Date   

Re: On ancestry

Gareth Morgan
 

This is not a DNA-problem.


No. Nothing is a problem for people who don't read the information past the first paragraph..



But the A00 gene has nothing to do with the human/chimp split.


Again, not a problem if you pretend Homo erectus didn't exist. Or Kenyapithecus, Samburupithecus, several species of robust and gracile Australopith, Paranthropus boisei, Homo habilis, Homo ergaster, Homo habilis or Homo heidelbergensis.

Just chimps. 

Then in 3 weeks, before they starved, they suddenly became aquatic humans on a volcanic rock.

Not a DNA problem? 
Some scientists believe that insanity does have a genetic component. 


From: AAT@groups.io <AAT@groups.io> on behalf of Allan Krill <krill@...>
Sent: Friday, October 8, 2021 2:22 PM
To: AAT@groups.io <AAT@groups.io>
Subject: Re: [AAT] On ancestry
 
On Fri, Oct 8, 2021 at 02:16 AM, Gareth Morgan wrote:
Here's just one example: - https://www.theatlantic.com/magazine/archive/2016/06/a-reasonable-doubt/480747/
In your example, Texas police misread the DNA evidence to convict two black men of a crime they did not commit. This is not a DNA-problem.

If a DNA-testing company can't tell the difference between male and female in a sample, they are swindling their customers by selling a worthless product. This is not a DNA-problem.

In your next message to this group, you write: Genetics proves (via A00 gene) that the human/chimp split happened 200,000 year ago. But the A00 gene has nothing to do with the human/chimp split. Other types of DNA show that the human/chimp split was millions of years ago, not a few hundred thousand years ago. No DNA-problem here either.


Re: On ancestry

 

On Fri, Oct 8, 2021 at 02:16 AM, Gareth Morgan wrote:
Here's just one example: - https://www.theatlantic.com/magazine/archive/2016/06/a-reasonable-doubt/480747/
In your example, Texas police misread the DNA evidence to convict two black men of a crime they did not commit. This is not a DNA-problem.

If a DNA-testing company can't tell the difference between male and female in a sample, they are swindling their customers by selling a worthless product. This is not a DNA-problem.

In your next message to this group, you write: Genetics proves (via A00 gene) that the human/chimp split happened 200,000 year ago. But the A00 gene has nothing to do with the human/chimp split. Other types of DNA show that the human/chimp split was millions of years ago, not a few hundred thousand years ago. No DNA-problem here either.


Out of Africa??

Marc Verhaegen
 

Morphological description and evolutionary significance of 300 ka hominin facial bones from Hualongdong, China
Dec.2021 Journal of Human Evolution 161:103052
xiu jie Wu Shuwen Pei Yanjun Cai Wu Liu
doi 10.1016/j.jhevol.2021.103052

Late Mid-Pleistocene hominins in Africa displaying key modern morphologies by 315 ka are claimed as the earliest Hs.
Evolutionary relationships among E.Asian hominins appear complex, due to a growing fossil record of late Mid-Pleistocene hominins from E.Asia, reflecting mosaic morphologies, that contribute to a lack of consensus on when & how the transition to Hs transpired.
Newly discovered 300-ka hominin fossils from Hualongdong provide further evidence to clarify these relationships in the region.

In this study, facial morphology of the juvenile partial cranium HLD-6 is described & qualitatively & quantitatively compared with other key Early-, Mid- & Late-Pleistocene hominins from E.Asia, Africa, W.Asia & Europe & a sample of Hs.
Qualitatively, facial morphology of HLD-6 resembles that of Early- & Mid-Pleistocene hominins from Zhoukoudian, Nanjing, Dali & Jinniushan in China & others from Java, Africa & Europe in some of these features (e.g. supra-orbital & malar regions) & Late-Pleistocene hominins & Hs from E.Asia, Africa & Europe in other features (e.g. weak prognathism, flat face & features in nasal & hard palate regions).
Comparisons of HLD-6 measurements to group means & multivariate analyses support close affinities of HLD-6 to Late-Pleistocene hominins & Hs.
Expression of a mosaic morphological pattern in the HLD-6 facial skeleton further complicates evolutionary interpretations of regional morphological diversity in E.Asia.
The prevalence of modern features in HLD-6 suggests:
the hominin population to which HLD-6 belonged may represent the earliest pre-modern Hs in E.Asia:
the transition from archaic to modern morphology in E.Asian hominins may have occurred at least by 300 ka: 80-100 ky earlier than previously recognized.


Re: Molecular Clock is dead using human/snail parasites from Puerto Rico pdf attached

Gareth Morgan
 

viral DNA....can give an accurate measure

Excellent. So genetics proves (via CERV2) that the human/chimp split happened 23 million years ago.

also...

Genetics proves (via A00 gene) that the human/chimp split happened 200,000 year ago.

Thank God for genetic science. We can all go home now. Job done.

G.


From: AAT@groups.io <AAT@groups.io> on behalf of Jack D.Barnes <needininfo@...>
Sent: Friday, October 8, 2021 1:03 PM
To: AAT@groups.io <AAT@groups.io>
Subject: [AAT] Molecular Clock is dead using human/snail parasites from Puerto Rico pdf attached
 
All,
This is an great paper.  What it is basically proves is the viral DNA is important and is highly conserved. That means endogenous viruses don’t change like protein coding genes and can give an accurate measure of the molecular clock.  What that means is the Human/Chimp split is 23mya (via CERV2) and NOT 5mya.

The deeply racist Out of Africa is dead, it’s just a matter of time until the greatest of scientific awakenings. I am 56 years old and am hoping I can be alive to see it.

Quote:
The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. 

https://academic.oup.com/gbe/article/13/10/evab204/6361599




-Jack


--
Welcome to the Aquatic Ape Theory Discussion Group


Molecular Clock is dead using human/snail parasites from Puerto Rico pdf attached

 

All,
This is an great paper.  What it is basically proves is the viral DNA is important and is highly conserved. That means endogenous viruses don’t change like protein coding genes and can give an accurate measure of the molecular clock.  What that means is the Human/Chimp split is 23mya (via CERV2) and NOT 5mya.

The deeply racist Out of Africa is dead, it’s just a matter of time until the greatest of scientific awakenings. I am 56 years old and am hoping I can be alive to see it.

Quote:
The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. 

https://academic.oup.com/gbe/article/13/10/evab204/6361599




-Jack


--
Welcome to the Aquatic Ape Theory Discussion Group


Re: On ancestry

Gareth Morgan
 

How often is DNA evidence wrong?

Last year, the bureau admitted that it had reviewed testimony by its microscopic-hair-comparison analysts and found errors in at least 90 percent of the cases.



In ancestry DNA testing, different companies give different results. Even the same company gives different results at different times for the same person. They fail to tell the difference between male and female. There is zero consensus. Here's just one example: - https://www.theatlantic.com/magazine/archive/2016/06/a-reasonable-doubt/480747/

Anyone treating DNA evidence as the 100% accurate gospel truth about things that happened millions of years ago are just deluding themselves.


From: AAT@groups.io <AAT@groups.io> on behalf of Allan Krill <krill@...>
Sent: Friday, October 8, 2021 11:22 AM
To: AAT@groups.io <AAT@groups.io>
Subject: Re: [AAT] On ancestry
 
On Thu, Oct 7, 2021 at 08:29 PM, alandarwinvanarsdale wrote:
Human geneticists learned about Out of Africa and made their data fit the Recent Out of Africa hypothesis by elevating the hypothesis to axiomatic status.
Reading DNA code of living animals is not like interpreting Australopithecus or Homo erectus. Paleoanthropologists never find a complete skeleton that was respectfully buried and preserved, and never find a fire-pit with the charred bones of animals that had been roasted and eaten. Geneticists are not making this stuff up about Out of Africa. DNA is like reading a book, where the text is actually legible. Anyone able to read, reads the same thing. In paleoanthropology, they have to guess all the time, based on the meager fossil evidence and the models in their heads. Their work can also be compared to reading a book, but they only have a few scraps of text to work with, and they won't let you test whether their text scraps are authentic.
 
--
AquaticApe.net


Re: On ancestry

Gareth Morgan
 

 DNA is like reading a book, where the text is actually legible. Anyone able to read, reads the same thing.

Ha ha ha ha ha!...


Go on then. Enlighten us. What does this say?



From: AAT@groups.io <AAT@groups.io> on behalf of Allan Krill <krill@...>
Sent: Friday, October 8, 2021 11:22 AM
To: AAT@groups.io <AAT@groups.io>
Subject: Re: [AAT] On ancestry
 
On Thu, Oct 7, 2021 at 08:29 PM, alandarwinvanarsdale wrote:
Human geneticists learned about Out of Africa and made their data fit the Recent Out of Africa hypothesis by elevating the hypothesis to axiomatic status.
Reading DNA code of living animals is not like interpreting Australopithecus or Homo erectus. Paleoanthropologists never find a complete skeleton that was respectfully buried and preserved, and never find a fire-pit with the charred bones of animals that had been roasted and eaten. Geneticists are not making this stuff up about Out of Africa. DNA is like reading a book, where the text is actually legible. Anyone able to read, reads the same thing. In paleoanthropology, they have to guess all the time, based on the meager fossil evidence and the models in their heads. Their work can also be compared to reading a book, but they only have a few scraps of text to work with, and they won't let you test whether their text scraps are authentic.
 
--
AquaticApe.net


Re: On ancestry

 

On Thu, Oct 7, 2021 at 08:29 PM, alandarwinvanarsdale wrote:
Human geneticists learned about Out of Africa and made their data fit the Recent Out of Africa hypothesis by elevating the hypothesis to axiomatic status.
Reading DNA code of living animals is not like interpreting Australopithecus or Homo erectus. Paleoanthropologists never find a complete skeleton that was respectfully buried and preserved, and never find a fire-pit with the charred bones of animals that had been roasted and eaten. Geneticists are not making this stuff up about Out of Africa. DNA is like reading a book, where the text is actually legible. Anyone able to read, reads the same thing. In paleoanthropology, they have to guess all the time, based on the meager fossil evidence and the models in their heads. Their work can also be compared to reading a book, but they only have a few scraps of text to work with, and they won't let you test whether their text scraps are authentic.
 
--
AquaticApe.net


Re: On ancestry

alandarwinvanarsdale
 

No fossil or genetic evidence for such fantasies. There is no fossil sequence of Aftrican people evolving into Eurasians, not even one step in the chain. Human geneticists learned about Out of Africa and made their data fit the Recent Out of Africa hypothesis by elevating the hypothesis to axiomatic status. _________________________________________________________________________________________________They do not understand many of the causes for genetic diversity and have been consistently wrong in their predictions. They predicted Neanderthals and our main ancestry were genetically isolated from each other, wrong. They predicted the transition from hunter gatherer to agriculture would increase genetic diversity, again wrong in the several cases known. _________________________________________________________________________________________________They predicted gene flow as out of Africa and not back in. The oldest known African genome at 14kya has been within the last couple of years shown to have considerable ancestry in Eurasia. They predicted the Khoi-San have been genetically isolated from non Sub-Saharans. Not only demonstrating remarkable ignorance of history, but again shown to be wrong (such as the strong Basque inflow of genes around 5kya). ______________________________________________________________________________________________Of course their beliefs are magical, and they even use phrases like Y Adam and mitochondrial Eve. They predicted the Neanderthal Y was very distant from extant Y, again within the last year, wrong. Because of good press, being wrong makes them some how reliable with people who do not understand how they operate or generate what is incorrectly presented by the press as “facts”. ________________________________________________________________________________________________They present Africa as a magical origin place of all of humanity, where evolution takes place while all other places it either does not take place or is some how erased by local extinctions or near extinctions. Creationism is not the same magical belief system as Out of Africa. Though both schools have similar origins. _____________________________________________________________________________________________________Read “Tarzan at the Center of the Earth” to better understand where Out of Africa was between Darwin and when it came back in paleoanthropology. In the period (decades) when no paleoanthropologist accepted Out of Africa (they were all Out of Asia or multiregionalists after 1948_. Weidenreich 1948 proposes all human populations at all times have had gene flow with each other. The Out of Africa school rejected that, as did the Nazi (the Nazi were considered the best paleoanthropologists in the World by their American and British peers until WW II broke out, and openly and greatly by them). ___________________________________________________________________________________________________Out of Africa is linear evolution, with blacks the lowest and whites the highest. So naturally where the most primitive humans are, is where humans originated. In Tarzan aquiline nose Native Americans and European aristocrats were the highest forms of humanity. Of course post WW II there has been a lot of white washing, which does not conceal the racism in Out of Africa for those familiar with the fantasy and it’s history. _____________________________________________________________________________________________________Most of my adult life the Khoi-San were some how living fossils, which the San have published is offensive to them through their political representation. Romanticism aside, a fundamentally racist dogma.

 

Sent from Mail for Windows

 

From: Allan Krill
Sent: Thursday, October 7, 2021 7:51 AM
To: AAT@groups.io
Subject: Re: [AAT] On ancestry

 

On Wed, Oct 6, 2021 at 06:07 PM, alandarwinvanarsdale wrote:

All the others start with the false axiom Africa is the Garden of Eden (or before in Out of Africa Africans were obviously the lowest extant form of human life so had to be basal in a linear evolution sense with other humans).

Thanks for explaining your views. Here are my thoughts on this: 

Only a few creationists still think there was some sort of Garden of Eden (in Africa or elsewhere) where humans originated. And only a few racists still think that black Africans are somehow closer to apes than Eurasians are. Those old beliefs don't have any influence on modern thinking by evolutionists (including geneticists.)

 

Geneticists are not influenced by religion or racism. They are simply reading and interpreting the genomes of living Homo sapiens. They read the genomes to say that all living humans descended from a population of fully evolved Homo sapiens that lived in Africa. It seems clear that there was a population bottleneck in Africa (more like Noah's Ark than the Garden of Eden) about 200,000 years ago and humans who came through that bottleneck then populated the entire planet. The most significant wave of those fully evolved people came out of Africa to Eurasia very recently, only about 70,000- 50,000 years ago https://en.wikipedia.org/wiki/Recent_African_origin_of_modern_humans. Genetics can't tell us where people evolved, or where in Africa this wave of people came from, or why there are so few fossils of humans or their stone tools or fireplaces before about 200,000 years ago. 

 

But genetics do tell us that the human-chimp LCA was about 6 million years ago. So humans and chimps had about 6 million years to evolve (between 6,000,000 - 200,000 years), during which time there are no mammal fossils of any kind in the areas where chimps live. And genetics tell us that the chimp-gorilla LCA was about 10 million years ago. Since the gorilla and chimp are so morphologically similar and well suited to their diets and habitats, it is reasonable to think that the chimp-gorilla LCA was similar to them, and not similar to humans. The humans must have had some sort of alternative diets and habitats that made them so morphologically different. And humans must have evolved in an isolated place, with gene flow and without predators. Prehumans without large brains, tools, and weapons could not have survived early stages of their evolution if there were predators. 

 
--
AquaticApe.net

 


Re: On ancestry

alandarwinvanarsdale
 

As Homo became more and more dominant great apes became more and more limited on what environments they usually lived in. Aquatic environments are often desirable and great apes were pushed out of them, or assimilated by Homo in more favorable environments for Homo. With gene flow being restricted to the point of Homo being a species different from great apes in Africa around 4-7 million years ago.

 

Sent from Mail for Windows

 

From: Marc Verhaegen
Sent: Thursday, October 7, 2021 1:25 PM
To: AAT@groups.io
Subject: Re: [AAT] On ancestry

 

"... Since the gorilla and chimp are so morphologically similar and well
suited to their diets and habitats, it is reasonable to think that the
chimp-gorilla LCA was similar to them, ..."


No: P & G evolved largely in // from our LCA:

the anatomical details & the embryology of P & G knuckle-walking are very different.
G is herbivorous, P & H are omnivorous. G is a lot larger, and polygynous. G evolved much thinner enamel. Etc.

From an aquarboreal hominid LCA late-Miocene,
- G & P evolved allopatrically in // from aquarboreal to KWing in wet forests:

longer ilia, much longer arms, longer canines etc.,
- H evolved in a special way: they became shallow-divers for shellfish etc.: indeed an alternative habitat & diet.

 

______

 



------ Origineel bericht ------
Van: alandarwinvanarsdale@...
Aan: AAT@groups.io
Verzonden: donderdag 7 oktober 2021 03:07
Onderwerp: Re: [AAT] On ancestry

Many measurements which are not very useful have been used to create highly inaccurate phylogenetic trees. In the past for example for humans, skin color, prognathy, brain size, body size, morphological closeness to Africans (Africans and Sahulians in the recent past being considered the most “primitive” humans and some how ancestral to all other humans). +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Whole genomic distances are just one more in a long series of blunders in human phylogeny. For those who understand modern evolutionary biology and natural selection, they know whole genomic distances can be like convergent evolution, and indicate similar niches, and not always accurately predict phylogeny. _____________________________________________________________________________________________________Linear evolution is widely thought to be a false concept in evolutionary biology now, and some paleoanthropologists have modern enough education to know this (Fuentes for example). We do not know which extant great ape humans are closest to (had their initial divergence from most recently). Morphologically, we are closest to orangutans (Schwartz et al, who have done the most detailed cladistic studies on this matter). _________________________________________________________________________________________________That we are closer to chimps than other extant great apes is yet another questionable artifact of the failed Out of Africa series of hypothesis (which assume some how Africa is the evolutionary Garden of Eden). The only Out of Africa hypothesis supported by real evidence is at 2.1,mya. All the others start with the false axiom Africa is the Garden of Eden (or before in Out of Africa Africans were obviously the lowest extant form of human life so had to be basal in a linear evolution sense with other humans). And establish themselves only on the assumption of a both false and magical premise which is to an axiom, and usually not even an hypothesis in all but one case. _____________________________________________________________________________________________________If we diverged from Pan before orangs, and last had strong gene flow with Pan, that does mot mean Pan is our closest relative. What this would suggest is that main human ancestry some how at some time became more geographically in contact with Pan than orangs (which supports OoA at 2.1 million years ago, with a hominin extinction or near extinction in Eurasian some time before 2.1mya). And ‘ or it suggests that of all the derived exotic great apes genes in humans, Pan genes were more favored than others. __________________________________________________________________________________________________________________________________It has been known for about five years all great apes today have derived genes from all other great apes, humans being a type of great ape. That means we had gene flow which survived until today, from every type of great ape’s ancestors alive today after they diverged from humans. No way to know why Pan genes are more common, it could be because of a later divergence (which is not supported either by the fossil record or extant morphology). Or it could just mean humans and Pan screwed around more with each other than they did with other great apes, and preferred similar niches favoring each others genes more as exotic genes.

Sent from Mail for Windows

From: Allan Krill
Sent: Wednesday, October 6, 2021 4:07 AM
To: AAT@groups.io
Subject: Re: [AAT] On ancestry

On Tue, Oct 5, 2021 at 06:32 AM, alandarwinvanarsdale wrote:

This reminds us that human genetics is a relatively new science, dominated by just a few European men who are not trained in and do not understand evolution or human evolution

Alan, This and your next post about DNA make no sense to me. Do you think that humans are more closely related to orangutans than they are to chimpanzees or gorillas? Or maybe you think ‘closely related’ is not a meaningful concept in evolution or human evolution??

I find your views and statements very confusing. You seem to think experts (paleontologists, evolutionists, ichnologists, geneticists) don’t understand the sciences they are said to be experts in.


--
AquaticApe.net

 

 

 


Re: wide incisors = frugivory

alandarwinvanarsdale
 

As modern stone tools came into use incisors became less wide. As there was less need for them with the teeth no longer being as much a “third hand”. Dental morphology also changes under natural selection due to diet, especially diet in periods of famine which is often different than diet in normal times. Because mortality is higher during famine so more selective pressure to be able to survive the famine on the teeth.

 

Sent from Mail for Windows

 

From: Marc Verhaegen
Sent: Thursday, October 7, 2021 2:32 PM
To: AAT@groups.io
Subject: [AAT] wide incisors = frugivory

 

Functional and phylogenetic variation in anthropoid incisor size

Jeremiah E Scott  2021 AJPA doi org/10.1002/ajpa.24375

 

Objectives

 

Previous studies have shown:

- frugivorous anthropoids have wider incisors than folivores vs body

mass,

- Catarrhini have rel.wider incisors than Platyrrhini.

This study re-examines these contrasts, using mandibular length as a

bio-mechanical standard, to quantify relative incisor width.

 

Materials & Methods

 

Dental, mandibular & body-mass data for 86 anthropoid spp were taken

from the literature.

Incisor width was size-adjusted, using shape ratios, with mandibular

length & body mass as the denominators.

Dietary & phylogenetic effects were examined, using  phylogenetic

generalized least squares.

 

Results

 

Mandible-based ratios provide a signal very similar to the one derived

from ratios computed using body mass.

Frugivores have rel.wider incisors than folivores, as expected.

There is limited support for a stronger dietary effect in Platyrrhini

when mandible-based ratios are used,

but neither type of ratio indicates an overall difference between Platy-

& Catarrhini.

 

Discussion

 

Both ratios support a link between incisor size & diet,  but there is

some evidence indicating:

mandible-based ratios are more sensitive to dietary variation at smaller

phylogenetic scales.

Understanding why these signals diverge may help clarify the functional

significance of variation in incisor width.

 

The results of this study undermine the view that Platyrrhini (as a

group) tend to have narrower incisors than Catarrhini, regardless of

diet:

the difference between the 2 clades noted in previous studies can be

explained by greater incisor functional  diversity in Platyrrhini.

 

 

 

 

 


wide incisors = frugivory

Marc Verhaegen
 

Functional and phylogenetic variation in anthropoid incisor size
Jeremiah E Scott 2021 AJPA doi org/10.1002/ajpa.24375

Objectives

Previous studies have shown:
- frugivorous anthropoids have wider incisors than folivores vs body mass,
- Catarrhini have rel.wider incisors than Platyrrhini.
This study re-examines these contrasts, using mandibular length as a bio-mechanical standard, to quantify relative incisor width.

Materials & Methods

Dental, mandibular & body-mass data for 86 anthropoid spp were taken from the literature.
Incisor width was size-adjusted, using shape ratios, with mandibular length & body mass as the denominators.
Dietary & phylogenetic effects were examined, using phylogenetic generalized least squares.

Results

Mandible-based ratios provide a signal very similar to the one derived from ratios computed using body mass.
Frugivores have rel.wider incisors than folivores, as expected.
There is limited support for a stronger dietary effect in Platyrrhini when mandible-based ratios are used,
but neither type of ratio indicates an overall difference between Platy- & Catarrhini.

Discussion

Both ratios support a link between incisor size & diet, but there is some evidence indicating:
mandible-based ratios are more sensitive to dietary variation at smaller phylogenetic scales.
Understanding why these signals diverge may help clarify the functional significance of variation in incisor width.

The results of this study undermine the view that Platyrrhini (as a group) tend to have narrower incisors than Catarrhini, regardless of diet:
the difference between the 2 clades noted in previous studies can be explained by greater incisor functional diversity in Platyrrhini.


Re: hominoid tail loss

Gareth Morgan
 

we present evidence that tail-loss evolution was mediated by the insertion of an individual Alu-element

Not quite convinced by this. 

In the tailless mice they are talking about, the tail just stops at a certain point, like a Manx cat. You see similar things in Thailand, where "Siamese" cats -- famous for the kink in their tails -- often have half the tail missing from the point where the kink "should" occur.

Our coccyx isn't like that. It tapers elegantly to a point, like every other mammal's tail. It's just very short.

That paper is looking at induced genetic defects. I don't consider congenital defects to be equivalent in any way to evolutionary adaptations. 

There could be some connection with the TBXT gene, but our coccyx is too well-designed to be an accident of jumping genes.

G.


From: AAT@groups.io <AAT@groups.io> on behalf of Marc Verhaegen <m_verhaegen@...>
Sent: Thursday, October 7, 2021 10:10 PM
To: AAT@groups.io <AAT@groups.io>
Subject: Re: [AAT] hominoid tail loss
 

The genetic basis of tail-loss evolution in humans and apes

Weimin Zhang cs 2021

doi org/10.1101/2021.09.14.460388

The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans & to the “anthropomorphous apes”.

This morphological re-programming in the ancestral hominoids has been long considered to have

- accommodated a characteristic style of locomotion,

- contributed to the evolution of bipedalism in humans.

Yet, the precise genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown.

Primate genome sequencing projects

- have made possible the identification of causal links between genotypic & phenotypic changes,

- enable the search for hominoid-specific genetic elements controlling tail development.

Here, we present evidence that tail-loss evolution was mediated by the insertion of an individual Alu-element into the genome of the hominoid ancestor:

this Alu element – inserted into an intron of the TBXT-gene (also called T or Brachyury) – pairs with a neighboring ancestral Alu-element encoded in the reverse genomic orientation, and leads to a hominoid-specific alternative splicing event.

To study the effect of this splicing event, we generated a mouse model that mimics the expression of human TBXT products, by expressing both full-length & exon-skipped isoforms of the mouse TBXT ortholog.

We found:

- mice with this genotype exhibit the complete absence of a tail, or a shortened tail, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype, albeit with incomplete penetrance,

- mice homozygous for the exon-skipped isoforms exhibited embryonic spinal cord malformations, resembling a neural tube defect condition, which affects ∼1/1000 human neonates.

We propose:

- selection for the loss of the tail along the hominoid lineage was ass.x an adaptive cost of potential neural tube defects,

- this ancient evolutionary trade-off may thus continue to affect human health today.







------ Origineel bericht ------
Van: m_verhaegen@...
Aan: AAT@groups.io
Verzonden: donderdag 7 oktober 2021 21:03
Onderwerp: [AAT] hominoid tail loss

The genetic basis of tail-loss evolution in humans and apes

10/06/2021 04:00:00 PM
Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest

NYU researchers are trying to understand an age-old question: Why do all the other animals have tails, but not me? The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans & the "anthropomorphous apes." The loss of tails has long been thought to have played a key role in bipedalism in humans.


The genetic basis of tail-loss evolution in humans and apes
The evolution of primate species are divided into hominoids — a group of tail-less primate species
that includes gorillas, chimpanzees & humans — and nonhominoids, which have tails and are
more distant primate relatives of humans.

This curiosity-based question was addressed by using bio-informatics tools to look at differences between the genomes of humans (& the other apes, which all lack tails) & monkeys (which all have tails, like most other mammals).

Bo Xia (in the labs of Jef Boeke & Itai Yanai) looked at sequence alignments of all genes known to be involved in tail development, and discovered a movable piece of DNA (a retro-transposon) inserted in the TBXT gene (a developmental regulator crucial for tail development). The reason it had not been spotted before was due its placement in non-coding (intron) DNA, where most people would not look for mutations.


Examination of the gene, which carried other copies of the Alu retrotransposon, led to a model for how the Alu might disregulate splicing of TBXT RNA. The researchers engineered a mouse model to test this hypothesis: indeed, many mice with a suitably altered genome lacked a tail. They also found that the mice without tails also suffered from spinal cord malformations. It's possible our ancestors who lost their tails also had this side-effect, which may contribute to some health problems even today.


The findings are published in BioRXiv.





Re: On ancestry

Marc Verhaegen
 

"... Since the gorilla and chimp are so morphologically similar and well
suited to their diets and habitats, it is reasonable to think that the
chimp-gorilla LCA was similar to them, ..."


No: P & G evolved largely in // from our LCA:

the anatomical details & the embryology of P & G knuckle-walking are very different.
G is herbivorous, P & H are omnivorous. G is a lot larger, and polygynous. G evolved much thinner enamel. Etc.

From an aquarboreal hominid LCA late-Miocene,
- G & P evolved allopatrically in // from aquarboreal to KWing in wet forests:

longer ilia, much longer arms, longer canines etc.,
- H evolved in a special way: they became shallow-divers for shellfish etc.: indeed an alternative habitat & diet.


______




------ Origineel bericht ------
Van: alandarwinvanarsdale@...
Aan: AAT@groups.io
Verzonden: donderdag 7 oktober 2021 03:07
Onderwerp: Re: [AAT] On ancestry

Many measurements which are not very useful have been used to create highly inaccurate phylogenetic trees. In the past for example for humans, skin color, prognathy, brain size, body size, morphological closeness to Africans (Africans and Sahulians in the recent past being considered the most “primitive” humans and some how ancestral to all other humans). +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Whole genomic distances are just one more in a long series of blunders in human phylogeny. For those who understand modern evolutionary biology and natural selection, they know whole genomic distances can be like convergent evolution, and indicate similar niches, and not always accurately predict phylogeny. _____________________________________________________________________________________________________Linear evolution is widely thought to be a false concept in evolutionary biology now, and some paleoanthropologists have modern enough education to know this (Fuentes for example). We do not know which extant great ape humans are closest to (had their initial divergence from most recently). Morphologically, we are closest to orangutans (Schwartz et al, who have done the most detailed cladistic studies on this matter). _________________________________________________________________________________________________That we are closer to chimps than other extant great apes is yet another questionable artifact of the failed Out of Africa series of hypothesis (which assume some how Africa is the evolutionary Garden of Eden). The only Out of Africa hypothesis supported by real evidence is at 2.1,mya. All the others start with the false axiom Africa is the Garden of Eden (or before in Out of Africa Africans were obviously the lowest extant form of human life so had to be basal in a linear evolution sense with other humans). And establish themselves only on the assumption of a both false and magical premise which is to an axiom, and usually not even an hypothesis in all but one case. _____________________________________________________________________________________________________If we diverged from Pan before orangs, and last had strong gene flow with Pan, that does mot mean Pan is our closest relative. What this would suggest is that main human ancestry some how at some time became more geographically in contact with Pan than orangs (which supports OoA at 2.1 million years ago, with a hominin extinction or near extinction in Eurasian some time before 2.1mya). And ‘ or it suggests that of all the derived exotic great apes genes in humans, Pan genes were more favored than others. __________________________________________________________________________________________________________________________________It has been known for about five years all great apes today have derived genes from all other great apes, humans being a type of great ape. That means we had gene flow which survived until today, from every type of great ape’s ancestors alive today after they diverged from humans. No way to know why Pan genes are more common, it could be because of a later divergence (which is not supported either by the fossil record or extant morphology). Or it could just mean humans and Pan screwed around more with each other than they did with other great apes, and preferred similar niches favoring each others genes more as exotic genes.

Sent from Mail for Windows

From: Allan Krill
Sent: Wednesday, October 6, 2021 4:07 AM
To: AAT@groups.io
Subject: Re: [AAT] On ancestry

On Tue, Oct 5, 2021 at 06:32 AM, alandarwinvanarsdale wrote:

This reminds us that human genetics is a relatively new science, dominated by just a few European men who are not trained in and do not understand evolution or human evolution

Alan, This and your next post about DNA make no sense to me. Do you think that humans are more closely related to orangutans than they are to chimpanzees or gorillas? Or maybe you think ‘closely related’ is not a meaningful concept in evolution or human evolution??

I find your views and statements very confusing. You seem to think experts (paleontologists, evolutionists, ichnologists, geneticists) don’t understand the sciences they are said to be experts in.


--
AquaticApe.net





Re: hominoid tail loss

Marc Verhaegen
 

The genetic basis of tail-loss evolution in humans and apes

Weimin Zhang cs 2021

doi org/10.1101/2021.09.14.460388

The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans & to the “anthropomorphous apes”.

This morphological re-programming in the ancestral hominoids has been long considered to have

- accommodated a characteristic style of locomotion,

- contributed to the evolution of bipedalism in humans.

Yet, the precise genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown.

Primate genome sequencing projects

- have made possible the identification of causal links between genotypic & phenotypic changes,

- enable the search for hominoid-specific genetic elements controlling tail development.

Here, we present evidence that tail-loss evolution was mediated by the insertion of an individual Alu-element into the genome of the hominoid ancestor:

this Alu element – inserted into an intron of the TBXT-gene (also called T or Brachyury) – pairs with a neighboring ancestral Alu-element encoded in the reverse genomic orientation, and leads to a hominoid-specific alternative splicing event.

To study the effect of this splicing event, we generated a mouse model that mimics the expression of human TBXT products, by expressing both full-length & exon-skipped isoforms of the mouse TBXT ortholog.

We found:

- mice with this genotype exhibit the complete absence of a tail, or a shortened tail, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype, albeit with incomplete penetrance,

- mice homozygous for the exon-skipped isoforms exhibited embryonic spinal cord malformations, resembling a neural tube defect condition, which affects ∼1/1000 human neonates.

We propose:

- selection for the loss of the tail along the hominoid lineage was ass.x an adaptive cost of potential neural tube defects,

- this ancient evolutionary trade-off may thus continue to affect human health today.







------ Origineel bericht ------
Van: m_verhaegen@...
Aan: AAT@groups.io
Verzonden: donderdag 7 oktober 2021 21:03
Onderwerp: [AAT] hominoid tail loss

The genetic basis of tail-loss evolution in humans and apes

10/06/2021 04:00:00 PM

NYU researchers are trying to understand an age-old question: Why do all the other animals have tails, but not me? The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans & the "anthropomorphous apes." The loss of tails has long been thought to have played a key role in bipedalism in humans.


The genetic basis of tail-loss evolution in humans and apes
The evolution of primate species are divided into hominoids — a group of tail-less primate species
that includes gorillas, chimpanzees & humans — and nonhominoids, which have tails and are
more distant primate relatives of humans.

This curiosity-based question was addressed by using bio-informatics tools to look at differences between the genomes of humans (& the other apes, which all lack tails) & monkeys (which all have tails, like most other mammals).

Bo Xia (in the labs of Jef Boeke & Itai Yanai) looked at sequence alignments of all genes known to be involved in tail development, and discovered a movable piece of DNA (a retro-transposon) inserted in the TBXT gene (a developmental regulator crucial for tail development). The reason it had not been spotted before was due its placement in non-coding (intron) DNA, where most people would not look for mutations.


Examination of the gene, which carried other copies of the Alu retrotransposon, led to a model for how the Alu might disregulate splicing of TBXT RNA. The researchers engineered a mouse model to test this hypothesis: indeed, many mice with a suitably altered genome lacked a tail. They also found that the mice without tails also suffered from spinal cord malformations. It's possible our ancestors who lost their tails also had this side-effect, which may contribute to some health problems even today.


The findings are published in BioRXiv.





hominoid tail loss

Marc Verhaegen
 

The genetic basis of tail-loss evolution in humans and apes

10/06/2021 04:00:00 PM

NYU researchers are trying to understand an age-old question: Why do all the other animals have tails, but not me? The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans & the "anthropomorphous apes." The loss of tails has long been thought to have played a key role in bipedalism in humans.


The genetic basis of tail-loss evolution in humans and apes
The evolution of primate species are divided into hominoids — a group of tail-less primate species
that includes gorillas, chimpanzees & humans — and nonhominoids, which have tails and are
more distant primate relatives of humans.

This curiosity-based question was addressed by using bio-informatics tools to look at differences between the genomes of humans (& the other apes, which all lack tails) & monkeys (which all have tails, like most other mammals).

Bo Xia (in the labs of Jef Boeke & Itai Yanai) looked at sequence alignments of all genes known to be involved in tail development, and discovered a movable piece of DNA (a retro-transposon) inserted in the TBXT gene (a developmental regulator crucial for tail development). The reason it had not been spotted before was due its placement in non-coding (intron) DNA, where most people would not look for mutations.


Examination of the gene, which carried other copies of the Alu retrotransposon, led to a model for how the Alu might disregulate splicing of TBXT RNA. The researchers engineered a mouse model to test this hypothesis: indeed, many mice with a suitably altered genome lacked a tail. They also found that the mice without tails also suffered from spinal cord malformations. It's possible our ancestors who lost their tails also had this side-effect, which may contribute to some health problems even today.


The findings are published in BioRXiv.


Re: On ancestry

 

On Wed, Oct 6, 2021 at 06:07 PM, alandarwinvanarsdale wrote:
All the others start with the false axiom Africa is the Garden of Eden (or before in Out of Africa Africans were obviously the lowest extant form of human life so had to be basal in a linear evolution sense with other humans).

Thanks for explaining your views. Here are my thoughts on this: 

Only a few creationists still think there was some sort of Garden of Eden (in Africa or elsewhere) where humans originated. And only a few racists still think that black Africans are somehow closer to apes than Eurasians are. Those old beliefs don't have any influence on modern thinking by evolutionists (including geneticists.)

 

Geneticists are not influenced by religion or racism. They are simply reading and interpreting the genomes of living Homo sapiens. They read the genomes to say that all living humans descended from a population of fully evolved Homo sapiens that lived in Africa. It seems clear that there was a population bottleneck in Africa (more like Noah's Ark than the Garden of Eden) about 200,000 years ago and humans who came through that bottleneck then populated the entire planet. The most significant wave of those fully evolved people came out of Africa to Eurasia very recently, only about 70,000- 50,000 years ago https://en.wikipedia.org/wiki/Recent_African_origin_of_modern_humans. Genetics can't tell us where people evolved, or where in Africa this wave of people came from, or why there are so few fossils of humans or their stone tools or fireplaces before about 200,000 years ago. 

 

But genetics do tell us that the human-chimp LCA was about 6 million years ago. So humans and chimps had about 6 million years to evolve (between 6,000,000 - 200,000 years), during which time there are no mammal fossils of any kind in the areas where chimps live. And genetics tell us that the chimp-gorilla LCA was about 10 million years ago. Since the gorilla and chimp are so morphologically similar and well suited to their diets and habitats, it is reasonable to think that the chimp-gorilla LCA was similar to them, and not similar to humans. The humans must have had some sort of alternative diets and habitats that made them so morphologically different. And humans must have evolved in an isolated place, with gene flow and without predators. Prehumans without large brains, tools, and weapons could not have survived early stages of their evolution if there were predators. 

 
--
AquaticApe.net


Prehistoric Settlements on the Red Sea Coast

Marc Verhaegen
 

Prehistoric Settlements on the Red Sea Coast of Eritrea:
Implications for assessing early human dispersals across the Red Sea basin
Amanuel Beyin 2018 Book Chapter
Early Maritime Cultures in East Africa and the Western Indian Ocean

This chapter focuses on a region that encompasses the Gulf of Zula & Buri Peninsula along the Red Sea coast of Eritrea.
Mid- & Later Stone Age sites uncovered from the area shed light on the exploitation of marine & coastal resources:

2 sites with MSA remains (Abdur elevated reef c 125 ka, Asfet diagnostic stone artifacts 200–50 ka) demonstrate:
the coast may have served as stepping-stones of Ancient Hs during their spread from Africa into Asia (N.ward into the Levant, or across the Red Sea into Arabia).

3 early to mid-Holocene (LSA) shell-middens documented from the region reflect the exploitation of different coastal environments.
- Misse E & Gelalo NW were dated to the 8th mill.BP.
Atactodea striata (bivalve, tidal flats near sandy beaches) & Terebralia palustris (gastropod, mangrove swamps) at the sites were likely served supplementary food-sources.
Gelalo NW also included a rel.large nr of shell-beads.
- Asfet Unit F (6th mill.BP) was also dominated by Terebralia palustris.
This coastal settlement is probably the result of adverse climatic conditions that prevailed in the hinterland during that period.


In higher organisms genetic diversity does not reflect populations size

alandarwinvanarsdale
 

 

 

From the previous paper “we are required to believe that higher organisms including man, mouse, and Drosophila and the horseshoe crab all have population sizes within a factor of 4 of each other. […] The patent absurdity of such a proposition is strong evidence against a neutralist explanation of observed heterozygosity.” __________________________________________________________________So by 1974 it was well understood there were serious problems with the neutral “theory”. Though it has only been in recent years, such as out of Drosophila research the neutral “theory” has been broadly disproven. _________________________________________________________________Just because a “theory” is incorrect does not mean it is not in some ways useful. However, false theories should not be relied upon to the point they generate new false theories and conclusions.


Re: genetic diversity paper

alandarwinvanarsdale
 

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