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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Tuesday, May 27, 2014

A shared Y chromosome lineage Neanderthals and Modern Humans



I am following up on some (there were quite a few) of the subjects that appeared while writing my most recent posts on the human Y chromosome.


Among them, are my very serious doubts regarding the markers used in classifying Y-chromosome haplogroups, the ages of the different sub-clades or haplotypes within them, and the different dates for common ancestors based on the estimated mutation rates for the human Y chromosome. As expressed in my previous posts, the methods, assumptions and convoluted statistical calculations seem far fetched and very uncertain. The fact that some confidence intervals are too large in my opinion invalidate the logic behind them, but then, I am a mere engineer not a geneticist.


The Y chromosomes of the Neanderthal


It is in this context that I read an interesting paper (Musaddeque Ahmed and Ping Lian, 2013) [1], from which I quote the following regarding Neanderthal Y chromosomes ... (bold font is mine):


"...the Y-chromosome of Neanderthals or paternal inheritance has yet to be examined. Comparisons of the Y chromosome sequence of Neanderthals with currently established Y-haplogroups for modern humans should provide some insights into the admixture hypothesis.
With respect to the recent finding of admixture of Neanderthals with non-African populations, the Neanderthal Y chromosome should not match the Y haplogroups A or B, as these haplogroups are the oldest of the clades and almost restricted to Africans and their descendants. Since haplogroup E is found in Africa, the Middle East, Southern Europe, and Asia, the Neanderthal Y chromosome may match this haplogroup, but it should not match the haplogroups E1b1a*, E2b1, or B2a1a, as they are specifically treated as Bantu expansion markers, while Neanderthals interbred only with non-Africans.
" [1]


I was very surprised by this paragraph, as I expected something similar to what we see in mtDNA, where the ancestral population of both humans and Neanderthals, split into two groups: one that would later evolve into modern humans, and another that would evolve into Neanderthals. Each would carry, in the beginning, the "original" archaic Y chromosome of the ancestral population, which, as each lineage accumulated mutations due to chance and positive selection would begin to grow in different directions, forming two distinct branches, which then in turn would continue branching as more mutations appeared.


So, the oldest human Y-chromosome haplogroups "A" and "B" found exclusively in Africa, were born from the branch leading to modern humans (the "root" of mankind), while, on a separate branch, (Neanderthals), the Y chromosome haplogroups of Neanderthals appeared.


However, towards the end of this post we will see that this reasoning may not be correct.


Nevertheless, mainstream science considers it to be the correct interpretation. According to Krause et al. (2007), [2] since the oldest common ancestor with human Y chromosomes dates back to 90 kya, and as Neanderthals and humans split long before that date, they "expect[ed] Neandertal Y chromosomes to fall outside the variation of modern human Y chromosomes unless there was male gene flow from modern humans into Neandertals"; in other words: Neanderthals would have their own peculiar Y chromosome haplogroups unless H. sapiens men mated with Neanderthal women and passed on their Y chromosomes to their human-neanderthal mixed male sons. But then these would not be pure Neanderthals but admixed ones, with 50% human genome in them and their Neander mom's mtDNA.



The following image shows what I expressed above, two branches: red for Neanderthals and black for us, humans, both splitting from our common ancestor:


Neanderthal and human Y chromosome tree
Hypothetical Y chromosome phylogenetic tree for humans and Neanderthal. Copyright © 2014 by Austin Whittall

Actually, we have not yet found Neanderthal Y chromosomes among modern human genomes and this is indeed curious since we have admixed with them. It could be due to several reasons:


(a) They are present in such low frequencies that they have not yet been sampled. Imagine a 0.001% frequency, that is, only 1 in 100,000 men would carry it (35,000 in the whole world, a very small number indeed).
(b) They are very similar to modern haplogroups (as suggested by Musaddeque and Ping, 2013. [1]) and we see them but have not yet realized that they are Neanderthal.... (More on this below, because it seems to be a very interesting possibility).


While studying the Neanderthal genome, Krause et al., (2007) [2] found that two of their Sidrón Neanderthal specimens (Sidrón 1253 and Sidrón 1351c) were males. They then tested them at the five positions that mark the main nodes of Human branches (i.e. the splitting points of our Y chromosome haplogroups) in both Eurasia and Africa. They noticed that "all 15 Y chromosomal products for the five assayed positions show the ancestral allele" [2]. In other words, the ancestral or chimpanzee-like state was found. They did not find any specifically Neanderthal-like state. This is odd, considering that 7 million years separate chimps from Neanders, why would they both share the markers in their Y chromosomes and humans, a mere 300 ky away don't. It may be an error in their sequencing.


Admitting the paucity in their sampling and that these Y-chromosomes may appear in extremely low frequencies among modern human populations, the authors conclude:"These [Neanderthal] Y chromosome results must derive, then, either from Y chromosomes that fall outside the variation of modern humans or from the very rare African lineages not covered by the assay..." [2], in other words, the Neanderthal Y chromosomes may be similar to those of modern humans that were not screened for.


I must point however, that according to Figure S1, the "markers" chosen by Krause et al., screened only certain branches of the Y chromosome tree: (i) and (ii) the split that leads to all haplogroups downstream from the A clade. (B, C,.... R2). (iii), The one leading to B. (iv) The one leading to P, (and therefore Q), R1, R2. And (iv) the one leading to A2.


So the Neanderthal Y chromosomes could belong to Haplogroups A1 and A3, which were not screened for. Or, an option that is evident, but they did not consider it at all: Neanderthal Y chromosomes are identical to those of Modern Humans and cannot be told apart from them.


Actually, isn't it surprising that not one Neanderthal Y (or X with its mtDNA) chromosome survived until our days? We have a considerable amount of autosomal genetic content introgressed from our relatives, the Neanderthals, but their mithocondria and their sex determining chromosomes did not survive. Why?



An extremely old Y chromosome lineage


Mendez et al., (2913) [3] , discovered a Y chromosome haplogroup (named A00) which shares its most recent common ancestor with the rest of mankind 338 kya, of course (as usual!) the confidence interval is 237 to 581 kya. So this is a very old and wide time frame which goes back well beyond the oldest known fossils of anatomically modern human (AMH) beings.


This haplogroup was found in the genes of an African American and later identified in the chromosomes of Mbo individuals from Cameroon, at very low frequencies: 0.19% [CI = 0.11%–0.35%].


They would predate the oldest modern human fossils, which are only 195 ky old. So the Mbo lineage should have split from humanity at least 40 ky before our species even appeared.


The paper also looked at the rest of our Y chromosome lineages, working up the other branches of the tree, finding that the African A0 hg diverged from the other branches 202 kya (CI = 125 - 382 kya), which is much older than previous estimates of 142 kya.


This in turn moves the split between African and non-African branches (hg C to T) backwards in time, making them older: 63 kya vs. the previous 39 kya date.


Orthodoxy strikes back
Of course, such an ancient root for modern humans is inconsistent with mainstream genetic beliefs so a rebuttal appeared (Eran Elhaik et al., 2014)[4], pointing out that it: "contradicts all previous estimates in the literature and is over 100,000 years older than the earliest fossils of anatomically modern humans.".
E. Elhaik et al believe that Mendez et al.'s paper overestimated mutation rates resulting in an artificially older age. Their analyisis "indicates that the A00 lineage was derived from all the other lineages 208300 (95% CI= 163900 - 260200) years ago." [4] Which as can be seen, falls suitably close to the oldest dated AMH fossils.


But let's get back to the very ancient A00 and the "unorthodox" point of view:


What are the implications of this finding? There are several possible scenarios:


1. Archaic admixture. These Mbo people inherited their A00 haplogroup from an achaic human population. These ancient African humans carried the A00 lineage in them, mated with AMH (within the last 195 ky) and passed on their Y chromosomes to their male offspring, their A00 passed from father to son in these AMH, which survived until now (Mbo's are their youngest descent). In the meantime, the archaic group became extinct.


Mendez et al. support this view: "Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya." [3]


2. Deeper time line. Maybe the depth of modern humans into the past is greater than the current (spotty) fossil record shows (roughly 200 kya).


The Confidence intervals given by Mendez et al., span from 237,000 to 581,000 years ago, this is well into the dark past of mankind, a time frame which encompasses many hominids in Eurasia and Africa: H. erectus (from 1.8 Mya until roughly 300 kya); Denisovans (until 30 kya), Homo heidelbergensis (600 to 400 kya), Neanderthals (600 to 25 kya) and H. rhodesiensis (300 to 125 kya).


Could this Y chromosome lineage belong to one of these hominids? Before answering let's just consider one additional piece of information.


Chuan-Chao Wang et al., [5] noticed that Y-chromosome STR haplotypes from different haplogroups converge; they looked for "possible haplotype similarities among haplogroups [and found] similar haplotypes between haplogroups B and I2, C1 and E1b1b1, C2 and E1b1a1, H1 and J, L and O3a2c1, O1a and N, O3a1c and O3a2b, and M1 and O3a2 ..." [5] .


In other words identical Short Tandem Repeat (STR) markers crop up among the different Y chromosome haplogroups indicating that the same mutations arise time and time again, unlike the markers of haplogroups which are much more sporadic and unique.


Making sense of this muddle


Above, I asked why didn't Neanderthal Y chromosomes survive among their descent (albeit admixed with modern humans)? Probably there were too few of them and too many of us, and their Y chromosomes got watered down, in successive admixtures, diluted until their frequencies are so low that they have not yet been detected.


Another option is that "Haldane's rule'' kicked in; the rule declares that if hybrids of one sex only are sterile, the afflicted sex is much more likely to be the male (XY) than the female (XX). Of course, why would hominds so close to each other bear sterile offspring? It is not like horses and donkeys, this is humans and Neanderthal, and we have their genes in us, so we did interbreed and the offspring survived (but Haldane's rule may mean that the girls survived but the boys were sterile).


A paper (Sankararaman et al., 2014) [6] supports the "Haldane's rule" notion: "...interbreeding of Neanderthals and modern humans introduced alleles onto the modern human genetic background that were not tolerated, which probably resulted in part from their contributing to male hybrid sterility".


The Neanderthal-deficient regions in modern humans are found in genes that "are specifically expressed in the testes, and in the female sex X chromosome. "This suggests that some Neanderthal-modern human hybrids had reduced fertility and in some cases were sterile. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome." [6]


But, this does not mean a total extinction of their sex chromosomes; not all of their offspring were sterile after all, we still carry their genes mixed with ours, why shouldn't their Y chromosomes survive too?


In my opinion, we actuall carry their Y chromosomes in us (in the men of course), but long before we admixed with them in Eurasia some 60 kya. The mutation rates that are used to date our Y lineages are wrong, allow me to explain why:


We look at populations (say Amerindians) and jot down their haplogroup markers, and we assume that they mutated when they reached America and then, we guess the date they entered America (say 15 kya). With this we calibrate our clock. We again look at the humans closest to Africa and jot down their haplogroups markers, and once again guess the date these people's ancestors left Africa (say 70 kya), and again calibrate our clock. We take another look at the oldest fossils of AMH in Africa (195 kya) and jot down the most divergent African haplogroups' markers, we recalibrate our clock again. But, as you can see, there are many assumptions in all of this (the dates and, above all, the assumption that these haplogroups are specifically human and mutated recently < 200 ky!).


But, What if they are not specific to us, but archaic? What if we carry slowly mutating Y chromosomes. The mutations found in certain haplogroups are valid, but they reflect ancient migrations. Maybe even the Out Of Africa (OOA) migration of H. erectus or, within the time range given by Mendez et al., the Y chromosomes of H. heidelberensis or Neanderthals?


This would explain why there are no Neanderthal specific branches to be found (the red ones in the image above). We all have the same tree our and their lineages coincide.


So what the date should we consider for the makers at the "non-African" CT groups (the OOA split)? Not the date modern humans left Africa. Instead it may be the date Neanderthals left Africa.


The split in Altai, with a Western route for our "R" hg and East for the "Q" hg may indicate divergence among the Neanderthals that lived there while AMH began to move out of Africa.


The archaic humans of China and even Lake Mungo people in Australia may be the branches of the South East Asian and Austronesian Y chromosome haplogroups, instead of modern humans that reached those regions much later.


The Q hg in America may not reflect a recent peoping of America at all, but an ancient one by Neanderthals.


The pan African E hg, may reflect the recent dispersal of AMH in the continent as well as in the Middle East, Southern Europe, and Asia after their OOA movement.


The dispersal of Q hg across the Arctic regions of America and Eurasia or the presence of the very old C hg in Asia and America may reflect the ancient migrations of primitive humans and not the recent (<20 kya) dispersal of modern humans.



Sources


[1] Musaddeque Ahmed and Ping Lian, (2013). Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome. Genomics Inform. Dec 2013; 11(4): 230–238. Published online Dec 31, 2013. doi: 10.5808/GI.2013.11.4.230
[2] Johannes Krause, et al., (2007). The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals. Current Biology 17, 1–5, November 6, 2007 ª2007 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2007.10.008
[3] Fernando L. Mendez et. al., (2013). An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. The American Journal of Human Genetics 92, 454–459, March 7, 2013. http://dx.doi.org/10.1016/j.ajhg.2013.02.002.
[4] Eran Elhaik, T. Tatarinova, A. Klyosov and D. Graur, (2014). The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. European Journal of Human Genetics (2014) 1-6. doi:19.1038/ejhg.2013.303
[5] Chuan-Chao Wang et al., (2013). Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction. pre-print Arxiv server on 21 October 2013.
[6] Sriram Sankararaman et al., (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354–357 (20 March 2014) doi:10.1038/nature12961



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Friday, May 23, 2014

Generation time is not 25 years


This post is just to provide some additional data regarding the "length" or "duration" of a generation. As seen in yesterday's post (which criticises Y chromosome mutation rates), calculations are based on a 25 year generational interval, which when input into the formulas used to calculate the ages of Y chrmosome lineages will give an incorrect date if, (and that is what we will clarify in this post) generations are either longer or shorter than 25 years.


Generations last more than 25 years


A long term study by Nancy Howell among the !Kung of Namibia and Botswana revealed that this contemporary hunter-gatherer group of people are relatively old at the time of bearing children: For women it averages 25.5 years, but for men (and this is important when it gets down to Y chromosomes): 31 to 38 years averaging 34.5 years. These people are very similar to the pre-agricultural society of our distant ancestors. [1]


A paper (Matsumura and Forster, 2008) [2] found that, among Eskimos, the father-son interval is 32.1 years. And point out (bold face is mine) : "The majority of the previous studies assumed that the generation time for mitochondrial DNA and Y-chromosomal DNA is 20 and 25 years, respectively (e.g. Harpending & Rogers 2000). We suggest that a higher value, 25–30 for mtDNA and 30–35 years for Y-chromosomal DNA, should be used in genetic inference." [2].


Fenner (2005) [3] indicates a male generation length of 31 to 32 years. [3]


So, it seems that 25 is too short a time for male generations, the value is at least 30 years, and perhaps higher. In polygynoous societies, older men would have monopolized women and the generation length have been even longer.


Sources


[1] N. Howell, (2009). Demography of the Dobe Kung. Transaction Publishers.
[2] Matsumura S, Forster P., (2008). Generation time and effective population size in Polar Eskimos Proc. R. Soc. B 7 July 2008 vol. 275 no. 1642 1501-1508
[3] Fenner JN, (2005) Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. American journal of physical anthropology 128. doi: 10.1002/ajpa.20188


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Thursday, May 22, 2014

Y Chromosome mutation rates


In my previous post I pointed out the differences found between the ages of different branches of the Y chromosome's Q haplogroup, and how papers tend to date Native American lineages so that they coincide with the date that mainstream science considers the correct one for peopling America: ca. 15 kya.


This made me wonder what certainty do we have of their accuracy, or how precise are these dating methods. The answer is surprising!: not very precise.


The complexity encountered in dating Y chromosome lineages is summarized very well by Chuan-Chao Wang and Li Hui (2014): "... Different time estimation methods use different algorithms and assumptions, thus alternative methods probably fit more or less well with sequence data in time estimations. In addition, the best-fit mutation model might vary for different STRs... some specific lineages might have their own unique best-fit STR mutation rates for time estimation." [4]


In other words, it is extremely fuzzy. Today's post will look into the issue of "dates", the calculations of haplogroup ages, of TMRC, and the fallacy of a "clock" behind Y chromosome mutations.


The complexities behind the Y chromosome


The Y chromosome is particular because it is passed along from father to son, basically unchanged -excepting random mutations- in a long line that links all modern men to an "ancestral Adam" who lived in Africa in the distant past of mankind and from which all Y chromosome haplogroups derive.


Y is one of the sex chromosomes found in mammals, and obviously, humans; the other is the X chromosome. An X chromosome and a Y chromosome ("XY") pair detrmine a male, a double X ("XX"), a woman.


Just like all other chromosomes, the Y chromosome also mutates: chance mutations and natural selection act upon it and create small differences that, if not negative (that is, killing its carrier), are passed on to the next generations.


Y chromosome's high mutation rates


The Y chromosome mutation rate is much higher than that of autosomes because it is restricted to the male germ line, and there, most cell divisions occur by meiosis [1]: Sperm is formed in a process of cellular division known as gametogenesis, inside the testis, and it is during this process, where mutations may take place in a way that can affect the future generations (if a Y chromosome in any other cell of the body mutates -i.e. a cell in the liver-, it will have no impact on the offspring of the bearer of the mutation).


Men produce sperm from pubrerty to death, while women are born with a given number of ovum one of which matures monthly from puberty till menopause. This means that sperm are subjected to many more rounds of cell divisions and may accumulate more chance mutations. If the men are older, the chances are even higher.


Unlike the X chromosome, excepting small regions at the telomers (tips), the Y chromosome cannot undergo recombination (where mutated parts are replaced with other "healthier" ones). This means that most of the Y chromosome (95% of it) forms a non-combining region where Single Nucleotide Polymorphisms (SNP) mutations accumulate without being "repaired".


This non-recombining situation arose because X and Y chrmosomes do not recombine among each other (as do the X chromosome pairs in women), to preserve them from gaining harmful genes from the opposite sex. Allowing Y chromosome to preserve male-specific genes.


These mutations allow geneticists to trace lineages and paternity by comparison. They would also allow calculating the age of lineages by comparing differences that accumulated in each line and the rate at which they accumulate. But this is easier said than done.


Calculating ages of Y-chromosome lineages


The key element in dating lineages or haplogroups is to know the mutation rate, and there are basically two methods for calculating it:


I. Direct Measurement or Pedigree estimates: Take two individuals, related by descent and identify the mutations in their Y-chromosome. As the time span that separates them is known (either in years or in generations), the mutation rate can be calculated directly. (it is a value given in: mutations per nucleotide per generation).


The direct measurement (Yali Xue et al., 2009) [1] of the substitutions in the Y chromosome of two related men, separated by 13 generations gave a "mutation-rate measurement of 3.0 × 10-8 mutations/nucleotide/generation... 1.0 × 10-9 mutations/nucleotide/year " [1].


The published human-chimpanzee comparisons are "2.3 × 10-8 – 6.3 × 10-8 mutations/nucleotide/generation... depending on the generation and split times assumed" [1].


The uncertainty is highlighted by the very ample confidence interval values (95% CI) 8.9 × 10-9 – 7.0 × 10-8 mutations/nucleotide/generation obtained.


II. Evolutionary estimates: they use STR polymorphisms or Microsatellites (defined by SNPs). These can be easily genotyped. So taking the microsatellite variation within Y chromosome lineages and knowing the historical dates of certain key events in these lineages history, a mutation rate can be calculated.


As an example, I will folllow the very cited paper by Zhivotovsky et al., (2004) [2], which has a lot of assumptions, plenty of formula and maths. I am an engineer and love maths, but I will spare you the details. Those interested can check the paper (see Statistical Analysis in [2]).


The calculated average "effective mutation rate" (w), was between 0.000312 and 0.000454 per 25 years for Polynesians and Gypsies respectively, however (and these are the things that surprise me!), these values are "adjusted" because they were considered underestimates. The correcting factor ASD0 or average squared difference was applied and voilá, a mutation rate w of 0.000705±0.000332 and 0.000725±0.000187 is obtained for Maori - Cook islanders and Bulgarian Gypsies respectively.


As can be seen the "adjustment" roughly doubled w (it increased 2.25 times in Polynesians and 1.59 times in Gypsies). Furthermore, the error bars are enormous (47% and 26% for each population).


These two values and another one estimated for "global" loci were then averaged resulting in the "magic number" most quoted, cited and used in current genetics papers: "an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9×10-4 per 25 years" [2].


Different mutation rates


As we can see the values calculated with each method (Pedigree and Evolutionary) are very different, and applying them to calculate ages of lineages will give very differing results.


Being an engineer with a scientific point of view, I believe that the real values are those that are measured, and that the theory should provide a good model that explains reality and sets of equations or formulae that can be applied with some simple parameters to obtain results that are very similar to reality.


The "laws" of mechanics are used because they are a reasonable model that fit the every day world and gives accurate predictions and practical results (you can design a car or a plane to withstand stress and accelerations, calculate the trajectory of a missile with precision, etc). But when it comes to "laws" in genetics, it seems things are much more blurred and lack precision.


Let's look at possible factors that may explain these differences in mutation rates:

  • Frequent mutations might occur within the few generations used in pedigree studies, while slowly mutating loci only become significant over a longer time interval. [2]
  • Evolutionary calculations use statistics of current variation which include reverse mutation of old alleles as well as forward mutation to new alleles; and these reverse mutation would reduce the number of alleles. On the other hand, Pedigree estimates count mutations on a per-meiosis basis so reversals are counted as new alleles. [2]

I would add that the mechanisms working here are not clearly understood so the model fails to replicate reality.


Factors that distort the estimations


Software and assumptions


Another factor to take into account when calculating the age of different haplotypes are the assumptions behind the calculations.


Modern geneticists employ software that runs simulations (i.e. rho statistics with Network, Bayesian analysis with Batwing), which are fed with these assumptions: weight assigned to different STR variants, exclusion of certain loci (those considered ambiguous or with multi nucleotide repeats), generation time, population sizes, mutation rates (which as seen above are also shrouded in uncertainties), and "others". [3]


Among these "others" are the assumptions that, after populations split, no further migration occurs between them, [3] or, for instance, that there is an exponential growth from an initally population with a constant size "N" [4]. These may not be true, as we will see below, together with other causes


Evolutionary Rate and Repeat unit size


Evolution rate is lower for STRs that have an increased repeat unit size (that is, "n" has more nucleotides).[6][7] In other words, penta or hexa nucleotides mutate slower (3.45 x 10-4 per 25 year generation) than tri or tetra markers (6.9×10-4 per 25 years -the figure given by Zhivotovsky et al., (2004) [2]). [7]


This is because (Dupuya et al., 2004) [8] there are "relatively more gains in short alleles and more losses in long alleles.". [8]


These mutation rates yields different coalescence dates for haplogroups; for instance the age estimate for haplogroup CF clade based on tri/tetra marker results is 42.2 ky which is much lower than 64.7 ky estimated with penta/hexa markers. [7]


The fact that mutation rate depends on allele size means that the different haplogroups (which are characterized by different and specific STRs) will mutate at different rates when compared to each other. [8] Yielding incorrect coalescence dates when compared.


More Factors that influence Y chromosome estimates


When comparing mtDNA timelines (these are based on women) and the male Y chromosome datings, differing patterns appear. These are due to:


1. Genetic drift. It acts strongly upon Y chromosomes: many males don't have sons (they may have only daughters, or die before reproducing) so their Y chromosome is not passed on, and is lost from the gene pool, reducing diversity. [9]


2. Polygyny (having more than one wife at a time) This custom would lead to a small number of males to spread their genes (including their Y chromosome) among a disproportionately large number of children. While others are excluded from the reproductive cycle and their Y chromosomes are lost. [9]


In our recent evolutionary past, humans lived in polygynous, extended families. Where male longevity (>50) would allow them to reproduce up to high ages via younger women, situation which is not found in monogamous societies where menopause effectively cuts off older men's reproductive cycle. Older male sperm may also accumulate more mutations than younger sperm, adding more diversity to the gene pool.


3. Lower effective Male Population Size. The higher Male mortality Rate and the reproductive sucess of males (i.e. due to polygyny) are factors that reduces Y chromosome diversity in populations compared to mtDNA and autosomes. [9] This is seen in the higher level of X chromosome (females) variability compared to that of Y chromosome (males). [10]


In their estimate, Zhivotovsky et al., (2004) [2] consider male and female population as equal, but they are not. And this influences the data on ratio of variance at Y chromosome STRs to that of autosomal STR loci. This ratio varies from 1.14 in "sub-Saharan African hunters" to 0.51 among "American farmers" (the global average is close to 1); and this is due to less males per female in the latter population. This lower ratio leads to a lower mutation rate.


4. Migration. Is an important cause of gene flow within a population. It will lead to overestimation of the accumulated STR variance used in evolutionary calculations.


If migrants admixing with a population are of the same haplogroup they cannot be told apart from the original population, so mutation rates would be overestimated for the admixed population.


The gender mix is also important: if more men migrate than women, this will influence the Y to autosomal STR variance as discussed above. [2] Patrilocality (the residence of a newly married couple with the husband's family or tribe) and Matrilocality (the opposite situation) also alters mtDNA to Y chromosome variance.


5. Generation times. "In present-day hunter-gatherer societies generation time is estimated to be approximately 32 and 26 years for males and females, respectively" [11] which is different to the 25 years postulated by Zhivotovsky et al., (2004) [2]. It may seem trivial but if a generation is 32 years instead of 25, the estimates will vary considerably 10 ky can actually mean 12.8 ky. Historical generation times as calculated by pedigree estimates may be very different from those of our evolutionary past.


My next post "Generation time is not 25 years", gives some sources and data to prove it is at least 30 years for males.


6. Variation in founding populations. The Y-STR variation of the founding population at time of arrival in a geographic region is taken into account in evolutionary estimates [2], if variation is lower, the mutation rate will increase and, for higher variation mutation rate will be lower. So if the founding male population has a substantial diversity it will lead to an incorrect (lower) divergence time calculation. [2]


7. Positive Selection. Natural selection also acts upon men, and will increase frequency of a given lineage if it is more benefical for those carrying it. [9] Or, may I add, it will also benefit Y chromosomes piggybacking on individuals with some other allele favored by selection.


8. Expansion and bottlenecks. Genetic diversity between two populations that shared the same original genetic structure may be due to expansion of one of them: because random mutations will arise more frequently in a larger population simply because there are more sperm cells in which they can arise. This will increase the diversity of the larger population. [9]


A bottleneck will have exactly the opposite effect: a paucity in genetic diversity of the decreasing population as lineages become extinct. [11]


Amerindians


When considering Native Americans we must look back towards their Paleo-Indian ancestors and see how some of the assumptions mentioned above apply to them:


They were not small isolated groups with a closed-shared ancestry. Instead they were dinamic groups that had fluid contacts and exchange between each other and their ancestral populations back in Asia. [12]


They were not a "neutral" system where mutations accrete regularly, they were instead subject to positive selection, war, disease, famine which modified the clock's rate of ticking. [12]


Last but not least is the sampling bias when studying populations. Most are not drawn in a random manner from large populations. Instead they come from tiny samples from small villages where the groups are mostly composed by relatives with shared ancestry. This of course modifies the basic premises of coalescent methods and leads to shorter coalescence times than the actual ones.


Another factor is that the current genes found in a population may not actually represent the historic or even the prehistoric mix of that population [12]. Amerindians suffered a severe bottleneck after the discovery and conquest of America (after 1492 CE) which wiped out many lineages (who knows how many Y chromosome or mtDNA haplogroups disappeared during this period?).


Anzic-1 remains


The remains of a Clovis youth from Montana, US (Anzic-1), which are 12.6 ky old, were typed (Rasmussen et al., 2014) [5] and found to belong to Q-L54*(xM3).


The paper indicates that they then calculated the date of divergence between haplogroups Q-L54*(xM3) (Anzic-1) and Q-M3 of contemporary Native Americans. It is a simple rule of three calculation:


They notice that Anzic-1 had 12 traversions (mutations) while modern ones have on average 48.7, then these 36.7 additional traversions must have arisen during the 12,600 years that elapsed between Anzic-1's death and today: so 12.6 x 48.7 ⁄ 36.7 = divergence date, which happened 16.72 kya.


Of course, to make it statistically neater for the paper, they then "implemented a Poisson process model for mutations on the tree and used the constrOptim() function in R to compute a maximum likelihood TMRCA estimate of 16.9 ky. We then repeated this for 100,000 bootstrap simulations to yield a 95% confidence interval of 13.0–19.7 ky." [5]. The outcome ratified their previous simple calculation.


Below is part B of their Extended Data Figure 2: [5]


Fig 2. Adapted from [5]

The figure's original caption reads: "Each branch is labelled by an index and the number of transversion SNPs assigned to the branch (in brackets). Terminal taxa (individuals) are also labelled by population, ID and haplogroup. Branches 21 and 25 represent the most recent shared ancestry between Anzick-1 and other members of the sample. Branch 19 is considerably shorter than neighbouring branches, which have had an additional ~12,600 years to accumulate mutations."


Cross checked and doubts


I checked this value using the transversions indicated in their figure.


So I took the values in brackets and added them up for each individual, the sum is shown on the far right in green (Q-M3 individuals) and red (Q-L54 ones). At the top is an example of the calculation. The sum is referred to the split that takes place at branch 26 (marked with the vertical green line).


As an example individual at branch 0, MXL NA19682, has 8 + 2 + 8 + 3 + 21 = 42 transversions.


For Q-M3 individuals I calculate an average of 40.33 extra transversions in moderns vs. Anzik-1 and an age of 17.96 ky. Using only the Q-L54 individual's values the average is 44.3 transversions and the age is 17.29 ky, using all modern values the figurs are 41.54 transversions and 17.72 ky. They differ slightly from the 16.9 calculated in [5].


Weird Maths or incorrect assumptions


The odd thing is that when the same methodology is applied to the Saqqaq remains (Branch 27), the age estimation goes awry!:


The paper mentions the Palaeo-Eskimo Saqqaq "sequence had a relatively high missing rate of 0.24 and is divergent with respect to the other hgQ lineages in the sample, its singleton branch should more properly be considered to be of length 71 (54 / 0.76) transversions" [5].


So when we take the age of Saqqaq (4 ky), its transversions from the root at the split of branch 28 (which are 71), and calculate the amount of transversions for modern samples (by adding the 31 that correspond to branch 26, to the previously calculated figures), we obtain an average for all moderns of 72.93 transversions, so the difference that accumulated over 4,000 years is only 1.93 transversions, which leads to: 4.0 x 72.93 ⁄ 1.93 = divergence happened 152 kya! Yes, one hundred and fifty two thousand years ago.


Furthermore the distance in transversions from the baseline (the green line in the figure above) ranges from 26 (on branch 3) to 52 (on branch 12), that is, twice the amount. But all belong to modern human populations, why would one group accumulate twice the quantity of transversions than another? the difference of 26 is 26/36.7 = 70.8% of those accumulated by Anzic-1, and if we apply the same criteria 0.708 x 12,600 y = 8,926 years should separate these populations. But no, they are contemporary. In other words, the amount of transversions does not reflect age as a direct proportion.


This clearly indicates that better calculation methods for Y chromosome lineage dating are necessary.


Subjects for future posts: no Y chromosome from Neanderthals is found in modern humans. Did Q haplogroup originate in America?. Where did the Q hg found in UK and Scandinavia come from?


Sources


[1] Yali Xue et al., (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Curr Biol. Sep 15, 2009; 19(17): 1453–1457, doi: 10.1016/j.cub.2009.07.032
[2] Lev A. Zhivotovsky, et al., (2004). The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time. Am J Hum Genet. Jan 2004; 74(1): 50–61. doi: 10.1086/380911
[3] Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
[4] Chuan-Chao Wang and Li Hui, (2014). Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates. bioRxiv posted online May 3, 2014. doi: http://dx.doi.org/10.1101/004705
[5] Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025
[6] Mari Järve, Lev A. Zhivotovsky, et al., (2009). Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit. PLoS One. 2009; 4(9): e7276. doi: 10.1371/journal.pone.0007276
[7] Järve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, et al. (2009). Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit. PLoS ONE 4(9): e7276. doi:10.1371/journal.pone.0007276
[8] B. Myhre Dupuya, M. Stenersena, , A.G. Flønesa, T. Egelandb and B. Olaisena, (2004). Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci. International Congress Series 1261 (2004) 76 – 78 doi:10.1016/S0531-5131(03)01791-6
[9] Cuan-Chao Wang, Li Jin, Hui Li1, Natural selection on human Y chromosomes. arxiv.org
[10] Michael F. Hammer, Fernando L. Mendez, Murray P. Cox, August E. Woerner, Jeffrey D. Wall, (2008). Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity. PLoS Genetics doi:10.1371/journal.pgen.1000202
[11] Labuda D, Yotova V, Lefebvre J-F, Moreau C, Utermann G, et al., (2013). X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations. PLoS ONE 8(11): e80710. doi:10.1371/journal.pone.0080710
[12] Peter N. Jones, American Indian mtDNA, Y Chromosome genetic data and the peoping of North America, Bauu Institute, 2004.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Tuesday, May 20, 2014

Out of America (into Asia)? Part 2


On the Y-Chromosome Q haplogroup


 


TThis is the second part (See First Part here) of my ramblings on a possible Out of America migration back into Asia.


I will carry on from where I left off: (Summary) some Asian (specifically Northern, Central and Northeastern Asians - from Siberia, NE China and Mongolia) have a small but noticeable content of specific genes of Amerindian content. Mainstream science has it that these Asians descend from the people that were also the ancestors of Amerindians therefore they do carry some of the same genes.


I posted that the Turkic people moved out from the Altai spreading West towards Europe and North, Northeast into Siberia (Sakha or Yakuts, Kets and Selkups) and that they probably admixed there with aboriginal Siberians who in turn had an American admixture due to an Out of America gene flow.


I pointed out tha the Kets have the highest frequency of Y chromosome haplogroup Q (Q hg) in all of Asia (93.7%), which is only found among Amerindians; The Selkups have the second-highest frequency of haplogroup Q (Q hg) in Asia (66.4%).


Other groups, Tuvans, Oroqen, Mongols, Hadza and Daur carry a much lower Amerindian content and is very likely due to admixing with the other Siberian peoples.


The Y-chromosome Q haplogroup (Q hg) mentioned above is very interesting due to its strong preponderance in the Americas. Could it be a signal of an Out of America back-migration into Asia?


The Y-Chromosome haplogroups in America


map Y-chromosome Q haplogroup
Global distribution of Q Y-Chromosome haplogroups

A paper analyzing American and Asian lineages of Y-Chromosome (Battaglia V., et al., 2013) [2] notes that of the two founding lineages of Y-chromosome found in America, (C and Q), Q is the oldest and most widespread (with 75% frequency), while C, is limited to North America and found at a lower frequency . This means that Q haplogroup (Q hg) reached America first and spread from Alaska to Tierra del Fuego, C hg is a later arrival.


Q haplogroup is found in two main lineages in America: Q1a3a1a-M3 (76.8%) and Q1a3a1-L54* (16.7%). It is however interesting to point out the great diversity of Q hg in America: another 8 haplotypes have been discovered, mainly found among Peruvians and Mexicans, and they add up to 6.4% frequency, much greater than the diversity found in Siberia. [2]


The M3 part of Q1a3a1a stands for the M3 marker which is believed by mainstream geneticists to have arisen in Beringia, except for some extant Far Eastern Siberians (it appears among Koryaks at a frequency of 40%) [2] it is only found among Native Americans. Its presence among Koriaks (see image below for Q1a3a1a* red and blue square) is believed to be "... the result of a back migration rather than be direct M3 Beringian descendants... [and] could also be due to recent contacts (gene flows) with modern northern Native Americans." [2] .


An alternative explanation could be that M3 originated in Asia and those that took it into America survived, while the Siberians that carried it, passed away without descent.


The other marker L54, is definitively American (with a higher frequency in Mexico and Central America and lower elsewhere), none were found in the "populations living along the entry route to the Americas" [2] , and "only a potential Q-L54* has been observed in one Chukchi from Northern Siberia" [2], the paper cautiously points out that "any interpretation of this result (new Asian lineage, remnant of an ancestral state, trace of forward or back-migration) is premature..." [2].


Eastern and Southern Siberian peoples, Mongolians from the Altai Region in Western Mongolia and southern Ataians are definded by the Q1a3a1c sub-clade defined by the L330 marker. Asian upstream intermediate is L53* is found in Northern-Altai and Mongolia, at very low frequencies.


The paper concludes that the Altai Mountains were the southern barrier for these people who carried an ancestral form of L54, which "in prehistoric times and long before the peopling of the New Continent, moved eastwards during the Beringian standstill." [2]


This is reasonable, but the dating of the different branches is very strange:


The Odd phylogenetic tree


What I find perplexing are the dates of the branches of Battaglia et al.'s Phylogenetic tree of Y-chromosome Q hg; where some branches are older than their roots!:


Below is my adaptation of Battaglia et al.'s figure 1; in red I shaded the American haplogroups (M3), and in blue the Asian ones. The number on the right is the age of each haplogroup, (kya). The branches that are "American" are shaded red. All other branches are fully Asian.


Q haplogroup tree
Phylogenetic tree of Y-chromosome haplogroup Q. From [2]
The ages are on the right. Blue= Asian, Red= Amerindian

We see an incongruity in the "main" branch MEH2 whose branches M120, MEH2* and M25 (with ages that range from 2.7 to 15.4 kya) are all younger than the offshoots of branch M346 which is at their same level.


Furthermore, M346 (dated by Zhong et al., [3] at 17.77 +⁄- 4.4 ky, then branches succesively into branch L53 which then branches into L54 and this one then branches into M3 which is the oldest in the tree with maximum ages between 21 and 23.6 kya.


Lets look at the details:

Dates (I round off the dates from Tables 2 and 3, in [2]):

  • America
    • Q1a3a1a-M3*. Most (from 66 to 100%) Amerindians belong to it: 22 kya for Central and Southern Americans, 3.4 kya for Na-Denes and 7.4 kya for Eskimo-Aleuts. Which is reasonable since the last two populations belong to a more recent migratory wave into Northern North America.
    • Q1a3a-L54*. The remaining American Natives belong to it: 23.6 kya old, except Na-Dene which, again, are younger: 5.6 kya.
  • Asia
    • Q1a1-M120 and Q1a2 - M25. Mongols were not dated in [2], however Table 1 in [3] gives 15.4 and 2.7 ky respectively.
    • Q1a*-MEH2. Koryaks = 3.5 kya and also the remains of the "Saqqaq" man from Greenland (Morten Rasmussen et al., 2009) [1] which are about 4,000 years old but belong to a later wave into America.

    • Q1a3a1c-L330. Mongols = 6.5 kya and Altaians: 2.9 kya.
    • Q1a3a*-M346, is dated at 17.77 +⁄- 4.41 kya [3]

Below I reproduce the data from Table 3 [2], showing the "average" ages for all Q haplogroups:


Age of Q haplogroup
Average age Q lineages. From [2]

Once more, American Q hg are between 21.1 and 23.4 ky old. The Asian ones range from 10.3 to 22.4 ky with a decreasing age cline as you move East to West from America into Siberia.


This would suggest that these Asian Q lineages originated in America and dispersed West, diversifying (mutating) along the way since the youngest are deeper in central Asia.


But that assumption is apparently wrong, because the markers follow the opposite order (that is, Americans have markers that Asians don't, implying that these markers appeared later, in Americans).


I guess I am going to have to do some deeper research into specific Haplogroup markers, but first, let's look into the Siberian Q haplogroups.


Siberian ancestors (?)


The presence of haplogroup Q (Q hg) among Siberians was pointed out in 2002 (Karafet et al., 2002) [4] at relatively low frequencies of 18.8% (when compared to Native Americans). Two populations concentrate 79.5% of the ocurrences: the frequency reached 93.8% among Kets and 66.4% among Selkups. The age of haplogroup Q was estimated at 17,700 +⁄- 4,800 years [4], in tune with the mainstream theory (it is just a bit older than the 15 kya date for entry into America).


These high frequencies were due to "intergenerational genetic drift coupled with founder effects... supported by very low levels of Y-STR diversity associated with haplogroup Q in both populations (0.149 and 0.159, respectively)..." [4]


In other words it was not natural selection, but chance that acted upon the small population sizes and their high mobility allowing Q hg to become predominant; therefore its frequency grew (intergenerational genetic drift), add to this the fact that small groups with Q hg survived while other haplogroups just died out (bottleneck); outcome: Thus the Q hg became the prevailing line among these people.


Different to Americans and different to each other


But, as we have already seen, these haplotypes are not the same as those found in Native Americans; a Russian language paper (Volkov, 2013) [5] provides an interesting phylogenetic tree, reproduced below:


phylogenetic tree Q1a3 haplogroup
Phylogenetic tree of haplogroup Q1a3. From [5]

At the split between Americans and Asians (Q1a3a-L53), two branches appear, one leading to all Siberian groups in blue. Another one, in orange one leads to American Natives (red branch M3) while another (yellow) leads to the Q haplogroup found in certain Europeans: Q1a2a2 L804, L805 (Sweden, Norway and via Vikings: UK) - this is worth looking into! [6]


The Q frequency (L330) among Siberians is in agreement with Karafet et al: Kets: 84%, Northern Selkups: 66.4% (and drops to: Evens: 4.2%, Nenets: 1,4%, Kanthy: 1%). [5]


But they are not the same Q haplotypes: Selkups, who originally lived in the Urals, share the same haplotype with the Chechens of the Caucasus (which is close by). On the other hand, the remaining Siberian populations and among them the Kets belong to another haplotype, with other downstream mutations: DYS347=14, and DYS437=13, DYS390=23 ("DYS" stands for DNA Y chromosome Short Tandem Repeat, with a lenght of "n").


Considering that Altai was the source of Amerindian Q haplogroup, Dulik at al., (2012) [7] explored the differences between the Q hg of Southern and Northern Altaian's (this is also reflected in the image above). They found that the latter were quite recent (Bronze Age) the former older -early Bronze Age or late Neolithic.


Then they calculated the divergence times between Southern Altaians and Native Americans, but their TMRCA ages fluctuate widely; from a too recent 7.74 kya (Pedigree Based) to a more reasonable 21.96 ky (Evolutionary-Based); the Split Time values were 4.95 and 13.42 kya for Pedigree based and Evolutionary based, respectively.


Seeing this 3 fold difference between the ages and taking into account that America was peopled more than 8 kya, the authors dismissed the Pedigree based values arguing ("that the evolutionary rate provided a more reasonable estimate.... making the use of the pedigree-based mutation rate questionable." [7]).


These "average" values are to young (even more recent than the 23 kya age estimated further up for the M3 and L54 haplotypes found in America. And, in my opinion it is due to the fact that the 95% confidence intervals for the Bayesian analyses are extremely broad: they range from 12,260 to 42,690 ya. for TMRCA and 5,220 to 30,430 ya. for Splilt Time.


Taking the oldest figures would mean that the ancestors of Americans could have shared a common ancestor with Altaians 42,690 years ago, which is really much more reasonable and consistent with the earliest dated Upper Paleolithic industries from Altai: 43.3 kya [4].


Dating and TMRCA values: Are they reliable?


Looking at these disparities it seems that a key issue is the dating, the timeline, the estimation on when groups split or when they shared a common ancestor.


As seen above, Pedigree estimations differ substantially from those based on evolutionary estimations. And these depend on the mutation rates adopted.


When reading the papers that deal with this subject, my doubts intensify. For instance, a paper by Poznik et al., (2013) [8] estimates mutation rates by adopting, as a "calibration point, the initial migration into and expansion throughout the Americas", based on the dates of known archaeological sites (Paisley Cave and Buttermilk Creek in the US and Monte Verde in Chile) they find Goebel et al. estimation that " humans colonized the Americas around 15 kya” acceptable, and use it for calibration purposes. [8]


But what if instead of 15 kya the date was really 30 kya or 45 kya? This would introduce a strong bias in their estimations. Once again we see how a "recent date" for the peopling of America impacts upon other branches of formal science.


The authors then use the Y haplogroup Q for their calibrations and assume that M3 arose "shortly subsequent to initial entry to the Americas", and in doing so, underestimate the impact that an earlier divergence (Between L54 and M3) in Siberia, prior to the entry into the New world could have had on their calibration. [8]


The strange dates produced by these estimations are higlighted by the case I mentioned in a Previous post on the useless mtDNA clock, where the dating of a novel Y-chromosome haplogroup (Mendez et al, 2013) named A00, gave a very old age: " 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils..." [9], strangely old date indeed. The clocks need to be checked.


Another example can be found in a paper on a Q hg sublineage (Q5) detected in India (Sharma et al., 2007) [10]; the ate estimated for it was 47.1 kya (34.2 – 75.6 ky), but the authors believe that it is "an over estimate than the age of haplogroup Q (15,000–18,000 Years Before Present)" and try to explain the distorted "old" age they calculated as caused by "enhanced diversity, probably as an effect of population expansions and severe bottlenecks or might be due to later migrations and admixture" [10], they then recalculate it as 14.4 ky old! (fitting it nicely into the assumed age range).


Summary


Y chromosome Q hg predominates in America, most of it belongs to the M3 subtype, the rest is L54. There is a very small presence of these two subtypes in East Beringia (Asia), most likely due to a back migration into Siberia from America.


Greater diversity within Q hg is found in America than in North East and central Siberia, this hints at a deeper and more ancient origin for the American lineages.


However the ages of the oldest Amerindian haplotypes are quite recent and have been calculated as being 22 -23 kya. Asian strains contrary to what would be expected from the theory of a trans-Beringian peopling of America appear to be much younger. Suggesting instead a migration Out of America and into Asia, carrying Q hg. We will see in a future post that there is additional proof from mtDNA and language of a migration from America into Eastern Siberia.


Despite doubts regarding age calculations, the oldest mainstream date of 43 kya for a split between the ancestors of Altaians and Americans seems to allow for an early peopling of America.


There is something with the ages that I find strange. But that will be the subject of another post, where I will deal with the dating methods (in particular after reading how Anzic-1 remains from Montana US were dated. By the way, he was a Q-L54*(xM3) 12,600 years old.


I will review the markers that indicate splits in Q hg, because a radiation out of America seems highly probable. I will also take a look at those odd Q hg found in Europe which some attribute to the Huns, but may have more ancient roots, the same ancient roots that Amerindian Q hg has... (I am thinking about Neanderthal here... however Neanderthal Y chromosome would be even older than the A00 haplogroup mentioned above, and quite different from the current Q hg that descends from A00).


Sources


[1] Morten Rasmussen et al., (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835
[2] Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, et al., (2013). The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q.. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390
[3] Hua Zhong et al., (2010). Extended Y-chromosome investigation suggests post-Glacial migrations of modern humans into East Asia via the northern route. Oxford Journals.
[4] Tatiana Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life, Human Biology, December 2002, v. 74, no. 6, pp. 761–789.
[5] VG Volkov, (2013). Ancient Samoyeds of Yenisey, and migration in light of Genetic Data. Tomsk magazine Ling. and Antropo. 2013. 1 (1) 79-96
[6] International Society of Genetic Genealogy
[7] Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
[8] G. David Poznik et al., (2013). Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science 2 August 2013: vol. 341 no. 6145 pp. 562-565 S. Inf. page 13. DOI: 10.1126/science.1237619
[9] Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
[10] Swarkar Sharma et al., (2007). A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India. BMC Evol Biol. 2007; 7: 232. doi: 10.1186/1471-2148-7-2327
[11] Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Friday, May 16, 2014

Out of America (into Asia)? Part 1


A paper (Morten Rasmussen et al., 2009) [1] reports the sequencing of the genome of a male from Greenland; it was obtained froma a hair (about 4,000 years old) that was found in the permafrost. The man belonged to a wave that peopled the New World long after the original and older migration of modern Amerindians.


The interesting part (from my perspective) is the information regarding Native Americans and how different they are from their purported Siberian ancestors.


The following image (Adapted from Fig. 3 in [1]) and, just by looking at it you can see some intriguing trends:


figure
Figure 3. From [1]

Part (b) of the figure (upper right corner of the image) shows a clear distribution where Siberians and East Asians are found on the upper branch, Europeans on the Right tip, where upper and lower branches meet, and Southern and Meso-American Natives are found on the bottom left tip of the lower branch.


It is very evident by the distance between them, the vector orientation and their placement in different branches, that current Siberians and Asians are not related to modern Amerindians.


Part (c) shows a plot generated by the ADMIXTURE39 algorithm with K = 5. It shows individuals from 35 extant Eurasian and American populations which are represented by stacked columns with five ancestry proportions (y axis indicates the fraction of each of the five inferred ancestral groups).


We can see that:


  1. (Blue color). There is an important western Eurasian component admixed into Siberians, Northernmost North Americans and Greenlanders. This drops off sharply with a North to South cline for the other Amerindian populations.
  2. (Brown or Burgundy color). The Amerindian component is prevalent with a decreasing South - North Cline, among all Native American groups. And is also found in minimum fractions among Chuckchis, Tuvinians, Altai, Selkups and Kets. (We will look into this further down)
  3. (Pale Yellow). Found in minimum frequencies in Eastern Siberia, it incrases to nearly 90% among West Beringian Koryaks and Chukchis, with a strong prevalence among Arctic Americans and Na-Dene natives. It drops off with a north to south cline from around 40% in Na-Dene to a <10% fraction among Southern Amerindians.
  4. The other components are absent among South American Natives.Orange, which is prevalent among Chinese, Japanese and East Asians, drops off towards Eastern Siberia. Dark Yellow, which grows with a West to East cline and is maximum in Central and Northern Siberia.

The Amerindian signature in Asia


The "brown component" found in small frequencies in Asia is quite interesting and exactly the same pattern appears in another paper (Li et al., 208) [2]; In this case the sample includes populations from African, Southern Asian, PNG and the Middle East. Below is its Figure 1 A:


Figure 1A. From [2]

The image indicates the ancestry of different populations at K = 7 (seven inferred ancestral groups). [2]


We see that the pattern is repeated and that the Amerindian component (Violet) appears predominantly (>90%) in South America (with a slight admixture of European and even less components from other regions).


The Amerindian "violet color" reappears in East Asia among the Yakut, but with extremely small frequencies among the: Oroquen of Heilongjiang (China), the neighboring Daur of Mongolia, Hazara (Afghanistan) and Mongols. It reappears again at relatively higher frequencies among the Russians.


Why do all these Eurasian people have a tiny proportion of Amerindian in them?


Orthodox view


The accepted theory is the following:


Modern Humans reached Siberia relatively late, the rest of the Old World was already peopled. The icy Siberian regions had effectively formed a barrier to all hominins until the superior skills of modern Homo sapiens (invention of needles to sew fur clothes and the mastery of glacial-condition survival skills) breached that last barrier.


This enabled Siberians from Central Asia to trek out on a Northeastern course, reach Beringia and stay there about 5,000 years during the peak of the last Ice Age, hunting mammoths and other tundra herbivores. During this time they became quite distinct from a genetic point of view from the relatives that stayed behind in Siberia. Then during deglaciation they packed their tents and gear and rapidly marched on into the vast and empty New World occupying it in less than 2,000 years.


A second wave of migrants admixed with the first, bringing some more recent Siberian alleles which are found among Na-Dene, Innuit and other North American natives. South America remained free from this admixture.


So, any similarity between Siberians and Amerindians is due to their common ancestry. There are differences of course, but these are due to the long sojourn in Beringia which gave time for unique Native American alleles to appear and also for founder effect (only a few clans of Siberians reached Beringia, so their set of genes was rather limited) and bottleneck (some clans died out and their lineages with them, further depleting Amerindian genetic diversity) to act and further separate Americans from Asians.


By the way, these people expanded into America in small isolated groups that did not mix frequently with their neighbors, so they developed in a very short period of time, hundreds of unique languages and their genomes took disparate courses which due to drift made them appear different, but actually all sharing the same recent Asian origin.


Last of all, enslaved Africans and Europeans admixed after 1492 C.E. as a consequence of the discovery of America by Europeans so any odd European or African genes found among Amerindians (even the most isolated groups) are due to this recent admxiture.


Another unorthodox view


The model outlined above does not even consider the possibility of a pre-sapiens peopling of America. The H. habilis from Dmanisi in Georgia, the H. erectus from China or even Neanderthals and Denisovans from Altai, could have continued onwards into America, but archaic sites with Acheulean or Mousterian tools are lightly dismissed by mainstream science as geofacts or of recent manufacture.


The recency in the peopling in America is taken as a proven fact and the data are used by other branches of science (i.e. genetics) when calibrating their methods. As seen in previous posts, the late peopling of America and Siberia is accepted without questioning. This in turn implies that Old World populations have "deeper evolutionary histories", and Amerindians, in contrast are "recent".


The bottleneck and founder effects are generally assumed to have taken place prior to or during the Beringian Standstill, thus restricting the gene pool that entered America. I have not seen papers that explicitly recognize that America was peopled by a popuation with a wide spectrum of alleles and that they became extinct due to the negative impact of mass deaths caused by disease, war and over exploitation of natives after the Discovery and Conquest of America. This overlooked event was an exceptionally strong force even as recently as the late 1800s, and early 1900s.


As an example, the population of Yaghans or Yamana, canoe people living in the fjords of Southern Tierra del Fuego and the Selknam hunter gatherers of the Fuegian mainland, dropped dramatically after contact with Europeans:


The Yaghans passed from 3,000 to 100 people between 1850 and 1916; in 1995 only 75 people of admixed Yaghan origin survived. The Selknam decreased from 3,500 to 800 during the same period, today only 696 persons of mixed Selknam descent survive. Whooping cough, tuberculosis, small pox and VD wiped them out.


These were the real bottlenecks that wiped out people who had lived in isolation from Old World illnesses for milennia. But let's get back to our main subject. The alternative theory for the peopling of America.


What to Yakuts, Oroquen, Daur, Hazara, Mongols, Russians, Chuckchis, Tuvinians, Altai, Selkups and Kets have in common that allows them to have minute quantities of Amerindian ancestry?


The map I prepared (see below) shows their approximate geographic location and the figure inside each oval is the rough percentage of Amerindian ancestry in each group (it indicates the average value within each population):


map of Amerindian Ancestry in Asia
Amerindian ancestry in different Asian populations. Copyright © 2014 by Austin Whittall

We see a high frequency of Amerindian ancestry among Chukchis, Kets and Selkups. And a drop towards the south: Altai, China, Mongolia and the Hadzas. Russians: it is hard to define a location for them since we do not have the data about where the samples were taken. But the value is high and uniformly distributed among them.


I believe that there was a back-migration from America into Eastern Siberia. This accounts for the high content among Chukchis (red arrow A in map).


The dispersal advanced further into East Asia along a northern corridor since to the south mountain ranges (Cherskiy and Kolyma) along the coast blocked the way. The route then crossed the Verkhoyansk Range and reached the Lena River Basin, and, further West, the Yenisei River Basin where it admixed with the aboriginal people living there. (red arrows B in map). To the south, the Iablonovy and Stanovoy Mountains blocked their advance into Manchuria, Mongolia and China. This was the maximum advance of these "Out-Of-America" migrants. (shaded pale red in map).


Much later, the current populations of Selkups, Yakuts and Kets moved north and east into these regions and admixed with these aboriginals, incorporating the Amerindian alleles into their genome (blue arrows in map).


And then, much more recently, further mixing towards the South along the Amur and then West through Mongolia incorporated these genes into the Oroqen, Daur and Mongols. Additional dispersal towards Altai and into Russia took place along the Northernmost Silk Road (Euasian Steppe Road); similar dispersal incorporated them into the Hadza in Afghanistan. (green arrows in map).

But who are these Selkups, Yakuts and Kets?


The Turkic people


The homeland of the Turkic people and their language is in the Altai region, where proto Turkic appeared ca. 400 BC. It expanded from there: the Tuvans and Sakha (or Yakut) moving East and Northwards, and others moving west around Aral, the Caspian and into Asia Minor (finally settling in Turkey).[3]


Let's take a look at the Asians who carry these American components:


The Sakha or Yakut left their Altai homeland forced by their neighbors. They advanced along the Lena River towards the northeastern forests of Siberia. They admixed with the local natives (some of which carried the ancient Amerindian component) and also with mongol people, which have left a strong Mongol - East Asian component in them.


The Kets, also from the Altai, and also forced north due to conflict with belicose neighbors. They have a very strong Amerindian component and also, the highest frequency of Y chromosome haplogroup Q in all of Asia (93.7%), which is only found among Amerindians. Currently they are a small population (<1,500 people) yet many name places in Siberia are Ket. They are linked to the later wave that peopled America through the Na-Dene - Yeniseian languages.


The Selkups (currently about 4,300 people) have the second-highest frequency of haplogroup Q in Asia (66.4%). They were not originally from Siberia, they migrated East from the Urals and mixed with Turkic elements in the Altai area and also with the aboriginal peoples of the Yeniseian region (Siberia) who carried the Amerindian alleles. [4][5]


The Y-chromosome Q haplogroup mentioned above is very interesting and worthy of the second Part of this post.


Continues in Part 2.


Sources


[1] Morten Rasmussen et al., (2009). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835.
[2] Li JZ, Absher DM, Tang H et al., (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 319: 1100–1104
[3] The Turkic Languages in a Nutshell
[4] The Red Book of the Peoples of the Russian Empire
[5] Tatiana M. Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life. Human Biology, December 2002, v. 74, no. 6, pp. 761–789.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Wednesday, May 14, 2014

A shared link on US languages


This is something that I have not done before, but, there is always the first timer for something, so here it is.


I don't intend to make a habit of it, but I may have woken up today feeling nice!


I received an e-mail, copied below, which I will share with you, together with the link in it:


Hi Austin,
We recently finished working on a graphic “Many Languages One America” which I thought I would share it with you in the hopes you might make some use of it. Here is the link: http://freepeoplesearch.org/blog/infographic-many-languages-one-america.html
I would highly appreciate it, if you could re-post it on your blog for your readers. Either way, I hope you’ll continue sharing the awesome contents through your blog. It has been a sincere pleasure to read.
Thanks & Regards,
Heather Brown


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Alcohol, genes and human migrations... Part 3


In two previous posts (Part 1 and Part 2) we looked into the Alcohol and Aldehyde Dehydrongenase (ADH and ALDH respectively) enzimes that metabolize alcohol in humans.


We noticed that they appear in all human populations but, in different genetic variations, which seem to be distributed globally following certain dispersal routes, acquiring higher frequencies among some peoples while in others they are absent or found at lower frequencies.


These variations in genes in turn affect how these people process their alcoholic intake. Some may have very ancient origins while others seem to be quite recent. Today we will present the final data and complete this third and last post of this series.


ADH and orthodoxy


A paper that is now 11 years old (Mulligan et al., 2003) [1] types Alcohol Dehydrogenase (ADH) and looks into the differente alleles for various populations. As expected, these are found in different frequencies for ADH1C / ADH1B among Amerindians, Asians and Africans (other populations were not included in this paper).


I was surprised at how the authors "edited" their data: (Bold mine) [1]


"For each of the five studied populations, all inferred haplotypes were removed if they did not significantly improve the model as assessed by a log likelihood ratio. Based on this criterion, the following numbers of unconfirmed haplotypes were removed from each population: American Indian, 3; Siberian, 2; Mongolian, none; Chinese, none; Nigerian, none.
The American Indian population had more unconfirmed haplotypes than the others, most likely because it had the largest sample size and contained relatives. However, all of the unconfirmed haplotypes were rare and increased the likelihood of particular individuals only trivially."


They used a program (MLOCUS) which conducts a probabilistic analysis and assigns log likelihood values, so as we can see above, they "removed... haplotypes" because they "did not significantly improve the model" or "increased the likelyhood... only trivially" [1].


Rare Amerindian haplotypes were therefore discarded (and in a high proportion compared to other populations), this surely biased the outcome, moreso since their impact on the "model" was minimum.


Then we must add the assumption that African and Eurasian genes are much older than Native American ones:


The assumption that Amerindians are "young"


Mulligan et al., conclude "No evidence of recombination was detected at the ADH or ALDH loci in the American Indian population. One Chinese and three Nigerian ADH haplotypes appear to have arisen by recombination and/or gene conversion, a result that is consistent with a deeper evolutionary history in these populations compared with American Indians." [1]


The fact is that the Chinese recombination is the one that originates Ht 6 affecting 8% of the Chinese population. It is not "deep" (i.e. old, archaic, ancient), actually this Ht6 "possessed the ADH1B*47His allele" which, as we have seen (Part 2 of this post) is very recent among Chinese:

Hui Li, et al., 2011 [2] gives the following dates for the ADH1B*47His alleles (this paper's nomenclature for them is H6 and H7): "The estimated ages of H6 and H7 both indicate relatively recent coalescents or expansion times of the haplogroups.The age of H7 is estimated at only around 2.8 thousand years... This young age is unexpected..." [2]


Clearly recent, so why do Mulligan et al. asume that the allele is "ancient"? [1]


I believe that they are trying to fit the paper to adjust to the current orthodoxy of a late peopling of America, therefore Asian lineages must be ancient and Amerindian ones young.


To do so, they also "manually" fit the Ht 7 found in Africans (Nigerians), which they believe to be the "ancestral" haplotype, between two Amerindian alleles, suggesting it is the most parsimonious setting for it; then they derive both Amerindian alleles, Ht 2 and Ht 3, from it; the write (my comments bold between brackets) [1]


The order of ADH1C HaeIII and ADH1C Ile349Val [that is, how to get from Ht3 to Ht2] could not be determined based solely on the American Indian data because of complete cosegregation of these markers [cosegregation: the genes and markers are inherited together]. However, Ht 7 in the Nigerians fit the cladogram most parsimoniously between Hts 2 and 3, which placed ADH1C Ile349Val after ADH1C HaeIII when moving outward in the cladogram....
Alternatively, Osier et al. (2002) inferred a haplotype in two American Indian populations that would reverse the order of ADH1C HaeIII and ADH1C Ile349Val.
[exactly the opposite to what Mulligan et al. suggest!] Osier et al. (2002) also inferred five additional ADH haplotypes present at low frequencies in four American Indian populations. Two of Osier and co-worker’s (2002) haplotypes, including the one that would reverse the order of ADH1C HaeIII and ADH1C Ile349Val, were removed from our dataset [they deliberately removed the data that contradicted their assumption] based on insignificant improvement of the model, suggesting that a more minimal set of haplotypes may exist for the populations investigated in Osier et al. (2002). [1]


What did Ossier et al. find?


Since Mulligan et al., mentioned Ossier et al., 2002, [3] we will take another look at Ossier & team's work (basically Table 4 and pp. 95):


Ossier et al., defined an Ancestral haplotype (212111) [corresponding to Ht 2 in Mulligan et al.], found in all populations aorund the world, with some minor exceptions, at relatively low frequencies (those with the highest value are shown in brackets): Africans: 0 - 10.6%, Europeans: 0.7 - 30.7% [Finns], East Asia: 0 - 9.8%, Pacific-PNG: 14.6 - 38%, Siberia: 13.1%, N. America: 11.7 - 48.1% [Mexican Pima], S. America: 3.2 - 10.8%.


I wonder why do Finns and Mexican Pima have such high frequencies


The Ancestral haplotype then mutated into two alleles:


  • 112111 [Ht 1 in Mulligan et al.] This is the ADH1C HaeIII site-absent allele, and it differs from the ancestral haplotype only at the ADH1C EcoRI site. (it is what Mulligan et al. named Ht1), which is found in most populations around the world and very common in Europe: Africa: 2.8 - 17.2%, Europe: 5.0 - 30.8% [Basque], East Asia: 0 - 14%, nil in Pacific - PNG, Siberia: 14%, N. America: 2.3 - 21%, S. America: 6.9 - 22.7%
  • 211111 [Ht 7]. Originated by "an independent mutation of the ADH1C Ile349Val site on the ancestral haplotype... This haplotype is rarely seen today but is present in the !Kung San (8.6%), Biaka Pygmies (10.8%), and African Americans (1.2%)". Some outliers: Yakut 1.3%, Micronesians 3%, Danes 1%, Irish 0.8%, San Francisco Chinese 1%. Zero elsewhere.
  • 221111 [Ht 3], is the mutation of 211111 and is "most common around the world" :
    Africa: 35.7 - 87.5%, Europe: 1.9 - 39%, East Asia: 9,4 - 20.5%, Pacific - PNG: 23.4 - 42.3%, Siberia: 42.4%, N. America: 28.6 - 68.3%, S. America: 64.9 - 82.3%. Note the very high frequencies in South America compared to much lower values in Asia - Siberia.

Who is correct? Mulligan or Ossier? You can decide based upon the evidence, please check both papers.


Unsurprisingly Mulligan et al. hint that the "difference in haplotype distribution may reflect the fact that different Asian and African populations were analyzed by Osier et al. (2002)." They also recognize that founder effects and possible population bottlenecks may have influenced Amerindian haplotype frequencies.[1]


Amerindian oddities


Nevertheless, the striking facts are that American Indians have, for both Mulligan and Ossier some peculiarities:

  1. The highest frequency of Ht 2 in the whole world (this is the Ancestral allele)
  2. The highest frequency of Ht 1 in the world (and this is only one mutation away from the ancestral allele, so it is evidently "old" too)
  3. The highest frequency of Ht 3 in the world if we consider only South American Natives (78.4%) or second highest 62.3% (for both North and South Amerindians) vs. 65.1% for Sub Saharan Africans. This is the most common allele worldwide, yet its highest frequency is found in Africa -cradle of Mankind- and... of all places, America!

An explanation is that a bottleneck effect in America eliminated some alleles leaving others, which later expanded to fill the void, hence a larger frequency of some alleles in comparison to the rest of the world.

I find this difficult to believe because there are some extremely rare alleles are present in America which are only found in Africa and in the Pyrenean foothills in Spain. A bottleneck would have eliminated these too, how did they survive? Were they present in even larger numbers before the bottleneck? Do we see the imprint of a once larger population? (I do believe that European contact in the 1500s wiped out a large number of alleles unique to Amerindians. So the "lack of diversity" does not mean a "recent" origin of Amerindians, it is merely the outcome of attrition due to disease and war).


Below are some Rare alleles and their frequencies [3]:


  1. 111111: 1.1% Karitiana, 9.2% Maya, 1.1% Arizona Pima. While in the rest of the world it is only found among: Basque 1.6%, North Moroccans 2.2%, !Kung San 2.3% and S.E. Bantu speakers: 1.4%. Zero in Asia, Siberia and the rest of the world.
  2. 121111: 1.1% Karitiana, 1.5% R. Suri, and (again) 1.6% Basque, 0.7% Catalans, 0.6 - 8.9% North Africans, !Kung San 2.6% and S.E. Bantu speakers: 4.2%. Zero in the rest of the world.

We could argue that Spanish genes admixed with those of Amerindian after the discovery of America: this would account for Catalan and Basque alleles. Additionally Moroccan genes surely got into the Spanish genome during the Moorish occupation of Spain (711 - 1491 C.E.), but, what about the Sub Saharan Africans? Did slave trade introduce !Kung San genes into America? I find it unlikely. Actually you would expect other African genes but not !Kung San genes.


Now, since Ht 1, Ht 2 (ancestral allele) and Ht 3 are all found in Africa you might expect them to have originated there. But the !Kung San do not carry Ht 1 and Sub Saharan Africans frequency for it is very low (6.1%), but not so in North Africa (13.6%) or Middle East (12%) so perhaps it originated out of Africa and back-migrated later, skipping East Asia and Siberia which also have low frequencies (3.7%), it is absent in PNG and Micronesia, but remained strong in America (11.8%) and in Europe (27.3%) where it probably originated.


Could they be a Denisovan allele? Not likely since it is not found among Papuans and they have the highest Denisovan admixture.


Perhaps it is Neanderthal. If so, its low rate among East Asians (which should have a very high Neanderthal admixture) is easily explained due to the exponential growth of the recent Ht 6 and Ht 7 haplotypes in that area, which were positively selected at the expense of the other alleles.


Closing Comments


As a summary of this "three part" post, I will highlight two things:


First; there is a tendency to "fit" the data to corroborate the orthodox theory of a late peopling of America by a small group of people with limited genetic diversity (founder effect and bottleneck). These then expanded in the New World filling it with people with a very different mix of genes than those found in the Old World.


This is akin to Astronomy before the "Big Bang" theory (the age of the Universe and the cosmological constant were "adjusted" to fit the prevailing theories) or Geology before Plate Tectonics.


Second, the different alleles found among American natives (and this is even more noticeable among South American natives, since North American ones have the imprint of a recent Asian migratory wave) are not similar to those found in East Asia. Some appear to be more similar to those of Caucasians or Africans than to those of Asians, which is unusual since one would expect Amerindians to resemble their supposed Asian ancestors.


Post discovery admixture, bottlenecks and founder effects are used to explain away these differences, but it is highly probable that a stronger archaic admixture is found among Amerindians than elsewhere. Probably due to an Admixture that took place in America, during a peopling event that predated the appearance of Modern East Asians or Siberians.


Part 1

Part 2


Sources


[1] Connie J. Mulligan, et. al., (2003). Allelic variation at alcohol metabolism genes (ADH1B, ADH1C, ALDH2) and alcohol dependence in an American Indian population. Hum Genet (2003) 113 : 325–336 doi: 10.1007/s00439-003-0971-z

[2] Hui Li, et al., (2007). Geographically Separate Increases in the Frequency of the Derived ADH1B*47His Allele in Eastern and Western Asia. Am. J. Hum. Genet. 2007;81:842–846. doi: 10.1086/521201
[3] Michael V. Osier, Andrew J. Pakstis, David Goldman, Howard J. Edenberg, Judith R. Kidd, and Kenneth K. Kidd., (2002). A Proline-Threonine Substitution in Codon 351 of ADH1C Is Common in Native Americans. doi: 10.1097/01.ALC.0000042013.13899.75, Alcohol Clin Exp Res, Vol 26, No 12, 2002: pp 1759–1763



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 
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