search this blog

Monday, May 1, 2017

Some strange stuff at bioRxiv lately


Should the submissions to bioRxiv be vetted in some basic way to prevent preprints like this from appearing there? Or is comic relief acceptable at bioRxiv every once in a while?

On The Peopling Of The Americas: Molecular Evidence For The Paleoamerican And The Solutrean Models

European Admixture In Chinchorro DNA

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

There's no way that any of these manuscripts will make it through the peer review process in any half decent journal, and keep in mind that a fair bit of crap does get through peer review even in the most prestigious and high-impact journals.

96 comments:

Richard Holtman said...

Thanks for this.

truth said...

Isn't that from Genetiker ? (The European admixture on the Chinchorro)

John Smith said...

> Isn't that from Genetiker ? (The European admixture on the Chinchorro)

Yep. He just linked to the paper on his blog.

Roy King said...

Yep---kinda makes you long for the peer review process despite the lengthy delays between lab results and eventual publication! I'm sympathetic to those who want speedier results uncovered, but the downside leads to junk.

John Smith said...

What evidence is there against the Chinchorro?

I found the autosomial results to be striking and I ignore them because they appear to be a dead end but that doesn't mean they didn't have Recent European Admixture. According to all the graphs they did what scientific evidence exists that they didn't? I hope they didn't because it would make things confusing but no one will even present any evidence against it but rather label it as heresy.

I am glad that Bioxriv finally gives us a ever small break from religious styled Academic Doctrine.

Nirjhar007 said...

So Genetiker is Robert Smith?.

Razib Khan said...

that's who i assume smith is too

Samuel Andrews said...

Geneticker admitted to writing that paper. So yeah Robert Smith is Geneticker. His paper is worth looking at to check if what he argues has much evidence.

Kristiina said...

Oh boy!

In the third paper, they have managed to push even yDNA A under F (58251 cleanly called SNPs). In the new mtDNA phylogeny, L0 is the youngest line, and all is under N (slow evolving SNPs). I admit that the position of L3 is problematic but this result exceeds all my expectations.

Moreover, I do not like the old fashioned racial classification used in the first paper. I do not think that it is supported by the ancient or modern evidence we currently have.

"These results strongly suggest that El Miron-related people
were among the direct ancestors of Anzick-1. Given the location of El Miron and the associated Magdalenian culture (immediately preceded by the Solutrean), the results here are most compatible with the Solutrean model." (Dejian Yuan, Shi Huang)

Simon_W said...

Robert Smith must be a pseudonym, because I have little doubt that Genetiker is a German. At least his nickname is German and I think I know who that guy is.

Gioiello said...

@ Davidski

I invited you many times to check all the data of the Shi Huang team. Now that no Kurgan autosome (thus no R1b except a few R-Z2103 subclades) are in the Balkans, thus less in Western Europe, you have all the time.
Not all of us are Levantinists, Kurganists, Caucasianists, Harvardians, Stanfordians etc etc

Davidski said...

Why should I have to show that up is not down? Shouldn't it be obvious?

If you don't know that these three papers are nothing more than the ramblings of madmen, then you're living in some sort of parallel universe. Good luck with that.

Matt said...

I guess that sunlight is the best disinfectant, as they say.

Gioiello said...

@ Davidski
To say that something is "obvious" without checking it, is anti-scientific. Read at least Karl Popper, another genial Ashkenazic man.

@ Kristiina
What you say is only the prejudice of these last years, that races don't exist. Examine Xyyman's mind and say to me if between his and ours there are 50000 or 2000000 years...

@ Roy King
With all the shit papers published in these years from renowned Universities, richly sponsored (I said names and surnames), at least these papers costed less.

Davidski said...

I guess that sunlight is the best disinfectant, as they say.

Indeed, I just hope that bioRxiv doesn't turn into a swamp full of this sort of thing.

Kristiina said...

Gioiello, I said old fashioned racial classification! I did not say that races do not exist. People look similar in the same geographical area and smoothly change appeareance with the increasing distance. Modern looks are a result of admixtures and evolution, and people surely did not look like modern humans 20 000-40 000 years ago.

Gioiello said...

@ Davidski

Dejian Yuan and Shi Huang read Karl Popper: "It must be emphasized that any result must be held as uncertain at best until it has been verified by at least one other independent approach unless that result is a logical deduction from selfevident axioms. Previous molecular results based on unrealistic assumptions have routinely contradicted trait evidence and common sense. In striking contrast, the results from our new molecular method, both here and in a previous work 19, have consistently found unity between molecules and traits. We expect this intellectually satisfying pattern to continue to hold in future studies of other evolutionary puzzles".
@ Kristiina

Also people like German Dziebel and others should be apologized. I am a literate, a poet and a critic, and intersted myself in genetics when we have pretty only the STRs, but I think having done a good use, if I formulated my 4 golden principles:
mutations happen around the modal
there is a convergence to the modal as time passes
sometime a mutation goes for the tangent
rarely there are multistep mutations.

Nirjhar007 said...

Anyway , this must mean that guys like Dave and others can also publish their researches at bioRxiv , I urge David to to do such in future and also he can push for Journals like Nature ,PNAS etc, although will require co-authors .

Joerg Hensiek said...

Davidski: I cannot comment on the scientific value of these papers (paper 1 and 3 seem to be from the same authors..). But I noticed one thing about the preprints on biorxiv: even they state that these preprints are not yet peer-reviewed, all the preprint articles that I know of were published just 1-2 months after they appeared on biorxiv...just an observation.

Gioiello said...

@ Kristiina
This is my true activity, but for understanding that you should be Italian, with a life spent in studying its literature (and of course many other foreign ones) and it would need another life to live:

ALLA NEGRA TERRA

Augura i 68 al tuo amico
sulla rete folle.
A 69 ci sono io, tu dovrai
aspettare ancora un anno...
Ma perché non un cenno
a sera compiuta?
La rete folle porta tutto
come quella che nel mare,
a strascico, l'acqua pura,
primordiale, e tutti gli scarti
di questo mondo folle, irredimibile.
Ora le tue ceneri
finalmente
hanno raggiunto
alla lapide disadorna
i poveri resti di colui
che fiorì l'albero
nella primavera inerte
senza l'estate
folle di frutti.
La vita ha compiuto il suo volo
e il suo cerchio.
Ora è perfetta, nessuno
potrà distruggerla, nessuno
potrà minacciare
la nera eternità
dell'amore.

Nirjhar007 said...

a friend on the crazy web who accomplishes 68 years

Nirjhar007 said...

yes ,he compares the crazy web to a net in the sea, then it says 'your ashes'.

The Poem is about a dead amico.

Olympus Mons said...

Wouldn't it be something if the guy that says sorry when he thinks he made a mistake ends up having his paper published?


Davidski said...

That'd be really something. But he'll have find a really shitty journal for that to happen.

Olympus Mons said...

@Davidski,
2017 seems to be the year you will have to swallow lots of frogs. Lets just hope genetiker will not be the next up.

Gioiello said...

@ postneo

I don't know why you choose this nickname: post does mean "after" and neo does mean "new". Are you afternew, perhaps a "novissimus"? The fact is that is just the theory of Shi Huang and colleagues that doesn't believe to the recent "out of Africa", but says that mankind derives from many branches separated 2 million years ago and mixed after, but they think that the actual Y and mt came from South East Asia. We may discuss about that, but I think that it merits to discuss that, and not giving for discounted that that cannot be true.
Of course Xyyman did his best for seeming in his reasonings more close to the ancestors or 2000000 years ago than to 50000... considering that anyway men mixed, we could say more to 300000 (the age of Y A00).

Grey said...

i don't know about the details of these papers but just as a general thing

https://phys.org/news/2017-04-humans-america-years-earlier-thought.html

if humans of some form could be blown across the atlantic/pacific 100,000 years ago then there's probably going to be other odd surprises before it's all figured out

Karl_K said...

@Davidski

"I just hope that bioRxiv doesn't turn into a swamp full of this sort of thing."

The physics and math ones are totally full of junk papers. It doesn't matter as long as more and more quality papers use it. Everyone is free to rip the junk ones to shreds.

Such as the one about the European ancestry in the mummy from the Americas. Show me the analysis to prove it isn't just contamination, like in so many hundreds of other cases where that was exactly the problem.

Karl_K said...

@Grey

That early humans in America paper is high on novelty, but very very low on evidence. Science and Nature occassionally let a few of these through just to boost readership. (Like the bacteria that 'used arsenic instead of phosphorus in its DNA' a few years ago.

andrew said...

The benefits of opening up the process of peer review of pre-prints to the general public and providing early access to research far outweighs the costs of some bad papers being shared with lots of people.

If you think the paper is weak, a brief comment can flag it for later peer reviewers, or you can just ignore it because you do not have a personal responsibility to correct every case in which someone might be wrong on the Internet.

John Smith said...

I doubt the Chinese paper about the phylogeny except that it shows how M is closer to L than N is I have seen this before but I wonder if this is true or what mutations would show this. The current phylogeny is correct. However for the mtdna it is very poorly resolved. The current phylogeny does not prove OOA. If someone published a paper 10 years ago on Nature that theorized without ancient dna evidence that U2, U6 and M mtdna as well as K2a y-dna and C1a and C1b y-dna were in Europe around 35-45kya years ago without ancient dna evidence they would be labelled as crazy (except for the U2 mtdna). OOW is a hypothesis that assumes paleolithic continuity into modern age with only mediocre evidence and no ancient dna evidence (oldest ancient y-dna in Africa is only 4kya which is essentially modern).

Alecia Madonado said...


I am Alecia used every single spell worker on the Internet, spent untold amounts of money and discovered they are all fakes…i was the fool though; doing the same thing over and over again and expecting different results. In the end, I decided that I wanted a tarot reading to know what my future held for me; I contacted a woman who lives locally to me and she told me about a man named (Dr Abalaka); he does not advertise on the Internet, has another job for income, has no set prices, makes no false promises and refuses to help anyone that cannot be helped and even helps for free sometimes, he will give you proof before taking money. He is a wonderful man and he was the only person who actually gave me real results. I really hope he doesn’t mind me advertising his contact on the Internet but I’m sure any help/ extra work will benefit him.contact him as dr.abalaka@outlook.com He travel sometimes.love marriage,finance, job promotion ,gambling voodoo,lottery Voodoo,poker voodoo,golf Voodoo,Law & Court case Spells,money voodoo,weigh loss voodoo,any sicknesses voodoo,Trouble in marriage,it’s all he does Hope this helps everyone that is in a desperate situation as I once was; I know how it feels to hold onto something and never have a chance to move on because of the false promises and then to feel trapped in wanting something
more. his cell phone number 760-935-3804 his website is coming up soon!

P Piranha said...

Completely agree with andrew. Peer review is quite insufficient to cut down on scientific incompetency; scientific consensus forms today in a highly organic process independent of the institutions associated with scientific papers. Might as well formally recognize this. Open review will lend ammunition to the crazies, but they were always going to be crazy.

batman said...

@ Kristiina

"Modern looks are a result of admixtures and evolution..."

Obviously.

Though, what does define the general term 'race' - as in 'etnicity' - in your opinion?

Grey said...

Karl_K said...
"That early humans in America paper is high on novelty, but very very low on evidence."

Fair enough.

There are Amerindian legends about fighting red-haired giants which i'm hoping turn out to be true so i'm a little biased.

batman said...

Matt

"I guess that sunlight is the best disinfectant, as they say."

Sure.

Shedding new light on old issues may certainly help adress unfortunate infections - such as mere prejudice, conforming presumtions and premature consent. Scientific progress is often sparked on the exeptional suggestions.

In the above cases we still have to await more thorough investigations to give any just and balanced judgement about any of them.

The presented study of the Chincorro-mummies happen to co-incide with the long-known discovery of Bradford and Stanford, proving a connection between the Solutrean and the pre-Clovis techno-complexes.

Since the crossin of oceans were proven to have existed among "ancient civilizations" the major argument against this hypothesis - presuming it was 'impossible' - have fallen. Which means that there are THREE different lines of evidence, from THREE different disciplines of science - claiming that there have been sea-voyages taking place between Eurasia and America during the last phase of the Late Paleolithic.

Moreover - during the last decades we've had numerous repports about Middle-Paleolithic/Late-Paleolithic humans in America. The recent discovery from San Diego is anything but a "stray object".

https://www.scahome.org/publications/proceedings/Proceedings.09Carter.pdf
https://en.wikipedia.org/wiki/Hueyatlaco

The recent article in NG gives a decent summary:
http://news.nationalgeographic.com/2017/04/mastodons-americas-peopling-migrations-archaeology-science/

Which actualizes your comment. The question is, though, WHAT of all this should to "desinfected"? The old view - or the new one?
http://press.uchicago.edu/ucp/books/book/chicago/G/bo21263519.html

Anthro Survey said...

Kristiina:

That is not always the case unless the following conditions are met: 1)both populations in question have resided in the area for a vey long time 2)Both populations are relatively primitive and at the extreme mercy of their respective environments 3)Fischerian selection doesn't take place 4)Mininal influx of other populations into both areas. The more consitions are met, the more this is going to be the case.

Some examples of discontinuity:

Georgians look more like Lebanese and Iraqis than like ethnic Russians despite geographical proximity. Tajiks look a lot more like Georgians than they do like ENA-heavy populations in closer proximity to them to the east. Iberians look a lot more like Southern French than like average Maghrebis who in turn look a lot more like average Egyptians or Saudis than the average Iberian.

Anthro Survey said...

Kristiina:

Having said what I've said, I'm not denying that smooth phenotypic clines are prevalent. It's just that those clines are more accounted for by the nature of human migrations in the last 12K years, not so much on the direct transition of environmental conditions across space. The nature of most migrations of a people B into territory of a people C has been that it tapered down as a function of distance penetrated. India is a perfect examples of this and so is Europe, for that matter.

German Dziebel said...

"Peers" are just groups of scholars sharing the same general assumptions. They are not Olympic gods of science. The Shi Huang papers challenge many of those assumptions. So, "peers" may not accept them into print simply because it's above their head. There needs to be an open discussion between Shi Huang's team and the "peers" regarding those assumptions. Geneticists working in the field of human dispersals is a motley crew of rotated drosophilologists, purely random one-eyed quant goblins, fox, feline, marsupial and other biologists, cancer and diabetes researchers - they are great at generating data and they have revolutionized our worldview through this new data. But they are not anthropologists trained to think through the big picture of human origins. I therefore welcome different schools of thought here.

The new Y-DNA and mtDNA trees generated by Shi Huang et al. make more sense than the mainstream trees, although Shi Huang needs to clean up some of his data capture, as I pointed out a couple of times.

http://anthropogenesis.kinshipstudies.org/2017/01/world-science-en-route-from-out-of-africa-to-out-of-america-first-stop-is-out-of-asia/

Shi Huang's American paper is just as confusing regarding the "origin of Amerindians" as any other. It's the current Zeitgeist: everybody has their own version of how America got a-peopled using this piece of data and then that.

The Chinchorro paper does not challenge assumptions, so it will be peer-reviewed and likely dismissed for a good reason.

Davidski is an Australopolocine of stagnant mental abilities. His little processor just got suspended and now spits out only insults. :) :) :)

Nirjhar007 said...

Well German you are getting some parallel researches and finds , I like your approach as I told you before, let see .

Karl_K said...

I just read that multiregional one straight through.

It is a disaster. They even claim that Neanderthals were Africans that recently moved into Eurasia and mixed with the humans living there. They didn't include Neanderthal and Denisovans as outgroups in their mtDNA and Y phylogenies. They claim that Africans are closer to Chimps because they don't know how SNPs were chosen for arrays.

I could go on and on. Total waste of time.

Simon_W said...

Anthro Survey said: "Having said what I've said, I'm not denying that smooth phenotypic clines are prevalent. It's just that those clines are more accounted for by the nature of human migrations in the last 12K years, not so much on the direct transition of environmental conditions across space. The nature of most migrations of a people B into territory of a people C has been that it tapered down as a function of distance penetrated. India is a perfect examples of this and so is Europe, for that matter."

Indeed, well said. I remember a 23andme customer with north Tuscan ancestry being confused about his high levels of northwest European ancestry. He believed the explanation was that northern Tuscany is on a more northern latitude than the southernmost parts of France. He couldn't understand the fact that there were migrations from central Europe into Tuscany and that this was the reason.

Gioiello said...

@ Simon_W
"Indeed, well said. I remember a 23andme customer with north Tuscan ancestry being confused about his high levels of northwest European ancestry. He believed the explanation was that northern Tuscany is on a more northern latitude than the southernmost parts of France. He couldn't understand the fact that there were migrations from central Europe into Tuscany and that this was the reason".

It is just what we are doing just examining the Y and the mt, that are less powerful of the autosme, but more centred to the purpose, and the question is open, also about the last sample of Bertolini, from Sassalbo, Tuscany, who resulted R-A366 (the old L277 haplogroup) but with DYS389II=+16 and not 15 which is modal in the R-L277, DYS392=13 and not 14 (or at least 15 in some Italian subclades) and above all YCAII=16-23 (and we have from Volterra. Pisa, an YCAII sample =16-22). Thus these Tuscans could be the first to break the series of SNPs at the L277 level, thus questioning all the data which would bring to Samara and Armenia as the origin of the haplogroup. Of course also these samples might have come from elsewhere. But always my question: but did all came here, and there didn't leave anyone?

Karl_K said...

On the other hand, it is kind of amazing how they can incorrectly use data, misinterpret the actual meaning of certain statistical methods, cherry pick SNPs, and 'eliminate noise', while adding completely unfounded rationales for 'better' phylogeny building in order to make a somewhat consistent story.

I wonder if they actually believe it, or if they just want attention and funding from the Chinese government. It is basically propaganda.

German Dziebel said...

@ Karl_K

"They even claim that Neanderthals were Africans that recently moved into Eurasia and mixed with the humans living there. They didn't include Neanderthal and Denisovans as outgroups in their mtDNA and Y phylogenies. "

This is a restatement of what they did.

"I could go on and on. Total waste of time."

You don't have to go on and on restating what they wrote. Do you have any reasons why it's a total waste of time? Neanderthals did come from Africa, didn't they? Neanderthals are not an ancient instance of the same species that we now know as Homo sapiens or are they? Or are they like Latin to French, an ancestral state that we can safely use as an outgroup?

Synome said...

It seems to be a longstanding policy of the Chinese anthropology community to promote multiregionalism and Chinese continuity since the LP. Chinese researchers have often claimed that AMH evolved in situ from ancient hominids in China based on supposed early Sapiens remains found there.

Unfortunately, this doesn't bode well for future aDNA studies coming from China. I hope that Qiaomei Fu can push for a change in direction.

German Dziebel said...

@Synome

What you wrote is true. But Western scholars are craftier. They invented out-of-Africa to hide their racial biases. It's called "repackaging." First, they assumed Africans (specifically, the descendants of African slaves in America who were their first "African" sample) must be ancestral, hence they invented a tree rooted in Africa. It just looked good for the press. Very progressive and politically correct. An affirmative action of sorts. Then they obtained Neanderthal DNA and rooted the human tree in Neanderthals. But Neanderthals are an African species, so again an African bias was employed.

The Chinese team doesn't share this strange Western fascination with Africa. They like China.

Gioiello said...

@ German Dziebel
"The Chinese team doesn't share this strange Western fascination with Africa. They like China".

And we shouldn't forget that we descend from the hunter-gatherers of the Siberian corridor and only there is our hope to survive.

Karl_K said...

@German

"Do you have any reasons why it's a total waste of time? Neanderthals did come from Africa, didn't they?"

I totally agree that pre-Neanderthals likely came from Africa. But that is not the point. The point is that they suggest that the admixture came from Modern Humans being all over Eurasia for millions of years, and even evolving there, and then some Neanderthals, who were not previously in Eurasia (according to them) came over and mixed with those Modern Humans. But, only in Eurasia, even though they came from Africa, where they didn't mix, but other quite unrelated Neanderthal relatives did mix with the Modern Humans who moved into Africa. So... some kind of hostage exchange situation?

I know that you like to do the same kind of 'fact' twisting as they do, so I am not surprised that you like the paper. Can you please explain how Native Americans are the most diverse population in the world based on the fixation index? That would be swell.

German Dziebel said...

@Karl_K

How are old are you? I assume it's not too late for you to go to graduate school and learn what facts are and what fact-twisting actually looks like. What I've been doing all along is untwisting of the "facts" that were placed into the foundation of out-of-Africa theory.

When you write "according to them" above you're forgetting that Shi Huang is only going with what we know for a fact and what plain logic says. Neanderthals are an Africa-derived species, hence they came to Eurasia. Agree? We don't know where modern humans originated, that's what we are trying to figure out, but we know that they have been present in Eurasia for at least 40,000-100,000 years (and now in America for 130,000 years maybe) and that there was admixture between them and Neanderthals. The oldest mtDNA haplotypes from Europe to (South)East Asia are all haplogroup R, which is geographically a most widely spread type now and 40,000 years ago. No African mtDNA types are found outside of Africa until slave trade times. It stands to reason - from what we currently know as a fact, I remind you, - that Africa must have been peopled from Eurasia and not the other way around.

I don't think this new interpretation can currently be supported by a sequence of skulls but this a thing of the future, not the present, because those archaeological and paleontological things accrue over time and we don't know what and when we're going to find. For now we have to go with what we know, not with what we wish were true, such as out-of-Africa.

Fst is a measure of intergroup allelic diversity. It's world highest in America followed by PNG, east Asia and only then Africa and Europe. Neanderthals and Denisovans were even higher on Fst than Amerindians, and they are the most ancient molecular species we currently have information about. Fst has gone down considerably in places like Western Eurasia in the past 10,000 years and we know why - because of massive waves of admixture. Intragroup diversity, on the other hand, increased in West Eurasia over the past 10,000 years. It stands to reason therefore that if we were to choose between two kinds of diversity as a proxy for population age, then we would choose Fst (intergroup diversity) and not intragroup diversity. The latter is a function of admixture and the places where it's world-highest (Africa and Europe) must be most admixed but not most ancient.

Does it make sense?

Karl_K said...

@ German

"The oldest mtDNA haplotypes from Europe to (South)East Asia are all haplogroup R, which is geographically a most widely spread type now and 40,000 years ago."

Wrong. We have both complete mtDNA, and some autosomal DNA from 430,000 year old hominins from Sima de los Huesos, Spain. The mtDNA is clearly related to Denisovans, to the exclusion of Modern Humans, and the autosomal DNA is clearly related to Neanderthals, to the exclusion of Modern Humans.

Karl_K said...

@German

"It stands to reason therefore that if we were to choose between two kinds of diversity as a proxy for population age, then we would choose Fst (intergroup diversity) and not intragroup diversity."

Wrong. No. It does not stand to reason. Strictly speaking, FST is NOT a genetic distance. It has zero relationship to genetic distance, and cannot ever accurately be used as a proxy for population age.

German Dziebel said...

@Karl_K

Again... where do you get your "wrong" claim? What "genetic distance"? Where do you see it upstring? There are two kinds of genetic diversity - intergroup (between-group) and intragroup (within-group). What is so hard about it? is it my English that creates a language barrier between us? I wasn't the first one to use high genetic diversity as an argument for population antiquity. Out-of-Africanists did. I just think it's the wrong kind of diversity to hang your hats on. But I'm willing to not use the "diversity" argument at all, as it does vary depending on actual historical circumstances. High intergroup diversity is a more solid predictor of age because it's actually attested in Mid-Pleistocene hominins whereas African high intragroup diversity increases not with antiquity but with recency. Since 1492, America is more diverse on this measure than Africa because of massive admixture from everywhere.

Karl_K said...

@German

"High intergroup diversity is a more solid predictor of age"

This just is not true. Fst has nothing to do with 'age' as you are describing it. You are implying that 'age' is genetic distance from other groups. Such that Native Americans would be the most divergent human group, and split off first, before the others diversified. In fact, this is an incorrect way to interpret these statistics.

German Dziebel said...

@Karl_K

Your counterarguments are all "from the hip." I'm not implying that "age is genetic distance." What kind of phrasing is it, in the first place? It's hard to talk to you because your language is fuzzy. Hence, I have to go back every time to an ex-cathedra mode.

What you need to understand is that there are population splits happening within and between a) continental; b) native and immigrant groups, and then there's admixture happening (or not) between those populations as well. Plus splits and admixtures happen at different times, so relative chronology of splits and admixture events is very important. E.g., when people say that Amerindians are admixed between Europeans and East Asians, this can't be right (without a special case of a bottleneck) because Europeans and East Asians have much higher intergroup diversities than Amerindians, so if they mix up then that diversity would go up (or at least stay the same) but no go down. What people see in the data are two ancient populations that got admixed in America (thus driving Amerindian Fst down from an even more ancient baseline attested in Neanderthals and Denisovans) after an expansion into East Asia and Europe. This is again plain logic because subpopulations that stayed behind would be more likely geographically to admix with each other than those populations that spread into 2 opposite directions and colonized 2 vastly different geographic masses. Since Fst is lower between any East Asian population and any West Eurasian population than it is between 2 Amerindian populations (already internally admixed!), Amerindians are older than either East Asians or West Eurasians. But they are related to both, hence East Asians and West Eurasians split from (proto) Amerindians, or expanded from America geographically.

Are we clear so far?

German Dziebel said...

@Karl_K

Notice that Shi Huang also has an admixture between East Asians and Europeans happening in America. This is a major departure from your wishful "Western consensus" that postulates the admixture to have happened in Siberia prior to a migration to America.

Huang's idea is good but not as good as my out-of-America model. This is because for his model to work he has to endorse the Solutrean hypothesis and assume that a) mtDNA X2 was present in Western Europe in the Solutrean times; b) its absence in Siberia is accidental. This is where his matter-of-fact approach faults because we don't have the evidence that he so badly needs. We know from several ancient samples that X2 shows up in Europe only in the last 10,000 years (the agricultural migration from the Near East, I presume). Until we have X2 ascertained in Solutrean aDNA, we have to go with the Beringian land route, and this Beringian land route must have been traveled from the New World into the Old World, not the other way around, because, again, the New World is mitochondrially connected to both East Asia and Western Eurasia.

Karl_K said...

@German

"Are we clear so far?"

Quite clear. I really like reading your comments.

I am just a little confused I guess. I only learned about this all last fall when my after middle-school group each sequenced our genomes on an Ion Torrent machine, then aligned the reads to a reference sequence on Raspberry Pi computers that we built and then extracted the SNPs inti vcf files, and built phylogenetic trees with our haplogroups, and learned about all the population genetics infos and definitions that were in our new textbooks.

So... I guess I'm a few decades behind you in knowing all this stuff.

Please go on. It's like I'm picking up free diamonds on the sidewalk.

Gioiello said...

@ German Dziebel
"We know from several ancient samples that X2 shows up in Europe only in the last 10,000 years (the agricultural migration from the Near East, I presume)".

That X2 isn't older in Europe than 10000 years I'd have many doubts. Not only Croatia is plenty of X2*, but I found very likely an old X2* also in Italy. I should find that.

German Dziebel said...

@Gioiello

Having heard legends about your superhuman foresight abilities, I'm trembling in fear. My only hope is that even if X2 is of a Solutrean date in Western Europe that they won't find a broken raft with a projectile point stuck in it that sailed from Portugal to the Bahamas 20,000 years ago.

:)

Karl_K said...

@German

"My only hope is that even if X2 is of a Solutrean date in Western Europe that they won't find a broken raft with a projectile point stuck in it that sailed from Portugal to the Bahamas 20,000 years ago."

Is this a joke? It seems funny... but with my limited English I can't tell if it is a joke or serious.

German Dziebel said...

@Karl_K

It's a joke.

:) is a smiley face. It just doesn't show up right.

Gioiello said...

@ German Dziebel

I ran again for you in the "Jame Lick calculator" the mt of Marco Lombardi:
HVR2: 73G 153G 225A 263G
CR: 750G 1438G 1719A 1888A 2706G 4769G 6221C 6371T 7028T 8860G 9449T 11719A 12705T 13966G 14470C 14766T
HVR1: 16092C 16278T (16519C)
It is X2 (G225A T16223C) with 3 extra-mutations: 1888A 9449T 16092C (16519C)

"Having heard legends about your superhuman foresight abilities, I'm trembling in fear".

Let's wait the BB Behemot.. and we'll speak again...

Karl_K said...

Thanks German!

I am gonna tell all my friends at school about that one! Awesome! :)

German Dziebel said...

@Gioiello

Yes, let's wait for the BB paper.

I'll be most happy if you turn out to be right.

@Karl_K

No joke.

Gioiello said...

@ German Dziebel

X2 19233.8 2640.9+/-
Behar 2012b. And don't forget the meager figure that Behar had with his tree from the Sardinian mt J2a1 with 7 extra-mutaion old 11000 years... when he thought that J2a1 were 10000 years old without extra-mutations.

Don't forget that I am a Tuscan...

"I'll be most happy if you turn out to be right".

You didn't forget that.

German Dziebel said...

@Gioiello

"You didn't forget that."

What are you talking about?

"Don't forget that I am a Tuscan.."

Where's that?

@Karl_K

Attention: Joke!

Gioiello said...

@ German Dziebel
"Don't forget that I am a Tuscan.."
Where's that?

Have you ever had news of Dante, Petrarca, Boccaccio, Masaccio, Brunelleschi, Leonardo, Alberti, Michelangelo, Galilei and 1000 others, and that Ashkenazim (27% of all the Nobel Prizes) Davdiski said having 51% Tuscan ancestry?

Anyway I hoped you were able to catch my irony...

Karl_K said...

@Gioiello

Hard to get through sometimes. Am I right? I doubt any irony made it over there.

Gioiello said...

Seen that you are using your real name, as I am doing, and very likely you are of German origin, I'd be curious to know your Y and mt, if you know them...

Gioiello said...

My post was for German and not for you. I couldn't foresee that you'd have posted in between...

Karl_K said...

@Gioiello

My father is Y R1b, and my mother mt K2b. When I am old enough, I will tell you if I am their child. Germany has very strict laws against revealing this kind of info for minors.

Gioiello said...

Karl, certainly you aren't a German. Too much Italian irony, and you are closely linked to me in both "your" uniparental markers: R1b1a2-L23-Z2110 , K1a1b1e.

Karl_K said...

@Gioiello

Don't worry. I am probably from a line of Italian Jews who mixed with a Western European population somewhere in Germany? Once we learn English, we are hilarious.

What's orange and sounds like a parrot?

Gioiello said...

@ Karl_K

If a knew your R1b subclade I could answer your question. The mt is certainly European.

Karl_K said...

So you can't say what is orange and sounds like a parrot without knowing that my father is R-M697?

German Dziebel said...

@Karl_K

"Germany has very strict laws against revealing this kind of info for minors."

Too bad, we don't have laws restricting Internet use for minors. But don't count on it. Grow up fast!

Lukasz M said...

From Biorxiv rules:)

"Articles are not peer-reviewed before being posted online. No endorsement of their methods, assumptions, conclusions or scientific quality by Cold Spring Harbor Laboratory is implied by their appearance in bioRxiv.

Articles are not typeset before being posted online. The author’s manuscript is either submitted as, or automatically converted into, a PDF file.

Articles appear in bioRxiv in the order in which they were received. They are retrievable via the web interface at no charge."

Lukasz M said...

So it's their policy. But it was always like that???

John Smith said...

Actually the mtdna tree will be updated and at least some part of it is very likely to be incorrect. Haplogroup K for example was used to thought to be different than U but its a subclade of U8. I remember nearly a decade ago when IWX was thought to exist. I think there is nearly 100% chance that a small part of the mtdna tree is wrong and will be updated. And I know 100% chance that it will be updated. Unlike the y-dna which finally has a good tree the mtdna tree is of extremely poor resolution. For example we still don't know who the closest relative to mtdna R0 (pre-HV) is , is it R2'JT is is U is it P is it B? Does anyone here have any access or even ideas on a more updated mtdna tree? In addition there is a rumor that M is closer to L3 than N is which would imply that M is much younger than N is there any truth to this what mutations would prove or disprove it? What branch of L3 is M closest to? Is it the same as the one N is closest to? Do most branches of M fall under a M0 which is akin to a R?

Anthro Survey said...

@Simon:

How much of 23andMe's "northwest Euro" component in Tuscany can be attributed to the first Kurgan-admixed migrants, to Bell Beakers, to later migrants from North Europe and to it simply just being a modal component in Western Europe due to very similar ancestral sub-populations?

What can the centimorgan thresholds tells us about the timing involved?

Btw, southern French, apart from Gascons, score relatively high on "NorthwestEuro"---as high as Po Valley folks. Gascons don't because a subpopulation there was used to construct a reference "Iberian". lol! So you get people from places like Tarn, Bearn or Spanish Euskadi w/90-100% Iberian. 23andMe cracks me up sometimes.

I'm sure our very own Maju would get a very high "Iberian" score. Maju, if you're reading and don't mind divulging, please do. Curious.

Anthro Survey said...

@SimonW I meant "or*" not "and" in my question.

Anthro Survey said...

@Gioiello:

How do we know Ashkenazis specifically had Tuscan ancestry and not from Po Valley? They are not such drastically different populations and sometimes, based on what I've seen from some Rumagnol's test results, identical. LOL

Some cities in the valley were quite formative in European Jewish identity----take Mantua and its Rapoport family.

If there's high-confidence data for this I'd be glad to see it.

Anyway, not surprised. Tuscany+most of the Po valley+even Umbria and Marche(to an extent) have been some of the most influential regions in Europe and the world in ways people don't realize. "Renaissance" is a concept that betrays a medieval golden age in Tuscany and much of the Po which was a source of cultural and techno achievements for the rest of "Frankish Europe" at the time. Long story. Anyway, much of this probably has to do with cognitive strength of its people which evolved under mysterious selective pressures.

Gioiello said...

@ Anthro Survey

"@Gioiello:

How do we know Ashkenazis specifically had Tuscan ancestry and not from Po Valley? They are not such drastically different populations and sometimes, based on what I've seen from some Rumagnol's test results, identical. LOL

Some cities in the valley were quite formative in European Jewish identity----take Mantua and its Rapoport family.

If there's high-confidence data for this I'd be glad to see it.

Anyway, not surprised. Tuscany+most of the Po valley+even Umbria and Marche(to an extent) have been some of the most influential regions in Europe and the world in ways people don't realize. "Renaissance" is a concept that betrays a medieval golden age in Tuscany and much of the Po which was a source of cultural and techno achievements for the rest of "Frankish Europe" at the time. Long story. Anyway, much of this probably has to do with cognitive strength of its people which evolved under mysterious selective pressures".

That Ashkenazim are 51% Tuscans (but Tuscans because they are in the 1KGP, but it did mean "Italians" very likely) was said from the same Davidski, but he gave also 29% (if I remember well) linked with Samaritans with which I didn't agree, thinking that the Middle Eastern component weren't more than 10/20% after the medieval bottleneck. But perhaps you know that I don't consider the autosome in my analyses, because so many times it changed and the same data gave different outputs from the same calculator in diferent times, as for instance GEDmatch (but is it really due to Ted Kandell? If so, no wander).
I study from more than ten years only the uniparental markers, and being K1a1b1e, close to the huge Ashkenazic haplogroup K1a1b1a, am saying from so long that they derive from me and not the other way around, being K1a1b1 European, etc, and that long before the poaper of Costa et al. 2013, for so long adversed in its publication from Jews. Frequently I published that single haplotypes in common between Jews and Italians, and thought of Jewish origin, demonstrated the other way around. Frequently Jews took away their data from public projects after that. I am interested above all to my R1b1 and subclades haplogroup, and so far only a few Jewish subclades seem almost old for being entered the Jewish pool before the diaspora, but next data should demonstrate that it wasn't so.

Simon_W said...

@ Anthro Survey


To my understanding the various 23andme ancestries don't go back very far. (BTW, I'm calling them ancestries rather than components, because they're not the same as ADMIXTURE components, due to the very different method.) The company aims at a time depth of about 500-600 years and filters out short (hence old) exotic segments that are placed inbetween long, well defined blocks. But of course recent ancestry is build up from ancient ancestry, and if a certain type of ancestry is important enough in the genome, some of the ancient, short segments are jumbled together into longer ones, even if the admixture took place longer ago. I suppose the northwestern and French&German ancestry in Tuscany is most of all from the Villanovans and to a lesser degree from Longobards, though in the very north IE Ligurians may also have brought some northern influence. I don't know what centimorgan threshold they use, but the smallest reported segments have a length of 0.1% of the autosomes.

Indeed, 23andme's Iberian ancestry peaks around the Basque area. But afaik Maju is only partly Basque by DNA, he's also got Romagnol and Spanish ancestry, IIRC.

Interesting what you say about the Po valley. Judging from the local differences in the incidence of light hair colour I suppose that the levels of Northwest Euro admixture differ quite lot between the regions. Though that was in the late 19th century, I guess nowadays modern Padanians are more mixed up among each other. But for example the area of Forli used to be particularly low on light hair, and to a lesser degree most of the Emilia-Romagna, at least the flat areas – which means that the Gaulish presence there was quite reduced by the Romans, which is in line with what the Romans themselves wrote.

Simon_W said...

@ Gioiello

You asked about German's ethnicity, well, according to his own site he's of Baltic or Russian Askenazi descent, IIRC. The surname Dziebel is from dialectal German and maybe also Yiddish and means onion, hence I first thought it was a joke. But yes, it's in fact his real name - Jewish surnames are often quite peculiar. ;-)

Gioiello said...

@ Simon_W

"@ Gioiello

You asked about German's ethnicity, well, according to his own site he's of Baltic or Russian Askenazi descent, IIRC. The surname Dziebel is from dialectal German and maybe also Yiddish and means onion, hence I first thought it was a joke. But yes, it's in fact his real name - Jewish surnames are often quite peculiar".

I tank you. I understand now why he didn't answer my question about his Y and mt. He feared that I demonstrated that he is Italian !!!!!

Gioiello said...

Onion? Italy is plenty of Cipolla, Cipolli, Cipollini etc etc

Ebizur said...

John Smith wrote,

"Do most branches of M fall under a M0 which is akin to a R?"

According to Supplementary Figure 14 of Sebastian Lippold, Hongyang Xu, Albert Ko, Mingkun Li, Gabriel Renaud, Anne Butthof, Roland Schröder, and Mark Stoneking, "Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences" (Investigative Genetics 2014, 5:13), M3, M4, M5, M18, M30, and M65 should share a MRCA significantly more recent than the MRCA of haplogroup M as a whole. This subclade of haplogroup M accounts for most members of haplogroup M in South, Central, and Southwest Asia that do not belong to M1, M2, or East Asian types of haplogroup M. This subclade also appears to include as a branch fairly close to its base M24, which has not been found in any South, Central, or Southwest Asians as far as I know, but rather has been found in a Cambodian and some Filipinos (specifically, "non-Negritos" on Palawan).

This hypothetical major South Asian subclade of haplogroup M may be relatively closely related to haplogroup M11, whose present-day distribution is centered on China. However, Supplementary Figure 14 has positioned Cambodian M51 as the nearest outgroup to a clade comprising M11 and the aforementioned South Asian subclade; on Wikipedia, someone has claimed that M51 should be relatively close to Chinese M20 and African & Mediterranean M1 instead.

As for M2, which has been billed as the "oldest mtDNA haplogroup in South Asia," that study's analysis has positioned it relatively close to Northeast Asian & American haplogroup D, which together would comprise one of the more basal branches of haplogroup M.

I think the small size of the mtDNA molecule and mutational limitations enforced by purifying selection restrict the phylogenetic resolution that may be afforded by research of human mtDNA. However, the results of Lippold et al. (2014) and other studies that I have seen do suggest quite strongly that East Asian haplogroup M is more diverse than South Asian haplogroup M, especially when M2 is considered separately from the rest of South Asian M.

Gioiello said...

Of course also the word is from Latin and very likely is Italian surname Cipolla. ZWIEBEL, f. (Swiss zibele, Bav. zwifel, Thuring. zippel), 'onion, bulb,' from the equiv. MidHG. zwibolle, zibolle (with the variants zwippel, zwifel, zibel, zebulle), m. OHG. zwibollo, zwivolle, m. A corruption of Lat. caepulla, ' onion,' whence also the Rom. words, Ital. cipolla, Fr. ciboule ; Dan. swible has been adopted from Ger. The genuine G. word for 3»it&el i8 93ol(e (properly ' bulb, ball'), on which MidHG. zwibolle was based. The E. word bulb is derived from the Lat. bulbus (Gr. /9oA£os), ' bulb, onion.'

Lee Albee said...

Looking at the Native American paper by Smith. It is very thin based on samples with really low number of SNP's

Would be better off looking at Marc1492 and Kennewick. Both show significant-non East asian/Native American ancestry.

Marc1492 is 7% western eurasian--this may or may not be real

Kennewick-very interesting genetic specimen.
Demonstrates ~20% Western Eurasian DNA.
Demonstrates long regions of homozygosity. Looks to be inbreed (in contrast to Aznick-1, Ma'lta, Marc1492)
Western Eurasian DNA is clustered into long runs through out his genome. unlike Aznick-1 or Marc1492 have the western eurasian alleles scattered without large blocks.(Gedmatch Eurogenes K13 or K36 test with chromopainting)
So western ancestry would have likely been relatively recent in relationship to his birth. Interestingly, while the snp are western eurasian and the regions are long--they do not match for significant lengths to any sample I compared them to.


So weird.


How
While he does have one allele for brown eyes--eye color is not driven by just one gene.

Kennewich (greenish/yellowish eye color)
TT at: rs916977 - Adds melanin. Some darkening.
CC at: rs3794604 - Blocks some melanin. Often gives light colored eyes.
GG at: rs7174027 - Blocks some melanin. Often gives light colored eyes.
CC at: rs1129038 - High Melanin production. Brown.
AA at: rs1105879 - Weak Amber Gradient
AA at: rs4778138 - Weak Amber Gradient
AA at: rs4778241 - Medium melanin on Anterior Epithelium. Brown.
AA at: rs12913832 - High melanin production on Anterior Epithelium. Adds yellow, amber, or brown. Some darkening. Contributes to brown.
CC at: rs12203592 - No pigmented Collarette.
CC at: rs4779685 - Flecks (Nevi).

Gioiello said...

@ German Dziebel

After the paper of Sarac et al., Maternal genetic Heritage of Southeastern Europe, Reveals a New Croatian Isolate and Novel, Local Sub-Branching in the X2 Haplogroup, Annals of Human Genetics (2014), 78, 178-194, it is clear that Lombardi belongs to another subclade of the X2h haplogroup, being negative for the three subclades even though partially tested from 23andMe:
Lombardi X2 (G225A T16223C)
73G 153G 225A 263G 750G 1438G 1719A 1888A 2706G 4769G 6221C 6371T 7028T 8860G 9449T 11719A 12705T 13966G 14470C 14766T 16092C 16223C! 16278T (16519C)
i4000775 MT 12397 A
rs28359178 MT 13708 G
i3001753 MT 16255 G/ 277 not tested
i4001101 MT 15310 T
i3001933 MT 153 G
i3001745 MT 16248 C
i3000535 MT 226 T
T16223C! but
8467 not tested
i4000648 MT 9033 A
Then no subclade but X2/G225A*
8639 not tested
12429 not tested
15892 not tested
i3001763 MT 16261 C
i3001905 MT 16399 A
It is ridiculous that Mr Van Oven didn't accept the results of the paper, being the FMS tested from "the Estonian Biocentre and Department for Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia" (p 181).
It is more difficult to support that X2 weren't in European Refugia during the LGM, and to German Dziebel I suggest to take in more account my results, also for his tentative in disproving the Solutrean theory about the peopling of America supported from Shi Huang and his colleagues.

Lee Albee said...

@Gioiello

I personally think that X2 dissemination in Europe is really complex.

I see that a very early variant--near the root of X2 could have entered europe either via North africa or through southern europe during the LGM.

I think this early spread resulted in X2a/j ending up in Europe and early X2b'd in europe--Iberia to be precise. X2a goes extinct but X2j hangs around for awhile. Though X2j could be unrelated to X2a and entered during a later near eastern population migration. X2B'd expands with early post glacial movements .... Can't prove it though.

Estimates of X2c place it in Iberia between Mesolithic and Neolithic (between 9 and 6K BC) but who knows when it really arrived..

X2e entered with the Steppe people......

Would it not be a kick in the head if C4 actually crossed the atlantic and then back migrated into asia from the Americas..... Probably not but fun to think about.

German Dziebel said...

@Gioiello

I looked at the ancient mtDNA types reported by Olalde and Mathieson, and all X2 samples are from the Neolithic and the Bronze Age. This is not consistent with Shi Huang's prediction but is consistent with my prediction. Please check for yourself, as I may have missed something.

Where's Tuscany again?

:)

Poise n Pen said...

Very open minded as usual lol

Normandie Kent said...

Yes, they also say they have been in the Americas forever since the dawn of time, of they crossed the ocean on rainbows. Why pick and choose which myth or oral tradition we believe?' One more thing, the Paiutes never said that those people were giants, just cannibals with red hair, which could of been Red Ocher, or some type of dye.

Normandie Kent said...

Opened minded yes, but don't let your brains fall out while your being " opened minded ".