New studies on the autosomal make-up of Native Americans

[curupira]

They differ from previous studies in that they argue there is a signal of an ancient shared ancestry with Australo-Melanesians.


How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict
populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not
directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full.pdf
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full


Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1, 2, 3, 4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5, 6, 7, 8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature14895.html

[curupira]

As for the Australo-Melanesian signal, these are the observations by the researchers:


The data presented here are consistent with a single ini-tial migration of all Native Americans and with later gene flow from sources related to East Asians and, more distant-ly, Australo-Melanesians. From that single migration, there was a diversification of ancestral Native Americans leading to the formation of ‘northern’ and ‘southern’ branches, which appears to have taken place ca. 13 KYA within the Americas. This split is consistent with the patterns of unip-arental genomic regions of mtDNA haplogroup X and some Y chromosome C haplotypes being present in northern, but not southern, populations in the Americas (18, 62). This di-versification event coincides roughly with the opening of habitable routes along the coastal and the interior corridors into unglaciated North America some 16 KYA and 14 KYA, respectively (63, 64), suggesting a possible role of one or both these routes in the isolation and subsequent dispersal of Native Americans across the continent.

We found that some American populations, including the Aleutian Islanders, Surui, and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as North American Ojibwa, Cree and Algonquin, and the South American Purepecha, Arhuaco and Wayuu (fig. S10). The Surui are, in fact, one of closest Native American populations to East Asians and Australo-Melanesians, the latter including Papuans, non-Papuan Melanesians, Solo-mon Islanders, and South East Asian hunter-gatherers such as Aeta (fig. S10). We acknowledge that this observation is based on the analysis of a small fraction of the whole ge-nome and SNP chip genotype datasets, especially for the Aleutian Islander data that is heavily masked due to recent admixture with Europeans (28), and that the trends in the data are weak.

Nonetheless, if it proves correct, these results suggest there may be a distant Old World signal related to Australo-Melanesians and East Asians in some Native Americans. The widely scattered and differential affinity of Native Americans to the Australo-Melanesians, ranging from a strong signal in the Surui to much weaker signal in north-ern Amerindians such as Ojibwa, points to this gene flow occurring after the initial peopling by Native American an-cestors.

However, how this signal may have ultimately reached South America remains unclear. One possible means is along a northern route via the Aleutian Islanders, previously found to be closely related to the Inuit (39), who have a rela-tively greater affinity to East Asians, Oceanians and Den-isovan than Native Americans in both whole genome and SNP chip genotype data-based D-tests (table S10 and figs. S10 and S11). On the basis of archaeological evidence and mtDNA data from ancient and modern samples, the Aleu-tian Islands are hypothesized to have been peopled as early as ca. 9 KYA by ‘Paleo-Aleuts’ who were succeeded by the ‘Neo-Aleuts’, with present-day Aleutian Islanders potentially resulting from admixture between these two populations (52, 53). Perhaps their complex genetic history included in-put from a population related to Australo-Melanesians through an East Asian continental route, and this genomic signal might have been subsequently transferred to parts of the Americas, including South America, through past gene flow events (Fig. 1). Evidence for this gene flow is supported by diCal2.0 and MSMC analyses showing a weak but recent gene flow into South Americans from populations related to present-day Northeast Asians (Koryak) (Fig. 2C and table S11C), who might be considered a proxy for the related Aleu-tian Islanders.

The detection of an Australo-Melanesian genetic signal in the Americas, however subtle, returns the discussion to the Paleoamerican model, which hypothesizes, on the basis of cranial morphology, that two temporally and source-distinct populations colonized the Americas. The earlier population reportedly originated in Asia in the Late Pleisto-cene and gave rise to both Paleoamericans and present-day Australo-Melanesians, whose shared cranial morphological attributes are presumed to indicate their common ancestry (23). The Paleoamericans were, in turn, thought to have been largely replaced by ancestors of present-day Amerindi-ans, whose crania resemble modern East Asians and who are argued to be descendants of later arriving Mongoloid populations (14, 23, 26, 54). The presence of Paleoamericans is inferred primarily from ancient archaeological specimens in North and South America, and a few relict populations of more recent age, which include the extinct Pericúes and Fuego-Patagonians (24, 25, 55).

The Paleoamerican hypothesis predicts that these groups should be genetically closer to Australo-Melanesians than other Amerindians. Previous studies of mtDNA and Y chro-mosome data obtained from Fuego-Patagonian and Paleo-american skeletons have identified haplogroups similar to those of modern Native Americans (55–57). Although these results indicate some shared maternal and paternal ancestry with contemporary Native Americans, uniparental markers can be misleading when drawing conclusions about the de-mographic history of populations. To conclusively identify the broader population of ancestors who may have contrib-uted to the Paleoamerican gene pool, autosomal genomic data are required.

We, therefore, sequenced 17 ancient individuals affiliated to the now-extinct Pericúes from Mexico and Fuego-Patagonians from Chile and Argentina (28), who, on the basis of their distinctive skull morphologies, are claimed to be relicts of Paleoamericans (23, 27, 58, 59). Additionally, we sequenced two pre-Columbian mummies from northern Mexico (Sierra Tarahumara) to serve as morphological con-trols, since they are expected to fall within the range of Na-tive American morphological cranial variation (28). We found that the ancient samples cluster with other Native American groups and are outside the range of Oceanian ge-netic variation (28) (Fig. 5 and figs. S32, S33, and S34). Simi-larly, outgroup f3 statistics (47) reveal low shared genetic ancestry between the ancient samples and Oceanians (28) (Figs. S36, S37), and genome-based and masked SNP chip genotype data-based D-statistics (46, 47) show no evidence for gene flow from Oceanians into the Pericúes or Fuego-Patagonians (28) (fig. S39).

As the Paleoamerican model is based on cranial mor-phology (23, 27, 58, 59), we also measured craniometric data for the ancient samples and assessed their phenotypic affin-ities to supposed Paleoamericans, Amerindians and world-wide populations (28). The results revealed that the analyzed Fuego-Patagonians showed closest craniometric affinity to Arctic populations and the Paleoamericans, while the analyzed female Pericúes showed closest craniometric affinities to populations from North America, the Arctic re-gion and Northern Japan (table S15). More importantly, our analyses demonstrated that the presumed ancestral ancient Paleoamerican reference sample from Lagoa Santa, Brazil (24) had closest affinities to Arctic and East Asian popula-tions (table S15). Consequently, for the Fuego-Patagonians, the female Pericúes and the Lagoa Santa Paleoamerican sample, we were not able to replicate previous results (24) that report close similarity of Paleoamerican and Australo-Melanesian cranial morphologies. We note that male Pericúes samples displayed more craniometric affinities with populations from Africa and Australia relative to the female individuals of their population (fig. S41). The results of analyses based on craniometric data are, thus, highly sen-sitive to sample structure and the statistical approach and data filtering used (51). Our morphometric analyses suggest that these ancient samples are not true relicts of a distinct migration, as claimed, and hence do not support the Paleo-american model. Similarly, our genomic data also provide no support for an early migration of populations directly related to Australo-Melanesians into the Americas.
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full.pdf

The remarks of the researchers of the second study:


The team named the mysterious ancestor Population Y, after the Tupí word for ancestor, “Ypykuéra.”

Reich, Skoglund and colleagues propose that Population Y and First Americans came down from the ice sheets to become the two founding populations of the Americas.

“We don’t know the order, the time separation or the geographical patterns,” said Skoglund.

Researchers do know that the DNA of First Americans looked similar to that of Native Americans today. Population Y is more of a mystery.

“About 2 percent of the ancestry of Amazonians today comes from this Australasian lineage that’s not present in the same way elsewhere in the Americas,” said Reich.

However, that doesn’t establish how much of their ancestry comes from Population Y. If Population Y were 100 percent Australasian, that would indeed mean they contributed 2 percent of the DNA of today’s Amazonians. But if Population Y mixed with other groups such as the First Americans before they reached the Americas, the amount of DNA they contributed to today’s Amazonians could be much higher—up to 85 percent.

To answer that question, researchers would need to sample DNA from the remains of a person who belonged to Population Y. Such DNA hasn’t been obtained yet. One place to look might be in the skeletons of early Native Americans whose skulls some researchers say have Australasian features. The majority of these skeletons were found in Brazil.
http://www.pasthorizonspr.com/index.php/archives/07/2015/genetic-studies-link-indigenous-peoples-in-the-amazon-and-australasia

[curupira]

From one of the studies:


Fig. 1. Origins and population history of Native Americans. (A) Our results show that the ancestors of all present-day Native Americans, including Amerindians and Athabascans, derived from a single migration wave into the Americas (purple), separate from the Inuit (green). This migration from East Asia occurred no later than 23 KYA and is in agreement with archaeological evidence from sites such as Monte Verde (50). A split between the northern and southern branches of Native Americans occurred ca. 13 KYA, with the former comprising Athabascans and northern Amerindians and the latter consisting of Amerindians in northern North America and Central and South America including the Anzick-1 individual (5). There is an admixture signal between Inuit and Athabascans and some northern Amerindians (yellow line); however, the gene flow direction is unresolved due to the complexity of the admixture events (28). Additionally, we see a weak signal related to Australo-Melanesians in some Native Americans, which may have been mediated through East Asians and Aleutian Islanders (yellow arrows). Also shown is the Mal’ta gene flow into Native American ancestors some 23 KYA (yellow arrow) (4). It is currently not possible for us to ascertain the exact geographical locations of the depicted events; hence, the positioning of the arrows should not be considered a reflection of these. B. Admixture plot created on the basis of TreeMix results (fig. S5) shows that all Native Americans form a clade, separate from the Inuit, with gene flow between some Native Americans and the North American Arctic. The number of genome-sequenced individuals included in the analysis is shown in brackets.
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full.pdf

http://i59.tinypic.com/5bsn46.jpg


Fig. 5. The Paleoamerican model. (A) Principal Component Analysis plot of 19 ancient samples combined with a worldwide reference panel, including 1,823 individuals from (6). Our samples plot exclusively with American samples. For plots with other reference panels consisting of Native American populations, see fig. S32. (B) Population structure in the ancient Pericú, Mexican mummy and Fuego-Patagonian individuals from this study. Ancestry proportions are shown when assuming six ancestral populations (K = 6). The top bar shows the ancestry proportions of the 19 ancient individuals, Anzick-1 (5), and two present-day Native American genomes from this study (Huichol and Aymara). The plot at the bottom illustrates the ancestry proportions for 1,823 individuals from (6). Our samples show primarily Native American (ivory, >92%) and Siberian (red, ca. 5%) ancestry. For the plot with K=13, see fig. S33.
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full.pdf

http://i62.tinypic.com/ra7tbq.jpg

[nicalandia]

thanks, so Mal'Ta boy was Native American?

[curupira]

thanks, so Mal'Ta boy was Native American?

He belonged to a population related - in part - to Native Americans. Native Americans would have an East Eurasian component which is missing in the Malta boy.

[Grab the Gauge]

He belonged to a population related - in part - to Native Americans. Native Americans would have an East Eurasian component which is missing in the Malta boy.

This is not true.

There is an East Eurasian component in Mal'ta. This unsuprising given the regional placement of Tianyuan and Oase 1 (both East Eurasian) in both Western and Eastern Eurasia. It's also confirmed by the Venus figurines of Mal'ta-Buret, which are typically Amerindian in facial and bodily form.

The figures for "Native Americans" include the Inuit who are heavily East Eurasian shifted. This skews the data making Amerindians look more East Eurasian than they really are. Abstracting the Indians from the data, Mal'ta has comparable East Eurasian admixture with modern Cheyenne. That is to say, less than the Inuit.

[nicalandia]

This is not true.

There is an East Eurasian component in Mal'ta. This unsuprising given the regional placement of Tianyuan and Oase 1 (both East Eurasian) in both Western and Eastern Eurasia.

The figures for "Native Americans" include the Inuit who are heavily East Asian shifted. This skews the data making Amerindians look more East Eurasian than they really are. Abstracting the Indians from the data, Mal'ta has comparable East Eurasian admixture with modern Cheyenne. That is to say, less than the Inuit.

wow thats so cool

[curupira]

This is not true.

I'm not saying it is true or not. I said the researchers alleged that. I'm not an expert on the subject. Here it is what they said:


Between 14 and 38 percent of American Indian ancestry may originate from gene flow from the Mal'ta Buret people, while the other geneflow in the Native Americans appears to have an Eastern Eurasian origin
https://en.wikipedia.org/wiki/Mal%27ta-Buret%27_culture


We estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians

The most parsimonious explanation for these results is that Native Americans have mixed origins, resulting from admixture between peoples related to modern-day east Asians and western Eurasians. Admixture graphs fitted with MixMapper27 model Karitiana as having 14–38% western Eurasian ancestry and 62–86% east Asian ancestry, but we caution that these estimates assume unadmixed ancestral populations

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/

[Grab the Gauge]

Again, when they say "Native American" they're including Inuit, DeNe, etc who skew the trend to East Eurasians on account of their closer affinities with them. When you abstract the real Indians, and disregard the Inuit and subarctic halfbreeds, the samples MA-1 and Plains Indians are much closer.

[Peterski]

thanks, so Mal'Ta boy was Native American?

No, he was Ancient North Eurasian (Ancient Siberian), which was unlike any of modern populations, including modern Siberians (see the PCA chart below), but contributed ancestry to several modern populations, including Native Americans, Western Eurasians and South Asians:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/

http://anthropogenesis.kinshipstudies.org/2013/11/ancient-dna-from-malta-and-afontova-gora-a-full-account/

https://www.academia.edu/7110954/Upper_Palaeolithic_Siberian_genome_reveals_dual_an cestry_of_Native_Americans-_Supplemental


(...) This suggests that populations related to contemporary Western Eurasians [Caucasoids] had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 [Mal'ta] lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that Western Eurasian [Caucasoid] genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans. (...)

Figure "B" shows that Mal'ta boy was genetically quite similar to modern populations such as Europeans, Western Asians and Central Asians, South Asians, Native Americans and Western Siberians, but NOT to modern East Asians:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/bin/nihms583477f1.jpg

This also overturns the Solutrean Hypothesis, as it shows that Caucasoid people got to North America from Siberia, not from Western Europe:

https://www.youtube.com/watch?v=hF1UO0-cHLs


https://www.youtube.com/watch?v=hF1UO0-cHLs

[Peterski]

So descendants of Mal'ta population contributed to both Native Americans and Europeans:

http://s14.postimg.org/i3yi0acq9/gene_flow.png

[Peterski]

This is not true.

There is an East Eurasian component in Mal'ta.

No there is not. Skulls of Mal'ta population did not resemble East Asian skulls:

"Gene flow from the MA-1 [Mal'ta] lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do NOT resemble those of east Asians2, 13."

Mal'ta population was more closely related to West Eurasians, not East Asians:

"This suggests that populations related to contemporary Western Eurasians [Caucasoids] had a more north-easterly distribution 24,000 years ago than commonly thought."

[Peterski]

Admixture graphs fitted with MixMapper27 model Karitiana as having 14–38% Western Eurasian ancestry and 62–86% East Asian ancestry, but we caution that these estimates assume unadmixed ancestral populations

Recent study reveals also a 3rd ancestral group to Karitiana people - Australasians (Australo-Melanesians):

http://dna-explained.com/2015/07/22/some-native-americans-had-oceanic-ancestors/

http://d1jrw5jterzxwu.cloudfront.net/sites/default/files/default/files/uploads/nature-dna-map.jpg

[Demon Revival]

Recent study reveals also a 3rd ancestral group to Karitiana people - Australasians (Australo-Melanesians):

http://dna-explained.com/2015/07/22/some-native-americans-had-oceanic-ancestors/

http://d1jrw5jterzxwu.cloudfront.net/sites/default/files/default/files/uploads/nature-dna-map.jpg

How much percent it is?

[curupira]

How much percent it is?

Read my two first posts on this thread. It explains it. Two studies were released, and they speak of it, though not in the same way.

[Demon Revival]

Read my two first posts on this thread. It explains it. Two studies were released, and they speak of it, though not in the same way.

Information is relatively vague. It only says that it was found on minor level, and that it wasn't found in the typically proposed peoples with an Australoid substratum (Fuegians and Pericus). I personally think that if this is under 10% level, they likely picked it somewhere in Asia. I also don't think it's truly Australian Aboriginal or Papuan like, but rather South Asian like (as in South Indians and such) or something ancestral to them.

[curupira]

Information is relatively vague. It only says that it was found on minor level, and that it wasn't found in the typically proposed peoples with an Australoid substratum (Fuegians and Pericus). I personally think that if this is under 10% level, they likely picked it somewhere in Asia. I also don't think it's truly Australian Aboriginal or Papuan like, but rather South Asian like (as in South Indians and such) or something ancestral to them.

It is not. Perhaps you did not really read it.


The team named the mysterious ancestor Population Y, after the Tupí word for ancestor, “Ypykuéra.”

Reich, Skoglund and colleagues propose that Population Y and First Americans came down from the ice sheets to become the two founding populations of the Americas.

“We don’t know the order, the time separation or the geographical patterns,” said Skoglund.

Researchers do know that the DNA of First Americans looked similar to that of Native Americans today. Population Y is more of a mystery.

“About 2 percent of the ancestry of Amazonians today comes from this Australasian lineage that’s not present in the same way elsewhere in the Americas,” said Reich.

However, that doesn’t establish how much of their ancestry comes from Population Y. If Population Y were 100 percent Australasian, that would indeed mean they contributed 2 percent of the DNA of today’s Amazonians. But if Population Y mixed with other groups such as the First Americans before they reached the Americas, the amount of DNA they contributed to today’s Amazonians could be much higher—up to 85 percent.

To answer that question, researchers would need to sample DNA from the remains of a person who belonged to Population Y. Such DNA hasn’t been obtained yet. One place to look might be in the skeletons of early Native Americans whose skulls some researchers say have Australasian features. The majority of these skeletons were found in Brazil.
http://www.pasthorizonspr.com/index.php/archives/07/2015/genetic-studies-link-indigenous-peoples-in-the-amazon-and-australasia

[Grab the Gauge]

So descendants of Mal'ta population contributed to both Native Americans and Europeans:

http://s14.postimg.org/i3yi0acq9/gene_flow.png

Yet again you post this retarded fucking Raghavan plot; this time with space-age MS Paint schematics. Look at the East Asian pool, it includes southeast Asians as East Asian. If you abstract Southeast Asians, the distance is far less. Just look at the Eskimo-Aleut (mongoloids) from your very own rat turd graph. They're closter to MA-1 than West Eurasians and Native Americans.

[Demon Revival]

It is not. Perhaps you did not really read it.


http://www.pasthorizonspr.com/index.php/archives/07/2015/genetic-studies-link-indigenous-peoples-in-the-amazon-and-australasia

Well, that's certainly not too much.

[curupira]

Well, that's certainly not too much.

Because it is a somewhat controversial subject still, the subject being complex, not simple (no Australo-Melanesian mtDNA and yDNA have been detected, f.e). It could be just the signal of a very ancient shared ancestry. If you read the first post on this thread, you'll notice according to these 2 studies from 2015 the basic model of the peopling of the Americans and of the composition of Native Americans remains basically the same. A single population from Siberia going into our continent, ancestral to the contemporary Native Americans, accounts for most of the ancestry of contemporary Native Americans.

Summing up the two studies:


How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full.pdf
http://www.sciencemag.org/content/early/2015/07/20/science.aab3884.full


Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1, 2, 3, 4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5, 6, 7, 8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature14895.html