On Wednesday, November 15, 2017 at 4:26:24 PM UTC-5, John Harshman wrote:
>> On 11/15/17 1:04 PM, J.LyonLayden wrote:
>>> Right now it looks like Artiodactyls and Xenarthra got their horn
>>> bosses from the same ancestor. Not confirmed, just looking that way.
>>> Since the explanation for horns in dinosaurs is "osteoderms" and
>>> early Xenarthrans had an osteoderm, it may have happened in the same
>>> way.
>> What make it look that way? And why should dinosaurs be relevant?
>
> Because early xenarthra is "near the root of the placental family
> tree," and artiodactyles had to get a pair of head horns from
> somewhere in order to have diverse head horns.

Xenarthra is no nearer the root than Afrotheria or Boreoeutheria, so why
single them out?

> Xenartha are the only
> other placental mammal group who have horns in the same place as
> Artiodactyls. Unless you count Cutaneous horns on humans, which I
> don't.

But the absence of horns in other groups, added to the places of both
these taxa in the tree, makes convergence the Occam's razor solution.

> A shared trait among two groups with a shared ancestor opens the
> possibility of the trait being found in the ancestor. Otherwise you
> have to claim "convergent evolution." Convergent evolution is an
> assumption of coincidence. Unless you have a reason for the
> development of the same trait evolving in both groups, it's another
> assumption.

Exactly, except that convergence is a conclusion drawn from the
distribution of the character on the tree, not an ad hoc assumption. Why
it happened is an interesting question, but we don't have to know the
answer to that question in order to recognize the pattern. Artiodactyls
are far from xenarthrans, and horns aren't even the primitive state in
artiodactyls.

> And so far I've found nothing as to how it could have arisen in
> mammals, or by what processes. Dinosaurs are only relavent because I
> need to know how horns can develop in amniotes. By what process do
> they form? Is bone from an osteoderm more likely than an extension of
> bone or something else?

You may not be able to know, but that doesn't matter to the distribution
of horns (and osteoderms too) on the tree of mammals.

[J.LyonLayden]

On Wednesday, November 15, 2017 at 6:56:52 PM UTC-5, John Harshman wrote:
> On 11/15/17 2:23 PM, J.LyonLayden wrote:
> > On Wednesday, November 15, 2017 at 4:26:24 PM UTC-5, John Harshman wrote:
> >> On 11/15/17 1:04 PM, J.LyonLayden wrote:
> >>> Right now it looks like Artiodactyls and Xenarthra got their horn
> >>> bosses from the same ancestor. Not confirmed, just looking that way.
> >>> Since the explanation for horns in dinosaurs is "osteoderms" and
> >>> early Xenarthrans had an osteoderm, it may have happened in the same
> >>> way.
> >> What make it look that way? And why should dinosaurs be relevant?
> >
> > Because early xenarthra is "near the root of the placental family
> > tree," and artiodactyles had to get a pair of head horns from
> > somewhere in order to have diverse head horns.
>
> Xenarthra is no nearer the root than Afrotheria or Boreoeutheria, so why
> single them out?

Because all my papers say you're wrong about that. I will get confirmation that you're wrong next week when I visit GSU with the same papers.

>
> > Xenartha are the only
> > other placental mammal group who have horns in the same place as
> > Artiodactyls. Unless you count Cutaneous horns on humans, which I
> > don't.
> But the absence of horns in other groups, added to the places of both
> these taxa in the tree, makes convergence the Occam's razor solution.

No. Horns could have become a liability for everyone but Artiodactyls. We don't have the transitional fossils to make your assumption.

Every Cretaceous mammal has so far been proven an offshoot of the main line that led to placentals. We don't have the one without an epipubic bone yet, so we must use circumstantial evidence to figure out what traits it had.

Osteoderms and horns can both become liabilities when adapting to a niche.

>
> > A shared trait among two groups with a shared ancestor opens the
> > possibility of the trait being found in the ancestor. Otherwise you
> > have to claim "convergent evolution." Convergent evolution is an
> > assumption of coincidence. Unless you have a reason for the
> > development of the same trait evolving in both groups, it's another
> > assumption.
> Exactly, except that convergence is a conclusion drawn from the
> distribution of the character on the tree, not an ad hoc assumption. Why
> it happened is an interesting question, but we don't have to know the
> answer to that question in order to recognize the pattern. Artiodactyls
> are far from xenarthrans, and horns aren't even the primitive state in
> artiodactyls.

You don't know what the primitive state was. The first Artiodactyl shows up 54 million years ago without horns but this means nothing, because Himalayecetus shows up only a million years later. We don't know whether the first placental who Artiodactyl diverged from lived 66 million years ago or 93 million years ago, so it could have had time to either shed horns or grow horns. We must use all available info and no bias, prejudice or assumption to determine which was the case.

If one answer is more plausible and negates the need for convergence, then it is the better answer.

>
> > And so far I've found nothing as to how it could have arisen in
> > mammals, or by what processes. Dinosaurs are only relavent because I
> > need to know how horns can develop in amniotes. By what process do
> > they form? Is bone from an osteoderm more likely than an extension of
> > bone or something else?
> You may not be able to know, but that doesn't matter to the distribution
> of horns (and osteoderms too) on the tree of mammals.
>
> >>> Only more data and more slicing will tell.
> >>>
> >>> If osteoderms provide the best explanation for horns, several
> >>> different mammal groups had scutes, and the first Xenarthra had an
> >>> osteoderm I will be getting closer to the most probable answer to the
> >>> question:
> >> How are "scutes" (=keratinous scales) relevant?

Osteoderms are made of scutes and bone. I've seen no proof that scutes exist in an animal without an ancestor who possessed osteoderms. Which came first, osteoderms or scutes?

Except for mammals, all creatures with scutes seem to have had an ancestor with an osteoderm. And no one has a definite answer about mammal scutes.

But I'm still looking for it.

> >>
> >>> Did the first placental have an osteoderm?
> >>>
> >>> Will my time traveling scientist see something that looks like an armadillo and be surprised or not?
> >>
> >> I see no reason not to invent such an animal. It's fiction, after all.

I like to blow minds and I like to stay relevant with the years to come.

I have no desire to read Clan of the Cave Bear again since it's oh so wrong, but Herbie Brennan's Shiva novels are still good with science despite 40 years of discoveries since their publication.

> >

[Peter Nyikos]

On Tuesday, November 14, 2017 at 8:58:54 PM UTC-5, John Harshman wrote:
> On 11/14/17 4:55 PM, Peter Nyikos wrote:
> > On Monday, November 13, 2017 at 12:07:10 PM UTC-5, John Harshman wrote:

> >> On 11/12/17 9:13 PM, J.LyonLayden wrote:
> >>> On Sunday, November 12, 2017 at 8:13:10 PM UTC-5, John Harshman wrote:
> >>>> On 11/12/17 2:38 PM, J.LyonLayden wrote:
> >>>>> On Sunday, November 12, 2017 at 5:22:13 PM UTC-5, John Harshman wrote:
> >>>>>> On 11/12/17 2:18 PM, J.LyonLayden wrote:
> >>>>>>> Mainly because Cingulata shows lest diversity of morphology than
> >>>>>>> Pilosa. The Cingulata genus Dasypodidae is the most basal form of
> >>>>>>> Xenarthra. Cingulata is made up of animals with armadillo morphology.
> >>>>>>> Also because the earliest members of Pilosa had exoskeletons or
> >>>>>>> scutes, some still do, and some still hold an armadillo-like
> >>>>>>> morphology themselves
> >>>>>>
> >>>>>> I would dearly love to see the evidence for each of these claims.
> >>>>>
> >>>>> Just look at Cingulata in wikipedia. It's all armadillos. Look at
> >>>>> Dasypodidae in wikipedia, it says it's most basal. Just look at the
> >>>>> Cyclopedidae in wikipedia, it's a Pilosa with scutes with an
> >>>>> armadillo morphology.
> >>>>
> >>>> I don't see any scutes. Are you sure? Now, if what you mean by "scutes"
> >>>> is nothing more than "scales", then there are a great many mammals with
> >>>> scaled tails, and that might be primitive for placentals. But that isn't
> >>>> just Xenarthra.
> >>>
> >>>

> >>> I was wrong about that. Thinking of the wrong animal. The earliest
> >>> members of the Pilosa clade had osteoderms. Giant sloth and ground
> >>> sloth.
> >>
> >> Did they? And why do you say they're the earliest members of the clade?
> >>
> >>> Osteoderm is a scute with bone- Xenartha is the only mammal group
> >>> with osteoderms, but pangolins and maybe others have scutes.
> >>>
> >>> Before DNA when they had pangolins and armadillos in the same group,
> >>> they used to think the ancestral Xenarthran had scutes or even an
> >>> osteoderm exoskeleton.
> >>
> >> Who are "they"?
> >>
> >>> The thinking was because of the idea that scutes evolve into hair or
> >>> scales or fur or osteoderms, but not vice versa. Or at least it's one
> >>> step back and one step forward, and more evolutionary effort.
> >>
> >> Whose thinking was that?
> >>
> >>> I don't know what they think now, but the recent steady I shared says
> >>> hair and fur and feathers came from scutes. I don't think they used
> >>> to think the LCA of Xenarthra was hairless, just that it also had
> >>> scutes.
> >>
> >> Who are "they"?
> >>
> >>> But while looking for the info i did find another study that says the
> >>> ancestral Eutherian mammal Karyotype is contained within Xenarthra:
> >>> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020109
> >>
> >> So do chimpanzees. What does that show?
> >>
> >>>>> And I'd be willing to bet it's the most basal form of extant Pilosa.
> >>>>
> >>>> Again, there is no such thing as "the most basal form". What "basal"
> >>>> means in terms of extant taxa is just "the less speciose of two basal
> >>>> branches".
> >
> > That seems like an artificial, ad hoc use of the word "basal" having
> > nothing to do with "being close to the LCA" which is what I have
> > always thought it meant.
>
> It might sometimes mean that in a paleontological setting,

Why all the hemming and hawing? can you think of a single
better use for the word in that setting?


> but here
> we're discussing trees made from molecular data, composed entirely of
> living species. Clearly all the species in the tree are equally close to
> the LCA.

Doesn't "Clearly" assume all parts of the tree evolve at the same rates?

I've read that the genomes of mice evolve many times (six is the number
I vaguely seem to remember) as fast as the genomes close to us in the
tree of Euarchontoglires. Are we still supposed to be equally close
to the LCA of that tree as they are?

Do you have any clue as to why the word "basal" was given such
a strange meaning?

But not to worry: according to your definition, Dermoptera is the
basal order of this superorder:

https://en.wikipedia.org/wiki/Euarchontoglires

That's not bad at all, but if rate of change is relevant, I would guess
that Scandentia is a bit more basal than Dermoptera.


> And "basal" is sometimes used unconsciously in the way I
> mention and with a false impression of what it implies, as Mr. L does here.



>
> > To make it worse, your definition of "basal" has the word "basal"
> > as an indispensable part of it.
>
> Not a problem, since it wasn't a definition of "basal"; it was a
> definition of "basal taxon".

Yeah, in terms of "two basal branches." So what's the definition
of "basal branch"? And how do they decide on which pair the
lucky two are?


> > If I put a command in my math program to define X by using a term
> > with X in it, the computer would go into a potentially infinite loop
> > which only built-in safeguards would keep the computer from continuing
> > indefinitely.
>
> This is an advantage humans have over computers. Some humans, at least.
>
> >>> Well that's what I mean. Least changed.
> >>
> >> That isn't what I just said. You perhaps don't know what "speciose"
> >> means. It means "having lots of species". "Less speciose" means "having
> >> fewer species.
> >
> > Yes, and that seems to make for a totally arbitrary choice. For instance,
> > what happens if a lot of species discovered in a remote New Guinea valley
> > make the formerly less speciose clade more speciose?
>
> That would switch the application. It should be apparent that I don't
> like the term, as to many people misunderstand its implications.

It wasn't apparent until now, so thanks for letting us all know that.

Peter Nyikos

> >>>> I would still like to see the evidence for each of your claims.
> >>>
> >>> Which ones?
> >>
> >> All the ones you made in the paragraph at the top of this post, for a
> >> start, at least the ones you haven't abandoned.
> >
> > Abandonment seems to be a common occurrence with JLL, but that's
> > not necessarily a bad thing.
>
> Agreed.

[erik simpson]

On Wednesday, November 15, 2017 at 4:34:21 PM UTC-8, J.LyonLayden wrote:
> <...>

> I have no desire to read Clan of the Cave Bear again since it's oh so wrong, but Herbie Brennan's Shiva novels are still good with science despite 40 years of discoveries since their publication.
>

There's something we can agree on! Paleolithic bodice-rippers are not needed.

[erik simpson]

As a topologist I would think you'd appreciate the use of "basal" as being
a description that unambiguously refers to the order of branching in a tree.
Unfortunately, the word has lots of connotations, and its use by different
people (or even the same person) isn't always consistent. "Rate of evolution",
on the other hand, doesn't present a clear definition. You could argue
endlessly over which branch had evolved 'more'. Kind of like old-school
phylogeny that depended more heavily on 'critical' characters. (Sorry, couldn't
help sticking that in.)