February 24, 2015

Mutation rate again (Lipson et al. 2015)

This estimate is in-between 1.2 and 2.5x10-8, the two most quoted values for this parameter. It seems like such an important number that I'm wondering if it would be possible to brute force estimate it. Maybe people who have whole genomes of parents-offspring should get together and do the mother of all meta-analyses to pin down this number.

From the paper:
For example, a recent method for estimating population split times from coalescent rates placed the median split of African from non-African populations at 60–80 ky and the split of Native Americans from East Asians at ∼ 20 ky, both assuming a per-generation mutation rate of 1.25 × 10−8 and an average generation interval of 30 years [28]. [...] Using our inferred rate also makes the dates more recent, but only by a factor of about 1.3 rather than 2, i.e., ∼ 46–61 and 15 ky (with some associated uncertainty both from the model and from our estimated rate), neither of which contradicts external evidence.
The first of these estimated splits overlaps the dates of estimated Neandertal admixture by the Ust' Ishim and Kostenki papers. For a variety of reasons that I've repeated ad nauseam, I think that the split of Africans from non-Africans first happened about 100ka with Out-of-Africa-into-Arabia. But, if there was back-migration into Africa, maybe this can be brought down. The 15ky value for the East Asian/Native America split seems too young: it's as late as could plausibly maintained for the colonization of the Americas, but the split of the two must have happened some time before that (because the ancestors of Native Americans and East Asians would have split long before a group of them made the crossing into the Americas).

bioRxiv http://dx.doi.org/10.1101/015560

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Mark Lipson et al.

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Classical methods based on sequence divergence have yielded significantly larger values than more recent approaches based on counting de novo mutations in family pedigrees. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.65 +/- 0.10 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.

Link

42 comments:

Sgt said...

Why an "average generation interval of 30 years" ?
RE Neolithic America:
Majority of females died by age 26: First Americans, National Geographic, January 2015
http://ngm.nationalgeographic.com/2015/01/first-americans/clues-graphic

It seems the generation-interval should be a changing variable, perhaps dependent on population size {Ne}

dwaggonerstr said...

It is logically impossible for Amerindians to have "split" from East Asians. The oldest Amerindian skulls are Amud 1, Predmost 3, Upper Cave 101, Skhul IV and Saint Cesaire 1. All are older than 27,000 years and as old as 105,000 years.

The oldest East Asian (Mongoloid) skulls are considedably less than 10,000 years old, appearing in Asia only way after Native Americans (Neanderthals) are alleged to have made their final migration to the western hemisphere.

Marcel F. Williams said...

The split between Africans and non Africans occurred 2.1 million years ago.

There hasn't been enough time since then for regional groups of human ancestors to become isolated long enough to become new species and to prevent gene flow.


Marcel

aniasi said...

'Majority of females died by age 26: First Americans, National Geographic, January 2015'

Probably true of the population as a whole. However, if you made it past the twenties, you could expect to live into your fifties. Life expectancies are heavily skewed by infant mortality, so historically it increased by age.

Disregarding life expectancy at birth makes sense in this case, since fertility is better related to life expectancy on beginning the teenage years. On that basis, an average generational age of 25 or 30 is very reasonable.

Tobus said...

@dwaggonerstr:
The oldest Amerindian skulls are Amud 1, Predmost 3, Upper Cave 101, Skhul IV and Saint Cesaire 1

None of those skulls are found in America, and none of them cluster particlarly closer to modern Amerindians than to other modern humans. I think you might want to look up what "logically" means.


@Marcel F. Williams:
The split between Africans and non Africans occurred 2.1 million years ago

Archaeology and modern genetics would disagree with you.

... what is this, Crackpot Week or something?

arch said...

100,000 years as the split of subsaharans from everyone else is not supported by any recent work I have noted, and almost every concedes its much older at this point.

Even Khoisan AFRICANS dont split from other africans until as late potentially as 150k -

http://www.nature.com/ncomms/2014/141204/ncomms6692/full/ncomms6692.html

The only real reasons to cling to 80-100,000k is that it throws a lifeline to the Neadertal centrics for whom everything is a crucial square peg into a round hole of protecting their interbreeding claims.. its not a surprise that Neandertals are mentioned right in this assessment.

Theory for a subsaharan split has been assessed at as far back as 250k years ago, in mainstream studies and often simply left at "much older than earlier though" in work where people fear getting in trouble or that is not the main focus of their paper -

http://www.nytimes.com/1999/03/16/us/study-alters-time-line-for-the-splitting-of-human-populations.html

There is often a need to control and POST DATE the split of non africans from africans to protect neandertal claims, and also because its simply not politically correct timeline to note.

Lastly.. all these dating schema are notoriously fallible and often wrong for the simple reason that the entire genome does not share a identical mutation rate,
some regions and loci are much more stable, and some are fast mutators,..

so simply looking for loci in common and then attempting to use that to settle on a mutation rate is likely to be automatically flawed because if you are targeting archaic sites that are slow mutators (and thus shared across archaic populations)it will skew all mutation rates and all findings for that matter.

Portia said...

Let me throw this study onto the fire. It appears that teen fathers children with a mutation rate six times that of fathers who are around 30. This whole business of estimating ages by mutations may be seriously flawed unless we have good data for generation age- which we don't. http://www.sciencedaily.com/releases/2015/02/150218101841.htm

eurologist said...

"Disregarding life expectancy at birth makes sense in this case, since fertility is better related to life expectancy on beginning the teenage years."

aniasi,

Yes, and in addition, the majority of the mutational load comes from the fathers, so the average life expectancy of females is irrelevant. Also, males can have offsprings into high age (with younger females).

One should note, though, that the number of mutations of male offsprings grows almost linearly with age, with an insignificant zero-offset. That means that generation length is irrelevant if one uses (and can use) a unit of mutations over time (instead of over generations, with a variable and somewhat unknown generation length).

Both pedigree-based methods and those based on only a few thousand years have severe shortcomings when applied to larger time intervals, due to the accumulation of deleterious mutations in combination, which short-term studies severally underestimate.

Even the lowest mutation rates are just an upper limit, with the true rate likely yet lower.

Sgt said...

@ aniasi

This was a study of adult skeletal remains. The text states that the women were "much smaller than the men with signs of malnourishment and domestic abuse ... most of whom died before age 26." There may be a good reason for a standard generational interval of 30 years across populations and eras, but not one I am aware of.

dwaggonerstr said...

Torbus:
"None of those skulls are found in America, and none of them cluster particlarly closer to modern Amerindians than to other modern humans. I think you might want to look up what "logically" means."

Amerindians cluster closest to these skulls and have been genetically proven as closer to them than other living people. Sorry Torus but it can no longer be denied. Amerindians are Neanderthals and Neanderthals are Amerindians. You need to stop being intimidated by the truth.

Tobus said...

@Portia: It appears that teen fathers children with a mutation rate six times that of fathers who are around 30

You read it wrong - it's six times higher than females of the same age: "mutations are six times higher in male sperm cells during onset of puberty than in female oocytes".

The paper actually states that teenagers have about the same number of mutations as older adults ("teenage boys have similar levels of DNA mutation in their sperm cells to men aged in their late thirties and forties") but this is higher than younger adults ("teenagers have approximately 30% higher rates of DNA mutation than those of young men in their twenties".

So there's a spike at puberty that drops in young adulthood and then slowly climbs again into old age. The "spike" itself isn't actually that large: around 2% as opposed to a general average abnormality risk of 1.5%. Unless there some reason to assume a disproportionate weighting of teenage and/or 35+yo fathers relative to 20-somethings, I imagine it would average out to be a fairly predictable constant rate across random fathers in random populations.

Portia said...

I should have said "It appears that teen fathers HAVE children with a mutation rate six times that of fathers who are around 30." This implies a "U" shaped curve for mutation rates, not one linear over time. This whole business of estimating ages by mutations may be seriously flawed unless we have good data for generation age- which we don't. Again heree is a link to the article http://www.sciencedaily.com/releases/2015/02/150218101841.htm

eurologist said...

Portia,

I saw that study, and I am skeptical. I qualitatively agree with the conclusion: "the number of cell divisions -- and consequently DNA mutation rates -- experienced by the germ cells of teenage boys is six times higher than for those of girls."

Something close to that was expected to fit the dominant male mutational load and an approximate zero offset (at age zero). If it is true that there is an age around puberty at which the male number of mutations are higher than in young adults (30% - not really Earth-shattering), I suspect this interval is extremely short and has nothing to do with cell divisions before puberty, because in that latter case, the mutations would be preserved and then still increase after puberty.

IOW, the article, as paraphrased by sciencedaily, makes no sense.

GailT said...

Sorry Torus but it can no longer be denied. Amerindians are Neanderthals and Neanderthals are Amerindians. You need to stop being intimidated by the truth.

It's always Crackpot Week in the comments section of this blog - it seems to be the last refuge for conspiracy theorists who can't find an audience anywhere else.

Tobus said...

@dwaggonerstr: Amerindians cluster closest to these skulls and have been genetically proven as closer to them than other living people.

Can you provide hard evidence to support these claims? (...and no, a German Dzeibel blogpost does not qualify)

Mark Moore (Moderator) said...

@ Tobus

You seem to have a good understanding of the article Portia linked to so I will ask you. Isn't that difference of 1.5% vs. 2% per generation, if the conditions persist, a little like compounding interest? That is to say, if one population bred early or late (on average of course) for 30 generations wouldn't the number of mutations be a LOT more than one half of one percent higher in that group as compared to one where most males sired most children in their twenties or early 30s?

I don't see it as a theoretical question because I see populations and subpopulations who reproduce at very different ages.

terryt said...

"It's always Crackpot Week in the comments section of this blog - it seems to be the last refuge for conspiracy theorists who can't find an audience anywhere else".

By no means everyone here is crackpot, but the statement, 'Amerindians are Neanderthals and Neanderthals are Amerindians' certainly fits that claim.

dwaggonerstr said...

WHAT is it with all the "T"s on this website?

Gail"T"
"T"obus
"T"erry"T"



All of whom seem to harbor the same baseless, dogmatic ideas about human origins.

What does tbe "T" stand for? Theocracy? Totalitarianism? Turd?

terryt said...

"What does tbe 'T' stand for? Theocracy? Totalitarianism? Turd?"

It stands for 'truth'.

German Dziebel said...

@Tobus

"German Dzeibel blogpost"

My blogposts feature only credible and peer reviewed findings and models. No surprise there are no positive references to Nameless Liar Tobus and his creationist sidekicks, GailT and TerryT.

Upper Cave 101 is indeed the closest to ancient Amerindian skulls in a sample of ancient and modern human skulls http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21425/abstract.

Tobus said...

@Mark Moore: Isn't that difference of 1.5% vs. 2% per generation, if the conditions persist, a little like compounding interest?

I guess it would be "if the conditions persist", but the "condition" is only a small window in the time frame of a man's reproductive life, and it only "persists" as a small window in the child's reproductive life. So overall I'd expect an averaging, not compounding, effect.

If you imagine the average male only having one or two kids before 20, and at least 5 or 6 between 20 and 35 (pre-modern families where even larger no?)... *most* of the next generation will be closer to the 1.5 than the 2%. This generation then mixes with each other and *most* of these are 1.5x1.5ers. As with any random distribution you'll get some 2x2% outliers (teenage father of a teenage father), but there'll be even more 1.5x2%-ers (teenage father of a 20+ father and vice versa) and so overall the mean will be kept pretty much in check. Five generations later it's only 2x2x2x2x2%ers that would show the full "compounding interest" effect and there'd be something like 3125 1.5x1.5x1.5x1.5x1.5ers for each one of them (assuming a 5:1 ratio)... plus a whole bunch somewhere in between. So the extra 30% in small number of samples would lift the mean a little bit, but I don't think it would lead to a runaway situation.


@dwaggonerstr:
It stands for "T"in foil hat - you should "git sum".

Tobus said...

@German:
My blogposts feature only credible and peer reviewed findings and models

Not quite, they also contain your personal interpretation and commentary that is often the opposite to what any rational thinking person would get from those same findings.

Upper Cave 101 is indeed the closest to ancient Amerindian skulls in a sample of ancient and modern human skulls

Modern Amerindians are the *least* like Upper Cave 101 in that data.

@dwaggonerstr:
This is a case in point re German's marketing expertise. Note how he slips the word "ancient" in there despite the very paper he links to showing that ancient and modern Amerindian skulls are markedly different - in it's very first sentence no less! Note also the use of "indeed" to reinforce the idea like this somehow validates Amerindians as closer to the entire range of skulls you claimed. The full paper he references can be found here: http://www.academia.edu/9059180/Paleoamerican_morphology_in_the_context_of_European_and_East_Asian_late_Pleistocene_variation_implications_for_human_dispersion_into_the_new_world.. I encourage you to read it and come to your own conclusion without German's marketing-babble commentary. I recommend you do this with every interesting idea you find on his site... in my experience, they very rarely hold up to independent scrutiny.

dwaggonerstr said...

Tobus, are you out oc your freaking mind? UC101 is Amerindian/UP Caucasoid this has been demonstrated since the skull was unearthed. That study German posted is one such proof of this reality, onky someone with severe dyslexia or a learning disability could say otherwise. MP Neanderthals are linked to Native Americans as are the Upper Paleolithic Europeans Predmost 3 and Saint Cesaire. From Coon:

"In the totality of facial features, with a few exceptions, the Upper Palaeolithic people may be said to have resembled modern white men. Some, however, probably looked like a certain type of American Indian, notably that of the North American Plains, and of the Onas and Tehuelche of southernmost South America. This comparison, we must remember, is wholly morphological, since we do not know Upper Palaeolithic man’s pigmentation, hair form, or hair distribution."

"
28 Morant, in his group “Fuegians, pooled,” mixed Ona skulls with those of the smaller and quite different Yaghans. If one abstracts the Ona crania from Lebzelter’s original tables, he will find that the European Upper Palaeolithic means of Morant are essentially duplicated"

You need to take a chill pill and learn to accept that your twisted and preconceived worldview is wrong.

German Dziebel said...

@Tobus

"Not quite, they also contain your personal interpretation and commentary that is often the opposite to what any rational thinking person would get from those same findings."

Au contraire. The version of the origin of American Indians that you entertain comes from pre-scientific thinking. As any historian of ideas knows, it originated with Father Jose Da Acosta (http://en.wikipedia.org/wiki/Jos%C3%A9_de_Acosta), and you are his faithful creationist follower. All my interpretations, on the other hand, follow the rules of reason supported by two doctorates in the field, not a religious tradition.

@dwaggonerstr

"German's marketing-babble commentary"? Next to it: ""Note how he slips the word "ancient" in there despite the very paper he links to showing that ancient and modern Amerindian skulls are markedly different - in it's very first sentence no less! Note also the use of "indeed" to reinforce the idea like this somehow validates Amerindians as closer to the entire range of skulls you claimed." This is Tobus's marketing baloney.

Lagoa Santa is indeed the closest to UC 101. Subsequent genetic research also showed that genetically modern Amerindians are related to ancient Amerindians. They are just very diverse cranially (see South Amerindian Craniofacial Morphology: Diversity and Implications for Amerindian Evolution, by Marina L. Sardi) which, I could add, is entirely consistent with their antiquity on the continent.

Tobus said...

@dwagonnerstr:
UC101 is Amerindian/UP Caucasoid this has been demonstrated since the skull was unearthed

Just read the paper Dwagonnerstr, you will learn something - a lot has changed since 1939.

@German:
As any historian of ideas knows, it originated with Father Jose Da Acosta ... and you are his faithful creationist follower

Yes, and Darwin was a Christian - by your "logic" that makes anyone who believes in evolution a Creationist too. I've said it once, and no doubt I'll say it again: You sir, are an idiot.

(...and while descending to idiocy, let's not ignore the first Out of America pioneer Jeffrey Goodman (author of "American Genesis: The American Indian and the origins of modern man" and discoverer of the infamous Flagstaff Stone!)... I'm assume you're up to date with his latest offering: "The Comets of God-New Scientific Evidence for God"?)

Lagoa Santa is indeed the closest to UC 101. Subsequent genetic research also showed that genetically modern Amerindians are related to ancient Amerindians. They are just very diverse cranially

So when Dwagonnerstr says "Amerindians cluster closest to these skulls" he is incorrect no? Unless you're purporting it's scientifically sound to use a 10,000 year old sample that is "diverse cranially" as a proxy instead of using the *actual* modern population samples we have? Modern East Asians, Polynesians, Europeans and even some Africans cluster closer to these skulls than modern Amerindians do... yes?

dwaggonerstr said...

Tobus:

Reality and facts do not have expiration dates. That UC 101 skull is a Neanderthaloid Amerindian just like the Aurignacian Europeans. Note that I said UC 101... NOT UC 102 OR UC 103, WHICH ARE FEMALE SKULLS AND THUS USELESS FOR CLASSIFICATION. ANY FEMALE OR ADOLESCENT SKULL FROM ANY RACE CAN BE LINKD TO "NEGROIDS" OR "EAST ASIANS", PARTICULARLY IN GROUPS WHERE SEXUAL DIMORPHISM IS HEAVILY PRONOUNCED, as it was in both Amerindians, Neanderthals and Aurignacians.

German Dziebel said...

@Tobus

"Yes, and Darwin was a Christian - by your "logic" that makes anyone who believes in evolution a Creationist too. I've said it once, and no doubt I'll say it again: You sir, are an idiot."

You can keep saying what you want. That's why you are Tobus Nameless Liar. There's a world of difference between a Jesuit missionary and Darwin. But to you they look the same because they were both educated in the way of the scriptures. Nice!

"(...and while descending to idiocy, let's not ignore the first Out of America pioneer Jeffrey Goodman (author of "American Genesis: The American Indian and the origins of modern man" and discoverer of the infamous Flagstaff Stone!)... I'm assume you're up to date with his latest offering: "The Comets of God-New Scientific Evidence for God"?)"

Yes, he's one of those archaeologists who migrated to the "dark side". His example discredits archaeology as a unique provider of physical proofs of human origins - in Africa or America. You, too, like to use relics as "proof" of human beginnings. I have nothing in common with JG. But you are on the same page with Father Jose de Acosta.

You should look up Ales Hrdlicka - a famous physical anthropologist and a passionate believer in human recency in the Americas (recent as in ~5,000 YBP). A faithful disciple of Father de Acosta. He would burn on the stake everyone who questioned his Bible-like chronology for humans in the Americas. Until he got disproved and died.

"Modern East Asians, Polynesians, Europeans and even some Africans cluster closer to these skulls than modern Amerindians do... yes?"

No, UC101 is an ancient skull and among ancient skulls it's the closest to ancient Amerindian skulls (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885431/). By some measurements it's close to UP Europeans (http://www.ncbi.nlm.nih.gov/pubmed/19863997). It showed no special affinity with modern East Asians. http://www.ncbi.nlm.nih.gov/pubmed/9503095. At the same time the earliest skulls with modern East Asian morphology are found in the Americas (see Brown's work) supporting my theory that there was a recent (12-10,000 YBP) back migration to Asia from the Americas that brought the "Mongoloid" type to Asia. This is in addition to the founding one.

@ Dwagonnerstr

Tobus is a convicted science offender. If you throw a fact at him, he will try to rip it apart just to create self-serving confusion. Sometimes he's being helped by terryT and GailT. It's safe to ignore any of them or all of them. You're not going to miss much. But Tobus is my preferred punching bag. He just bounces back nicely.

Grognard said...

Looks like this mutation rate nonsense will never die. Too bad there's nothing to suggest it has any validity. Following this kind of logic we should expect everyone on PCA charts to whiz away from each other in the same directions of their current distances. Obviously that doesn't happen, usually the opposite over time.

German Dziebel said...

@ Dwagonnerstr

"NOT UC 102 OR UC 103, WHICH ARE FEMALE SKULLS AND THUS USELESS FOR CLASSIFICATION. ANY FEMALE OR ADOLESCENT SKULL FROM ANY RACE CAN BE LINKD TO "NEGROIDS" OR "EAST ASIANS", PARTICULARLY IN GROUPS WHERE SEXUAL DIMORPHISM IS HEAVILY PRONOUNCED, as it was in both Amerindians, Neanderthals and Aurignacians."

This is unacceptable. I first tried to shield you from the attacks of Tobus & Co. but looks like you belong in the same pseudoscientific "clade" with them.

Tobus said...

@dwagonnerstr:Reality and facts do not have expiration dates

On the contrary, scientific "reality" is being continually revised and refined as time goes on, vis a vis Copernicus -> Newton -> Einstein etc. Modern advances in science have revolutionised the field of human origins in the last 10 years, somewhat exponentially. You should update your "reality", by reading some of recent discoveries that Dienekes kindly collects for us in this blog.


@German:
UC101 is an ancient skull and among ancient skulls it's the closest to ancient Amerindian skulls

If you're going to insist on comparing ancient skulls against UC101 instead of just using the modern samples, then you need to use ancient samples that are all the same age - the "ancient" UP skulls in the data are 10-20ky "more ancient" than the "ancient" Amerindian ones, so you are comparing apples to oranges.

Unfortunately there's no 10kya paleo-Eurasian/African skulls in the data to compare against the paleo-Indian samples, but we do have 3 paleo-Indian and 3 modern Amerindian samples. We can use these 6 samples to work out how much different 10ky makes, and thus what we might reasonably expect 10kya paleo-European, -African and -East Asian ancestors to score based on their modern scores. You can work out from the data that the average effect of the last 10,000 years on the Amerindian samples is an increase in distance of about 66%, meaning that we'd need to multiply the modern scores by about 0.6 to get their expected 10,000kya scores. Once you do this you can see that virtually all the modern samples, bar Amerindians, would have had ancestors closer to UC101 than Amerindians did at 10kya. To make it simple for you, modern samples with a score less than 54 will have a score lower than 33 (the lowest paleo-Indian distance) when calibrated for the same shift that we see between ancient and modern Amerindians.

So, modern Amerindians are the *least* like UC101 when compared to modern samples. Paleo-Indians are the *least* like UC101 when compared to calibrated "paleo-" samples. The only way you are claiming Amerindians are the closest to UC101 is by mixing the sample ages and comparing the paleo-Indian samples against modern samples (or against UP samples twice as old). You make it sound reasonable so I give you 10/10 for marketing chicanery, but it falls apart under scrutiny... so 0 out of 10 for science.

German Dziebel said...

@Tobus

You are ignorant as always: UC101 is likely 12,000 years old (Kamminga 1992). So it's comparable in age to Lagoa Santa and other Paleoamerican skulls to which it's closest craniometrically.

But in any case, all the modern skulls between 10,000 and 50,000 form a cluster contrasted with both Holocene skulls and AMH skulls in Africa.

Your writeup is a typical pseudoscientific nonsense.

Tobus said...

@German:UC101 is likely 12,000 years old (Kamminga 1992). So it's comparable in age to Lagoa Santa and other Paleoamerican skulls to which it's closest craniometrically.

EXACTLY!!! That's why you *can't compare* the paleo-Indian scores against modern samples to decide who is the "closest" - the paleo-Indians will appear closer due to 10,000 years less drift! You need to compare modern Amerindians' scores against modern Europeans'/Africans'/East Asians'. If for some bizarre reason you really really need to use the paleo-Indian scores instead of modern Amerindians', then you must make some effort to adjust for the extra 10,000 years drift that all the modern scores will contain.

German Dziebel said...

@Tobus

"hat's why you *can't compare* the paleo-Indian scores against modern samples to decide who is the "closest" - the paleo-Indians will appear closer due to 10,000 years less drift! "

I'm only interested in noting the special affinity between UC101 and Paleoindian skulls. You are the one who's comparing UC101 to modern samples.

Tobus said...

@German:I'm only interested in noting the special affinity between UC101 and Paleoindian skulls.

Cool, so you're happy to accept that when dwagonnerstr said "Amerindians cluster closest to these skulls" that he was in fact mistaken - Amerindians are actually the *least* like UC101 of all modern samples.

As to your particular interest, you may want to consider that the "special affinity" might not be so "special" if there were contemporaneous Eurasian samples included in the data. The differing age of the samples is no doubt confounding in a direct comparison of the final scores.

German Dziebel said...

@Tobus

"Amerindians are actually the *least* like UC101 of all modern samples."

They are not the least like UC101 of all modern samples. Just study the data.

"The differing age of the samples is no doubt confounding in a direct comparison of the final scores."

Nonsense. They all form a cluster compared to AMH and to modern samples.

"As to your particular interest, you may want to consider that the "special affinity" might not be so "special" if there were contemporaneous Eurasian samples included in the data. "

Special affinity between UC101 and Paleoindian samples is a fact. Whether you like it or not.

Tobus said...

@German:
They are not the least like UC101 of all modern samples. Just study the data.

I did. Amerindians' average distance from UC101 is 55, next closest pop is Africans with an average of 46. Table 3 of Hubbe 2011 - check it for yourself.

Nonsense.

Are you saying the age of the sample is *not* relevant when comparing affinity? Funny, you said the exact opposite when the Ust'-Ishim sample came up with the most Neanderthal DNA.

Special affinity between UC101 and Paleoindian samples is a fact.

It's certainly interesting but I'm not sure you can call it "special" when there's no other contemporaneous populations in the data to compare against (ignoring that UC101 could possibly be considered a paleo-East Asian sample to start with). It's a bit like that Dad joke of saying "you're the biggest boy in the whole room" when you're the only one in there - you appreciate the sentiment, but given the lack of competition it's devoid of any real meaning.

German Dziebel said...

@Tobus

"I did. Amerindians' average distance from UC101 is 55, next closest pop is Africans with an average of 46. Table 3 of Hubbe 2011 - check it for yourself."

What about other populations?

"It's certainly interesting but I'm not sure you can call it "special" when there's no other contemporaneous populations in the data to compare against (ignoring that UC101 could possibly be considered a paleo-East Asian sample to start with). "

Special affinity between UC101 and Lagoa Santa is important in the context of the non-Mongoloid status of Paleoindian skulls. That's the context of that whole stream of research we tapped into.

"Are you saying the age of the sample is *not* relevant when comparing affinity?"

With skulls I'm only interested in broad patterns and clusters. Your pseudoscientific age calibration exercises are not something that's relevant to the present discussion.

Tobus said...

@German
What about other populations?

The two averages I quoted are the two highest, the other modern populations are all lower than these. But surely you can read this table yourself?

Special affinity between UC101 and Lagoa Santa is important in the context of the non-Mongoloid status of Paleoindian skulls.

Great, but let's be careful not to insinuate that this Indian affinity carries through to modern Amerindians.

Grognard said...

Tobus, if you are talking about migration it makes zero sense to compare bones from the same time period.

Tobus said...

@Grognard:if you are talking about migration it makes zero sense to compare bones from the same time period

We're talking about similarity, not migration, age is a confounding factor.

Comparing UC101 affinity between paleo-Indians and modern pops is like comparing my grandchildren with my brother - my brother is closer to me than my grandchildren are, but does that mean my brother's grandchildren are closer to me than my own?!?

Grognard said...

Your make a HUGE unwarranted assumption that we already know who is related to who, when that is what we are trying to find out.

If you insist on following this line, take a look at sitting bull's skull, compare it to neanderthal skulls and to magdalenian skulls. Obviously there's a huge affinity.

Now if you really insist you could only compare modern to modern then there's no helping you. Obviously nothing can EVER be determined that way....

Tobus said...

@Grognard:Now if you really insist you could only compare modern to modern then there's no helping you.

You misunderstand, German is comparing the difference between an ancient and an ancient sample against the difference between and ancient and a modern sample, but not allowing for the 10,000 years of extra divergence that the ancient-to-modern difference will always have.

A comparison of both modern Amerindians and modern East Asians against UC101 shows that modern East Asians are closer... a *LOT* closer.