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holderlin
08-11-18, 23:20
I think this is new, although there may be a thread about the pre-print. It's hard for me to keep track of when we had discussed pre-prints months before the actual publication.

https://www.cell.com/action/showPdf?pii=S0092-8674%2818%2931380-1



Genome-wide analysis of 49 Central and South Americans up to ∼11,000 years old





Two previously unknown genetic exchanges between North and South America





Distinct link between a Clovis culture-associated genome and the oldest South Americans





Continent-wide replacement of Clovis-associated ancestry beginning at least 9,000 years ago



"We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions."

The peopling mechanism is elucidated, or narrowed down a bit more.

berun
09-11-18, 18:17
We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago,

very interesting, maybe linguists could find related linguistic families in such areas, such time depth is similar to Mycaenian Greek or Semitic Akkadian.

Angela
09-11-18, 19:33
I think this is new, although there may be a thread about the pre-print. It's hard for me to keep track of when we had discussed pre-prints months before the actual publication.

https://www.cell.com/action/showPdf?pii=S0092-8674%2818%2931380-1



Genome-wide analysis of 49 Central and South Americans up to ∼11,000 years old





Two previously unknown genetic exchanges between North and South America





Distinct link between a Clovis culture-associated genome and the oldest South Americans





Continent-wide replacement of Clovis-associated ancestry beginning at least 9,000 years ago



"We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions."

The peopling mechanism is elucidated, or narrowed down a bit more.

Very interesting. As per the data for EDAR:

"Our data show that a variant in EDAR that affects tooth shape, hair follicles and thickness, sweat, and mammary gland ductal branching and that occurs at nearly 100% frequency in present day Native Americans and East Asians…was not fixed in USR1, Anzick-1, a Brazil_LapaDoSanto_9600BP individual and a Brazil_Laranjal_6700BP individual, all of whom carry the ancestral allele. Thus, the derived allele rose in frequency in parallel in both East Asians and in Native Americans."

Razib Khan argues that:

"These are on the older side as far as samples in the paper go. The numbers are small, but looking at modern Amerindian groups to have this much ancestral variant is surprising. The authors’ conclusion seems highly likely. The EDAR locus, and probably this particular SNP, was segregating in the ancient proto-East Asian/Amerindian metapopulation, and during the Holocene, there was selection on both sides of the Pacific.Why? Unlike some people, I don’t think it was sexual selection for silky hair with full body. EDAR does a lot of things. From GeneCard:

The EDAR gene provides instructions for making a protein called the ectodysplasin A receptor. This protein is part of a signaling pathway that plays an important role in development before birth. Specifically, it is critical for interactions between two embryonic cell layers called the ectoderm and the mesoderm. In the early embryo, these cell layers form the basis for many of the body’s organs and tissues. Ectoderm-mesoderm interactions are essential for the formation of several structures that arise from the ectoderm, including the skin, hair, nails, teeth, and sweat glands.
This locus doesn’t seem to have been targeted elsewhere during the Holocene. Why not? Perhaps there’s another locus (or set of loci) that do similar things and were the targets of selection in other cases."

halfalp
10-11-18, 06:15
Is the Ancestral-B somehow related to the R1* found in some natives? Clovis seems to be 100% represented with Q, wich at least somehow kills the demic " Solutrean Hypothesis ". I really wonder about that Australasian ancestry found in some Southern Natives from some times now, is there no y-dna haplogroups, even a minority found with it? It's only 3% and was already shown in Mesoamerica following the f-statistics.

bicicleur
10-11-18, 10:04
Is the Ancestral-B somehow related to the R1* found in some natives? Clovis seems to be 100% represented with Q, wich at least somehow kills the demic " Solutrean Hypothesis ". I really wonder about that Australasian ancestry found in some Southern Natives from some times now, is there no y-dna haplogroups, even a minority found with it? It's only 3% and was already shown in Mesoamerica following the f-statistics.

along the lines of Y-DNA, Anc-A is Z780 and Anc-B is M3, who entered America in 2 consecutive waves

R1 in North America was spread in the 18th century by the Ojibwe tribe
they got fire-arms and a switch in Y-DNA from French traders

bicicleur
10-11-18, 12:08
Very interesting. As per the data for EDAR:

"Our data show that a variant in EDAR that affects tooth shape, hair follicles and thickness, sweat, and mammary gland ductal branching and that occurs at nearly 100% frequency in present day Native Americans and East Asians…was not fixed in USR1, Anzick-1, a Brazil_LapaDoSanto_9600BP individual and a Brazil_Laranjal_6700BP individual, all of whom carry the ancestral allele. Thus, the derived allele rose in frequency in parallel in both East Asians and in Native Americans."

Razib Khan argues that:

"These are on the older side as far as samples in the paper go. The numbers are small, but looking at modern Amerindian groups to have this much ancestral variant is surprising. The authors’ conclusion seems highly likely. The EDAR locus, and probably this particular SNP, was segregating in the ancient proto-East Asian/Amerindian metapopulation, and during the Holocene, there was selection on both sides of the Pacific.Why? Unlike some people, I don’t think it was sexual selection for silky hair with full body. EDAR does a lot of things. From GeneCard:

The EDAR gene provides instructions for making a protein called the ectodysplasin A receptor. This protein is part of a signaling pathway that plays an important role in development before birth. Specifically, it is critical for interactions between two embryonic cell layers called the ectoderm and the mesoderm. In the early embryo, these cell layers form the basis for many of the body’s organs and tissues. Ectoderm-mesoderm interactions are essential for the formation of several structures that arise from the ectoderm, including the skin, hair, nails, teeth, and sweat glands.
This locus doesn’t seem to have been targeted elsewhere during the Holocene. Why not? Perhaps there’s another locus (or set of loci) that do similar things and were the targets of selection in other cases."

I have a simpler theory.
2 waves of 'first Americans', 16 ka with Y-DNA Z780 and 14 ka with Y-DNA M3 (also check their TMRCA dates)
Anzick was Z780 but this line is extinct today, except in Mexico and Central America
M3 has spread all over America

What if M3 had EDAR, and Z780 didn't?

Question is was EDAR advantageous in America, as it was in Siberia? It also was in Europe, but there it didn't spread.
Because it remained in America, even when M3 merged with autosomal of the first Z780 wave.
Did EDAR help the M3 wave to dominate the Z780 wave?

halfalp
10-11-18, 12:47
I have a simpler theory.
2 waves of 'first Americans', 16 ka with Y-DNA Z780 and 14 ka with Y-DNA M3 (also check their TMRCA dates)
Anzick was Z780 but this line is extinct today, except in Mexico and Central America
M3 has spread all over America

What if M3 had EDAR, and Z780 didn't?

Question is was EDAR advantageous in America, as it was in Siberia? It also was in Europe, but there it didn't spread.
Because it remained in America, even when M3 merged with autosomal of the first Z780 wave.
Did EDAR help the M3 wave to dominate the Z780 wave?

Do Southeastern Asian have the EDAR gene? EDAR seems to be linked with what some anthropologists call the Sinodonts mongoloids, while Southeastern Asians are Sundadonts. It is possible that the first wave of migration was something Ainu-like with a little bit of Australasian ( Sundadont ), while the second was more proto-Sinodonts? Kennewick man is clearly Dolicocephalic, and is physically an outlier over Mongoloid peoples.

Angela
10-11-18, 18:08
I have a simpler theory.
2 waves of 'first Americans', 16 ka with Y-DNA Z780 and 14 ka with Y-DNA M3 (also check their TMRCA dates)
Anzick was Z780 but this line is extinct today, except in Mexico and Central America
M3 has spread all over America

What if M3 had EDAR, and Z780 didn't?

Question is was EDAR advantageous in America, as it was in Siberia? It also was in Europe, but there it didn't spread.
Because it remained in America, even when M3 merged with autosomal of the first Z780 wave.
Did EDAR help the M3 wave to dominate the Z780 wave?

That's certainly possible.

Either way, what I don't completely understand is why it was so beneficial even in vastly different climates.

What seems most likely to me to be a target of selection is not the shape of the teeth or the thickness of the hair, but perhaps the thickness of the skin. That is a distinction between East Asians and West Eurasians, so that sort of confounds the authors' theory that other snps in West Eurasians perform the same function. It certainly may explain why they age better, and why you need a thicker needle when treating them, as I've heard from a few doctors, or even why there might be more pain tolerance. In terms of strong selection, I can see how it might be advantageous in terms of cold weather, but the Amazon?

Perhaps we don't understand some advantage it gives in terms of organs themselves?

bicicleur
10-11-18, 18:19
That's certainly possible.
Either way, what I don't completely understand is why it was so beneficial even in vastly different climates.
What seems most likely to me to be a target of selection is not the shape of the teeth or the thickness of the hair, but perhaps the thickness of the skin. That is a distinction between East Asians and West Eurasians, so that sort of confounds the authors' theory that other snps in West Eurasians perform the same function. It certainly may explain why they age better, and why you need a thicker needle when treating them, as I've heard from a few doctors, or even why there might be more pain tolerance. In terms of strong selection, I can see how it might be advantageous in terms of cold weather, but the Amazon?
Perhaps we don't understand some advantage it gives in terms of organs themselves?
this is a woman from the bororo tribe in equatorial Brasil

https://upload.wikimedia.org/wikipedia/commons/1/1b/Bororo_American_Indian_Mongoloid.png

she has some Mongoloïd traits

the fat around the eyes, the shape of the nose are protections against the eastern Siberian cold and drougth

she don't need this any more
it looks more like a relic she has from her Siberian ancestors >16 ka

Ygorcs
10-11-18, 23:00
I have always had a hard time putting myself to believe that Native Americans did indeed with the huge linguistic diversity that existed in Pre-Columbian America (not just diversity of languages, but of different typologies and of apparently unrelated or at least very distantly related language families). The fact that the recent (2017?) paper on the peopling of the Americas found evidences to support the "Beringian standstill" hypothesis and that the data point out to two very early and independent branches led me to start speculating: what if the Americas were first peopled by two populations that were similar genetically, but culturally and linguistically different enough to follow totally different routes and compete with each other?


The Proto-Amerinds seem to have been pretty mixed themselves (probably an East Asian element mixing into the indigenous ANE/Paleolithic Siberian one), and they supposedly had millennia to diverge linguistically and also to mix and homogeneize in Beringia (or near it) itself. It is thus possible that the two populations already arrived in the Americas speaking different languages or even different language families, even if they were reasonably homogeneous genetically (what if there were still strongholds of "ANE language" amidst the acculturated East Asian-derived languages, like in Bronze Age or even Iron Age Europe, e.g. Iberians and Etruscans do not seem to have been particularly different genetically from their IE neighbors?).


The subsequent intra-Americas movements the scientists have found in this paper can further enhance our understanding of the linguistic diversity of the Americas, because it does not seem like there was just one big settlement event 13,000-16,000 years ago, but subsequent partial or complete replacements, maybe leaving a mix of older language families with newer arrivals. In South America, a Clovis-related layer could've survived in some points (the ethnic diversity was too large in my opinion to be accurately represented by these relatively few samples), a latter dominant layer came in, and finally the 4,200-year-old arrival from North America (this is particularly intriguing to me, because AFAIK linguists have never identified any South American link with North American language families, but the existence of these migration events fits well with the spread of agricultural crops from North America to South America and vice-versa).

Ygorcs
10-11-18, 23:32
Is the Ancestral-B somehow related to the R1* found in some natives? Clovis seems to be 100% represented with Q, wich at least somehow kills the demic " Solutrean Hypothesis ". I really wonder about that Australasian ancestry found in some Southern Natives from some times now, is there no y-dna haplogroups, even a minority found with it? It's only 3% and was already shown in Mesoamerica following the f-statistics.

To answer that the best thing would be to find more ancient DNA of the Botocudo/Aimoré people who inhabited parts of southeastern Brazil and spoke Macro-Jê (generic term for "non-Tupi-Guarani languages" in fact, the Macro-Jê in fact spoke several distinct language families that were not necessarily closely related, the distinction was mainly because to European missionaries the default Brazilian languages were Tupi-Guarani, the rest were, well, much more insignificant to them). The 17th century Botocudo DNA that was retrieved some years ago showed the clearest signal of Melanesian/Ancient Southeast Asian ancestry.

From this Brazilian report on this study (https://g1.globo.com/ciencia-e-saude/noticia/2018/11/08/estudo-contradiz-teoria-de-povoamento-da-america-e-sugere-que-rosto-de-luzia-era-diferente-do-que-se-pensava.ghtml), I learned that 9 of the samples were done exactly in the same archaeological site where they had found the oldest skull of the Americas, Luzia (which incidentally is also close to the homeland of the Botocudos in the early colonial era of Brazil). Luzia was previously found to have physical features more similar to Australian Aboriginals than to Siberians or modern Amerindians, but the new genetic results and facial reconstructions change that story quite a lot. Scientists were maybe assuming too much from the "non-Amerindian-like" cranial measures of Luzia and maybe unconsciously reconstructed her face to fit a "Melanesian" narrative better. The new reconstruction looks much more Amerindian-like.

https://s2.glbimg.com/CMYLT_SZXtP5d7hjebPh5K-DOtY=/0x0:1623x930/984x0/smart/filters:strip_icc()/i.s3.glbimg.com/v1/AUTH_59edd422c0c84a879bd37670ae4f538a/internal_photos/bs/2018/Y/x/4BlrKzTAyuh9orA5BJlw/luzia.jpg

I think that the Melanesian ancestry should still be explained, but it probably did not come with a fully Southeast Asian/Oceanian population, rather it may have come with a Northeast Asian branch of Proto-Amerinds who had intermarried with Southeast Asian-derived migrants somewhere. Maybe there was a third branch of Paleo-Amerind people, with Melanesian ancestry, that was much less successful and smaller than the others and as of yet kind of invisible in the aDNA record elsewhere, but they were very mobile and eventually pushed to the easternmost parts of South America, where small traces of their presence survived in some Brazilian natives?

P.S.: By the way, Luzia was one of the MILLIONS of scientific findings that had been lost to the awful fire that destroyed the 200-year-old National Museum in this September. Thankfully, though, last month the rescuers found the cranium still reasonably preserved inside an iron box. Unfortunately millions of other objects, including Egyptian mummies, Native American objects and decisive parts of Brazilian history (e.g. the very Abolition Law that freed the slaves in 1888), were not as lucky.

ToBeOrNotToBe
10-11-18, 23:56
along the lines of Y-DNA, Anc-A is Z780 and Anc-B is M3, who entered America in 2 consecutive waves

R1 in North America was spread in the 18th century by the Ojibwe tribe
they got fire-arms and a switch in Y-DNA from French traders

There's no way the R1 in North America unmixed natives is from a modern European source. No population is exclusively R1b in Europe (or R1 for that matter). France is barely majority R1b, so you should see lots of (for example) J2 Ojibwe, but you don't.

WHY DON'T WE KNOW THE PHYLOGENY! I legitimately believe something is fishy here, has anybody ever seen an unmixed Native American R1 Y DNA sample?

halfalp
11-11-18, 00:08
To answer that the best thing would be to find more ancient DNA of the Botocudo/Aimoré people who inhabited parts of southeastern Brazil and spoke Macro-Jê (generic term for "non-Tupi-Guarani languages" in fact, the Macro-Jê in fact spoke several distinct language families that were not necessarily closely related, the distinction was mainly because to European missionaries the default Brazilian languages were Tupi-Guarani, the rest were, well, much more insignificant to them). The 17th century Botocudo DNA that was retrieved some years ago showed the clearest signal of Melanesian/Ancient Southeast Asian ancestry.

From this Brazilian report on this study (https://g1.globo.com/ciencia-e-saude/noticia/2018/11/08/estudo-contradiz-teoria-de-povoamento-da-america-e-sugere-que-rosto-de-luzia-era-diferente-do-que-se-pensava.ghtml), I learned that 9 of the samples were done exactly in the same archaeological site where they had found the oldest skull of the Americas, Luzia (which incidentally is also close to the homeland of the Botocudos in the early colonial era of Brazil). Luzia was previously found to have physical features more similar to Australian Aboriginals than to Siberians or modern Amerindians, but the new genetic results and facial reconstructions change that story quite a lot. Scientists were maybe assuming too much from the "non-Amerindian-like" cranial measures of Luzia and maybe unconsciously reconstructed her face to fit a "Melanesian" narrative better. The new reconstruction looks much more Amerindian-like.

https://s2.glbimg.com/CMYLT_SZXtP5d7hjebPh5K-DOtY=/0x0:1623x930/984x0/smart/filters:strip_icc()/i.s3.glbimg.com/v1/AUTH_59edd422c0c84a879bd37670ae4f538a/internal_photos/bs/2018/Y/x/4BlrKzTAyuh9orA5BJlw/luzia.jpg

I think that the Melanesian ancestry should still be explained, but it probably did not come with a fully Southeast Asian/Oceanian population, rather it may have come with a Northeast Asian branch of Proto-Amerinds who had intermarried with Southeast Asian-derived migrants somewhere. Maybe there was a third branch of Paleo-Amerind people, with Melanesian ancestry, that was much less successful and smaller than the others and as of yet kind of invisible in the aDNA record elsewhere, but they were very mobile and eventually pushed to the easternmost parts of South America, where small traces of their presence survived in some Brazilian natives?

P.S.: By the way, Luzia was one of the MILLIONS of scientific findings that had been lost to the awful fire that destroyed the 200-year-old National Museum in this September. Thankfully, though, last month the rescuers found the cranium still reasonably preserved inside an iron box. Unfortunately millions of other objects, including Egyptian mummies, Native American objects and decisive parts of Brazilian history (e.g. the very Abolition Law that freed the slaves in 1888), were not as lucky.

I guess Native Americans are a specific context in humanity, 15'000 years without real other contacts that with themselves or ancestrally related people, it's long. Probably enough long to create multiple language families, + i'm not sure at what level of academic, amerindian languages are studied. It's probably not a trend like IE or Altaic languages. Plus there is already hypothesis like the Na-Dené-Caucasian, wich even if it's not confirmed, maybe shows cultural link that tell us a story. I also believe that the australasian ancestry is probably coming from Beringia, but it was in a population that we still dont have ancient samples of, and only survived here and there in meso and south america. It's not the signal of some Polynesians adventurers for instence. Also apparently there is no sign of african ancestry, wich also somehow cut down the hypothesis that some pre-siberian people from africa came first in south america. You can found in all populations those very prognathic faces ( thrust ) that remainds " Negroids " Africans. I have a work collegue 100% Swiss who looks almost completely like Sungir 2 and i dont even kidding.

Ygorcs
11-11-18, 01:12
I guess Native Americans are a specific context in humanity, 15'000 years without real other contacts that with themselves or ancestrally related people, it's long. Probably enough long to create multiple language families, + i'm not sure at what level of academic, amerindian languages are studied. It's probably not a trend like IE or Altaic languages. Plus there is already hypothesis like the Na-Dené-Caucasian, wich even if it's not confirmed, maybe shows cultural link that tell us a story. I also believe that the australasian ancestry is probably coming from Beringia, but it was in a population that we still dont have ancient samples of, and only survived here and there in meso and south america. It's not the signal of some Polynesians adventurers for instence. Also apparently there is no sign of african ancestry, wich also somehow cut down the hypothesis that some pre-siberian people from africa came first in south america. You can found in all populations those very prognathic faces ( thrust ) that remainds " Negroids " Africans. I have a work collegue 100% Swiss who looks almost completely like Sungir 2 and i dont even kidding.

Na-Dené has been linked to Yeniseian with reasonable credibility in the linguistic community, but it's very little to solve that puzzle, because Na-Dené-speaking people seem to have derived their language from the much later colonization of the Americas by Paleo-Eskimos, who lent the Athasbaskan and Na-Dené populations part of their ancestry (and thus probably their language, too). Na-Dené has probably little or no direct relationship to the other American language families that derive from the first languages brought by Proto-Amerinds (Inuit excepted, as it came with the latest Siberian colonization a mere 2,000-1,000 years ago).

I also believe it's very unlikely that the Australasian ancestry could've come directly from Southeast Asia or more specifiically Polynesia, and it would've failed to leave any impact in the Pacific Coast of South America, but would've been preserved in the easternmost portion of South America close to the Atlantic Ocean.

Yes, I think the prognathic features and other measures of the skull were responsible for the earlier reconstruction of Luzia looking so "African" or at least Melanesian. She may have even had some Melanesian ancestry (who knows? She lived roughly in the same region where Botocudos many millennia later also had slight Melanesian admixture), but it's very unlikely she was part of a "Melanesian population", instead of a Melanesian-admixed Amerindian people.

halfalp
11-11-18, 01:24
Na-Dené has been linked to Yeniseian with reasonable credibility in the linguistic community, but it's very little to solve that puzzle, because Na-Dené-speaking people seem to have derived their language from the much later colonization of the Americas by Paleo-Eskimos, who lent the Athasbaskan and Na-Dené populations part of their ancestry (and thus probably their language, too). Na-Dené has probably little or no direct relationship to the other American language families that derive from the first languages brought by Proto-Amerinds (Inuit excepted, as it came with the latest Siberian colonization a mere 2,000-1,000 years ago).

I also believe it's very unlikely that the Australasian ancestry could've come directly from Southeast Asia or more specifiically Polynesia, and it would've failed to leave any impact in the Pacific Coast of South America, but would've been preserved in the easternmost portion of South America close to the Atlantic Ocean.

Yes, I think the prognathic features and other measures of the skull were responsible for the earlier reconstruction of Luzia looking so "African" or at least Melanesian. She may have even had some Melanesian ancestry (who knows? She lived roughly in the same region where Botocudos many millennia later also had slight Melanesian admixture), but it's very unlikely she was part of a "Melanesian population", instead of a Melanesian-admixed Amerindian people.

Does it really matter at the end, it's only 3%? There was more CHG in Mal'ta than Australasian in Amerindians. It probably means that an influx of melanesians, maybe related with Filipino Aetas give little genetic impact into some people of northeast asia that would later become some Amerindians. Because Americas were so isolated, that ancestry persist there. I already said multiple times that i give way more credit to haplogroups than to audna. If some Melanesians or some Africans gived ancestry to Native Americans, we would see lineage related, there is no way. Even 0.1% of all Brazil makes 200'000 individuals that should show some Melanesian or African specific lineages. Now another intersesting question is, is that Australasian specific ancestry was found in the recent siberian paper? wich i doubt sadly.

bicicleur
11-11-18, 09:56
There's no way the R1 in North America unmixed natives is from a modern European source. No population is exclusively R1b in Europe (or R1 for that matter). France is barely majority R1b, so you should see lots of (for example) J2 Ojibwe, but you don't.
WHY DON'T WE KNOW THE PHYLOGENY! I legitimately believe something is fishy here, has anybody ever seen an unmixed Native American R1 Y DNA sample?
yes, this admixture is not restricted to R1, there are also other European Y-DNA in it, but R1 is the main branch
there is not much literature about this, but if you dig deeper you'll find it, a list somewhere of Y-DNA of a population large enough to represent Native Americans
I've read such study once a few years ago
a large list, it included black Americans and Native Americans

also check the history of the Ojibwe tribe, and you'll understand
it's not the whole of France that visited the Ojibwe, just a few traders with fire-arms and - who knows - a few priests

bicicleur
11-11-18, 10:04
To answer that the best thing would be to find more ancient DNA of the Botocudo/Aimoré people who inhabited parts of southeastern Brazil and spoke Macro-Jê (generic term for "non-Tupi-Guarani languages" in fact, the Macro-Jê in fact spoke several distinct language families that were not necessarily closely related, the distinction was mainly because to European missionaries the default Brazilian languages were Tupi-Guarani, the rest were, well, much more insignificant to them). The 17th century Botocudo DNA that was retrieved some years ago showed the clearest signal of Melanesian/Ancient Southeast Asian ancestry.
From this Brazilian report on this study (https://g1.globo.com/ciencia-e-saude/noticia/2018/11/08/estudo-contradiz-teoria-de-povoamento-da-america-e-sugere-que-rosto-de-luzia-era-diferente-do-que-se-pensava.ghtml), I learned that 9 of the samples were done exactly in the same archaeological site where they had found the oldest skull of the Americas, Luzia (which incidentally is also close to the homeland of the Botocudos in the early colonial era of Brazil). Luzia was previously found to have physical features more similar to Australian Aboriginals than to Siberians or modern Amerindians, but the new genetic results and facial reconstructions change that story quite a lot. Scientists were maybe assuming too much from the "non-Amerindian-like" cranial measures of Luzia and maybe unconsciously reconstructed her face to fit a "Melanesian" narrative better. The new reconstruction looks much more Amerindian-like.
https://s2.glbimg.com/CMYLT_SZXtP5d7hjebPh5K-DOtY=/0x0:1623x930/984x0/smart/filters:strip_icc()/i.s3.glbimg.com/v1/AUTH_59edd422c0c84a879bd37670ae4f538a/internal_photos/bs/2018/Y/x/4BlrKzTAyuh9orA5BJlw/luzia.jpg
I think that the Melanesian ancestry should still be explained, but it probably did not come with a fully Southeast Asian/Oceanian population, rather it may have come with a Northeast Asian branch of Proto-Amerinds who had intermarried with Southeast Asian-derived migrants somewhere. Maybe there was a third branch of Paleo-Amerind people, with Melanesian ancestry, that was much less successful and smaller than the others and as of yet kind of invisible in the aDNA record elsewhere, but they were very mobile and eventually pushed to the easternmost parts of South America, where small traces of their presence survived in some Brazilian natives?
P.S.: By the way, Luzia was one of the MILLIONS of scientific findings that had been lost to the awful fire that destroyed the 200-year-old National Museum in this September. Thankfully, though, last month the rescuers found the cranium still reasonably preserved inside an iron box. Unfortunately millions of other objects, including Egyptian mummies, Native American objects and decisive parts of Brazilian history (e.g. the very Abolition Law that freed the slaves in 1888), were not as lucky.

this study looked for it and didn't find it, they even checked the Lago do Santo population with the odd skulls

I have another question for you : how old are the Na-Dene and the Athabaskan languages?
USR1 11.5 ka shows affinity to Shuka Kaa 10.3 ka, which is in the Tlingit area, but there is no affinity between Shuka Kaa and extant Tlingit people
whatever, by 10.3 ka there must have been a passageway through the icecap between central Alaska and the southeast Alaskan coast

Ygorcs
12-11-18, 10:09
this study looked for it and didn't find it, they even checked the Lago do Santo population with the odd skulls

I have another question for you : how old are the Na-Dene and the Athabaskan languages?
USR1 11.5 ka shows affinity to Shuka Kaa 10.3 ka, which is in the Tlingit area, but there is no affinity between Shuka Kaa and extant Tlingit people
whatever, by 10.3 ka there must have been a passageway through the icecap between central Alaska and the southeast Alaskan coast

I think the secondary migration wave that is now thought to have brought Na-Dené languages to the Americas was the one linked to Paleo-Eskimos, so some 5-6kya, as Paleo-Eskimo ancestry is most prevalent in modern Inuit (those who replaced the Paleo-Eskimos and probably absorbed them too) and Na-Dené populations. It's unlikely a 10kya individual would have any relationship to the spread of Dené-Yeniseian languages. I couldn't find an estimate for the time span of Proto-Dené-Yeniseian, but one analysis for Na-Dené languages alone estimated at most 8.5kya, another source says "at least 5,000 or 6,000 years old". So the split between Na-Dené and Yeniseian would've certainly happened even earlier, maybe as much as 10kya? An early date would explain the very tenuous relationship that has been found between both language families.

Gnarl
12-11-18, 11:54
There's no way the R1 in North America unmixed natives is from a modern European source. No population is exclusively R1b in Europe (or R1 for that matter). France is barely majority R1b, so you should see lots of (for example) J2 Ojibwe, but you don't.

WHY DON'T WE KNOW THE PHYLOGENY! I legitimately believe something is fishy here, has anybody ever seen an unmixed Native American R1 Y DNA sample?

Y-DNA has a tendency to explode. Admixture in the Ojibwe was probably not even, but came from a low number of individuals.

Angela
12-11-18, 19:18
As to whether Southeast Asians carry the EDAR gene.
https://i.imgur.com/IqaUlM7.png

Megalophias
12-11-18, 21:02
There's no way the R1 in North America unmixed natives is from a modern European source. No population is exclusively R1b in Europe (or R1 for that matter). France is barely majority R1b, so you should see lots of (for example) J2 Ojibwe, but you don't.
What's your source for Ojibwe Y haplogroups?
Bolnick et al (2006), "Asymmetric male and female genetic histories among Native Americans from Eastern North America" - Chippewa (n=97) had 51% R1-M173, 15% Q-M242, 4% C-M130, 2% DE-YAP, and 28% other (i.e. not C, DE, or P1-M45). So of what's not Q and C 65% is R1 (presumably mostly R1b) and 35% other (presumably I, J, E, etc). That seems unremarkable coming from intermarriage with Northwest European men.

Salento
15-11-18, 23:51
The great adventure of the Native Americans
Razib Khan

.... In 1492 Christopher Columbus made definitive and lasting contact between Europe and the New World....

... The story of the native peoples of the New World, called Native Americans in the United States of America, First Nations, Aboriginal or indigenous elsewhere, begins over 30,000 years ago at the “top of the world.” The Asian landmass adjacent to the Arctic...

...Modern Native Americans are overwhelmingly descendants of these ancient Beringians. Modern Native Americans are therefore ~40% Ancient North Eurasian, and 60% descended from a group of ancient East Asians...

... This fusion likely occurred by ~20,000 years ago. But the archaeology seems to indicate that the native people of the New World did not begin to spread across the landscape of North and South America until ~15,000 years ago. The reason is simple: ice sheets blocked migration south and west. But by ~15,000 years ago we see evidence of humans as far as south as Chile! The movement seems to have been rapid and immediate....
...........

https://blog.insito.me/the-20-000-year-adventur-eof-the-29850081166a

berun
18-11-18, 15:18
The case of a Mesoamerican migration towards South America also is seen in the recent paper "Early human dispersals within the Americas":

This analysis indicates most present-day South American populations do not form a clade with Lagoa Santa, but instead derive from a mixture of Lagoa Santa and Mesoamerican-related ances-tries ... The ~5.1 ka Patagonian Ayayema genome is an exception; it forms a clade with the Lagoa Santa population. This sug-gests the arrival of the Mesoamerican-related ancestry oc-curred post-5.1 ka, and/or that it did not reach the remote region inhabited by the Ayayema individual’s ancestors. ... The diCal2 results are consistent for the Karitiana, Aymara, and Suruí showing their demographic histories involved a mixture between a Lagoa Santa-related and a Mixe-related source (13).

berun
18-11-18, 16:06
What is interesting with the Mesoamerican gene flow is that it could be linked with the first ceramincs in Peru and the cultivation of maize.

64logh
03-12-18, 12:40
There's no way the R1 in North America unmixed natives is from a modern European source. No population is exclusively R1b in Europe (or R1 for that matter). France is barely majority R1b, so you should see lots of (for example) J2 Ojibwe, but you don't.

WHY DON'T WE KNOW THE PHYLOGENY! I legitimately believe something is fishy here, has anybody ever seen an unmixed Native American R1 Y DNA sample?

I would like to see some research showing precolumbian peoples with R-YDNA .