tag:blogger.com,1999:blog-7785493.post4378082286045841248..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Phylogeny of mtDNA haplogroup M in India (Chandrasekar et al. 2009)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger50125tag:blogger.com,1999:blog-7785493.post-29914744617760468172009-10-20T21:42:42.997+03:002009-10-20T21:42:42.997+03:00At least, I made you read Peirce (note the correct...At least, I made you read Peirce (note the correct spelling, smartie pants!) if not in the original. I have a whole chapter on Peirce in my book because he was one of the first students of kinship-based or relational logic in the 19th century.<br /><br />"M and N sister clade is not L3 as such but the various L3 sublineages as mentioned above." <br /><br />Very good. Now D lineages form an outgroup to all Asian and North-East African M lineages, while A, X, S and some other Eastern N lineages form an outgroup to the European-North African (Western) N lineages (including U). Some of the M and N lineages are found in Africa as well as outside of Africa, while all African "L3" lineages are restricted to Africa. African L3 sublineages are derived from certain lineages grouped under Western N submacrohaplogroup, U lineages included. I'm still working on the rest of African L lineages (L0, etc.) but most likely they're derived from X, B and some other "Eastern" lineages. <br /><br />This is the tree topology that fits phylogeography, linguistics, kinship, etc. better. And it'll have fewer homoplasies than the current one.<br /><br />Don't argue with it. It's a working hypothesis. I'll publish a revision at some point with all details in it.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-14280653549107572972009-10-20T21:18:33.636+03:002009-10-20T21:18:33.636+03:00Que no! M and N sister clade is not L3 as such but...Que no! M and N sister clade is not L3 as such but the various L3 sublineages as mentioned above, you are stubborn in this regard because you don't want to face reality. Do your homework and make some self-criticism. <br /><br />For what I can read at Wikipedia-Scientific method, some guy named Charles Sanders Pierce, stated that the following are from worst to best the ways of finding the truth among humans:<br /><br /> 1. The method of tenacity — persisting in that which one is inclined to think.<br /> 2. The method of authority — conformity to a source of ready-made beliefs.<br /> 3. The method of congruity or the a priori or the dilettante or "what is agreeable to reason" — leading to argumentation that gets finally nowhere.<br /> 4. The scientific method — whereby inquiry actually tests itself and criticizes, corrects, and improves itself.<br /><br />You are stuck in method 1, you don't even care about method 2 and you are very far away from method 4 (science). You just have to be right no matter what. <br /><br />It's boring, annoying and dismaying to discuss with you.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-43016433536970894212009-10-20T21:00:21.512+03:002009-10-20T21:00:21.512+03:00The fact that people call a clade to which M and N...The fact that people call a clade to which M and N supposedly belongs "L3" is simply an out of African driven convention. M, N and L3x are sister clades with a tenuous connection to L1, L2 or L0. Think of D and E in Y-DNA as an example. Nobody calls Y-DNA D lineages E lineages. In the same way as D is at least as diverse as E or maybe more, L3 is as diverse or maybe less than M or N.<br /><br />How can a person who isn't a scientist judge what science is and what is not? I have two doctorates and 20 years of experience across several science fields, including pop genetics. You are an amateur with huge gaps in knowledge, logic and ethics. At times your prose falls somewhere in the gray area between spam and cyberbullying.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-27130662818247264542009-10-20T20:29:53.691+03:002009-10-20T20:29:53.691+03:00Now your job is to buy the book...
I'm not go...<i>Now your job is to buy the book</i>...<br /><br />I'm not going to buy that book. I already know more than what I need to know about your kinship-based hypothesis and I know also that it is bad science. Maybe if it was fantasy genre...<br /><br /><i>L3 is closer to M and N than either of them to L0, L1, L2, L5, etc. But being closer to doesn't mean they derive from L3</i>.<br /><br />The branch that you seem to be calling "L3" in Maca-Meyer 2001 is actually L3b (or if you wish L3b'd'e'j), not all L3(xM,N). Only L3b and L3e (both within L3b in the most recent PhyloTree nomenclature) are analyzed in that study among "African" L3(xM,N)<br /><br />Nomenclature changes and the least you could do is to check PhyloTree for the most actualized references. Do your homework, please (I'm not getting paid for these lessons).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-83642848933293883932009-10-20T16:28:08.412+03:002009-10-20T16:28:08.412+03:00Luis: "Anyhow, Mungo Man's apparent mtDNA...Luis: "Anyhow, Mungo Man's apparent mtDNA was extreme but still within the range of modern humans."<br /><br />Check Adcock et al. 2001, Fig. 2A and you'll see that the range of variation in ancient Australian sequences overlapped with modern human sequences with LM3 falling outside of it. Nuclear insert overlaps with LM3 but is entirely outside of modern human variation.<br /><br />"I sincerely think that the comments sections in various blogs are not the place to post your caveats re. the mtDNA phylogeny."<br /><br />You started it by providing people with your grand theory of human haplotype dispersals. I just asked you about your rooting sequence. You didn't know what it was. I explained.<br /><br />All my personal comments are relevant to the Chandrasekar paper under discussion, which again reiterated the lack of ancient M and N lineages in Africa and the lack of L3 lineages in India. This has implications for mtDNA phylogeny. I wrote a whole book and a post on anthropology.net outlining my views, so I think I did my job at this time. Now your job is to buy the book, educate yourself about kinship systems and linguistics and if you have any concerns you can write a post anywhere with a critique of the data presented. But your dogmatic belief in the infallibility of the out of Africa theory (mind you, you are not even a scientist, so what are your stakes?) deprives us of a minimal common denominator to interact without bickering.<br /><br />I am planning to revise the mtDNA phylogeny to make it more consistent with phylogeography, demography, kinship systems and linguistics and to remove the "noise." However at this point I'm still waiting for a good genetics publication to provide me with a springboard.<br /><br />"Anyhow, I only pointed you to MM because of vane hopes that you could maybe understand that, in spite of your extremely heterodox beliefs, M and N belong to L3, nothing else."<br /><br />L3 is closer to M and N than either of them to L0, L1, L2, L5, etc. But being closer to doesn't mean they derive from L3. This is up in the air for me because of homoplasies, lack of the necessary mutations on the actually attested sequences, phylogeography, etc.<br /><br />"As for Mungo Man. The tests were done apparently with little guarantees, for what I've read, and the fact that the remains have been "returned" to the Aboriginals, making any counter-test nearly impossible, makes us unable to discern the truthfulness or error in this oddball case."<br /><br />This case looks "oddball" only because out of Africa was prematurely made into a measuring stick. There was nothing wrong with the Mungo man research. Yes, it's an unusual case of DNA extraction from a specimen of such antiquity and in such low latitudes (although the DNA from the Windover brain in Florida was also a case of remarkable preservation) but this doesn't make it invalid. Especially since it overlapped with an independently attested nuclear insert. It'd be good to replicate the results, sure, but if this is impossible I'd focus on trying to extract DNA from one of those African skulls to see how far in time L lineages go.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-70265911597440365082009-10-20T06:31:56.055+03:002009-10-20T06:31:56.055+03:00"the current Australian populations are the r..."the current Australian populations are the result of 2 separate migrations within the past 20,000 years. Hence, linguistically Australia is not as diverse as Papua New Guinea or America". <br /><br />I'd agree with two (or more) migrations to Oz. However I'd put the first at more like 50k although I agree that many lines involved in that arrival have died out. A second migration seems to have arrived between 20k and 15k. The accepted reason for the lack of linguistic diversity through much of Oz (ignoring the far northwest) is that extreme drought exterminated the population through Central Oz but this region was later recolonised from within the continent. <br /><br />"X chromosome's basal lineage (B006) is most frequent in Amerindians, Y-DNA YAP+ lineages probably migrated into African from Asia and they account for the majority of African Y-DNA diversity". <br /><br />I agree completely that haplogroups don't tell the full story by any means. Individual genes move through individual species. <br /><br />"Mungo Man's remains were ony tested once in what seems to be a very controversial case with not enough guarantees". <br /><br />That is correct and so I agree we can't rely too much on the particular research.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-15482232023090861652009-10-20T06:12:28.737+03:002009-10-20T06:12:28.737+03:00And btw, I sincerely think that the comments secti...And btw, I sincerely think that the comments sections in various blogs are not the place to post your caveats re. the mtDNA phylogeny. You should research the matter and publish something first, at least a series of blog pots, so the rest of the universe can follow your hypothesis consistently.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-21409321734020442902009-10-20T06:10:00.204+03:002009-10-20T06:10:00.204+03:00I would have changed the word "obsolete"...I would have changed the word "obsolete" if I would have been able to edit. It's not really adequate. Anyhow, I only pointed you to MM because of vane hopes that you could maybe understand that, in spite of your extremely heterodox beliefs, M and N belong to L3, nothing else. <br /><br />I wonder if this concept has already penetrated your mind or not. <br /><br />I bet that when we cross paths again in the net you will again insist that M and N are not L3 and all that discourse that just can't hold. <br /><br />As for Mungo Man. The tests were done apparently with little guarantees, for what I've read, and the fact that the remains have been "returned" to the Aboriginals, making any counter-test nearly impossible, makes us unable to discern the truthfulness or error in this oddball case. <br /><br />Individual doubtful cases without a context have always been considered with some disregard and extreme caution. Otherwise we'd be talking vividly of the late Acheulean of NW Iberia, contemporary with Magdalenian and other oddball doubtful cases that are normally, when lacking further evidence, archived and disregarded until further evidence appears. <br /><br />This practice is quite standard in prehistory and extends to many cases. <br /><br />Anyhow, Mungo Man's apparent mtDNA was extreme but still within the range of modern humans. If you check figure 1 in <a href="http://www.pnas.org/content/100/11/6593.full.pdf" rel="nofollow">Caramelli 2003</a>, you can perfectly see that he is within modern human range, with modern day individuals being in some cases further away in the PCA. <br /><br />Maybe more strange is to me that Cro-Magnon mtDNA is right in the middle of today's European range. Of course they are not that old.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-59681532376232866662009-10-20T01:40:41.021+03:002009-10-20T01:40:41.021+03:00Luis: "I don't think that Hermann's [...Luis: "I don't think that Hermann's [read Herrnstadt's - GD] quote changes anything either (after all it's quite obsolete data, from the times L0 and the minor Ls were not even described)."<br /><br />Luis, Herrnstadt is 2002, while Maca Meyer that you pointed me to is 2001. Which one is more obsolete?<br /><br />Luis: "Mungo Man's remains were ony tested once in what seems to be a very controversial case with not enough guarantees."<br /><br />As Kosmo put it the other day in a comment on a different article here, Mungo man results "have been essentially thrown out for no other reason than their wild divergence from expectation."<br /><br />Well put.<br /><br />Luis: "Sadly, I don't think that Mungo Man can be used for anything other than speculation at this point."<br /><br />Everything that you write, including this last sentence, is a huge speculation. I hope you're aware of this.<br /><br />Terry: "Unlike German I'm quite prepared to accept the current interpretation of haplogroup evolution."<br /><br />Terry, X chromosome's basal lineage (B006) is most frequent in Amerindians, Y-DNA YAP+ lineages probably migrated into African from Asia and they account for the majority of African Y-DNA diversity.<br />The nuclear insert is found at high frequencies in America and at low frequencies in Africa, which according to Adcock et al. (the authors of the Mungo man study) implies that humans came to Africa, rather than originated there. African L lineages aren't found outside of Africa in either extant populations or in ancient remains. Non-African M and N lineages aren't indigenous to Africa. Ward et al 1991; Bandelt 2007 estimated that one single Amerindian tribe harbors mtDNA diversity worth of 80,000 years (sic!) of evolution.<br /><br />All this seems to indicate very consistently that the conventional version of haplotype evolution is wrong. The first mtDNA study, by Johnson et al. 1983 as well as the subsequent study by Excoffier and Langaney 1987 identified out of Asia/out of America as a possible alternative to out of Africa.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-31137570678464580272009-10-19T20:09:53.415+03:002009-10-19T20:09:53.415+03:00There's a theory by which the earliest Austral...There's a theory by which the earliest Australians represent the first migration of anatomically modern humans out of Africa/ Levant (Mungo man's skull seems to cluster with Skhul/Qafzeh in some studies), while the rest of the world was peopled by the second migration (out of Africa, if you're a pygmy-hugger, or out of America if you're a serious scholar) of anatomically and behaviorally modern humans. The first migrants to Australia didn't survive, and the current Australian populations are the result of 2 separate migrations within the past 20,000 years. Hence, linguistically Australia is not as diverse as Papua New Guinea or America.<br /><br />The nuclear insert is consistent for all mankind: it has all the synapomorphies of modern humans and none of those of Neandertals.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-23880557342378358912009-10-19T15:21:48.820+03:002009-10-19T15:21:48.820+03:00*shakes head*
Mungo Man's remains were ony te...*shakes head*<br /><br />Mungo Man's remains were ony tested once in what seems to be a very controversial case with not enough guarantees. The remains were given to native tribals (a practice that I strongly oppose in what regards to remains older than say, 1000 years) and will never again be available for comparative re-testing most probably. <br /><br />Sadly, I don't think that Mungo Man can be used for anything other than speculation at this point. <br /><br />I see now what the nuclear insert is. IMO, unless it can be shown that somehow the fragment has resisted recombination havoc and is consistent for all humankind, it seems to me that it will also cause many problems and confusion. The Chimpanzee or maybe better the averaged Pan sequence seems the safest so far, though admittedly soon we will be able to contrast the modern human genome with a good quality array of several Neanderthal sequence, which should anyhow produce the same results. <br /><br />Probably it has already been done, even if only informally, but I'm not aware of it. But otherwise, there would be for sure someone crying foul already.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-29598675780008682462009-10-19T08:07:04.334+03:002009-10-19T08:07:04.334+03:00"The Mungo man sequence was the most divergen..."The Mungo man sequence was the most divergent, hence, by definition, it fell outside of the modern human mtDNA variation". <br /><br />And that's the really interesting part, not descnded from L. The fact it appeared in Australia and is clearly 'modern' human sugests that the surviving haplogroups spread through a pre-existing population. And the modern haplogroups may not have their ultimate origin in Africa. They may derive from haplogroups immigrant to Africa. Unlike German I'm quite prepared to accept the current interpretation of haplogroup evolution.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-34759684768016607962009-10-19T06:00:54.593+03:002009-10-19T06:00:54.593+03:00The nuclear insert (just like X chromosome's b...The nuclear insert (just like X chromosome's basal B006, it's frequent in Amerindians, rare in Africans, with all others in-between) was used to root the Mungo man sequence. <br /><br />Zischler, H., Geisert, H., von Haeseler, A., Paabo, S., 1995. A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans. Nature 378, 489–492.<br /><br />The Mungo man sequence was the most divergent, hence, by definition, it fell outside of the modern human mtDNA variation. Anything of this sort can be used as a rooting outgroup.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-20276520361960852652009-10-19T04:24:18.849+03:002009-10-19T04:24:18.849+03:00Neanderthal, Mungo man, the nuclear insert are bet...<i>Neanderthal, Mungo man, the nuclear insert are better rooting tools</i>.<br /><br />Mungo Man is no valid root: he clearly belonged to H. sapiens. He's no outgroup. <br /><br />Neanderthal could be valid but the sequence was not known until 2003 and, anyhow, being aDNA, known only in a few specimens, guess it still arises some caution. <br /><br />No idea what's "the nuclear insert".Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-24595944385106368912009-10-19T04:00:46.997+03:002009-10-19T04:00:46.997+03:00What's wrong with rooting using a chimpanzee s...What's wrong with rooting using a chimpanzee sequence? Would you prefer it'd be an American animal like a sloth?<br /><br />Neanderthal, Mungo man, the nuclear insert are better rooting tools. Without them you can't decide which state was ancestral. Some trees are left unrooted, other trees are rooted. <br /><br />The rest of your prose is full of apologies. mtDNA studies always had "noise" in them despite the 20 years of research. I would know - I was there.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-10886053938304421892009-10-19T03:39:33.764+03:002009-10-19T03:39:33.764+03:00What's wrong with rooting using a chimpanzee s...What's wrong with rooting using a chimpanzee sequence? Would you prefer it'd be an American animal like a sloth? It would not make any difference, as long as it is an outgroup. <br /><br />In 2001, L3 was still a tag not applied to N and M, as the phylogeny was still being worked out. However you can clearly see in fig. 1 how L3d and L3b are much more closely related to M and N (and viceversa) than to any other lineage. This is precisely the point of Maca-Meyer.<br /><br />I'm not sure exactly when the tag L3 began to be used for all the macro-lineage but it's clear that this paper estabilishes the basics of such nomenclature, even if it still doesn't use it. <br /><br />You're not going to fool me with semantics/nomenclature but I wonder if you can fool yourself. Whatever the name you give to that clade parallel to L2 in fig. 1, it is clear that it is monophyletic. We normally call that L3 and is virtually "official" nomenclature now. <br /><br /><i>Finally, Maca-Meyer's tree contains a bunch of homoplasies: 16278 occurs 5 times in different parts of the tree</i>. <br /><br />It can be a recurrent mutation or most likely different mutations at the same locus. This is sadly not too unusual in mtDNA, specially at control area regions (as is the case of all 16... loci) but not enough to blurr the phylogeny. Remember that the mitochondiral DNA is much shorter than any chromosome's and that the control region is just a small fraction of it (however mutating frequently enough as to give some useful keys). <br /><br />Even if you remove the HVS mutations, the phylogeny stands. I don't think that Hermann's quote changes anything either (after all it's quite obsolete data, from the times L0 and the minor Ls were not even described). Two of those locus define L3 right now (per PhyloTree again). Basically he was noticing, it seems to me mutations describing L3. Back then only L3, L2 and L1 were known I believe (if we don't count M and N), so finding those specificities for L3 surely helped reinforce the distinct personality of this macro-haplogroup. <br /><br />The current, quite solid, tree was not built in a single paper: it took the accumulative work of many researchers along maybe 15 years or more.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-11436476227859974362009-10-19T01:44:05.880+03:002009-10-19T01:44:05.880+03:00Maca-Meyer rooted the tree in a chimp sequence. Th...Maca-Meyer rooted the tree in a chimp sequence. This is too far in the past and too hypothetical. Plus L3, M and N, even in Maca-Meyer's interpretation, are parallel lineages. Try to root the tree in the Mungo man sequence. It was more divergent than any L lineages. Note also this: "African L3 haplotypes are characterized by the absence of L1/L2-specific polymorphisms at nucleotide positions 769, 1018, 3594, 4104, 7256, 7521, and 13650″ (Herrnstadt et al. 2002. Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups. Am J Hum Gen 2002 70 (5).) Finally, Maca-Meyer's tree contains a bunch of homoplasies: 16278 occurs 5 times in different parts of the tree.<br /><br />Again, this is a hypothesis which, in my opinion, doesn't withstand a test.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-76127596123182040302009-10-18T19:51:49.093+03:002009-10-18T19:51:49.093+03:00I have my own priorities, which obviously are not ...I have my own priorities, which obviously are not the same as yours. <br /><br /><i>M and N are not subclades of L3 unless you prove your phylogeny</i>.<br /><br />M and N are subclades of L3 because its phylogeny <a href="http://www.biomedcentral.com/1471-2156/2/13" rel="nofollow">has been proven</a>: all tested M and N samples have the L3 defining mutations. There is nothing to discuss unless you have evidence of the opposite.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-74363486364089614552009-10-18T19:20:47.667+03:002009-10-18T19:20:47.667+03:00I understand how genetics works, no need to worry....I understand how genetics works, no need to worry. But if you want to help science, rather than simply consume some of its products, you can consider other alternatives. An alternative is already a contribution to science: regurgitation is not.<br /><br />M and N are not subclades of L3 unless you prove your phylogeny. So far phylogeography disproves it, as well as linguistics, kinship and other cultural elements. Archaeology is neutral, as it can accommodate pretty much any scenario. There're millions of ways in which trees can be generated. There're different tree topologies fitting the same data. Work from X chromosome to Y chromosome to mtDNA to look for alternatives. I suggested to you a few venues to explore.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-16947513303094477292009-10-18T19:10:09.212+03:002009-10-18T19:10:09.212+03:00You describe a hypothesis but you don't prove ...<i>You describe a hypothesis but you don't prove it</i>.<br /><br />Man: I'm not writing any scientific paper, I'm not the one who has laid out all those theories. I'm just falling into my altruistic outspoken side and trying to help you understand how genetics works. If you don't like it, then it's up to you. <br /><br /><i>... you don't find L lineages next to M or N</i>...<br /><br />Whatever. I have told you already a zillion times that M and N are subclades of L3. <br /><br />You just want to prove that Earth is flat. Fine: it must be an entertaining but unrewarding endeavour.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-5893028685810727752009-10-18T17:32:00.771+03:002009-10-18T17:32:00.771+03:00You describe a hypothesis but you don't prove ...You describe a hypothesis but you don't prove it. Phylogeography seems to disprove your phylogeny, as you don't find L lineages next to M or N in the same geographic area or in the same population. The only place where they're found in the same area is North and Northeast Africa and here M and N are derived from non-African M and N and not from L.<br /><br />The same concerns America: if America was peopled, you would expect to find R, M and N lineages next to A, X, B, C and D at decreasing frequencies from North to South or you would find only R, M and N lineages because A, X, B, C, and D are either rare or non-existent in geographic areas of Asia leading to America. In actuality, you have the opposite: rare and supposedly recent lineages with a narrow geographic range were brought into America, while more common, older and hence more widely distributed lineages are not found in America.<br /><br />You and others postulate lineage loss between Africa and, say, India and between Siberia and America but this doesn't explain the special selectivity of these losses twice in human history.<br /><br />This is exactly how a false theory looks: new facts are retrofitted into a pre-existing idea, namely that America was peopled late in human history, while Africa, with its short and dark tropical people, is the homeland of modern humans.<br /><br />My theory has no discontinuities: mutations frequently found in Amerindians are original and have the largest geographic distribution. African mutations are derived and have the most restricted geographic distribution. This corresponds to the linguistic map very closely: 140 families in America vs. 20 in Africa.<br /><br />Instead of arguing with me and showcasing your fundamentalist proclivities, try to devise an mtDNA tree that will illustrate the current distribution of linguistic families. Work with different <br />tree topologies, root trees using Neanderthal, Mungo man or nuclear insert sequences (nuclear insert is from Zischler et al. 1995), simulate bottlenecks on route to Africa, add gene flow, etc. Use X chromosome, with basal B006 outside of Africa, as a model for a mtDNA phylogeny.<br /><br />Take 9 bp deletion as an example. This mutation is found in Asia-America, in India and in Africa (high frequencies in Pygmies). What assumptions about mutation rate and bottlenecks do we have to make in order to postulate the common origin of this mutation plus a few SNPs also shared between the sequencies carrying this indel in Asia-America and in Africa?German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-60803866504152939102009-10-18T15:31:07.971+03:002009-10-18T15:31:07.971+03:00"So you think that X2 might not exist... Inte...<i>"So you think that X2 might not exist... Interesting."<br /><br />Actually it's X1</i>.<br /><br />From your quoted text: [X1] "lacks the two transitions (195 and 1719) that characterize X2. These two nucleotides are rather mutable"...<br /><br />And if you check PhyloTree, it is clear that the transition at 1719 is the only coding region mutation defining <br />X2, not X1. <br /><br />Anyhow, what would seem is that there are some reasons to consider the X1/X2 as at least somewhat doubtful. However X stands and so do the lineages under the X1/X2 nodes, which are essentially West Eurasian (with one or two American exceptions). <br /><br /><i>Alexe uses primate sequences to root a tree - this has been criticized</i>.<br /><br />By whom? AFAIK what has been criticized is the use of the supposed but hardly clear Homo-Pan split <b>age</b> for MCH calculations. It is clear that using Pan sequences to root the human phylogeny makes all sense, why wouldn't it?<br /><br /><i>Without properly rooting a tree, it's hard to say which mutations are basal and which ones are derived</i>.<br /><br />Seriously, I do not understand what you mean. It's as simple as all human sequences having the defining mutations of L1-6, except those that belong to L0. That makes the root to be between L0 and L1-6. The same method applies to all branches at any level. <br /><br /><i>I'd interpret M and N mutations as ancestral, while L1-L3 mutations as derived</i>. <br /><br />You can't because these are sets and subsets. L3 includes M but M does not include L3. M has all the defining mutations of L3 (plus others) but L3 has none of the defining mutations of M. <br /><br />That's how you root a tree: the inclusive set is always an upstream clade, the distinct subset is always a downstream clade. <br /><br />Do your homework, seriously.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-4865991850698704232009-10-18T07:00:43.472+03:002009-10-18T07:00:43.472+03:00"So you think that X2 might not exist... Inte..."So you think that X2 might not exist... Interesting."<br /><br />Actually it's X1.<br /><br />Alexe uses primate sequences to root a tree - this has been criticized. What about the nuclear insert? Without properly rooting a tree, it's hard to say which mutations are basal and which ones are derived. However, phylogeographic observations can be suggestive of the directionality of mutations. If L1, L2, L3 are African-specific, while M and N are found everywhere, including North Africa, I'd interpret M and N mutations as ancestral, while L1-L3 mutations as derived. The diversity within these lineages doesn't really matter as larger population size and gene flow in Africa will make its lineages more diverse than the lineages of more isolated populations with smaller effective population sizes outside of Africa. <br />By making L1-L3 mutations look ancestral phylogenetically (which is evolution only on a computer screen), the out of Africa theory arrives at a phylogeographic stalemate, with no L lineages found outside of Africa and with no early offshoots of M and N detected in Africa.<br /><br />Also, Alexe's Fig 3 shows the trifurcation of M, N and L3 and not the subordination of M and N to L3. This looks somewhat like the D-E situation in Y-DNA. <br /><br />"out of America fantasy."<br /><br />Out of Africa is a lie, and the bigger the lie the more people believe in it.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63474937081480157622009-10-18T06:10:03.405+03:002009-10-18T06:10:03.405+03:00So you think that X2 might not exist... Interestin...So you think that X2 might not exist... Interesting. <br /><br />I don't think it changes much, specially when X1 is defined by a single control region marker (which looks much more feeble to me in principle). <br /><br /><i>A, X and (Australian) S are closely related lineages</i>.<br /><br />Not anymore than anything else under N: they are just three of 12 known lineages that apparently hang from that node, including macro-haplogroup R. <br /><br />But anyhow, FYI, I recall that <a href="http://www.springerlink.com/content/q225678542442u22/" rel="nofollow">recent study by Alexe et al.</a>, who researched all the mtDNA tree all over (using a different method than the usual one of SNPs: K-means analysis) and, while they recycled completely the Eurasian (and American, etc.) part of the tree, even scrapping macro-haplogroup R and other "heresies", the basic structure of the global tree stood their efforts: L1, L2 and L3 (including what we still call M and N) persisted even against such titanic and unconventional efforts, only the structure of M and N (always under L3) was altered. <br /><br />Anyhow, I think that the paper had little merit - though it's always good to read something that challenges it all, even if it fails. You may enjoy reading it but it's not going to give you the reason on your out of America fantasy.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-16377737152206905162009-10-18T04:44:39.498+03:002009-10-18T04:44:39.498+03:00I'd be curious to know how do you, Luis, root ...I'd be curious to know how do you, Luis, root your trees? Do you use a primate sequence, a Neanderthal sequence, a Mungo man sequence, or a "nuclear insert" in mtDNA?<br /><br />Reidla et al. (2003, 1181) published an interesting caveat regarding the phylogeny of X haplogroup: "Moreover, haplogroup X is subdivided into two major subhaplogroups, designated “X1” and “X2.” Subhaplogroup X1, represented by a single Druze mtDNA in figure 1, differs from the root of haplogroup X by eight coding and three control region transitions and lacks the two transitions (195 and 1719) that characterize X2. These two nucleotides are rather mutable (Finnila ̈ et al. 2001; Herrnstadt et al. 2002); thus, it cannot be completely ruled out that X1 is indeed a subset of X2 that reverted at both nucleotide positions."<br /><br />I personally haven't seen an article in which X was given a Beringian origin but A, X and (Australian) S are closely related lineages, hence I doubt X emerged in West Asia, as A and S aren't found there. East Asia, Beringia or America make more sense as its places of origin.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.com