Many people suspected this because of the difficulty to access the Americas from Eurasia: this must have limited gene flow between the two regions to a handful of migrants and a restricted set of time periods where geological and climatic conditions were advantageous. The much reduced genetic diversity of Native Americans also argues in favor of them being a relatively simple population, with low heterozygosity and a handful of unique "founder lineages" in both the Y-chromosome and mtDNA.
Nonetheless, there are also several theories in the realm of alernative history, involving Solutreans from Europe, trans-Pacific boat riders, bearded "White Gods", Minoans/Phoenicians/Atlanteans/Ancient Egyptians, "African" Olmecs, "Caucasoid" Paleo-Indians, lost Israelite tribes, to mention only a few of the most well-known ones.
The new study does not, of course, disprove any of the proposals in the preceding paragraph: one can still claim that diverse groups once inhabited the Americas and Rasmussen et al. (2014) just happened to chance upon one that looked just like modern native Americans. But, this certainly improves the odds of early "Native American simplicity", offering no evidence for the complexity postulated by many of the alternative theories.
Moreover, while the existence of other human groups in the Americas cannot be disproved by the study of a single ancient individual, what can be proved is the antiquity of the ancestors of Native Americans. Rather than being late arrivals arriving from Asia after the initial colonization, perhaps with derived Mongoloid physical morphology, we now know that they were already there as early as ~13 thousand years ago. It is remarkable that a single ancient DNA sample can sweep away much of the nonsense that has been written on the topic in the past.
A piece in Nature News addresses some of the "ethics" debate that seems ever-present in studies involving Native American remains. I don't know how this study will be perceived by living Native Americans: a possibility is that they'll be more receptive to ancient DNA research now that a team of scientists have stretched the time depth of their ancestry in the Americas to the earliest studied sample, revealing themselves not to be the evil-doers that western scientists are generally assumed to be according to a certain kind of mentality. A different -and more alarming- possibility, is that radical anti-science elements will be emboldened by these findings to claim that continuity with the earliest Americans (which in itself seems true enough) adds support to claims of ownership to pretty much all archaeological samples whose relationship to living Amerindians was hitherto uncertain in light of the many alternative theories.
In any case, it is remarkable that this ~13 thousand year old genome now exists while the genomes of modern native Americans that can be had for a fraction of the cost and technical difficulty do not. Indeed, not even genotype data exist from most Amerindian groups from the USA, which creates the rather bizarre state of affairs that the Anzick-1 genome had to be compared with native groups from several countries in the Western hemisphere except the one in which it was found.
Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025
The genome of a Late Pleistocene human from a Clovis burial site in western Montana
Morten Rasmussen et al.
Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (BP) (13,000 to 12,600 calendar years BP)1, 2. Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum4. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years BP (approximately 12,707–12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.
Link
293 comments:
«Oldest ‹Older 201 – 293 of 293"Amerindians are the closest among modern humans to Denisovans and Neandertals".
I have told you before, and I tell you again, that is simply not true. Unless you're now claiming Australian Aborigines and Papuans are not 'modern humans'. Actually I would not be at all surprised to learn that is exactly what you believe.
"terry, we're talking about a very specific chart in Prufer".
And ignoring everything else. And you call yourself a 'scientist'!
"Do your due diligence!"
Listen to your own advice.
"I'm a scientist who challenges other scientists".
No you're not. You're a wannabee scientist who challenges real scientists.
"the phylogeography suggests that African-specific lineages were absorbed from an archaic African substratum. Otherwise, Y-DNA hgs A and B would've been found outside of Africa"
The only reason you are able to suggest that to be so is because you absolutely refuse to see an African origin for humans. Once you accept an African origin it makes complete sense that some African haplogroups are not found outside that continent. On the other hand the absense of these haplogroups outside Africa poses a huge problem for 'out of America' which you can only solve by denying the veracity of the haplogroup phylogeny as currently understood.
"Anthropology is the best of science and the best of humanities"
Depends what you're studying it for. If it is to learn how ideas and information is spread through tribal groups with the idea of using that information for your own salesmanship then is can hardly be called an objective science. I understand it is common for advertising executives to study anthropology.
"human origins is an anthropological problem by definition".
Human origins is only partly an anthropological problem. Other sciences are equally, or even more, important.
@TerryT
"I have told you before, and I tell you again, that is simply not true. Unless you're now claiming Australian Aborigines and Papuans are not 'modern humans'. Actually I would not be at all surprised to learn that is exactly what you believe."
Terry, why don't you look at the chart I was referring to? On that chart Amerindians (followed by Papuans) are the closest to Denisovan and Altai Neandertal. It's true that Papuans and Australian aborigines share more alleles with Denisovans than Amerindians (but Amerindians have more Denisovan ancestry than, say, Han, Europeans or Africans), but my comment referred to the Prufer chart. The two pieces of evidence are very consistent with each other, even if sometimes Amerindians follow Papuans and sometimes Papuans follow Amerindians. In any case, Africans, who have been shown to have both Denisovan and Neandertal alleles are the most removed from those two archaic hominins from Eurasia. The pattern we're talking about is fully consistent with linguistics that shows that the New World has 2/3 of world linguistic diversity, not including Papua New Guinea, while Europeans and Africans are the most homogeneous linguistically.
"You're a wannabee scientist who challenges real scientists."
This is demonstrably not true. What is true is that you're an ignorant cryptocreationist.
"The only reason you are able to suggest that to be so is because you absolutely refuse to see an African origin for humans."
I know that in your creationist world one is supposed to first find an idea to believe in and then force all the evidence into it.
"On the other hand the absense of these haplogroups outside Africa poses a huge problem for 'out of America' "
Only using a perverted logic of a believer like yourself. Y-DNA A and B, mtDNA hgs L0, L1, L2 are not found outside of Africa. They are African specific but have unique matches with chimp sequences. We also know that they are more divergent than the other lineages found in modern humans, including such African-specific lineages as Y-DNA hg E and mtDNA hg L3. mtDNA L3 is increasingly thought of as a subset of the non-African clade, most closely related to Asian mhg M, just like Y-DNA hg E, which is most closely related to Asian hg D. We do find Denisovan and Neandertal alleles in Africa and those species are non-African (Denisovan is Asia-specific, Neandertals are European and Asian). Geneticists are now very comfortable with the idea that modern humans mixed with archaics and we have paleobiological evidence showing admixture in Africa (Iwo Eleru). So the most natural conclusion is that Africa was colonized by modern humans from Asia. In the process, they absorbed genes from African "archaics."
"I understand it is common for advertising executives to study anthropology."
Wrong again. I first studied anthropology, published two books, then became an advertising executive. This makes me both highly qualified to talk about human origins and objective when it comes to evaluating academia-generated theories. Nick Patterson did the opposite: first he worked in investment banking, then became a geneticist.
"Human origins is only partly an anthropological problem. Other sciences are equally, or even more, important."
Anthropology is a multidisciplinary field. Your "other sciences" should be part of anthropology when it comes to human origins. The genetics of modern human populations is called "anthropological genetics" for a reason.
"This is demonstrably not true. What is true is that you're an ignorant cryptocreationist".
And it is equally true that you are a very stupid person. Perhaps it is simply that you have an unrequited desire to be different that drives you.
"I know that in your creationist world one is supposed to first find an idea to believe in and then force all the evidence into it".
More stupidity on your part. Waht is 'creationist' about out of Africa? How about some facts from you instead of opinion for a change.
"Y-DNA A and B, mtDNA hgs L0, L1, L2 are not found outside of Africa. They are African specific but have unique matches with chimp sequences".
Obviously they formed earlier on the haplogroup tree. Where's you problem?
"We also know that they are more divergent than the other lineages found in modern humans"
Yes, again showing they are more ancient.
" We do find Denisovan and Neandertal alleles in Africa and those species are non-African (Denisovan is Asia-specific, Neandertals are European and Asian)".
Yes, and we can tell from that there has been a movement back into Africa from Eurasia. Once more, what's your problem?
"So the most natural conclusion is that Africa was colonized by modern humans from Asia".
Wrong. We can tell 'that Africa was [partly] colonized by modern humans from Asia'. I see your problem emerging. You are prepared to ignore any evidence that fails to fit your hypothesis.
"In the process, they absorbed genes from African 'archaics'".
Proving that even in the unlilkely event of your knowing everything about anthropology you knoe absolutely nothing about gnetics or evolution. If the 'African archaics', as you call them, are completely interfertile with modern humans they are the same species. We can argue all day and all night as to whether Neanderthals and Denisovans were the same species as modern humans, but but they appear to have had limited hybrid forming ability. Various African groups are completely interfertile.
"This makes me both highly qualified to talk about human origins and objective when it comes to evaluating academia-generated theories".
But your apparent lack of any biological knowledge, including evolutionary biology and genetics, renders you impotent with regard to your claim.
"terry, we're talking about a very specific chart in Prufer".
You'll have to remind me of which paper the chart is in, but one Prufer paper has this to say:
"We estimate that the Denisovan
contribution to mainland Asian and Native American populations is
,0.2% and thus about 25 times smaller than the Denisovan contribution to populations in Papua New Guinea and Australia".
Link:
http://pgl.soe.ucsc.edu/pruferAltai14.pdf
" It's true that Papuans and Australian aborigines share more alleles with Denisovans than Amerindians (but Amerindians have more Denisovan ancestry than, say, Han, Europeans or Africans)"
But you're claiming Amerindians have 'the most' Denisovan ancestry. Clearly that is not correct.
@German:
Amerindians are the closest among modern humans to Denisovans and Neandertals.
You can repeat that mantra as much as you like, but it won't change the facts: Denisovans and Neanderthals are *NOT* the the closest populations to Amerindians. The populations that are closest to Amerindans (and hence best represent Amerindian demographics) are Papuans and Eurasians.
You're like a real estate agent talking up a house because it's "the closest house to the beach in all of El Paso!".... in other words, nowhere near the beach. Trying to insinuate associations where no associations exist might be good marketing, but it's bad science.
You don't appeal to authority and opinions when the conversation is about facts.
I didn't - it was you appealing to your own supposed authority that lead the discussion this way... trying to justify your denial of the science remember?
Yes, you are a science denier. And yes it's a fact.
... and yet I accept the science, and you deny it! Go figure.
Just use your mathematical skills to demonstrate that Russians cluster with Papuans and hence f3 plots are full of noise.
Russians and Papuans cluster on the X-axes of EDF 5a and 5e. I never said the plots of "full of noise", I said that you're interpretation of them is invalid. If you interpret them the way they are meant to be interpreted they are very straightforward, with no "noise" at all.
I've furnished tons of data.
Then furnish it again, it must have been lots in all the self-aggrandisement and bullying behaviour.
I'm curious about your thoughts on the theory of relativity, now that I'm going to show you Albert Einstein in an Indian garb.
Einstein did base his theory on the time he spent dressed up like this, he used maths and logical reasoning. You on the other hand claim your "playing Indian" PhD makes you better than every other scientist on the planet.. so it's not an accurate comparison. Everything you say turns out to be a misreprentation of the facts, an invalid conclusion from the data or just a plain outright lie.
@terry:You'll have to remind me of which paper the chart is in
He's talking about Figure S9.1 in the Supplementary Info of the same paper you linked to. It's a version of Extended Data Figure 1 (page 8 in your PDF) that gives separate scores for each of the African and non-African populations samples represented by the range bars in EDF 1.
His interpretation is basically a marketing trick - using the word "closest" to imply some form of similarity between two very disparate populations. In reality, despite their position at the bottom of the non-African cluster making them technically "the closest" to the next highest-scoring population, Amerindians are very close to other non-Africans, and not close to Denisovans at all.
What's really interesting is that he continues to use this figure as evidence Amerindians had a Denisovan-like demographic history despite it being obvious that it's totally untrue... do you think he's actually fallen for his own trick here? Or has it just worked before so he's going to keep trying it over and over even though we've seen through it?
@Tobus
"You can repeat that mantra as much as you like, but it won't change the facts: Denisovans and Neanderthals are *NOT* the the closest populations to Amerindians. The populations that are closest to Amerindans (and hence best represent Amerindian demographics) are Papuans and Eurasians."
Yes, I will repeat what is a fact: Amerindians are the closest among modern humans to Denisovans and Neandertals. You can keep denying it and misrepresent my statements (committing a strawman fallacy) but this doesn't change the fact.
"Trying to insinuate associations where no associations exist might be good marketing, but it's bad science."
Trying to deny facts is a typical creationist strategy, but it's a bad practice when it comes to science. We can talk about marketing at a different blog.
"I accept the science"
Sure, a creationist can say this, too, when it suits him. Listen to the recent Nye-Ham debate.
"PhD makes you better than every other scientist on the planet.. so it's not an accurate comparison. Everything you say turns out to be a misreprentation of the facts, an invalid conclusion from the data or just a plain outright lie."
I haven't misrepresented anything. And I don't lie. I do have two doctorates. I didn't know I needed three. For a breakdown of specific competencies see here http://anthropogenesis.kinshipstudies.org/sample-page/.
"Then furnish it again, it must have been lots in all the self-aggrandisement and bullying behaviour."
Go back to the string and memorize all the facts about "human origins" that I've brought up. What you misinterpret as "self-aggrandizement and bullying behavior" are just facts about you as a science denier and unethical commenter.
"Trying to insinuate associations where no associations exist might be good marketing"
No surprises there. That is what German's training has set him up for.
"Then furnish it again, it must have been lots in all the self-aggrandisement and bullying behaviour".
Like you, I don't remember any 'data' German has supplied. There you go, German. Let's have a scientific paper that supports your belief. Just one will do.
"Everything you say turns out to be a misreprentation of the facts, an invalid conclusion from the data or just a plain outright lie".
Amen. How's that for a creationist comment?
@TerryT
"You'll have to remind me of which paper the chart is in>"
We were referring to Prufer Fig. S9.2, S10.10 and some others.
"But you're claiming Amerindians have 'the most' Denisovan ancestry. Clearly that is not correct."
You need to read what people write and follow the conversation closely. I wrote "It's true that Papuans and Australian aborigines share more alleles with Denisovans than Amerindians (but Amerindians have more Denisovan ancestry than, say, Han, Europeans or Africans)." But in terms of "intergroup diversity" Amerindians are the closest to Denisovans and Altai Neandertals compared to other human populations. The two metrics must be related as both of them, in very general terms, contrast Africans and Europeans, on the one hand (the least Denisovan, the least Neandertal, the least intergroup diversity) and Amerindians/Papuans as most Neandertal, most Denisovan, with most intergroup diversity. Amerindians and Papuans are also the two groups with highest linguistic diversity, while Africans and Europeans are the least diverse linguistically. Pretty neat picture!
@TerryT
"Obviously they formed earlier on the haplogroup tree. Where's you problem? "
They are not found outside of Africa along the putative ancient routes of the colonization of the world by modern humans. But they are found aplenty among African Americans, which represent the only clear out-of-Africa migration.
"Waht is 'creationist' about out of Africa?"
It's not easy to find someone in the blogosphere who's more feeble-minded than you, Terry. There's nothing creationist about out-of-Africa per se, just like there's nothing fundamentalist about the Bible, but when people turn it into a dogma and refuse to test it against data, then they exhibit creationist behavior.
"Yes, again showing they are more ancient."
What makes them automatically "modern" human in the absence of direct DNA evidence from "archaic" hominins in Africa? They were created modern ex nihilo by God, weren't they, Padre?
"Yes, and we can tell from that there has been a movement back into Africa from Eurasia. Once more, what's your problem?"
The absence of any evidence for a migration out of Africa and the presence of such evidence for out-of-Asia-into-Africa.
"But your apparent lack of any biological knowledge, including evolutionary biology and genetics, renders you impotent with regard to your claim."
Evolutionary theory and population genetics are part of anthropological education.
"If the 'African archaics', as you call them, are completely interfertile with modern humans they are the same species."
The overall lineage encompassing Neandertals, Denisovans, those African "archaics" and modern humans was capable of interbreeding. Just like today's indigenous Amerindians and immigrant African Americans can interbreed, so modern humans from Asia interbred with African "archaics." And we have paleobiological evidence for such interbreeding. What is your problem?
'He's talking about Figure S9.1 in the Supplementary Info'
'What's really interesting is that he continues to use this figure as evidence Amerindians had a Denisovan-like demographic history despite it being obvious that it's totally untrue... do you think he's actually fallen for his own trick here? Or has it just worked before so he's going to keep trying it over and over even though we've seen through it?'
The figure shows that Amerindians are most reminiscent of a period that human groups were less heterozygous than nowadays. Africans don't comply to this picture at all, what may be the result of extensive admixture and more hominine lineages involved. If this can be comfirmed, a completely different picture emerges of modern human evolution. Departing from human (family) groups as homozygous as Neanderthal and Denisovans, then Amerindians were an early split-off from the human hybrid gene-pool. Amerindian homozygosity, though, is not high enough to deny a dual origin, hence also the considerable difference though being "closer". However, it's low enough to consider a quite early split-off, Eurologist's ~35 kya being a good shot.
A pity MA-1 and Anzick are not on the picture, to possibly exclude forthcoming East-Asian admixtures in case their heterozygosity was indeed even lower.
BTW., remarkable is also the Australian's higher heterozygosity than Papuans, most probably confirming the suggested Holocene admixtures from India in Australia. Papuan higher heterozygosity than Amerindians indicates that hybridization remained an important element in the process towards modernity ever since this 35 kya estimate, everywhere. Intermediate Eurasian figures for Dai/Han and French/Sardinians may reveal the gravity of this admixture process in the non-African world.
@German:
I will repeat what is a fact: Amerindians are the closest among modern humans to Denisovans and Neandertals. You can keep denying it and misrepresent my statements (committing a strawman fallacy)
Are you or are you not using this technical fact to imply Amerindians had a demographic structure more similar to Denisovans than to modern humans? (Because on March 5 you said: "these values are exceeded by such populations as Denisovans and Altai Neandertals suggesting that Amerindians followed by Papuans have a demographic structure closest to Mid-Pleistocene hominins... those values were much higher prior to the admixture and probably matched Denisovans and Altai Neandertals much more closely").
If not, how is your "closest" observation relevant to the discussion of relatively low Amerindian heterozygosity indicating relatively low internal admixture?
Trying to deny facts is a typical creationist strategy, but it's a bad practice when it comes to science
So do you accept or deny that modern Eurasians better represent Amerindian heterozygosity (and hence demographic structure) than the archaics do?
@Rokus:
Departing from human (family) groups as homozygous as Neanderthal and Denisovans, then Amerindians were an early split-off from the human hybrid gene-pool.
Effective population estimates for Neanderthal and Denisovans are in the low thousands whereas estimates for sapiens surpassed this well before leaving Africa, reaching 100,000+ before the suggested 32kya Amerindian divergence. So I doubt that modern humans were as homozygous as Neaderthals and Denisovans at any time in Eurasia.
BTW., remarkable is also the Australian's higher heterozygosity than Papuans, most probably confirming the suggested Holocene admixtures from India in Australia.
I think it's also likely that Australians admixed within themselves to a much larger degree than Papuans. Australians live on a big flat plain that is easily traversed and the lack of linguistic diversity indicates they were not isolated. Papuans live in isolated mountain villages and are the most linguistically diverse population on earth. It seems logical that admixture (genetic exchange) and language (cultural exchange) would follow a similar distribution pattern... Amerindians fit with this low admixture/lots of languages correlation.
#Tobus
"His interpretation is basically a marketing trick - using the word "closest" to imply some form of similarity between two very disparate populations. In reality, despite their position at the bottom of the non-African cluster making them technically "the closest" to the next highest-scoring population, Amerindians are very close to other non-Africans, and not close to Denisovans at all.
What's really interesting is that he continues to use this figure as evidence Amerindians had a Denisovan-like demographic history despite it being obvious that it's totally untrue... do you think he's actually fallen for his own trick here? Or has it just worked before so he's going to keep trying it over and over even though we've seen through it?"
Of course, all creationists think of "scientific evidence" as a "trick." And scientists as "tricksters." Bur the fact remains that among all modern humans populations, Amerindians are the closest to Denisovans and Altai Neandertals. Africans are the most removed.
@Rokus
"The figure shows that Amerindians are most reminiscent of a period that human groups were less heterozygous than nowadays. Africans don't comply to this picture at all, what may be the result of extensive admixture and more hominine lineages involved. If this can be comfirmed, a completely different picture emerges of modern human evolution. "
Exactly. Virtually the same data is reported in Table S36 in http://www.sciencemag.org/content/suppl/2012/08/29/science.1224344.DC1/Meyer.SM.pdf
"Departing from human (family) groups as homozygous as Neanderthal and Denisovans, then Amerindians were an early split-off from the human hybrid gene-pool. Amerindian homozygosity, though, is not high enough to deny a dual origin, hence also the considerable difference though being "closer". However, it's low enough to consider a quite early split-off, Eurologist's ~35 kya being a good shot."
It's better than the current consensus but not old enough IMO. But it's close to the emergence of modern humanity in the world archaeological record at 50-40,000 years ago, so we're getting close. BTW, Hadza in Africa will probably be the only African population that would fall in the area of Amerindians, Papuans and Australians. And by some counts they are considered to be the most divergent linguistically in the oldest African language family, Khoisan.
@Tobus
"Are you or are you not using this technical fact to imply Amerindians had a demographic structure more similar to Denisovans than to modern humans? (Because on March 5 you said: "these values are exceeded by such populations as Denisovans and Altai Neandertals suggesting that Amerindians followed by Papuans have a demographic structure closest to Mid-Pleistocene hominins... those values were much higher prior to the admixture and probably matched Denisovans and Altai Neandertals much more closely"). "
This is exactly what the data suggests: "Amerindians followed by Papuans have a demographic structure closest to Mid-Pleistocene hominins." Among modern human populatiosn, Amerindians are the closest to mid-Pleistocene population realities than modern Africans, hence Zhivotvsky, at Cavalli's suggestion, used them as a model for an African ancestor.
Just let go of it already. Another biased attempt to shoot down a perfectly fine model.
"those values were much higher prior to the admixture and probably matched Denisovans and Altai Neandertals much more closely" - this referred to the idea that Amerindians used to be even closer to Denisovans and Neandertals but internal admixture drove their intergroup values down.
"Papuans live in isolated mountain villages and are the most linguistically diverse population on earth."
Amazonian Indians are strictly speaking the most linguistically diverse because they count the greatest number of isolates. But for all practical purposes New World is most diverse.
"Australians live on a big flat plain that is easily traversed and the lack of linguistic diversity indicates they were not isolated. "
Australia was geologically conjoined with PNG, so its homogeneity is just like the homogeneity of northern North America covered with Na-Dene languages. Definitely a pre-agricultural, Holocene language expansion but it needs to be considered as part of the Sahul linguistic zone.
"Effective population estimates for Neanderthal and Denisovans are in the low thousands whereas estimates for sapiens surpassed this well before leaving Africa."
This interpretation is precisely the one being questioned. So don't use it as a fact. As the Hadza example demonstrates, modern Africans used to be more like Amerindians, but then hominin admixture likely kicked in.
@German:Among modern human populatiosn, Amerindians are the closest to mid-Pleistocene population realities than modern African
Sorry German but you failed to answer the question... are you saying that this "closest" relationship means that Amerindians had a demographic structure more like Denisovans than like modern Eurasians?
This interpretation is precisely the one being questioned. So don't use it as a fact.
I'll refer you to Atkinson 2008 Fig. 2. It's a fact.
"do you think he's actually fallen for his own trick here? Or has it just worked before so he's going to keep trying it over and over even though we've seen through it?"
I think he just refuses to accept the most obvious explanation because he wants to believe Amerindians represent the 'earliest' human population in spite of the mountain of evidence to the contrary. He has this huge desire to be 'different'.
"Australia was geologically conjoined with PNG"
Probably not actually. The two regions are remarkably different from what we would expact if they had actually been joined for much of prehistory.
"Go back to the string and memorize all the facts about 'human origins' that I've brought up".
What facts'? I don't recall a single relevant fact you have brought up. Just misrepresentations of data from various papers. I again invite you to provide a link to a single scientific paper that supports your belief.
"You need to read what people write and follow the conversation closely. I wrote 'It's true that Papuans and Australian aborigines share more alleles with Denisovans than Amerindians (but Amerindians have more Denisovan ancestry than, say, Han, Europeans or Africans)'".
Surely that means Papuans and Australian aborigines have more Denisovan admixture than do any other modern human population, including Amerindians. Something you continually deny.
"But in terms of 'intergroup diversity' Amerindians are the closest to Denisovans and Altai Neandertals compared to other human populations".
which has nothing at all to with whether they have significant Denisova/Neanderthal admixture at all, or not. That 'intergroup diversity' obviously developed in America, after they arrived there.
"They are not found outside of Africa along the putative ancient routes of the colonization of the world by modern humans".
Give me one valid reason why they should be.
"Evolutionary theory and population genetics are part of anthropological education".
Obviously a very inadequate part.
"It's not easy to find someone in the blogosphere who's more feeble-minded than you, Terry".
You are providing me with very close competition.
@Tobus,
'Effective population estimates for Neanderthal and Denisovans are in the low thousands whereas estimates for sapiens surpassed this well before leaving Africa, reaching 100,000+ before the suggested 32kya Amerindian divergence.'
Effective population estimates never took into consideration hybridization processes, and so far were never substantiated by paleogenetic evidence. Why effective population sizes would be so different without major cultural differences before the Upper Neolithic?
@Rokus:Why effective population sizes would be so different without major cultural differences before the Upper Neolithic?
There were obviously major differences (cultural or otherwise) because modern humans were expanding in size and territory while the Neanderthals were dwindling... the simplest answer is that modern humans were better adapted to environmental conditions/disease/inter-species warfare, etc.. If things had been equal there'd still be Neanderthals around today.
Interesting site. Well, seeing as these have to be approved I have a few questions for the moderator... who I'm assuming is the 'actual guy'.
Interesting these days to be able to offer an opinion or explain things from our point or view. I can see there's quite a difference between what happened in the US as opposed to Canada. The US has a lot of crazy beliefs that resulted in unneeded laws and I can see why they're not open to dna tests, etc.
Down there they seem to be very 'rare' and limited to certain areas but in Canada we're all over the place with a rapidly growing population. So, on behalf of North American Natives we honestly thought all this dna stuff was done a long time ago. Plus so many skeletons ended up all over the world we kind of thought they would've had whatever they needed.
Just within the last year too I see world history has almost been completely rewritten what all this Denisovan/Neanderthal/Mal'ta boy/Clovis stuff. I heard "white people" didn't even become white until recently too, hehe. I only mention it because that was the whole point of all these crazy beliefs (Solutrean, Kennewick, etc etc), that they were white.
Anyway, I'm a Native guy from Canada, specifically "Ojibway". All this stuff is very confusing to any average joe and I'm no different. I don't suppose you could tell me something about Ojibway people?
I see there were 3 migrations apparently and if I'm reading things right Ojibway people are descendants of the first wave. Is that right? To be honest I just want to know if Ojibway people related to this Clovis boy, are we?
Finally, from what I've read on sciencedaily not too long ago, the Native American "genome" was around by at least 22,000 BC but it didn't start moving into the Americas until about 13,000 BC.
What does this mean exactly? Does it mean what I think it means and Native Americans are actually much older than people realize? When/where (approx) did we actually genetically become Native American?
(btw I hope this shows up right cause it doesn't look right in the preview)
@Tobus
" are you saying that this "closest" relationship means that Amerindians had a demographic structure more like Denisovans than like modern Eurasians?"
I understand that chart reading is not your skill but this is the correct answer: Amerindians are closer to Denisovans than Papuans and East Asians, even closer than Europeans and much closer than Africans. Out of all the modern human populations, Amerindians are the closest to Denisovans on all the referenced charts.
"I'll refer you to Atkinson 2008 Fig. 2. It's a fact."
This study is outdated, as it didn't use any data from Eurasian hominins and for African hominins we don't have any data, only simulations.
"Finally, from what I've read on sciencedaily not too long ago, the Native American 'genome' was around by at least 22,000 BC but it didn't start moving into the Americas until about 13,000 BC. What does this mean exactly? Does it mean what I think it means and Native Americans are actually much older than people realize? When/where (approx) did we actually genetically become Native American?"
It is 'presumed' that the population that became the first Americans became isolated in Beringia for some time after it had formed from a mix of East Asian and Central Eurasian populations and before they actually entered America. I guess we can imagine them as being 'genetically Native American' while isolated in Beringia from 22,000 BC even though they didn't actually enter America until 13,000 BC.
Tobus,
'There were obviously major differences (cultural or otherwise) because modern humans were expanding in size and territory while the Neanderthals were dwindling... the simplest answer is that modern humans were better adapted to environmental conditions/disease/inter-species warfare, etc.. If things had been equal there'd still be Neanderthals around today.'
Actually, I meant to say above that effective population sizes wouldn't be so different without major cultural differences before the Upper Paleolithic, although the most obvious departure from Mid-Paleolithic (early Late Pleistocene) hunter-gatherer family groups - and low effective population sizes - only happened since the Neolithic.
IMO this suggests that hybridization/mixture must have played a far greater role in the origin of modern heterozygosity than mere HSS-confined population growth.
So far the fossils 'indicate that the appearance of modern human biology in portions of western and eastern Eurasia occurred in the early Late Pleistocene, long before the appearance of Upper Paleolithic (sensu lato) behavioral complexes' (Liu et al., 2010). Shen et al. (2002) couldn't tell HSS apart either, but suggested 'a possible coexistence in China of two distinct hominid populations or species in the late Middle Pleistocene or early Late Pleistocene.'
@German:I understand that chart reading is not your skill but this is the correct answer: Amerindians are closer to Denisovans than Papuans and East Asians
Perhaps you need to look at the chart again - Amerindians are only slightly below Papuans and East Asians but are a very long way from Denisovans. Thus Amerindians had a demographic structure much more similar to other non-Africans than to Denisovans.
You're using marketing-spin logic again. Amerindians may technically be the best example we could use for Denisovans (albeit still a very poor one), but Denosivans are no where near the best example we can use for Amerindians - modern Eurasians are much, much better.
@Rokus: IMO this suggests that hybridization/mixture must have played a far greater role in the origin of modern heterozygosity than mere HSS-confined population growth.
I think you are correct to some degree, but internal hybridization/mixture between the various HSS groups was more widespread than between HSS groups and archaics. IIRC the Stuttgart sample has a much higher heterozygozity than modern Europeans while Loschbour's is much lower even than Karitiana. This suggests to me that modern heterozygosity is more a result of continuous HSS "intrabreeding" than of isolated HSS/archaic interbreeding, although both would obviously be factors.
@Tobus
"Perhaps you need to look at the chart again - Amerindians are only slightly below Papuans and East Asians but are a very long way from Denisovans. Thus Amerindians had a demographic structure much more similar to other non-Africans than to Denisovans.
You're using marketing-spin logic again. Amerindians may technically be the best example we could use for Denisovans (albeit still a very poor one), but Denosivans are no where near the best example we can use for Amerindians - modern Eurasians are much, much better."
No, you are biased and prone to spreading negative publicity when you can't defend your beliefs with logic and facts. Amerindians are the closest to Denisovans among modern humans, and the rest of non-Africans haven't moved too far from the Amerindian baseline among modern humans.
@German: No, you are biased and prone to spreading negative publicity when you can't defend your beliefs with logic and facts
Fact: Modern Eurasians are much closer to Amerindians in Prufer's graph than Denisovans are.
Logic: Therefore modern Eurasians provide a much better example of Amerindian demographic history than Denisovans.
Case closed?
@Tobus
"Fact: Modern Eurasians are much closer to Amerindians in Prufer's graph than Denisovans are.
Logic: Therefore modern Eurasians provide a much better example of Amerindian demographic history than Denisovans. Case closed?"
You are so naive! You are trying to sell me another piece of flawed logic and sincerely want me to buy it. I wish your arguments evolved beyond a sales pitch.
Fact: Modern Amerindians are the closest to Denisovans (an ancient sample!) among modern human populations. They are the least removed from the Mid-Pleistocene demographic reality.
Conclusion: Modern humans evolved from an Amerindian-like demographic structure. Modern Eurasian and African demographic structures are progressively derived from an Amerindian-like ancestral prototype. Amerindians provide the best example of Eurasian and African demographic history.
Case closed.
@German: Amerindians provide the best example of Eurasian and African demographic history.
.. and vice versa, the point being that Denisovans don't. Agreed?
@Tobus
".. and vice versa, the point being that Denisovans don't. Agreed?"
Wrong again. Why can't you get it right after trying for an umpteenth time?! If you look at S9.1., p. 67 in Prufer, you'll see that Karitiana are roughly equidistant from Denisovans/Altai Neandertals and San on a heterozygosity scale (or even a little closer to Denisovans than to San). Denisovans is an ancient hominin species in geographic proximity to the New World. History goes from past into future. So, Denisovans support the antiquity of the Amerindian demographic structure compared to other modern human populations. San demography evolved from an Amerindian-like demography
@ German:
"Modern humans evolved from an Amerindian-like demographic structure".
I remember trying to point out your failure of logic the very first time I read anything of yours at anthropolgy.net. You are still amking the same wrong assumptions. Yes, ancient human demographic structure may well survive best in Amerindian and Australian Aborigine societies. But that doesn't mean at all that those societies are the ancestral source. They are merely the last surviving remants of a once widespreaqd social structure.
"Modern Eurasian and African demographic structures are progressively derived from an Amerindian-like ancestral prototype".
Quite possibly true. Those societies have changed. Amerindian and Australian Aborigene societies have not, or have changed to a much lesser extent.
"Amerindians provide the best example of Eurasian and African demographic history".
The best 'surviving' example of Eurasian and African demographic history. That is far from being the same as 'Eurasian and African demographics derive from Amerindian demographics'.
@German:So, Denisovans support the antiquity of the Amerindian demographic structure compared to other modern human populations. San demography evolved from an Amerindian-like demography
Correlation is not causation German, and especially not arbitrary correlations like this one. I figure your humanities training didn't teach you this, but you know now so how about you stop making the same mistake over and over.
In this case Denisovans aren't directly ancestral to modern humans - Tianyuan, Ust-Ishim or even MA-1 are better examples of modern human demographic history than Denisovans ever could be. Since modern East Asians and other non-African populations are much closer to modern Amerindians in both heterozygosity and age, you need to explain Amerindian demographic structure in terms of other modern Eurasians, not in terms of an archaic population that only made a marginal contribution to Amerindians. Remember you are supposedly explaining how East Asians were the same population as Amerindians at the time of the MA-1 sample yet don't share any of the DNA this ancestral population supposedly gave to him.
@Tobus
"Correlation is not causation German, and especially not arbitrary correlations like this one. I figure your humanities training didn't teach you this, but you know now so how about you stop making the same mistake over and over."
I know you've picked up the "correlation vs. causation" distinction somewhere but you haven't learned how to apply it. This distinction is not even relevant here.
"Since modern East Asians and other non-African populations are much closer to modern Amerindians in both heterozygosity and age, you need to explain Amerindian demographic structure in terms of other modern Eurasians, not in terms of an archaic population that only made a marginal contribution to Amerindians."
Nonsense. We are trying to understand the origin of all modern humans, not just Amerindians. You are creating an artificial problem. A degree in any academic field - humanities or sciences - would help you overcome this intellectual disorder. Considering that East Asians and West Eurasians haven't contributed any ancestry to Amerindians but drew ancestry from it, a shift to Denisovans and Altai Neandertals is a natural solution. A marginal contribution is better than no contribution.
"Remember you are supposedly explaining how East Asians were the same population as Amerindians at the time of the MA-1 sample yet don't share any of the DNA this ancestral population supposedly gave to him."
Can you rephrase it? I don't even know what you are referring to?
@German:
This distinction is not even relevant here.
Yes it is. You've picked an arbitrary (and marginal) "correlation" and then assumed a "causation" that decreased heterozygosity must indicate order of ancestry. There are many reasons (lack of admixture for example) that could cause one contemperaneous population to exhibit a lower heterozygosity than another. This is a pattern of thinking I've observed in you a number of times now - you jump to a conclusion that a single theory must be the sole "cause" without giving due consideration to other possibilities... you go straight to "must be" when it's really only "might be", and often the other "might be"s are more plausible and fit with other data that your "must be" is rejected by. Prufers chart in no way proves that "San demography evolved from an Amerindian-like demography".
Consider also that the Loschbour sample shows an estimated population size that is much lower than Amerindians and thus much closer to Denisovan population structure (Laziridis 2014 EDF2) - are you going to drop OOAm and sign up to OOEu now? Or are you going to posit alternative explanations for why a population may exhibit a "closeness" to Denisovans in this regard and then fail to apply it Amerindians in your own reasoning?
Considering that East Asians and West Eurasians haven't contributed any ancestry to Amerindians but drew ancestry from it,
Well if that's you're starting assumption it's no wonder you're so mixed up.
I don't even know what you are referring to?
Short memory hey? You posited this supposed similarity with Denisovan population structure to explain the lack of heterozygosity in what you proposed was a deeply diverged and then throughly admixed Amerindian population. Since it's clear from the data that modern Amerindians, East Asians, Oceanians and Europeans all share a very similar demographic history compared to the ancients, this explanation falls short and you are back at square one - unable to explain the lack of East Asian affinity in MA-1 under a scenario where he received admixture from the closest living relative of East Asians, and not the other way round.
@Tobus
"In this case Denisovans aren't directly ancestral to modern humans - Tianyuan, Ust-Ishim or even MA-1 are better examples of modern human demographic history than Denisovans ever could be."
From the little we know about Ust-Ishim, it falls next to Karitiana on the scale of Neandertal admixture LD (http://dienekes.blogspot.com/2014/04/svante-paabo-talk-at-nih.html). The continuum is exactly the same as the heterozygosity continuum in S9.1., p. 67 in Prufer: Ust-Ishim > Karitiana > Han > Dai > Europeans. Understandably, Ust-Ishim is 45,000 years older than Karitiana, hence it has longer chunks of Neandertal DNA but out of all the modern human populations Karitiana is next. 45,000 years ago Karitiana was likely even more Neandertal-like than Ust-Ishim, although it's of course hard to say for sure. (Just ignore Paabo's claim that by the extent of LD you can measure the time to the admixture event, since clearly, if recent out-of-America were true, Karitiana would've been the most removed from Ust-Ishim in terms of "generations" but in fact it's the closest to it, which means LD decay doesn't work in a clockwork fashion but instead reflects extent of inbreeding and population size.
@ Tobus:
"Remember you are supposedly explaining how East Asians were the same population as Amerindians at the time of the MA-1 sample yet don't share any of the DNA this ancestral population supposedly gave to him".
You're again wasting your time. German has carefully avoided explaining that problem away, because he can't. He has found he can convince enough people to satisfy his ego if he just ignores the huge difficulties with his belief.
@ German:
"I don't even know what you are referring to?"
Really???
"A degree in any academic field - humanities or sciences - would help you overcome this intellectual disorder".
It obviously hasn't been so in your case.
"We are trying to understand the origin of all modern humans, not just Amerindians".
But you always carefully avoid considering any non-American human population except for those that show some small level of affinity with them. You next proceed to ignore all evidence from those non-American populations that contradict your belief. How can that possibly lead to an understanding of 'the origin of all modern humans'? It doesn't even help in understanding the origin of Amerindians.
"Considering that East Asians and West Eurasians haven't contributed any ancestry to Amerindians but drew ancestry from it"
How can that possibly be so? East Asians and West Eurasians are far more different from each other than are any two populations within America, and yet you insist that this relatively homogeneous America population gave rise to two completely different Eurasian populations. If you had even the slightest knowledge of genetics or evolution you would immediately see that what you're proposing is a crock of s..t.
"you jump to a conclusion that a single theory must be the sole 'cause' without giving due consideration to other possibilities..."
No, no, no. Not correct at all. The explanation is far simpler. German has a belief, and simply ignores any evidence that proves beyond doubt that this belief is incorrect. In contrast he jumps immediately on any evidence capable of being distorted enough that he can interpret it as 'proving' his belief. He has it all back to front if he wants to consider himself a 'scientist'.
"you go straight to 'must be' when it's really only 'might be'"
That's because the amount of 'evidence' capable of supporting his belief is so very minute he is forced into the 'must be' position. It would not advance his belief at all if he just offered the 'might be' position.
"Or are you going to posit alternative explanations for why a population may exhibit a 'closeness' to Denisovans in this regard and then fail to apply it Amerindians in your own reasoning?"
Consistency has never been German's strong point.
@Tobus
"You've picked an arbitrary (and marginal) "correlation" and then assumed a "causation" that decreased heterozygosity must indicate order of ancestry."
Nonsense. The distinction is not appropriate because everything that we have in human origins research is correlational until we test it. Then something becomes causational, something becomes falsified. Out-of-Africa posited that the decline in heterozygosity from Africa to America means a serial bottleneck out of Africa. Why don't you go ahead and accuse the out-of-Africa believers in admitting a confusion between correlation and causation. But you seem to endorse the out of Africa model. My case is different: Denisovan, Ust-Ishim and Altai Neandertals are ancient populations and they all show a profile, which among modern populations is best represented by Karitiana. There's no correlation vs. causation confusion here. It's a logic of historical reconstruction. You test it further against more ancient samples but you don't question it on spurious incredulity grounds, while creating a double standard for hypothesis evaluation.
"Prufers chart in no way proves that "San demography evolved from an Amerindian-like demography"."
It's a model to be tested against other data. Hadza, for instance, is a unique population in Africa that leans toward Amerindians on the heterozygosity scale and they speak the most divergent Khoisan language. This supports my inference that San demography evolved from an Amerindian-like demography.
"Consider also that the Loschbour sample shows an estimated population size that is much lower than Amerindians and thus much closer to Denisovan population structure (Laziridis 2014 EDF2)."
Yes, that's interesting. I would need to see other metrics for Loschbour, including Fst, LD, heterozygosity, etc. But as you notice Stuttgart is the most removed from Amerindians among ancient Eurasian samples and it has the largest eff pop size values suggesting that Eurasian history involved a transition from more Karitiana-like demography to more African-like demography, in refutation of the serial bottleneck out of Africa model.
"Or are you going to posit alternative explanations for why a population may exhibit a "closeness" to Denisovans in this regard and then fail to apply it Amerindians in your own reasoning?"
We need to see them plotted together and add Anzick into the mix. My prediction is that Anzick which is just 2,000 years older than Loschbour will be closer to Denisovans.
"Well if that's you're starting assumption it's no wonder you're so mixed up."
No, that's the most parsimonious interpretation of the data.
"unable to explain the lack of East Asian affinity in MA-1 under a scenario where he received admixture from the closest living relative of East Asians, and not the other way round."
You are just utterly confused! I've explained it multiple times already - the Amerindian component in MA-1 IS the ancient East Asian "component." You have West Eurasian, Papuan, South Asian and Amerindian-as-ancient-east-Asian components in MA-1. Everything is very normal. Modern East Asians are derived from the Amerindian-as-ancient-East-Asian component in post 24,000 years times. Modern East Asians don't have the West Eurasian component that MA-1 has.
@German: From the little we know about Ust-Ishim
I'm going to wait till I can read the full Ust-Ishim paper before trying to interpret what it means... and no offense, but I certainly won't be ignoring what Paablo says in preference to what you say, PhD in pretending to be Native American or not.
So back to the topic, you've proven that Amerindian demographic structure is similar to that of other modern humans, ruling out a theory of deep divergence and subsequent admixture... do you have another explanation or are you ready to accept that Amerindian gene flow into MA-1 is an impossibility given the pattern of modern and ancient genetic affinities?
@Tobus
"I'm going to wait till I can read the full Ust-Ishim paper before trying to interpret what it means... and no offense, but I certainly won't be ignoring what Paablo says in preference to what you say, PhD in pretending to be Native American or not."
Just look under the hood of my credentials: http://anthropogenesis.kinshipstudies.org/sample-page/. You write your thesis but it doesn't reflect the actual range of work that you've done. Now look at the data presented by Paabo and think for yourself: modern Karitiana has the fewest number of "generations" elapsed since the admixture event with Neandertals. Only Ust-Ishim has fewer generations to admixture event. Ust-Ishim is 45,000 years old according to C14. Unless there were Neandertals greeting future Amerindians at the entry to the Americas 15,000 years ago, "molecular clock" clearly is at fault because different populations have a different demographic structure and a different rate of admixture LD decay. Paabo has a history of making mistakes about human origins because you can't just be a lab geneticist - as great as you are at that - if you are in the business of human origins. You need to have a more well-rounded education and a bullshit detector. My research into American Indian reenactors has taught me the latter.
"you've proven that Amerindian demographic structure is similar to that of other modern humans, ruling out a theory of deep divergence and subsequent admixture... do you have another explanation or are you ready to accept that Amerindian gene flow into MA-1 is an impossibility given the pattern of modern and ancient genetic affinities?"
Another try to sell me your perverted logic. I've proven that Amerindians are the closest among modern human populations to Denisovans. Now I can prove that they are closer on the heterozygosity scale to Denisovans and Altai Neandertals than to Africans. See Table S2.2 in the latest Suppl Mat of Lazaridis. So we have proof of Amerindian deep divergence. But Amerindians still have higher heterozygosity than Denisovans and Neandertals. This suggests that they've admixed since their deep divergence. If Amerindians were a product of gene flow from two Eurasian populations with higher heterozygosity values than Amerindians (East Asians and West Eurasians), Amerindians would have been next to Africans and not next to Denisovans on the heterozygosity scale. So you are wrong, as always.
@Tobus
"PhD in pretending to be Native American."
One last thing on this. You can consider my book The Genius of KInship (http://www.amazon.com/The-Genius-Kinship-Phenomenon-Terminologies/dp/1934043656/ref=sr_1_1?ie=UTF8&qid=1397781382&sr=8-1&keywords=dziebel) as my third Ph.D. It introduces a multidisciplinary approach to human origins and outlines out-of-America as a new theory. It was peer reviewed by scholars from Stanford, Russia and the U.K. There's a Kindle version of it just in case your superior mathematical talents haven't put enough cash in your pocket to buy a physical copy.
@German:
I've proven that Amerindians are the closest among modern human populations to Denisovans. Now I can prove that they are closer on the heterozygosity scale to Denisovans and Altai Neandertals than to Africans. See Table S2.2 in the latest Suppl Mat of Lazaridis. So we have proof of Amerindian deep divergence.
1 + 1 = 5?? Proof of lower heterozygosity doesn't prove deep divergence. You're making the same "only consider one possibility" (ie. "correlation is not causation") mistake again. The pattern of Amerindian's low genetic diversity - a high level of microsatellite variation compared to heterozygosity - is inconsistent with a deep divergence and instead indicates a recent bottleneck followed by rapid expansion... a cause of low heterozygosity you have (deliberately?) failed to consider.
If Amerindians were a product of gene flow from two Eurasian populations with higher heterozygosity values than Amerindians (East Asians and West Eurasians), Amerindians would have been next to Africans and not next to Denisovans on the heterozygosity scale.
... unless of course Amerindians underwent a recent bottleneck since the admixture, and guess what! This is *exactly* what the genetic evidence indicates.
You can consider my book ... as my third Ph.D.
I could, by why would I? Nobody else does. You seem to think that having PhD's takes the place supplying facts and evidence for your claims - it doesn't! You could have 5 PhD's and still be wrong if the facts are against you. So please, no more appealing to your own authority, it doesn't prove anything and just makes you look like arrogant twerp.
"I certainly won't be ignoring what Paablo says in preference to what you say, PhD in pretending to be Native American or not".
I too am far more inclined to accept what Paabo says over what German beleives every time. In fact German's motives are clear: it is absolutely necessary he adopt that position otherwise he has to admit his belief is completely demolished. He even admits, 'since clearly, if recent out-of-America were true'. He is absolutely, religiously, committed to his strange belief. Not prepared for a moment to consider that perhaps out-of-America may not be true.
"One last thing on this. You can consider my book"
Ever the salesman.
@Tobus
"unless of course Amerindians underwent a recent bottleneck since the admixture, and guess what! This is *exactly* what the genetic evidence indicates."
How can genetic evidence "indicate" anything if it's based on an assumption that all the genetic evidence got lost (via a "bottleneck")? More pseudoscience from Tobus!
"Proof of lower heterozygosity doesn't prove deep divergence. You're making the same "only consider one possibility" (ie. "correlation is not causation") mistake again. The pattern of Amerindian's low genetic diversity - a high level of microsatellite variation compared to heterozygosity - is inconsistent with a deep divergence and instead indicates a recent bottleneck followed by rapid expansion... a cause of low heterozygosity you have (deliberately?) failed to consider."
Deep divergence is measured by Fst. This is precisely how divergence is measured. Fst tends to be world highest in America. Denisovans and Altai Neandertas are most homozygous on that list and they are more divergent from each other than Africans from Europeans. Your microsatellite sentence doesn't make sense.
"So please, no more appealing to your own authority, it doesn't prove anything and just makes you look like arrogant twerp."
As a science denier you obviously deny scientific credentials. And I'm just stating simple facts. And you need to start respecting facts, whatever they are.
"it doesn't prove anything and just makes you look like arrogant twerp".
I would have added 'egotistical'.
@German:
How can genetic evidence "indicate" anything if it's based on an assumption that all the genetic evidence got lost (via a "bottleneck")?
Yes German, every single gene got lost when Amerindians migrated into America. You do talk nonsense sometimes.
If you read Tishkoff (2009) she explains it in there - basically a population at equilibrium will have similar diversity estimate from macrosatellite variance as from heterozygosity. In a bottleneck scenario the heterozygosity is lowered more significantly than the microsatellite variance while conversely, in the absence of a bottleneck, heterozygosity increases faster than microsatellite variance as the population expands. So a comparison of these two measures of diversity can be used to indicate the demographic history of a population. Amerindians show a significantly higher diversity in their microsatellite variance than in their heterozygosity, something the could not happen without a significant and recent bottleneck event.
Your microsatellite sentence doesn't make sense.
It does make sense, you just don't understand it - read the source material and you'll get there.
What doesn't make sense if why you are using Denisovans and Neanderthals, who both diverged from the sapiens line well before 500kya and from each other well before sapiens evolved at 200kya, as a reference point for modern human genetics - especially for Amerindians who only diverged ~15kya? It's like discussing oranges and lemons in terms of coconuts and jellyfish.
As a science denier you obviously deny scientific credentials
Remember that pattern I detected? Here it is again - you just denied the scientifically verified conclusions of Tishkoff, and yet are calling *me* a "science-denier" when I haven't denied any scientifically accepted fact. You are committing the irrationality that you are falsely accusing me of.
And I'm just stating simple facts
Not "just". You are stating simple facts and them asserting a causal correlation between them. I have no issue with the verifiable facts (such as high Fst in Amerindians and low homozygosity in both Neanderthals and Denisovans), but your assertion that these are somehow related or causally connected to each other follows no scientifically proven or logically conclusive rationale... it seems like you're just connecting similar words without really understanding what those words mean in context, and then assigning causation based purely on correlation without considering other causes known to provide a similar effect.
@Tobus
"Yes German, every single gene got lost when Amerindians migrated into America."
This is nearly what you postulated. All of East Asian and West Eurasian heterozygosity got lost and Amerindians became as homozygous as Denisovans.
"will have similar diversity estimate from macrosatellite variance as from heterozygosity."
I'm not going to discuss Tishkoff et al. 2009. You're leadfrogging from one source to another. Whatever she wrote is already old and is not informed by any ancient DNA insights. The discrepancy between heterozygosity and microsatellite variation has nothing to do with the age of the bottleneck. Tishkoff just assumed that Amerindians are recently derived from Asia and then she retrofitted this cultural notion into an interpretation of a genetic pattern.
"What doesn't make sense if why you are using Denisovans and Neanderthals, who both diverged from the sapiens line well before 500kya and from each other well before sapiens evolved at 200kya, as a reference point for modern human genetics - especially for Amerindians who only diverged ~15kya? "
Yes, and the Earth is 6000 years old.
Amerindians didn't diverge 15 KYA ago. MA-1 proves that Amerindians are at least 24,000 years old. And we share genes with Denisovans and Neandertals, so they can be product of admixture or common descent. And Amerindian population structure is similar to those Eurasians "archaics." Ust-Ishim seems to show that Amerindians carry the longest chunks of Neandertal DNA among all modern populations.
"the scientifically verified conclusions of Tishkoff, and yet are calling *me* a "science-denier" when I haven't denied any scientifically accepted fact."
there's nothing in Tishkoff that's scientifically verifiable. The whole paradigm she worked in got undermined by ancient DNA evidence. And you continue to deny it reaching out for some increasingly outdated sources to prove a point.
"You are stating simple facts and them asserting a causal correlation between them. I have no issue with the verifiable facts (such as high Fst in Amerindians and low homozygosity in both Neanderthals and Denisovans), but your assertion that these are somehow related or causally connected to each other follows no scientifically proven or logically conclusive rationale... it seems like you're just connecting similar words without really understanding what those words mean in context, and then assigning causation based purely on correlation without considering other causes known to provide a similar effect."
We already finished talking about your spurious correlation vs. causation argument. Out-of-Africa, and not out-of-America is a perfect example of untested assumptions.
@Tobus
"If you read Tishkoff (2009) she explains it in there - basically a population at equilibrium will have similar diversity estimate from macrosatellite variance as from heterozygosity. In a bottleneck scenario the heterozygosity is lowered more significantly than the microsatellite variance while conversely, in the absence of a bottleneck, heterozygosity increases faster than microsatellite variance as the population expands. So a comparison of these two measures of diversity can be used to indicate the demographic history of a population. Amerindians show a significantly higher diversity in their microsatellite variance than in their heterozygosity, something the could not happen without a significant and recent bottleneck event."
No, I can't resist the temptation to punish you again, Tobus. Here's a quote from Tishkoff et al. 2009 (Suppl Mat):
"The ratios of θ inferred from variance and heterozygosity for the current dataset are shown in Fig. S3. The ratio of variance and heterozygosity is the largest in Native American and Papuan and Melanesian populations followed by East Asians, all with values greater than one, intermediate in most Europeans, Middle Easterners, and Indians, with values near one, and with values less than one in most African populations and a few Middle Eastern and European populations. This observation is consistent with previous findings, suggesting a strong bottleneck followed by a recent and rapid expansion in Native Americans and Australo-Melanesians, and expansion but lack of a recent strong bottleneck in Africans (S75, S77). Interestingly, the San and the Hadza hunter-gatherers have the highest ratio of variance relative to heterozygosity among almost all African populations, with a ratio value slightly greater than 1.0 (Fig. S3). The only African population with a larger ratio is the Dogon. The Hadza and San are also apparent outliers in the plot of θ inferred from heterozygosity shown in Fig. S2B. These results are consistent with relatively stable small population sizes in these hunter-gatherer
populations..."
Although for a cryptocreationist like you, all academic scientists are angels, clearly, Tishkoff is not particularly scientific in this instance. She holds a double standard for Amerindians vs. San. In the case of the former, she's talking about a recent bottleneck (thus recycling the cultural stereotype I'm debunking), in the case of the latter "stable small population sizes." But the underlying pattern is the same: San, Hadza and Dogon are the most Amerindian among Africans in their ration of heterozygosity to microsatellite variation, and they are postulated as the "most basal" among Africans and all of modern humans. Plus, Papuans are not known to go through a recent bottleneck but they follow Amerindians, so Tishkoff's logic is flawed on several counts.
So, basically, it's another confirmation that Amerindians best preserve an ancient demographic structure from which all other modern human demographies derive. Naturally, African hunter-gatherers are among the closest to Amerindians among all African populations.
"Plus, Papuans are not known to go through a recent bottleneck but they follow Amerindians, so Tishkoff's logic is flawed on several counts".
An example of what Locrian was talking about. Are you telling me that a completely representative sample of the ancient Sunda population crossed Wallace's Line to New Guinea? Surely if you had even the most basic biological knowledge you would immediately know the whole idea is ridiculous. In fact there is a rasonable amount of evidence that the New Guinea population has undergone several separate expansions, presumably following bottlenecks of some sort.
"MA-1 proves that Amerindians are at least 24,000 years old".
For the eleventy-twelfth time: no, it doesn't. It proves that a population like MA-1 provided part of the Amerindian genetic backgound.
"there's nothing in Tishkoff that's scientifically verifiable".
God reveals himself again.
@German:
All of East Asian and West Eurasian heterozygosity got lost and Amerindians became as homozygous as Denisovans.
Where on earth do you think I postulated that? It's *you* who keeps saying Amerindian heterozygosity is like Denisovans and *me* who points out that it's much, much more similar to other Eurasians than any of the ancients.
The discrepancy between heterozygosity and microsatellite variation has nothing to do with the age of the bottleneck. Tishkoff just assumed that Amerindians are recently derived from Asia and then she retrofitted this cultural notion into an interpretation of a genetic pattern.
Science-denier!! The relationship bewteen population demographics and the microsatellite/heterozygosity ration wasn't invented by Tishkoff and has been empirically confirmed. Read the paper!
And Amerindian population structure is similar to those Eurasians "archaics."
No... "closest" is not always "close". Amerindian population structure is nothing like the archaics and very similar to other modern Eurasians - check your Prufer data again.
there's nothing in Tishkoff that's scientifically verifiable.
Science-denier!! Funny how you said "Tishkoff et al is a good source." when I first brought it up, but now deny it when it fails to support your argument!
She holds a double standard for Amerindians vs. San.
You missed the bit where she says "This observation is consistent with previous findings" - Amerindians number in the millions and inhabit the largest land mass of any population ("rapid expansion") whereas the San number in the thousands and inhabit a very small region of Africa ("stable small population"). Unlike you, Tishkoff doesn't take a single measurement and attempt to divine the entire evolution of humanity from it - she combines it with other data and reaches a workable conclusion.
"Funny how you said 'Tishkoff et al is a good source.' when I first brought it up, but now deny it when it fails to support your argument!"
I'm sure you don't find that in the least bit surprising! That has been German's tactic all along.
@Tobus
"Where on earth do you think I postulated that? It's *you* who keeps saying Amerindian heterozygosity is like Denisovans and *me* who points out that it's much, much more similar to other Eurasians than any of the ancients."
Admixture drives heterozygosity up, bottleneck drives it down. Learn the basics!
"The relationship bewteen population demographics and the microsatellite/heterozygosity ration wasn't invented by Tishkoff and has been empirically confirmed. Read the paper!"
I read it and blogged about it a few years ago. They didn't confirm anything empirically. They assume that America was peopled early based on non-existent archaeological evidence and then they retrofit their data to illustarte this flawed assumption. But when they encounter the same situation in Africa, they invent a different scenario. Sorry, Padre, God is dead.
"No... "closest" is not always "close". Amerindian population structure is nothing like the archaics and very similar to other modern Eurasians - check your Prufer data again."
All the data at hand is consistent with the idea that Amerindians are the closest to Eurasian archaics in terms of their population structure than other modern human populations, and all the values plot nicely as a function of distance from America to Europe and Africa. But a science denier like you will obviously deny it.
"Science-denier!!"
No, a scientist who's better educated than any of the authors you are reading, who holds 2 doctorates from top schools and who published two peer-reviewed books, is disproving other scientists using hard evidence, superior logic and crisp research ethics.
"You missed the bit where she says "This observation is consistent with previous findings" - Amerindians number in the millions and inhabit the largest land mass of any population ("rapid expansion") whereas the San number in the thousands and inhabit a very small region of Africa ("stable small population"). Unlike you, Tishkoff doesn't take a single measurement and attempt to divine the entire evolution of humanity from it - she combines it with other data and reaches a workable conclusion."
No facts, just a hysterical fit from a powerless, ignorant and pseudonymous creationist Tobus.
@German:
No facts, just a hysterical fit from a powerless, ignorant and pseudonymous creationist
Funny, I could say the same thing about your post... and you completely failed to address the only relevant point: How does LB plot relative to Europeans on the Kartiana axis in EDF 5a?
"No, a scientist who's better educated than any of the authors you are reading, who holds 2 doctorates from top schools and who published two peer-reviewed books, is disproving other scientists using hard evidence, superior logic and crisp research ethics".
Proof, if any were needed, of what an arrogant, ignorant, egotistical toad you are.
@Tobus
"and you completely failed to address the only relevant point: How does LB plot relative to Europeans on the Kartiana axis in EDF 5a?"
How does it the only relevant point? The only relevant point in EDF 5a is that all Eurasians are Amerindian-shifted. LB is an ancient sample, so you can't even talk about it in terms of a "modern European cluster" because it predated it and the latter evolved from an LB-like population. As Lazaridis showed, LB falls with other ancient European samples in terms of its Amerindian affinity. That's another relevant point. But you've missed both and instead you've invented an illogical and ahistorical idea into which you're trying to fit the data.
"Funny, I could say the same thing about your post."
Sure you can. In a true creationist spirit, you just won't be able to adduce any evidence to bolster your claim.
@German:How does it the only relevant point?
Because it's all I'm arguing - that LB's Amerindian affinity is within the range shown by modern Europeans.
As Lazaridis showed, LB falls with other ancient European samples in terms of its Amerindian affinity.
The Lazaridis data actually shows that Stuttgart has significantly *LESS* MA-1 (and thus presumably Amerindian) than modern Europeans (EDT2), that La Brana has significantly less MA-1 and Amerindian than Loschbour who in turn has significantly less than Motala (SI14), and a similar pattern is seen with Aj58 in Skoglund (S13). So instead of "LB falling with other ancient Europeans", we actually see a wide range of MA-1 and Amerindian affinities across ancient Europe - much wider than in modern Europe, and ranging from less than modern Europeans to more than modern Europeans with LB at the lower end. LB's Amerindian affinity relative to other ancient samples doesn't preclude him from being in the same range as modern Europeans.
@Tobus
"Because it's all I'm arguing - that LB's Amerindian affinity is within the range shown by modern Europeans."
If this is what you're arguing, it's ahistorical because this affinity is ancient not Viking-age, hence it's either modern Europeans fall into the range circumscribed by an ancient cluster or it's nothing. But your original foray into your indefensible position stemmed from the desire to show that LB, MA-1 and Amerindians are related to each other as genetic "West Eurasians." So you decided to use modern West Eurasians as a paragon of West Eurasianness. I'm glad to see you walk away from this baloney into what is borne out by all the available facts, namely that LB, MA-1 and Amerindians share Amerindian affinity.
"The Lazaridis data actually shows that Stuttgart has significantly *LESS* MA-1 (and thus presumably Amerindian) than modern Europeans (EDT2), that La Brana has significantly less MA-1 and Amerindian than Loschbour who in turn has significantly less than Motala (SI14), and a similar pattern is seen with Aj58 in Skoglund (S13). So instead of "LB falling with other ancient Europeans", we actually see a wide range of MA-1 and Amerindian affinities across ancient Europe - much wider than in modern Europe, and ranging from less than modern Europeans to more than modern Europeans with LB at the lower end. "
This is a useful writeup. Keep up a good work. Stuttgart is still closer to Amerindians than to other ENA, per Lazaridis. So, ancient Europeans are related to Amerindians with or without MA-1, it seems.
@German:
If this is what you're arguing, it's ahistorical because this affinity is ancient not Viking-age, hence it's either modern Europeans fall into the range circumscribed by an ancient cluster or it's nothing
However you want to phrase it and however you want to explain it - this data shows LB has a shared drift with Amerindians that is within the range shown by modern Europeans... agreed?
This is a useful writeup. Keep up a good work.
Why thank you.
Stuttgart is still closer to Amerindians than to other ENA, per Lazaridis. So, ancient Europeans are related to Amerindians with or without MA-1, it seems.
Where do you get the notion that Stuttgart is "without MA-1"? The data only says she has *less* than modern Eurasians, not none at all.
Your conclusion seems premature - is there something I missed that suggests Stuttgart has less MA-1 than Amerindian/ENA?
@Tobus
"Where do you get the notion that Stuttgart is "without MA-1"? The data only says she has *less* than modern Eurasians, not none at all."
Lazaridis, version 1, p. 9: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans."
"However you want to phrase it and however you want to explain it - this data shows LB has a shared drift with Amerindians that is within the range shown by modern Europeans... agreed?"
No, LB is ancient sample and when plotted against another ancient sample it shows that LB's shared drift with Amerindians exceeds that of modern Europeans. EDF 5a is good as an overall picture of Amerindian admixture in Eurasia, ancient and modern, but not as a specific drill-down into the placement of individual ancient samples.
@German:
Lazaridis, version 1, p. 9: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans."
I see, you think MA-1 is included in "other eastern non-Africans"?
Look two lines higher where they define what "eastern non-Africans" means: "Eastern non-Africans
(Oceanians, East Asians, Native Americans, and Onge, indigenous Andaman islanders)"... note no MA-1. The raw data they made these conclusions from is in S12 (first version - S14 latest) - see the subsection called "Relationship of ancient samples to eastern non-Africans" and table S12.5 (S14.7), note how MA-1 is listed under "Ancient Eurasian", not "eastern non-African" (ENA) in this data.
LB is ancient sample and when plotted against another ancient sample it shows that LB's shared drift with Amerindians exceeds that of modern Europeans.
NO! The MA-1 axis shows shared drift with MA-1 not Amerindians!!
When LB is plotted against an ancient sample it shows LB's shared drift with that ancient sample, not with some other population. Shared drift with Amerindians is shown on the Karitiana axis.
@Tobus
"NO! The MA-1 axis shows shared drift with MA-1 not Amerindians!!"
Pseudoscientist still on the loose! It's shared drift with MA-1 AND Amerindians as the most MA-1-like modern population on the plot. MA-1 and Amerindians on the X axis are just like Sardinians and other Europeans on the Y axis.
"I see, you think MA-1 is included in "other eastern non-Africans"?"
The two seem to be the same in their relationship to Stuttgart. Comp.: 1)" "Eastern non-Africans are all more closely related to ancient hunter gatherers than to Stuttgart" (p. 97, latest Lazaridis); 2) "MA1 is closer to all European hunter-gatherers than to Stuttgart." (p. 92, latest Lazaridis); 3) "ENA share more alleles with MA1 than with Stuttgart" (p. 104); 4) "Loschbour and MA1 are symmetrically related to ENA (because they both lack Neolithic Near Eastern ancestry)" (p. 104); 5) "Stuttgart has a proportion of “Basal Eurasian” ancestry while Loschbour and MA-1 share the non-African>X>W drift for the entirety of their ancestry" (p. 104). But: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans."
Could you comb through those Lazaridis tables to find a number that supports that Stuttgart is closer to Amerindians than to MA-1 (because Amerindians are behind both Ancient North Eurasian and Basal Eurasian, while MA-1 is an ANE-only population)?
@German:
It's shared drift with MA-1 AND Amerindians
No, it's absolutely not. The f3 is (Yoruba; MA-1, X) - there's no comparison with Amerindians in the calculation.
Amerindians as the most MA-1-like modern population on the plot. MA-1
Mistake! Being "closest" doesn't mean you are the same. By your logic the Karitiana axis would be shared drift with Amerindians AND East Asians, since East Asians are the the most Amerindian-like population on the plot... the Sardinian axis would be shared drift with Sardinians AND LB, etc. etc. The reason there are different graphs for MA-1 and Karitiana is because the results are different - shared drift with MA-1 is demonstrably not the same as shared drift with Amerindians.
Amerindians on the X axis are just like Sardinians and other Europeans on the Y axis.
I already pointed out the vast differences between an MA-1/Amerindian comparison and a Sardinian/European comparison. Your use of "just like" is unfounded.
Could you comb through those Lazaridis tables to find a number that supports that Stuttgart is closer to Amerindians than to MA-1
I did comb through the data but couldn't find any evidence of this - that's why I asked where you got the idea from, in case I'd missed something. But as you said above you got it from a misunderstanding of what Lazaridis meant by "eastern non-African". These f4 data do not, in fact, show whether Stuttgart is closer to MA-1 or Amerindians, although the PCA projections (latest S10.1, 10.2 etc.) and common logic would suggest the former.
@Tobus
"No, it's absolutely not. The f3 is (Yoruba; MA-1, X) - there's no comparison with Amerindians in the calculation."
Amerindians are some of those X populations. You lost the debate long time ago. Stop appealing to the judges!
"Mistake! Being "closest" doesn't mean you are the same. "
Sure, not the same. MA-1 is an admixed Amerindian-West Eurasian population. But it's ancestrally related to Amerindians, hence they are mutually interchangeable when it comes to comparisons with other populations. EDF 5d confirms this.
"shared drift with MA-1 is demonstrably not the same as shared drift with Amerindians."
MA-1 has an additional West Eurasian layer to it that Amerindians don't have, but they are identical in their Amerindianness.
"I already pointed out the vast differences between an MA-1/Amerindian comparison and a Sardinian/European comparison. Your use of "just like" is unfounded."
Your argument was invalid. Just because Sardinians are modern Europeans and MA-1 is an ancient Amerindian-derived population, the logic of the plot is the same.
"I did comb through the data but couldn't find any evidence of this - that's why I asked where you got the idea from, in case I'd missed something."
Well, you missed a lot. Comb again. MA-1 must behave like a typical ENA population in relationship to Stuttgart, while Amerindians have an additional affinity to Stuttgart that ENA/MA-1 don't have. Just a repost: Comp.: 1)"Eastern non-Africans are all more closely related to ancient hunter gatherers than to Stuttgart" (p. 97, latest Lazaridis); 2) "MA1 is closer to all European hunter-gatherers than to Stuttgart." (p. 92, latest Lazaridis); 3) "ENA share more alleles with MA1 than with Stuttgart" (p. 104); 4) "Loschbour and MA1 are symmetrically related to ENA (because they both lack Neolithic Near Eastern ancestry)" (p. 104); 5) "Stuttgart has a proportion of “Basal Eurasian” ancestry while Loschbour and MA-1 share the non-African>X>W drift for the entirety of their ancestry" (p. 104). But: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans."
Go ahead and compare all the Stuttgart statistics for MA-1, Amerindians plus a fourth population.
"MA-1 is an admixed Amerindian-West Eurasian population".
How can MA-1 be 'admixed' with anything? I was under the distinct impression you were claiming all modern humans descend from Amerindians yet here you go saying MA-1 is admixed with a non-existent 'West Eurasian population'. Another example of your consistent inconsistency? Or are you now conceding that Eurasians descend in large part from a non-Amerindian population? If the latter is the case then you've just destroyed your own belief.
"But it's ancestrally related to Amerindians"
I agree totally. It's just that you're totally confused as to the direction of that ancestry.
@German:
Amerindians are some of those X populations.
In EDF 5d we have Amerindians compared with MA-1, Europeans compared with MA-1, East Asians compared with MA-1, LB compared with MA-1, etc. etc. We never have any of these X populations compared with Amerindians... understand?
But it's ancestrally related to Amerindians, hence they are mutually interchangeable when it comes to comparisons with other populations.
Your logic must be flawed - when we interchange them we get completely different results. compare EDF 5d with 5a for instance.
but they are identical in their Amerindianness.
Yes, identical in a small part of their genomes, but completely unrelated in the rest. That's why a population like LB can show increased affinity to one but not the other.
Your argument was invalid. Just because Sardinians are modern Europeans and MA-1 is an ancient Amerindian-derived population, the logic of the plot is the same.
Let's see - plots where Europeans cluster with Sardinians: EDF 5a, b, c, d and e (both axes in each). Plots where MA-1 clusters with Amerindians: nil. Hmmm... "Just like"? "The same"? I don't think so.
MA-1 must behave like a typical ENA population in relationship to Stuttgart
MA-1 is ANE, not ENA. First you say MA-1 is Amerindian, now you're trying to paint him as East Asian?! Hmmm...
Go ahead and compare all the Stuttgart statistics for MA-1, Amerindians plus a fourth population
I have, there's no evidence that Stuttgart is closer to Amerindians than MA-1.
@Tobus
"In EDF 5d we have Amerindians compared with MA-1, Europeans compared with MA-1, East Asians compared with MA-1, LB compared with MA-1, etc. etc. We never have any of these X populations compared with Amerindians... understand?"
All individual European populations cluster with each other, all individual Asian populations cluster with each other, LB clusters with Amerindians, Amerindians is the most MA-1 population of them all. Like I said, you are welcome invent an f100 statistics to measure all of those populations' relationship with each other "directly." But the data is explicit enough as it is.
"Your logic must be flawed - when we interchange them we get completely different results. compare EDF 5d with 5a for instance."
What different results? MA-1 is West Eurasian shifted in 5a because it's an admixed population. In 5d Amerindian divergence is lower than in 5a. This is again because MA-1 is West Eurasian-admixed. The value that Amerindians have on the X axis anchored in MA-1 is the same value as MA-1 has on the x axis anchored in Karitiana. But both 5d and 5a show Amerindians as rightmost on the X axis. If MA-1 were an ancestrally West Eurasian population, we would've seen the West Eurasian cluster as rightmost on the MA-1 anchored axis. If MA-1 were ancestrally an East Asian (Han-like) population, we would have seen modern East Asian as rightmost on the MA-1 anchored axis. But we don't...
"Let's see - plots where Europeans cluster with Sardinians: EDF 5a, b, c, d and e (both axes in each). Plots where MA-1 clusters with Amerindians: nil."
MA-1 does not need to cluster with Amerindians (or the other way around) - as an ancient sample, with post-Amerindian admixture in it, it only needs to be Amerindian-shifted compared to other populations.
"MA-1 is ANE, not ENA. First you say MA-1 is Amerindian, now you're trying to paint him as East Asian?! "
ANE is a fictitious population. ENA is "eastern non-Africans," a conglomerate of real modern populations. MA-1 is an Amerindian-derived ancient Eurasian population. Where's the contradiction?
"I have, there's no evidence that Stuttgart is closer to Amerindians than MA-1."
Could you post the runs you've looked at? Thanks.
@German:
, you are welcome invent an f100 statistics to measure all of those populations' relationship with each other "directly." But the data is explicit enough as it is.
As you say, the data is explicit, but you should consider all of it. LB shares the same amount of shard drift with MA-1 as Amerindians do (EDF 5d), and he shares the same amount of shared drift with Amerindians as modern Europeans do (EDF 5a). The obvious explanation for him having increased affinity to MA-1 but not to Amerindians is that his affinity to MA-1 is not shared affinity to Amerindians.
What different results? MA-1 is West Eurasian shifted in 5a because it's an admixed population. In 5d Amerindian divergence is lower than in 5a. This is again because MA-1 is West Eurasian-admixed
Exactly the ones you are listing! The X populations get different scores on the MA-1 axis to the Karitiana axis, hence MA-1 and Amerindians are empirically *not* "mutually interchangeable when it comes to comparisons with other populations".
If MA-1 were an ancestrally West Eurasian population, we would've seen the West Eurasian cluster as rightmost on the MA-1 anchored axis.
Europeans had already diverged before MA-1's time and have admixture with other populations that diverged even earlier (eg EEF). Amerindians had diverged much earlier but then received DNA from a population much closer to the MA-1 sample than most Europeans. In terms of the shared drift measurement, it's plausible (and evident) that Amerindians and MA-1 have more similar allele frequencies in their shared Eurasian component than modern Europeans and MA-1 do.
MA-1 does not need to cluster with Amerindians (or the other way around)
They need to if your suggestion that "Amerindians on the X axis are just like Sardinians and other Europeans on the Y axis" has any merit. They don't, so it doesn't.
ANE is a fictitious population. ENA is "eastern non-Africans," a conglomerate of real modern populations. MA-1 is an Amerindian-derived ancient Eurasian population. Where's the contradiction?
The contradiction is that you posit different populations that MA-1 is supposedly genetically representative of depending on the theory you are trying to make. In reality MA-1 doesn't fit very well as any single modern population, hence the use of the "fictitious" ANE population to represent his specific lineage. He's not Amerindian, he's decidedly un-East Asian and no particular modern European population represents him very well. The quotes you took from Lazaridis do not include MA-1 when referring to "ENA" or "eastern non-Africans", so stop trying to make out that they do.
Could you post the runs you've looked at? Thanks.
I've looked through all the f4s in Lazaridis EDTs 1 and 2 and S14 (latest version) ... none of them suggest Stuttgart is closer to Amerindians than to MA-1. You're welcome.
@Tobus
"LB shares the same amount of shard drift with MA-1 as Amerindians do (EDF 5d), and he shares the same amount of shared drift with Amerindians as modern Europeans do (EDF 5a). The obvious explanation for him having increased affinity to MA-1 but not to Amerindians is that his affinity to MA-1 is not shared affinity to Amerindians. "
LB shares more affinity with Amerindians than modern Europeans (EDF 5d), it falls within Amerindian variation (this means some Amerindians, especially Anzick are more like MA-1 than LB) in EDF 5d (Anzick from Rasmussen). But overall of course LB and MA-1 share West Eurasian affinity than neither of them shares with Amerindians (EDF 5a). This is why there was no West Eurasian gene flow into Amerindians.
"The X populations get different scores on the MA-1 axis to the Karitiana axis, hence MA-1 and Amerindians are empirically *not* "mutually interchangeable when it comes to comparisons with other populations"."
Obviously MA-1 has West Eurasian admixture. It most closely related to Amerindians, followed by West Eurasians.
"In terms of the shared drift measurement, it's plausible (and evident) that Amerindians and MA-1 have more similar allele frequencies in their shared Eurasian component than modern Europeans and MA-1 do."
There's no shared Eurasian component between MA-1 and Amerindians. It's the pan-American component that MA-1 and modern Amerindians share. Modern Europeans have less of it than MA-1 and modern Amerindians.
"They need to if your suggestion that "Amerindians on the X axis are just like Sardinians and other Europeans on the Y axis" has any merit. They don't, so it doesn't."
No, MA-1 has mixed Amerindian-West Eurasian ancestry with the direction of gene flow being from Amerindian to MA-1. Hence, MA-1 and Amerindians will be like Sardinians and modern Europeans when an axis is anchored in MA-1 but not like Sardinians and modern Europeans when an axis is anchored in Karitiana.
"The contradiction is that you posit different populations that MA-1 is supposedly genetically representative of depending on the theory you are trying to make. In reality MA-1 doesn't fit very well as any single modern population, hence the use of the "fictitious" ANE population to represent his specific lineage. He's not Amerindian, he's decidedly un-East Asian and no particular modern European population represents him very well. The quotes you took from Lazaridis do not include MA-1 when referring to "ENA" or "eastern non-Africans", so stop trying to make out that they do."
MA-1 is an admixed population. It's ancestrally Amerindian and it's closer to modern Amerindians than to any other single continental population. So ancestrally it fits well with Amerindians. No need for ANE.
"I've looked through all the f4s in Lazaridis EDTs 1 and 2 and S14 (latest version) ... none of them suggest Stuttgart is closer to Amerindians than to MA-1. You're welcome."
Can you get more specific and show me how you arrived at your conclusion and if you've found instead that MA-1 is closer to Stuttgart than Amerindians are. Figure S14.11 seems to suggest that MA-1 is a better surrogate for ANE than is Karitiana and since Stuttgart is not an ANE population it may be closer to Amerindians than to MA-1 and hence Karitiana is a better surrogate for Basal Eurasians than MA-1 is. There must be something in the data to justify their assertions that Stuttgart is closer to Karitiana than to ENA but that ENA share more alleles with MA-1 than with Stuttgart.
@German:
LB shares more affinity with Amerindians than modern Europeans (EDF 5d)
Incorrect. EDF 5d shows LB shares more affinity with MA-1, not Amerindians.
Obviously MA-1 has West Eurasian admixture. It most closely related to Amerindians, followed by West Eurasians.
"Closer" notwithstanding, MA-1 and Amerindians are not interchangeable.
There's no shared Eurasian component between MA-1 and Amerindians
Every expert in the field would disagree.
Hence, MA-1 and Amerindians will be like Sardinians and modern Europeans when an axis is anchored in MA-1 but not like Sardinians and modern Europeans when an axis is anchored in Karitiana.
The Sardinian/European continental cluster exists on every single axis. If your supposed MA-1/Amerindian continental cluster only exists of a single specific axis then it's got no meaning, it's just the results of one f3.
It's ancestrally Amerindian and it's closer to modern Amerindians than to any other single continental population. So ancestrally it fits well with Amerindians. No need for ANE.
MA-1 is decidedly not ancestrally Amerindian because he doesn't share the East Asian affinity that Amerindians do. Lazaridis tried to build ancestry models without ANE but found it hard to account for all relationships. Hence there certainly is a need for ANE.
Can you get more specific and show me how you arrived at your conclusion and if you've found instead that MA-1 is closer to Stuttgart than Amerindians are.
I arrived at my conclusion by looking at the data and not finding any f4 stats that show Stuttgart is closer to Amerindians than MA-1. No, I did not find the opposite is true, hence why I'm not saying it is (although, as I pointed out, there are strong indications of it in the f3 trees, ADMIXTURE and PCA data).
since Stuttgart is not an ANE population it may be closer to Amerindians than to MA-1 and hence Karitiana is a better surrogate for Basal Eurasians than MA-1 is
It may also *not* be and hence they're *not*. You need actual evidence to support your speculation. Incidentally they use a similar ratio in EDF 5 and Stuttgart plots on the MA-1 side.
There must be something in the data to justify their assertions that Stuttgart is closer to Karitiana
They don't assert this.
@Tobus
"EDF 5d shows LB shares more affinity with MA-1, not Amerindians."
That's be perfectly fine with me as MA-1 has West Eurasian affinities shared with LB, which Amerindians don't have. It's reflected in EDF 5a, though. EDF 5d shows that LB has affinities with MA-1 and Amerindians.
""Closer" notwithstanding, MA-1 and Amerindians are not interchangeable."
Depending on the content.
"Every expert in the field would disagree. "
I'm an expert in the field and I would agree. Your claim is therefore falsified.
"The Sardinian/European continental cluster exists on every single axis. If your supposed MA-1/Amerindian continental cluster only exists of a single specific axis then it's got no meaning, it's just the results of one f3."
MA-1 are the closest to modern Amerindians among all modern human populations. It's a cluster validated by all experts in the field. MA-1 has additional West Eurasians affinities, while the European/Sardinian cluster just had time to equilibrate and net out on its own component, hence it looks tighter that the Amerindian/MA-1 cluster.
"MA-1 is decidedly not ancestrally Amerindian because he doesn't share the East Asian affinity that Amerindians do. "
This proves that Amerindians did NOT descend from East Asians. What the data shows is that MA-1 has not East Asian affinity to the exclusion of Amerindians, which is another way of saying that West Eurasians are related to East Asians only via a New World Amerindian source and not via any "Eurasian" unity.
"They don't assert this."
They do. They explicitly say that Stuttgart is closer to Karitiana than ENA. But Stuttgart has a Mesolithic substrate, so it's not clear if this is just a rollover from the stronger association between European hunter-gatherers and Karitiana, or it's because Stuttgart's Neolithic ancestry is also Karitiana-skewed.
"I'm an expert in the field and I would agree. Your claim is therefore falsified".
No-one, apart from yourself, would consider you to be 'an expert in the field'. In fact the evidence has long been overwhelming that you are particularly ignorant in the matter of human origins. Therefore Tobus' comment is by no means falsified.
"MA-1 has additional West Eurasians affinities"
I notice with intense interest that you are still dodging the question of what those 'West Eurasians affinities' actually are. At present they remain non-existent.
@German:
I'm an expert in the field and I would agree
You are not an expert in the field. Dressing up like a Native Americans and traipsing around Russia for a few years doesn't make you an expert in human genetics. Sorry.
It's a cluster validated by all experts
I've yet to see any (genuine!)expert refer to an "MA-1/Amerindian cluster". The two poulations don't cluster on *any* of these f3 plots.
This proves that Amerindians did NOT descend from East Asians
No, it proves that MA-1 did NOT descend from Amerindians. The data is entirely consistent with Amerindians and East Asians having a common recent ancestor.
They do. They explicitly say that Stuttgart is closer to Karitiana than ENA
No, they don't, because MA-1 is not ENA, as I pointed out earlier and as they themselves define in S14. EDF 5 shows that what you are claiming is incorrect, Stuttgart is in fact closer to MA-1 than to Karitiana.
Note that *all* Europeans are closer to Karitiana than to ENA, yet all of them are still closer to MA-1 than to Karitiana.
@Tobus
"You are not an expert in the field. Dressing up like a Native Americans and traipsing around Russia for a few years doesn't make you an expert in human genetics. Sorry."
And Darwin used to hang out with pigeon breeders in London! I can only fathom what a creationist like you would make out of it. A theory of natural selection is compromised! I studied population genetics in the best universities of Russia and the U.S. I published two peer-reviewed books drawing on this and and other disciplines, which I also studied meticulously. And yes I'm also an expert in the psychology of wannabes such as yourself who dresses as a scientist but who's a creationist inside. One can be an expert in different fields, you know.
"I've yet to see any (genuine!)expert refer to an "MA-1/Amerindian cluster". The two poulations don't cluster on *any* of these f3 plots.
I'm just an expert who's faster than other experts. Amerindians are the closest to MA-1 out of ll modern human populations. This is Fig 1C in Raghavan. In Olalde EDF 5a the distance between Amerindians and MA-1 is the same as the value around which Amerindians cluster in EDF 5d anchored in MA-1. Anzick is even further on the right on the MA-1 anchored axis than modern Amerindians. BTW, do you see the MA-1 star anywhere on EDF 5d?
"No, it proves that MA-1 did NOT descend from Amerindians. The data is entirely consistent with Amerindians and East Asians having a common recent ancestor."
So, how come East Asians are not close to MA-1, while all of Amerindians are? Your logic would've worked if you postulated that Amerindians entirely descended from West Eurasians with no East Asian contribution. Then East Asians would've diverged from Africans separately and had nothing to do with West Eurasians and Amerindians, and with MA-1. But you want to have the cake and eat it, too. But the stubborn reality is that if West Eurasians share genetic affinity with a descendant (Amerindian), there must be genetic affinity between West Eurasians and the putative ancestor (East Asian). If it's East Asians and West Eurasians who are the descendants and Amerindians an ancestor, then, with no gene flow between the descendants, they should be divergent from each other. Facts support the latter interpretation. The only reason Raghavan didn't put the correct interpretation forth is because it would've required from him to admit that East Asians must have descended from Amerindians (in addition to postulating Amerindian gene flow into West Eurasia!) and this would have been a double violation of a cultural taboo and he didn't have the guts for it.
I think your fundamental mistake is that you convinced yourself that the Amerindian component in MA-1 is a West Eurasian component. This is false. It's a separate Amerindian component and as such it should carry an East Asian affinity with it if Amerindians descended from East Asians prior to admixture with West Eurasians.
My recommendation is for you to re-read Raghavan and the lengthy discussion he devoted to the issue of the directionality of gene flow in MA-1 vs. Amerindians. You imagine it to be an easy solve, while it's not.
"And Darwin used to hang out with pigeon breeders in London!"
Showing your ignorance once more. Darwin learned a considerably amount about evolution from those same pigeon breeders. Something you could learn a lot from also. Have you ever bothered to read 'On the Origin of Species'?
"I'm just an expert who's faster than other experts".
And so humble. Do you actually have any friends?
"So, how come East Asians are not close to MA-1, while all of Amerindians are?"
Tobus and I have explained that to you multiple times but you are so obsessed by your creationist beliefs that you refuse to see sense. But I repeat: MA-1 and East Asians are two completely different populations. They mixed and produced Amerindians. There is no other possible explanation that covers ALL the evidence. You are able to maintain your creationist belief only by ignoring a substantial body of that evidence.
"But the stubborn reality is that if West Eurasians share genetic affinity with a descendant (Amerindian), there must be genetic affinity between West Eurasians and the putative ancestor (East Asian)".
That statement is completely stupid. I agree it might be the case if Amerindians were ancestral to the two. But, because it is not the case you belief cannot be correct. Why, if Amerindians are a hybrid between East Asians and West Eurasians, need East Asians and West Eurasians show any affinity at all? Certainly they would both show affinity with Amerindians, which is in fact the case.
"If it's East Asians and West Eurasians who are the descendants and Amerindians an ancestor, then, with no gene flow between the descendants, they should be divergent from each other".
Rubbish. An amazing statement from someone who has just claimed to have, ' studied population genetics in the best universities of Russia and the U.S. I published two peer-reviewed books drawing on this and and other disciplines, which I also studied meticulously'. How come you can still make such a stupid comment? If both East Asians and West Eurasians are the descendants of Amerindians then even with no subsequent gene flow between the descendants they would hardly be divergent from each other. After all, both East Asians and West Eurasians would share ancestry and so demonstrate close affinity.
"The only reason Raghavan didn't put the correct interpretation forth is because it would've required from him to admit that East Asians must have descended from Amerindians"
Wrong. He did put the correct interpretation forth. East Asians do not descend from Amerindians. You are only able to believe they do by ignoring a mountain of evidence.
"this would have been a double violation of a cultural taboo and he didn't have the guts for it".
What 'cultural taboo'? If any actual evidence existed I'm sure he would have been the first to agree with your belief. As far as I'm aware there is no cultural reason at all why anyone opposes what you wish us to believe. Just a total lack of evidence to support it.
"It's a separate Amerindian component and as such it should carry an East Asian affinity with it if Amerindians descended from East Asians prior to admixture with West Eurasians".
This is false. Your comment lacks logic.
@German:
I'm also an expert in the psychology of wannabes such as yourself who dresses as a scientist but who's a creationist inside
That's great, except that I'm *not actually* a creationist, your self-appointed expertise has led you astray once again.
I'm just an expert who's faster than other experts.
Unless you're actually going the wrong way and the real experts have left you far, far behind.
No-one talks about an "MA-1/Amerindian" cluster because there isn't one - you have to fabricate it with some nonsense about what they get on some other graph, but do we need to do that for any other cluster? No, we don't, because "cluster" means they cluster. MA-1 and Amerindians don't cluster on any of these plots.
BTW, do you see the MA-1 star anywhere on EDF 5d?
No, because they don't include the axis populations in the plotted samples (I'm guessing the didn't calculate f3(Yoruba, MA-1, MA-1) etc.) - LB isn't on the charts with an LB axis and if you count the dots you'll see there's one less European population on the Sardinian plots and etc. for the rest.
So, how come East Asians are not close to MA-1, while all of Amerindians are?
Because East Asians didn't receive any MA-1 admixture, only Amerindians did. (duh!)
if West Eurasians share genetic affinity with a descendant (Amerindian), there must be genetic affinity between West Eurasians and the putative ancestor (East Asian).
Why? You've repeated this claim many times but it makes no sense - if population A is a mix of B and C, what makes you think population B would show affinity to C? The two source populations would stay distinct and only the admixed descendants would show affinity to both.
If it's East Asians and West Eurasians who are the descendants and Amerindians an ancestor, then, with no gene flow between the descendants, they should be divergent from each other
No, in that scenario whichever population diverged first should be *equally* divergent from the other two. In a single wave scenario Europeans and East Asians should be equidistant from the lineage that stayed in America. In a two-wave scenario Europeans should be equally distant from both East Asians and modern Amerindians (who were a single population at the time and stayed in America and only split later). The data doesn't support either scenario.
I think your fundamental mistake is that you convinced yourself that the Amerindian component in MA-1 is a West Eurasian component.
I was convinced of this by examining the data, it's the only possible scenario given the pattern of genetic affinities we see today. You seem to be an intelligent person so I'm confident you'd arrive at the same conclusion if you made an honest appraisal of the data without projecting your preconceived belief structure onto it.
@German (cont):
My recommendation is for you to re-read Raghavan and the lengthy discussion he devoted to the issue of the directionality of gene flow in MA-1 vs. Amerindians.
Like this bit (SI 11.3): "While the optimized admixture graphs above modeled Karitiana as having MA-1- related ancestry, it is possible that the affinity between the two could also be explained with gene flow in the other direction. To test the statistical support for the direction of gene flow, a bootstrap analysis was performed where an a priori migration edge from the Denisova lineage to the ancestry of the Papuan was included, and TreeMix was then used to optimize a second migration edge. Over 100 bootstrap pseudoreplicates, a migration edge from MA-1 to Karitiana was observed in 99 cases, and a migration edge from Karitiana to MA-1 in 1 case. This analysis was repeated including all three migration edges inferred for m=4 in the first analysis, except the one including MA-1 and Karitiana. Here, all 100 bootstrap pseudoreplicates supported the gene flow direction from MA-1 into Karitiana."?
Or this one (SI 12): "When adding the Karitiana genome to this scaffold tree, 422 of 500 bootstrap pseudoreplicates were found to fit Karitiana as a mix between the Sardinian and Han lineages, with 73.7% (95% CI: 61.8-85.7%) of its ancestry being derived from the Han lineage and the remainder 26.3% (14.3-38.2%) from the Sardinian lineage (Figure SI 18; Table SI 12)."... and "Subsequently, Karitiana was fitted as a three-way mixture between MA-1 (modeled as a mixture as above, see SI 14) and Han, since it is likely that populations related to MA-1 mediated the mixture event between western Eurasians and Native Americans. Here, 496 bootstrap replicates supported Karitiana as having 26.1% (7.7-44.4%) ancestry from the MA-1 lineage and the remainder from Han, consistent with the previous analysis."?
I know you'd really like it to be the other way, but the data is clear that gene flow went from MA-1 into Amerindians.
@Tobus
"That's great, except that I'm *not actually* a creationist, your self-appointed expertise has led you astray once again."
You are a cryptocreationist: you use scientific words but your thinking is pre-scientific and relies on apriori beliefs, which you think of as immutable and the people you got them from as omniscient, and not on data or method.
"Unless you're actually going the wrong way and the real experts have left you far, far behind."
Yes, right, they quickly got everybody into the out-of-Africa myth, but I'm the first one to dispel it. The "experts" you adore aren't anthropologists. And genetics is just a subset of the skill set necessary to solve human origins. I have it, they don't. But I'm happy to learn what they think about the origins of Drosophila.
"No-one talks about an "MA-1/Amerindian" cluster because there isn't one - you have to fabricate it with some nonsense about what they get on some other graph, but do we need to do that for any other cluster? No, we don't, because "cluster" means they cluster. MA-1 and Amerindians don't cluster on any of these plots."
Right. Because MA-1 is an admixed population. Once you remove it's West Eurasian ancestry, it will cluster with modern Amerindians.
"No, because they don't include the axis populations in the plotted samples (I'm guessing the didn't calculate f3(Yoruba, MA-1, MA-1) etc.) - LB isn't on the charts with an LB axis and if you count the dots you'll see there's one less European population on the Sardinian plots and etc. for the rest."
Right. Then where do you see MA-1 being a more Amerindian population that modern Amerindians?
"Because East Asians didn't receive any MA-1 admixture, only Amerindians did. (duh!)"
So, East Asians and West Eurasians are not related via a common Eurasian ancestral population?
@Tobus (contd.)
"Why? You've repeated this claim many times but it makes no sense - if population A is a mix of B and C, what makes you think population B would show affinity to C? The two source populations would stay distinct and only the admixed descendants would show affinity to both."
You yourself are saying that Amerindians are very East Asian like and that Amerindians are closer to East Asians than to West Eurasians. This would make MA-1 East Asian like, too.
In addition, your logic is flawed: "if population A is a mix of B and C, what makes you think population B would show affinity to C." You need to prove that Amerindians are a mix of two populations, not assume this to be the case. If populations B and C diverged from population A and stayed in isolation from each other ever since, then they both will be variably related to population A but not to each other. This is exactly what we see with West Eurasians vs. East Asians. The whole "admixture" framework is wrong in this case because ALL of West Eurasians and ALL of East Asians show Amerindian affinities, not subsets of both.
"No, in that scenario whichever population diverged first should be *equally* divergent from the other two. In a single wave scenario Europeans and East Asians should be equidistant from the lineage that stayed in America. In a two-wave scenario Europeans should be equally distant from both East Asians and modern Amerindians (who were a single population at the time and stayed in America and only split later). The data doesn't support either scenario."
Where do you get your idea that East Asians and West Eurasians are not equidistant from Amerindians (assuming that East Asians absorbed an additional late gene flow from America which explains the physical similarity between the two and brings modern populations closer together)? Where do you get your idea that Papuans and West Eurasians are not equidistant from Amerindians (assuming Papuans absorbed a Denisovan substrate)?
The data supports a number of out-of-America scenarios. A single wave to East Asia/the Sahul and to West Eurasia with subsequent migration of North Amerindians into East Asia only would fit all the data. What the data doesn't support are any into-the-Americas scenarios currently on the table (exclusively from East Asians or from a mixed East Asian-West Eurasian population).
"I was convinced of this by examining the data."
Since it's not in the data (Amerindians and not West Eurasians are most like MA-1; the Amerindian component is distinct from the West Eurasian component in ADMIXTURE runs), you must have been examining something else. Which is exactly what creationists do.
@Tobus (contd.)
"Like this bit (SI 11.3)...the data is clear that gene flow went from MA-1 into Amerindians."
Their calculations are irrelevant because they assumed from the beginning that Karitiana is East Asian-derived and not the other way around. This assumption is present throughout the paper and in SI is stated in the following way: "If the gene flow was mainly from Native American ancestors to the MA-1 lineage, an affinity would also be expected between East Asians and MA-1." (SI, p. 67). Or in the main body of the paper: "The genetic affinity between Native Americans and MA-1 could be explained by gene flow after the split between east Asians and Native Americans, either from the MA-1 lineage into Native American ancestors or from Native American ancestors to the ancestors of MA-1."
In the main paper they state "...D statistic...estimated from outgroup-ascertained SNP data reveal significant evidence (Z>3) for Middle Eastern, European, central Asian and southAsian populations being closer to Karitiana than to HanChinese (Fig. 3b and Supplementary Information, section 14.5). Similar signals were also observed when we replaced modern-day Han Chinese with data from chromosome 21 from a 40,000-year-old east Asian individual (Tianyuan Cave, China), which has been found to be ancestral to modern-day Asians and Native Americans (Supplementary Information, section 14.5). Thus, if the gene flow direction was from Native Americans into western Eurasians it would have had to spread subsequently to European, Middle Eastern, south Asian and central Asian populations, including MA-1 before 24,000 years ago."
The latter is precisely what out-of-America postulates.
But here their fundamental assumption kicks in: "Moreover, as Native Americans are closer to Han Chinese than to Papuans (Fig. 3c), Native American-related gene flow into the ancestors of MA-1 is expected to result in MA-1 also being closer to Han Chinese than to Papuans."
But this doesn't need to be the case because Papuans have additional Denisovan admixture and East Asians have additional, later, post-MA-1 North American Indian admixture. Lazaridis confirms that ancient West Eurasians are closer to East Asians than they are to Papuans.
"The two source populations would stay distinct and only the admixed descendants would show affinity to both".
A PhD in Dances with Indians prevents one from being able to see anything that is so obvious to any even half-trained geneticist or evolutionary biologist.
"You seem to be an intelligent person so I'm confident you'd arrive at the same conclusion if you made an honest appraisal of the data without projecting your preconceived belief structure onto it".
No. I think the first statement in that sentence is incorrect and so the remainder doesn't necessarily follow.
"You yourself are saying that Amerindians are very East Asian like and that Amerindians are closer to East Asians than to West Eurasians. This would make MA-1 East Asian like, too".
I have asked you repeatedly to provide even a single reason why MA-1 should be East Asian under any scenario. So far you have made no attempt to explain why you believe that is a necessity. I can only conclude you don't actually believe it yourself but you find it necessary to continually set up a straw man argument so that you can remain your old smug self. And you are conveniently forgetting that if both MA-1 and East Asians descend from Amerindians that MA-1 should have an East Asian affinity. It doesn't. Therefore MA-1 cannot possibly descend from Amerindians, who do have East Asian affinity.
"You need to prove that Amerindians are a mix of two populations, not assume this to be the case"
You seem more than happy to assume Amerindians gave rise to both East Asians and MA-1 without offering the slightest proof, of even evidence, to support your assumption. This rubbish for example:
"If populations B and C diverged from population A and stayed in isolation from each other ever since, then they both will be variably related to population A but not to each other".
On the contrary B and C would show considerable affinity with each other. Their common ancestry would ensure that to be so. But of course your PhD in Dances with Indians prevents you from being objective in this matter.
"This is exactly what we see with West Eurasians vs. East Asians".
The fact that this is so argues eloquently against the idea the two have a common Amerindian ancestry.
"If the gene flow was mainly from Native American ancestors to the MA-1 lineage, an affinity would also be expected between East Asians and MA-1."
That statement is absolutely correct and rules out gene flow from America to either MA1 or East Asians.
@German:
You are a cryptocreationist: you use scientific words but your thinking is pre-scientific and relies on apriori beliefs, which you think of as immutable and the people you got them from as omniscient, and not on data or method.
Not at all, try to look at things from my perspective - every expert and every paper that comes out says the same thing and then up pops a blog troll flinging insults and repeatedly insisting that "MA-1 is Amerindian" and other such nonsense. Read back what you just said to me and tell me who it better applies to, yourself, or every reputable scientist in the industry.
You need to prove that Amerindians are a mix of two populations, not assume this to be the case.
It's your logic THAT is flawed - you are saying that A *can't* be a mixture of B and C because B has no C... I'm asking why you think that is the case.
Yes, right, they quickly got everybody into the out-of-Africa myth, but I'm the first one to dispel it
... and the last - it will be here long after you're in Anthropology heaven.
Once you remove it's West Eurasian ancestry, it will cluster with modern Amerindians.
.. and once you remove it's Amerindian affinity it will cluster with modern Europeans - what's your point?
Where do you get your idea that East Asians and West Eurasians are not equidistant from Amerindians
Where do you get your idea that Papuans and West Eurasians are not equidistant from Amerindians
From the data... you have actually looked at the f3's we've been discussing haven't you?
You yourself are saying that Amerindians are very East Asian like and that Amerindians are closer to East Asians than to West Eurasians. This would make MA-1 East Asian like, too.
WHY???? In a scenario where MA-1 is not Amerindian nor East Asian, why do you keep saying he should have an East Asian affinity?
Their calculations are irrelevant because they assumed from the beginning that Karitiana is East Asian-derived and not the other way around.
Not in this measurement they don't - that's why I chose it. Read it and weep.
@Tobus
"Not at all, try to look at things from my perspective - every expert and every paper that comes out says the same thing and then up pops a blog troll flinging insults and repeatedly insisting that "MA-1 is Amerindian" and other such nonsense. Read back what you just said to me and tell me who it better applies to, yourself, or every reputable scientist in the industry."
Again, facts is an easy way to adjudicate between the two possibilities. I'm a person with a real name, real books, real blogs and real credentials working with cross-disciplinary data. You are a troll without any. If I challenge the authors who are more like me than like you, I have all the wherewithal to do that. If you want to read those people and those people only, you're free to do it and stop wasting my time. But since you're talking to me you should respect my rules of engagement. And those are: don't think of those authors as omniscient and don't doubt the scientific value of my perspective. Because from my perspective (which is always data-driven) and by my standards (which are always reciprocal) you are a cryptocreationist.
"It's your logic THAT is flawed - you are saying that A *can't* be a mixture of B and C because B has no C... I'm asking why you think that is the case."
I never said it can't be a mixture of B and C. We just have no evidence for it. MA-1 is not a mix of East Asians and West Eurasians. Neither is Anzick. Anzick is Amerindian, while MA-1 is ancestrally Amerindian with additional basal West Eurasian affinities. MA-1's haploid lineages are not found in the Americas, while an Amerindian mtDNA lineage that has a West Eurasian affinities (hg X) is not found in MA-1 or anywhere in Siberia. Tianyuan's mtDNA lineage is the same as the one found in Amerindians (hg B) but it's not a mix of West Eurasians and East Asians autosomally.
There's a very simple way to explain why B has no C, while they both have A. This is because they diverged from A and didn't admix with each other ever since.
"... and the last - it will be here long after you're in Anthropology heaven."
True. Creationists continue to teach the Bible as Science long after Darwin has gone to his.
".. and once you remove it's Amerindian affinity it will cluster with modern Europeans - what's your point?"
My point is that it's an admixed population. Amerindians, on the contrary, always stay pretty stable on the right.
"From the data... you have actually looked at the f3's we've been discussing haven't you?"
Oh, f3 is now a measurement of genetic distance?
"WHY???? In a scenario where MA-1 is not Amerindian nor East Asian, why do you keep saying he should have an East Asian affinity?"
MA-1 is part Amerindian but not at all East Asian. So your "scenario" is falsified even before it made it to the big screen.
"Not in this measurement they don't ."
Oh, yes they do. They projected admixture edges onto an existing "tree." And this tree has Amerindians as part of the East Asian clade. See SI12, SI 13. Notice that MA-1 is closest to Europeans and Karitiana is closest to Dai and Han on the tree, while in f3 stats MA-1 is the closest to Karitiana.
"But since you're talking to me you should respect my rules of engagement".
I've just read one of your comments where you admit to arbitrarily offering data interpretations. Are we all to adopt that idea just to maintain your little private joke?
"facts is an easy way to adjudicate between the two possibilities".
I would have thought so but you seem to have an allergy when it come to facts. You just arbitrarily make up 'facts' to suit the joke you are working on at the time.
"If I challenge the authors who are more like me than like you"
Are you able to name any authors who are more like you? I presume we would be dealing with a very short list.
"MA-1 is not a mix of East Asians and West Eurasians".
Straw man again. No-one has ever suggested MA-1 is a mix of East Asians and West Eurasians.
"while MA-1 is ancestrally Amerindian"
Yes, ancestral to Amerindians. Everybody apart from you readily accepts that to be so. You are the only person who tries to manipulate the data to show anything else.
"with additional basal West Eurasian affinities".
Yes. But how do you reconcile that statement with your apparent claim that all modern humans descend from Amerindians? I presume the whole idea is just another example of your arbitrary sense of humour.
"MA-1's haploid lineages are not found in the Americas"
Therefore MA-1 cannot possibly descend from Amerindians.
"an Amerindian mtDNA lineage that has a West Eurasian affinities (hg X) is not found in MA-1 or anywhere in Siberia".
Not correct. X2e has been found in Altai and X2b in Evenks. Other X haplogroups may also be present in Siberia as my data is incomplete. For example I don't know where the Amerindian X2a2's closest relation X2a1 is found. You claim to be omniscient so perhaps you could tell us. Its absence in MA-1 is hardly evidence of its contemporary absence in Siberia. Unless your knowledge of genetics is so limited that you believe individuals can contain several different mt- and Y-DNA haplogroups.
"Tianyuan's mtDNA lineage is the same as the one found in Amerindians (hg B)"
It is not the 'same' as the B haplogroup found in Amerindians. That is equivalent to saying Polynesian B is the same as the B found in Amerindians. You are demonstrating your lack of genetic knowledge once more.
"but it's not a mix of West Eurasians and East Asians autosomally".
Correct. It lived long before anyone had reached America, and even before the hybridisation events that gave rise to the ancestral Amerindians.
"MA-1 is part Amerindian but not at all East Asian. So your 'scenario' is falsified even before it made it to the big screen".
Here we go again. You have carefully avoided explaining exactly why you believe that MA-1 should have any East Asian genetic element at all. Exactly the same approach you adopt when confronted by evidence that completely demolishes your creationist beliefs. Neanderthals in America for example. MA-1 would only have an East Asian genetic element if it descends from Amerindians. It doesn't have any East Asian (as you admit) therefore it doesn't descend from Amerindians. Case dismissed. You are an idiot.
@Tobus
To elaborate on ("I never said it can't be a mixture of B and C. We just have no evidence for it. MA-1 is not a mix of East Asians and West Eurasians. Neither is Anzick. Anzick is Amerindian, while MA-1 is ancestrally Amerindian with additional basal West Eurasian affinities. MA-1's haploid lineages are not found in the Americas, while an Amerindian mtDNA lineage that has a West Eurasian affinities (hg X) is not found in MA-1 or anywhere in Siberia. Tianyuan's mtDNA lineage is the same as the one found in Amerindians (hg B) but it's not a mix of West Eurasians and East Asians autosomally") further. I understand if you were arguing for Amerindians being a mixture of Neandertals (a West Eurasian hominin) with Denisovans (an East Asian hominin). For this we do have some evidence. And this is what it looks like: Nenadertal and Denisovans are mutually divergent. Both Neandertal genes and Denisovan genes show up in Amerindians but not the other way around. There's genomic evidence for mixture between Neandertals and Denisovans in East Asia (we don't have evidence for the mixture of West Eurasians and East Asians in Asia as MA-1 is decisively not East Asian and Tianyuan is decisively not West Eurasian). Both populations are more homozygous than Amerindians, so the mixture between the two can plausibly result in Amerindian-like heterozygosity values. The two Neandertals tested for blood groups turned up blood group O, which is at near fixation among Amerindians (alternatively, bg B found in world-highest frequencies in Asia is virtually absent in America).
But you are not arguing for this. I am arguing for this sort of theory and approach. Now compared to this kind of argument your modern East Asian-modern West Eurasian admixture idea is clearly without any merit.
@German:
And those are: don't think of those authors as omniscient and don't doubt the scientific value of my perspective.
And if I look into the scientific value of your perspective and find it is a series of misunderstandings, misinterpretations, misrepresentations and bald-faced lies, am I allowed to doubt it then?
I never said it can't be a mixture of B and C.
We're getting somewhere! You agree it's *possible* that Amerindians could be a mix of West Eurasians and East Asians.
We just have no evidence for it.
Look again - Raghavan provides evidence for it in multiple measurements.
MA-1 is not a mix of East Asians and West Eurasians.
Correct!
Neither is Anzick. Anzick is Amerindian
Oh! So close - Anzick shows affinities to both East Asians and West Eurasians in greater amounts than either of these two show to each other. *IF* the MA-1 into Amerindians theory is true (which you acknowledge is possible above), then this is exactly what we'd expect to see. So Anzick *could* be a mix of East Asian and West European, just like you agreed Amerindians *could* be above.
while MA-1 is ancestrally Amerindian with additional basal West Eurasian affinities
Now you're just being obstinate - we're talking about the *possibility* that Amerindians are a mix of MA-1 and East Asians, but you've gone back to assuming the opposite. Try to keep an open mind.
There's a very simple way to explain why B has no C, while they both have A. This is because they diverged from A and didn't admix with each other ever since.
That means:
/\
/ /\
A B C
B and C (West Eurasians and East Asians) should be closer to each other than either is to A (Amerindians). So not true.
Raghavan posits:
/\
/\/\
B A C
A (Amerindians) has greater affinity to both B and C (West Eurasians and East Asians) than either have to each other. Confirmed by the data.
True. Creationists continue to teach the Bible as Science long after Darwin has gone to his.
Darwin went to his long ago and the widespread acceptance of modern evolutionary theory is his legacy. Out of America is already obsoleted by recent studies and once you're gone it will have zero proponents. Apples and oranges... but hey, you spent years pretending you were a Native Americans, now you're pretending you're on the level of Darwin - knock yourself out!
Oh, f3 is now a measurement of genetic distance
To the A population, yes.
Oh, yes they do. They projected admixture edges onto an existing "tree."
No: "TreeMix3 (version 1.12) was used to build ancestry graphs assuming 0 to 10 migration
edges, the placement and weight of each being optimized by the algorithm" (SI 11.2) - your "existing 'trees'" weren't existing at all, but were created as bet fit ancestry models using the data. The authors didn't just assume or make up how Amerindians fit into the tree, it was dictated as fact directly by the data, and then this fact was used in the subsequent analyses (S12/S14).
@Tobus
"And if I look into the scientific value of your perspective and find it is a series of misunderstandings, misinterpretations, misrepresentations and bald-faced lies, am I allowed to doubt it then? "
You are mistaken in your assessment. This is because you're incompetent and biased.
"We're getting somewhere! You agree it's *possible* that Amerindians could be a mix of West Eurasians and East Asians."
Your whole question is pseudoscientific. Any population can be a mix of any other populations. It's just there's no evidence that Amerindians are a mix of West Eurasians and east Asians.
"Look again - Raghavan provides evidence for it in multiple measurements."
His measurements are invalid as he assumes that Amerindians cluster with East Asians in the first place. f3,f4 stats prove the tree clustering wrong.
"That means:
/\
/ /\
A B C
B and C (West Eurasians and East Asians) should be closer to each other than either is to A (Amerindians). So not true.
Raghavan posits:
/\
/\/\
B A C
A (Amerindians) has greater affinity to both B and C (West Eurasians and East Asians) than either have to each other. Confirmed by the data."
Nonsense. You're simplifying an actual situation by referencing a couple of ideal models. If you look at Olalde 5a, you'll see that on your favorite Karitiana-anchored axis East Asians and West Eurasians are closer to each other than either of them to Amerindians. If you, say, open a PCA at Fig. 3b of http://www.nature.com/nature/journal/v463/n7282/fig_tab/nature08835_F3.html, you'll see again that East Asians are closer to Europeans than to Amerindians on PC2 and Europeans are closer to East Asians than to Amerindians on PC1.
Plus if you use Raghavan's tree model with A in the middle, just add admixture arrows from A to B on the left and from A to C on the right, and you'll get it all consistent with the data at hand. If you use your first graph, just add admixture arrows from the most divergent A to both B and C and you'll get a model that's again consistent with the data at hand.
Finally, your modeling only works for panmictic populations. From a subdivided population perspective, Amerindian populations are internally most structured but still closer to each other than to either East Asians and West Eurasians. This means that you have an AA (Amerindian) cluster splitting into an AB cluster (East Asian) and an AC cluster (West Eurasian). AC and AB clusters are equidistant from each other (or at least contain the same amount of A) but both of them are less Amerindian than Amerindians. Most divergent = most Amerindian. This fits the data perfectly.
You are deeply mistaken about the nature of the evolutionary process in human populations. You have only cosmological beliefs about the world. When the data doesn't fit the model you invent a "theory" whereby the lack of East Asian affinities in an ancient MA-1 sample is an indication that East Asians had already diverged prior to 24,000 years, while the presence of a clearly differentiated Amerindian component in MA-1 as indication that it's in fact not Amerindian but West European. It's by way of such trickery that you get the West Eurasian + East Asian = Amerindian equation.
@Tobus (contd.)
"Darwin went to his long ago and the widespread acceptance of modern evolutionary theory is his legacy. Out of America is already obsoleted by recent studies and once you're gone it will have zero proponents. Apples and oranges... but hey, you spent years pretending you were a Native Americans, now you're pretending you're on the level of Darwin - knock yourself out!"
Out of America is fully supported by most recent studies. Out of Africa and Recent-into-the Americas are consistently being refuted by them. And everyone acknowledges it. Darwin hasn't converted too many creationists just like it's hard for me to convert cryptocreationists such as yourself. And there are a lot of open-minded people who are perfectly comfortable with out of America.
"No: "TreeMix3 (version 1.12) was used to build ancestry graphs assuming 0 to 10 migration
edges, the placement and weight of each being optimized by the algorithm" (SI 11.2) - your "existing 'trees'" weren't existing at all, but were created as bet fit ancestry models using the data. The authors didn't just assume or make up how Amerindians fit into the tree, it was dictated as fact directly by the data, and then this fact was used in the subsequent analyses (S12/S14)."
It's the same maximum likelihood underneath TreeMix. See more at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002967. TreeMix is like a self-fulfilling prophecy. It's a hybrid model that creates admixed populations. Comp. Skoglund's reverse tree S7 here: http://www.sciencemag.org/content/suppl/2014/04/23/science.1253448.DC1/Skoglund.SM.pdf.
@Tobus (contd.)
Oh! So close - Anzick shows affinities to both East Asians and West Eurasians in greater amounts than either of these two show to each other. *IF* the MA-1 into Amerindians theory is true (which you acknowledge is possible above), then this is exactly what we'd expect to see. So Anzick *could* be a mix of East Asian and West European, just like you agreed Amerindians *could* be above.
Too bad there's no evidence for this. Anzick is Amerindian and not part East Asian-part West Eurasian. MA-1 is part West Eurasian-part Amerindian. Tianyuan is not a mix of East Asians and West Eurasians. It doesn't matter what "could have been." What matters is that the data rejects your beliefs. You are a wannabe scientist with couldabe theories.
@Tobus (contd.)
"you spent years pretending you were a Native Americans, now you're pretending you're on the level of Darwin."
I never pretended to be a Native American. You, on the contrary, are a clear wannabe scientist. You use scientific words, read scientific works, worship scientists, all while disparaging a person with all the scientific degrees, not building a single argument of one's own or providing valuable data. As for Darwin, he came from a rural society with a long history of animal breeding, he socialized with pigeon breeders in London and he developed a theory of natural selection. Does his background invalidate his theory? No. Do creationists like you try to undermine science with stupid snooping around in search of compromising material? Yes.
"Out of America is fully supported by most recent studies".
Such as? You are yet to demonstrate that anyone other than you believes anything like 'out of America'. Even googling 'out of America' comes up only with what you have written, nothing else. So, please, either show us a respected scientist who agrees with your belief or just forget your whole idea.
"You are deeply mistaken about the nature of the evolutionary process in human populations".
You demonstrate a complete ignorance of any aspect of evolutionary biology. And it is this ignorance enables you to claim, 'It's just there's no evidence that Amerindians are a mix of West Eurasians and east Asians'. You are obviously unable to understand the mountain of evidence that shows Amerindians are undoubtedly a mix of West Eurasians and east Asians.
"Out of Africa and Recent-into-the Americas are consistently being refuted by them. And everyone acknowledges it".
Everyone? Please give us even just a single example of someone other than yourself who ' acknowledges it'.
"while disparaging a person with all the scientific degrees"
You cannot be referring to your self here as your own information tells us you do not have any science degrees. Your degrees are in humanities, and your comments prove you don't understand science, and certainly not genetics of evolutionary biology. As demonstrated by:
"As for Darwin, he came from a rural society with a long history of animal breeding, he socialized with pigeon breeders in London and he developed a theory of natural selection. Does his background invalidate his theory?"
With this comment you are yet again demonstrating your complete ignorance of evolutionary biology. It is actually far more minute than was Darwin's, and he had no idea of genetics. That background was exactly what enabled Darwin to come up with his great idea.
@German:
Out of America is fully supported by most recent studies. Out of Africa and Recent-into-the Americas are consistently being refuted by them. And everyone acknowledges it.
You can no doubt show me one of these "recent studies" that everyone acknowledges "refutes" Out of Africa then?
It's the same maximum likelihood underneath TreeMix
TreeMix builds the maximum likelihood tree each time: "In this paper, we present a unified statistical framework for building population trees.." and "Our approach to this problem is to first build a maximum likelihood tree of populations." There's no arbitrary preconceived tree being used - it's built each time by analysing the input genomes. The differing trees in Skoglund S6 and S7 is demonstrable proof of this... if it were the same tree with admixture just layered on top it would change from run to run now would it?
Comp. Skoglund's reverse tree S7 here
It too shows that the admixture went from MA-1 into Amerindians, not the other way round.
Too bad there's no evidence for this.
Rhagavan S11, S12, S14. Skoglund S6, S7.
. Does his background invalidate his theory? No
Did he try to use his background to support his theory? No, he used facts and logic. If you don't want the flaws in your education to be brought up, don't bring up your "superior education" as an argument. Bring facts and logic, not self-aggrandisement.
@Tobus
"You can no doubt show me one of these "recent studies" that everyone acknowledges "refutes" Out of Africa then?"
You just need someone's stamp of approval, don't you? Here you go: ALL of them acknowledge that Serial-Bottleneck-Out-of-Africa has been disproved with the discovery of "archaic admixture" in Eurasia (and in Africa). Now, I take it one step further and remind them that "Amerindian admixture" is another phenomenon that disproves out-of-Africa.
"There's no arbitrary preconceived tree being used - it's built each time by analysing the input genomes."
But clustering is done first. And admixture edges are added after. That's the nature of the software.
"It too shows that the admixture went from MA-1 into Amerindians, not the other way round."
"The other way around" comes from Amerindians and Australians being closer to the root than MA-1. The reason they connected MA-1 and Amerindians with an admixture arrow is to show that they share something that Australians lack. But Australians and Amerindians share something that MA-1 lacks. That's a good example of how TreeMix works and the challenges it creates. It effectively produces two mutually exclusive clusters. A scholar then is left with making a choice between putting Australians and Amerindians together and showing an arrow from MA-1 to Amerindians or putting Amerindians and MA-1 first with an arrow from Amerindians to Australians. They didn't show the latter but it would've been perfectly reasonable if we assume that MA-1 and Amerindians share a node.
So we again end up with all of these populations sharing material with Amerindians but not with each other. A tree that would be true to these facts should have a substructured Amerindian population branching off first followed by MA-1 and Australians as individual branches in whatever order.
"Did he try to use his background to support his theory? No, he used facts and logic. If you don't want the flaws in your education to be brought up, don't bring up your "superior education" as an argument. Bring facts and logic, not self-aggrandisement."
I don't have any flaws in my education. It's perfectly suited for human origins and a number of other topics. I studied and practiced all the key sciences currently generating data for human origins research in top schools and have my own data at the intersection of linguistics and population genetics the analysis of which yielded a Ph.D. and two peer-reviewed books. Your argument would have been valid if I provided an alternative theory of Drosophila origins. But I didn't.
" ALL of them acknowledge that Serial-Bottleneck-Out-of-Africa has been disproved with the discovery of 'archaic admixture' in Eurasia (and in Africa)".
And that proves out of America ... how?
"Now, I take it one step further and remind them that 'Amerindian admixture' is another phenomenon that disproves out-of-Africa".
That is a giant leap, not a 'step', even for a creationist like yourself. Can you please remind us of someone other than you who claims 'Amerindian admixture' equals 'American ancestry'?
"So we again end up with all of these populations sharing material with Amerindians but not with each other. A tree that would be true to these facts should have a substructured Amerindian population branching off first followed by MA-1 and Australians as individual branches in whatever order".
That conclusion is possible only to some-one with a very limited knowledge of evolutionary biology and genetics. If all human populations descend from Amerindians surely all populations should be far closer to each other than they actually are. Your conclusion regarding the matter is obviously faulty.
"I don't have any flaws in my education".
You just carry on believing that for now and I'm sure the pills will eventually take effect.
@German:
You just need someone's stamp of approval, don't you?
No, just some actual evidence that what you say is indeed true. As it turns out you were just making it up, there're aren't any "recent studies" that refute the Out of Africa theory at all, and your statement that "everybody acknowledges it" is just pure bunkum.
But clustering is done first. And admixture edges are added after. That's the nature of the software.
There's no assumptions made in the clustering, just like the admixture edges, it's determined directly by the data.
The reason they connected MA-1 and Amerindians with an admixture arrow is to show that they share something that Australians lack.
No, the reason is because it represents the best fit given the data. There was no purpose behind it, it's just a statement of fact.
A tree that would be true to these facts should have a substructured Amerindian population branching off first followed by MA-1 and Australians as individual branches in whatever order.
And a tree that is true to *all* the facts, in proportion to their importance, would look exactly like the one generated. Your model might fit a few isolated facts, but when all the data is considered together, the tree shown in Raghavan is the result.
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