tag:blogger.com,1999:blog-7785493.post40403284478316566..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit (Järve et al. 2009)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger73125tag:blogger.com,1999:blog-7785493.post-5991800901974192652009-10-11T21:50:35.951+03:002009-10-11T21:50:35.951+03:00Or to go to a extreme comparison: there has been a...Or to go to a extreme comparison: there has been a very fast demic expansion in America (not just the USA but the whole continent/s) in the last few centuries, surely with rates of demic replacement that Neolithic farmers could only dream of. Do you see any of your model's ideas become real in America? Or rather you see a series of local founder effects with no or very limited phylogenies? <br /><br />Maybe there's a limited founder effect's trail expanding from Pennsylvania to Oregon but this will never be the same as the founder effect that extends from Cuba to Tijuana or from Panamá to Peru. These are just assumed examples, just in case. <br /><br />Plus in America you also have a "Celtic fringe" of sorts: a Native fringe where the pre-colonial peoples and their lineages are much more frequent than elsewhere, for instance the Andes or the Arctic. All this, that is just common sense even for the extreme case of massive demic replacement like the modern colonialist one, is missing in your equation.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32431851072184537362009-10-11T21:35:07.835+03:002009-10-11T21:35:07.835+03:00Forget about the SNPs. It's not my main point,...Forget about the SNPs. It's not my main point, just another element of consideration. <br /><br />My main point is the impossibility of a recent demic expansion causing the "Celtic fringe" type of distribution of R1b in Europe. This can only be the product of a demic expansion not of R1b itself but of something else (Neolithic, Indoeuropeans). <br /><br />And there is not one single Neolithic but several and you are avoiding all the time to answer to this crucial issue that simply makes impossible the kind of expansion you propose. You are just using the SNP/tandem repeat apparent contradiction to divert the real issues here. <br /><br />If you'd be telling me: "I think that, as my TRMCA estimates give me a "recent" expansion and the pattern is in concordance with Tardenoisian expansion in the Epipaleolithic, then it must be Epipaleolithic". If you said something like that, I'd say: ok, it's a most interesting possibility. But you are all the time talking Neolithic, as if Neolithic was a single culture and its expansion a single process. So I have to say: no way!Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-47721316104126483582009-10-11T19:20:00.994+03:002009-10-11T19:20:00.994+03:00But this says nothing about the fact that you are ...<i>But this says nothing about the fact that you are trying to push four SNPs into a fraction of what we would expect them to take to evolve and become fixated just because of blind faith on the MCH, or rather in an extremist revised version of it. </i><br /><br />First, I am not pushing anything. I am looking at data and understanding it. There is no "push" involved.<br /><br />Second, do you have an idea about the Y-SNP mutation rate and the length of the Y-chromosome? If you do, then you know that there is roughly one new SNP produced each generation. So three or six or eight SNPs in a lineage over 30 generations is barely even remarkable.<br /><br />Further, if you want to believe those three SNPs between R-M269 and R-L11 account for 10,000 years instead of 800 then what do you think about the 60 or so SNPs between R1 and R1b1b2? Is R1 really 200,000 years old in your conception of things? I sincerely hope not.<br /><br />And there is no refuge for your logic further up the tree, I'm afraid. Look the the 23andMe dataset. How many SNPs between F and Q? About 80. How many between F and O? 32 or fewer, depending on which branch of O you count.<br /><br />The point is, the universe of known Y-SNPs is extremely skewed by ascertainment bias. Only a rigorous approach can make that skewed sample into a clock, and counting the SNPs on the ISOGG tree is not such a rigorous approach.Vincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-20237459199662831362009-10-11T18:10:37.419+03:002009-10-11T18:10:37.419+03:00Please. I always think to the root of the human tr...Please. I always think to the root of the human tree or maybe to something as remote as the F node. I would not dare to estabilish a chronology between the ill studied R1ba and the highly studied R1b1b2a1a - it would be at best a mere crude exercise with virtually no value. <br /><br />But this says nothing about the fact that you are trying to push four SNPs into a fraction of what we would expect them to take to evolve and become fixated just because of blind faith on the MCH, or rather in an extremist revised version of it. <br /><br />You are entitled to do that but I'm entitled not to believe a word and to say it loudly. Based on the SNP data, which for me is not worse than the MCH, much less than your peculiar revised version of it, there should be a pause and not acceleration of growth between R1b1b2a1 and R1b1b2a1a, i.e. between the arrival of R1b to Western Europe and its likely main expansion. This suggests a time to drift, maybe the LGM, before R1b1b2a1a expanded and no MCH speculations will make me think otherwise, specially if they are so blatantly in contradiction with the archaeological data. <br /><br />Where are the two distinct founder effects in "Cardial" Mediterranean Europe and "Linear" Central Europe? Considering the random nature of FEs, they should be any two (or even fifteen) different "West Asian" or at least "Balcanic" lineages but they are nowhere! Hence it cannot be Neolithic, at least most probably not. <br /><br />Think again, please. You need drift to produce what we see and you need a cultural and demic phenomenon that extended through the Western half of Europe as a set, not one through Central Europe and another through the Mediterranean (and a whole array of different ones like slow growing mushrooms throughout the Atlantic).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-61952020940566132432009-10-11T17:42:37.827+03:002009-10-11T17:42:37.827+03:00I know of the severe limitations of using the SNP ...<i> I know of the severe limitations of using the SNP tree for MC analysis but I also know that a more or less random sample of the actual SNPs is already there for the longer and best studied branches.</i><br /><br />I would think even a novice could see that the published SNP tree is nothing remotely like a random sample of "actual SNPS".<br /><br />Take R1b1b as an example.<br /><br />How many SNPs in the ISOGG tree between the R1b node and a living man in R-L21? Sixteen.<br /><br />How many SNPs in the ISOGG tree between the R1b node and a living man in R-L23? Nine.<br /><br />How many SNPs in the ISOGG tree between the R1b node and a living man in R-M73? Three.<br /><br />How many SNPs in the ISOGG tree between the R1b node and a living man in R-P25? Two.<br /><br />The time elapsed between the R1b MRCA and now (e.g. today) is a single, definite length. Yet according to the ISOGG tree one of these guys differs from the R1b MRCA by 8 TIMES as many SNPs as another. It should be quite obvious that all those branches have not been sampled equally.<br /><br />In short, is possible to use SNPs as a molecular clock but not by simply gathering up whichever SNPs happen to be lying about close at hand. Karafet et al. are only ones to have published an attempt, at least with Y-SNPs and they make clear reference to the limitations that ascertainment bias imposes: limitations that should not be ignored.<br /><br />VVVincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-17643994558039051052009-10-11T05:54:06.386+03:002009-10-11T05:54:06.386+03:00No species of big game got extinct except mammoth ...No species of big game got extinct except mammoth (early on in the UP, I think), the woolly rhinoceros and the cave bear (if Neanderthals had left any). All the major species survived, though reindeer and maybe bison migrated northwards, where they were followed by some groups maybe (though most likely they followed seals instead, IMO). Aurochs, deer and wild goat, which made up a good deal of the UP diet in the FC region (and many other places surely too), survived and did not have to migrate. Deer (and similar species) in fact was favored by the expansion of the woodlands northwards, and the same must have happened with boars. <br /><br />More important may have been the migration of seals in my opinion and that may account for an increased consuption of ivertebrate seafood. <br /><br />I have no particular reason to think that the population of Europe got negatively affected by warming. The archaeological data rather suggests continuity and even limited expansion. What may have increased, as the big herds moved north, was semi-sedentarism, already existent in the UP anyhow. As people relied more on aurcohs, deer, boar, wild goat, fish and seafood, instead of migratory herds like bison and reindeer, they probably needed to migrate much less behind their "livestock".Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-83485919348969614152009-10-10T22:57:25.493+03:002009-10-10T22:57:25.493+03:00"Can you document that? I don't see that ..."Can you document that? I don't see that clear at all. AFAIK there was a shift in the focus of the economy, more focused on smaller animals and seafood". <br /><br />We know that the large grazing animals dissappeared, and we can safely assume that 'smaller animals and seafood' had always been a part of the diet, so life would certainly have become more difficult. The example of 'people migrating to Scandinavia and Scotland, almost as fast as the ice receeded' is quite a while after the animals had died out, same for the Magdaleian/Azilian transition.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-6844075533989119742009-10-07T15:56:11.712+03:002009-10-07T15:56:11.712+03:00The Adriatic is of course a bit inconclusive, sinc...<i>The Adriatic is of course a bit inconclusive, since much or it is under water, now</i>. <br /><br />Sure. Although that also applies to other areas with large continental platform, like SW France or Doggerland. We can only extrapolate from the still existing land's findings. <br /><br /><i>My guess is that later travels (Phoenicians, Etruscan, Greeks) had a much larger impact</i>. <br /><br />In some specific regions maybe but in others it's pretty clear that the impact was strictly limited to some colonies and outposts (emporia). For instance I would not expect any strong genetic influence in Iberia from either colonial ethnos. Now, I am quite intrigued by the possible role of less famed "colonialist powers" of the Bronze and Iron age, like post-Mycenaean Cyprus or whatever was driving the cultural exchanges across the E-W Mediterranean axis in the pre-Mycenaean Copper/Bronze Age (Troy?, Cyclades?, Crete?). <br /><br />But I still suspect that most of the East Mediterranean genetic impact in "the Hesperides" was anyhow Neolithic, just that it was initially very localized in some specific areas of true colonization like the Valencia-Alicante area, getting diluted only with time. <br /><br />You make a difference between North and South Europe on mere anatomical evaluation but there is a real autosomal genetic evaluation (Bauchet 2007 for example) that clearly defines more than one South European group. Iberians for example, while carrying a god deal of East Mediterranean blood, are essentially just Iberians (a distinct group). Basques too (with much lower exotic input). So either the affinities are older or they are merely caused by climatic adaptation (i.e. the big differences/affinities are in pigmentation in fact, not in other anatomical aspects). <br /><br /><i>But the more Northern populations should have originated from the same LGM refugia</i>...<br /><br />That's something we don't know for sure. We know that the Magdalenian cultural package expanded in such a pattern but the case for a total depopulation of Central Europe in the LGM has been questioned a lot and may in the end happen that Central Europeans (and by extension Northern Europeans too) are largely derived from local pre-LGM populations, or at least that they were until the arrival of Neolithic. <br /><br /><i>One thing is clear: once the climate improved, the large grazing animals vanished, life became harder again, and population density likely was relatively low before the advent of agriculture</i>. <br /><br />Can you document that? I don't see that clear at all. AFAIK there was a shift in the focus of the economy, more focused on smaller animals and seafood, a shift in some cultural manifestations (rock art for example vanished in many areas, it seems) and a microlithization of the toolkit. But I have never seen any evidence that population decreased. In fact many areas that were once uninhabitable became available instead. You see people migrating to Scandinavia and Scotland, almost as fast as the ice receeded but you also see people colonizing inner Iberia, that was mostly a desert before. <br /><br />For example <a href="http://en.wikipedia.org/wiki/File:Magdalenian_and_Azilian_in_the_Basque_Country.gif" rel="nofollow">in the case of the Basque Country</a>, the number of important archaeological sites grows in Azilian in contrast to the Magdalenian period, partly driven by that colonization of the south but not only. And Epipaleolithic is much shorter than the Magdalenian period.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-55698082672685985822009-10-07T04:50:49.667+03:002009-10-07T04:50:49.667+03:00Thanks for the link. The Adriatic is of course a ...Thanks for the link. The Adriatic is of course a bit inconclusive, since much or it is under water, now.<br /><br />I agree that populations in the plains would always be larger, as long as good sustenance is possible: it's basically 2-D versus a bit over 1-D (fractal) along a coast, and the possibility of hunting grazing animals that often don't exists close to coasts.<br /><br />I think one could make a good case for the Danubian to be a bit of a melting pot in the 500 or so years of transition before agriculture truly took of. Both the Danubian and the Mediterranean coastline IMO had their own reasons why initially there was little genetic impact from the Anatolian agriculturalists (except in the southern Balkans, of course):<br /><br />before the advent of large sea-faring populations, agriculture could spread in a filtered way along the coastline through existing populations with very little genetic input. My guess is that later travels (Phoenicians, Etruscan, Greeks) had a much larger impact.<br /><br />At the Danubian, agriculture just got stuck for the numerous reasons I have often mentioned. But there are indications that the region was already "up-and-coming" with some of their own plantings and separation of labor (fishing, stone collecting and tool making).<br /><br />Since agriculture was just being tested and was marginal, you really didn't have that single genetically overwhelming population there coming in from Anatolia: in fact, at the NW boundary agriculture obviously for centuries was so marginal that population growth seized altogether.<br /><br />And when it did take off, it pretty much started with some random locally assortment of haplogroups. Some of it local H, some of it likely Anatolian, and some of it just idiosyncratic (N1a).<br /><br />I still don't know what to make of today's anatomical differences between Northern Europeans and Mediterraneans, that are neither reflected in Y or Mt-DNA nor in linguistics. The latter are clearly more closely related to the original Southern groups and later (mostly bronze age and historic) Mediterranean newcomers. <br /><br />But the more Northern populations should have originated from the same LGM refugia - with the only difference of a more significant, homogeneous agricultural wave, and subsequent waves of invasions from the East. Some of that seems to make sense, but much of it is not reflected in the genetic data (outside of autosomal).<br /><br />It would be so much easier if one could pin-point later population groups to specific refugia, but that seems to be somewhere between wishful thinking and extremely difficult, at this point. <br /><br />One thing is clear: once the climate improved, the large grazing animals vanished, life became harder again, and population density likely was relatively low before the advent of agriculture.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-58582062005180561132009-10-07T03:10:30.048+03:002009-10-07T03:10:30.048+03:00I think during LGM, southern Iberia, southern Ital...<i>I think during LGM, southern Iberia, southern Italy, and Greece were probably much, much less hospitable than just before</i>.<br /><br />The case I know best is Mediterranean Iberia (or just Iberia for short) and the opposite is actually the case: in the LGM is when Gravettian culture arrived (Aurignacian settlement was very sparse) and soon after hybridates with Solutrean, generating the most original culture of the regional UP: the Iberian Gravetto-Solutrean (which IMO may be at the origin of Oranian, but that's another story). <br /><br />Even if it got colder, it was always warmer than the rest of Europe. It had a quality of refugium, that's quite clear, but it's not likely that it actively participated in any post-LGM recolonizations. For that you have to look at the Franco-Cantabrian region mostly. In this sense, I always regret the little attention that Occitania (Southern France) is being paid by geneticists. <br /><br /><i>In the above, I just wanted to point out the huge East-West gradient of temperature and precipitation both away from the Atlantic (long scale), and away from the Mediterranean (shorter scale). Even today, about a factor 3 in precipitation away from the Adriatic, and over 10C colder in the winter, within just a little over 500 km - that's roughly the equivalent of a 2,000m altitude change!</i> -<br /><br />That's largely because of the orography of Europe, with all the mountains being rather close to the Mediterranean. The transition when you cross those chains is very intense. There's nothing of the like at the Atlantic-Interior axis. But that says nothing against human life being possible and even good quality at the Mediterranean coasts. The differences between the Med and the Atlantic/Continental areas seems more a product of ecology: the steppes (or at least some of them) may have been more productive than the forests. In the very particular case of the FC province, the rather harsh steppe conditions were largely ameliorated by the Ocean, being somewhat warmer and more humid. It is also several degrees to the south in comparison to the Central or East European provinces. <br /><br />Whatever the case, <a href="http://www.ohll.ish-lyon.cnrs.fr/pages/documents_Aussois_2005/pdf/Jean-Pierre_Bocquet-Appel.pdf" rel="nofollow">it is quite demonstrated</a> that the FC region hosted most of the population of Europe through all the Ice Age. All the others were secondary provinces. <br /><br /><i>As to the cave art, AFAIK there are remains of paint on several southern German caves. However, most caves are of material and/or situated in regions that do not allow much surface preservation over long time</i>. <br /><br />Maybe I'm totally wrong when suggesting this but the case is that the Bramanti paper (and other aDNA data, like Chandler's Portuguese) would seem to suggest certain duality between Southern and Central Europe that just doesn't fit well with the cultural processes of the tool kits. That's why I am considering other possible variables; because obviously Neolithic did not expand from Portugal or anywhere in SW Europe, so H must have existed in other parts of southern Europe, like the Balcans or Middle Danube. <br /><br />It might be totally unrelated to any particular cultural element excepting maybe the somewhat dual early colonization of the continent, as Mellars suggested. Or it might be that the spread of U5 may be associated with Gravettian specifically but only at the origin (Central Europe), with the situation elsewhere being different. It might even be that both spread with Gravettian and that SW Gravettian arrived from Italy and not Germany (though Gravettian was late and weak in the FC province). <br /><br />Largely speculating in search of the best possible answer(s). What I think is that the Taforalt data strongly suggests that H existed in SW Europe in Gravettian times (LGM roughly for that region), as it's been apparently estabilished that North African H almost totally of Iberian derivation. Chandler's Portuguese data seems to ratify this idea, as does arguably the Paglicci samples.<br /><br />Just food for thought.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53803713311954925652009-10-07T02:14:15.425+03:002009-10-07T02:14:15.425+03:00Thanks, Maju.
I knew about Moravia, and that - as...Thanks, Maju.<br /><br />I knew about Moravia, and that - as well as the Italian refugium - could very well be candidates for the "central axis" of Y-haplogroup I (perhaps I2, only).<br /><br />I think during LGM, southern Iberia, southern Italy, and Greece were probably much, much less hospitable than just before.<br /><br />In the above, I just wanted to point out the huge East-West gradient of temperature and precipitation both away from the Atlantic (long scale), and away from the Mediterranean (shorter scale). Even today, about a factor 3 in precipitation away from the Adriatic, and over 10C colder in the winter, within just a little over 500 km - that's roughly the equivalent of a 2,000m altitude change!<br /><br />As to the cave art, AFAIK there are remains of paint on several southern German caves. However, most caves are of material and/or situated in regions that do not allow much surface preservation over long time. Clearly, Hohle Fels and other Danubian caves have shown that portable art and musical instruments were pretty much part of the people right when they came to the area, 35,000 to 40,000 years ago, or at least a second wave.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-59777830755031922882009-10-06T14:36:00.415+03:002009-10-06T14:36:00.415+03:00Eurologist: Hungary, or at least parts of it (as w...Eurologist: Hungary, or at least parts of it (as well as of nearby Austria and very specially Moravia) were inhabited in long Ice Age periods, however the LGM as such is not clear enough. Moravia in particular is claimed to have been an LGM "oasis" (i.e. it had patches of forest even in that extremely cold period) and may have hosted some of the Central European "survivors" of the time (but I know of no material fossils).<br /><br />Now for the material record, in Hungary there seems to be a late "Solutrean", before even Magdalenian expansion (but after the LGM). In NW Germany there seems to have been late Aurigancian around the LGM, that is claimed sometimes as the inspiration for Magdalenian (though this culture evolved as such in SW France). <br /><br />You are right about Romania (and in general the Balcans) being quite empty (at least in what regards to the fossil record) in the UP. Romania specifically nevertheless was colonized from Ukraine in the Epipaleolithic. <br /><br />And you're right too that the East Adriatic should correlate with Italy more than anything else. <br /><br />However, beyond industries ("cultures"), there is a cultural divide in UP Europe that I never fully understood: there are areas with rock art and others where all art is portable. This may be trivial or not. The areas with rock art are the Franco-Cantabrian region (very specially), Iberia, southern (but not northern or central) Italy, Dalmatia and, out of Europe as such and rather late, southern Turkey and southern Egypt. The rest, including Central-North France, Central Europe, most of Italy and Eastern Europe only show portable art (venuses and other stuff). <br /><br />The main climatic areas (excluding arctic/tundra/taiga) seem to be:<br /><br />1. Loess steppe (rather rich) in the Rhine and the Danube basins, as well as in southern East Europe.<br />2. Continental steppe (hostile) in Northern France, the Balcans and central Iberia. These areas were mostly devoid of humans.<br />3. What I would call Ice Age Oceanic (semi-steppe but milder and more humid) in most of the Franco-Cantabrian region. Possibly the best climate.<br />4. Ice Age Mediterranean in most of Italy, coastal Iberia and surely most of Greece too, dominated with deciduous forests. Not so good for humans attending to the abundance of remains but quite temperate.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-43927871536747735452009-10-06T12:30:52.481+03:002009-10-06T12:30:52.481+03:00That may be because people pictured Italy just lik...That may be because people pictured Italy just like most of (Southern) Spain, Greece, and much of SW Anatolia: a dry wasteland that could not sustain pines nor oaks nor berries or other sources of vegetable food, nor relevant animals other than perhaps Rabbits, and had few reliable sources of fresh water (except at the base of the highest mountains). None of this is of course true for the contiguous region I outlined above.<br /><br />Just looking at modern data as a proxy:<br /><br />Ljubljiana: three months below freezing, average low -1C to -4C, average precipitation: around 100mm year-round<br /><br />Zagreb is similar in the winter with an average rainfall of 70mm.<br /><br />Craiova, on the other hand, has much lower extremes, averages ~-8C in January and February, with ~5 months of average below-freezing temps, and about half of Ljubljiana's precipitation.<br /><br />Budapest today is just slightly warmer in the winter, but as dry year round.<br /><br />In comparison, Kaiserstuhl, southern upper Rhein valley, still disputed if it could have harbored any humans at all during LGM has an almost Mediterranean climate in comparison.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-46444998781564338062009-10-06T08:14:35.440+03:002009-10-06T08:14:35.440+03:00I spoke on this some years ago on "Genealogy-...I spoke on this some years ago on "Genealogy-dna" before they banned me. But in those times the refugia were in Spain, Balkans, South Russia and nobody spoke of Italy. This was what was unacceptable for me. Now someone speaks also of Italy as a refugium and for me is already something.Gioiellohttps://www.blogger.com/profile/00999270356447668208noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-86027682774801045562009-10-06T06:06:31.857+03:002009-10-06T06:06:31.857+03:00My theory is that from Italy there was an expansio...<i>My theory is that from Italy there was an expansion to the Balkans...</i><br /><br />Gioiello,<br /><br />Also, don't forget that the geography and climate strongly hint that the Northern Italian and NW Balkan LGM refugia may very well be identical:<br /><br />The northern part of the Adriatic (now under water), together with the Po valley and the NE Adriatic coastline formed one continuous source region, and probably by a wide margin the most abundant one in the general area. However, during summers and milder years, it had easy access to both the very nearby small inland plains and the farther, larger ones (around today's Ljubljana and Zagreb). In addition, the NE Adriatic cost receives and likely received at earlier times some of the most rainfall (and snowfall) in the region.<br /><br />In contrast, most of today's Hungary and Romania must have been brutally dry and cold (they are even today, in comparison) - perhaps someone with better regional knowledge can tell me about their suitability to animal grazing during LGM.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-49095101445220288142009-10-06T03:53:13.727+03:002009-10-06T03:53:13.727+03:00I cannot accept that you claim the MC as "sci...I cannot accept that you claim the MC as "scientific method". It's essentially conjectural, nothing else. <br /><br />The scientific method basically has three phases:<br /><br />1. Hypothesis, including predictions (this is the stage of the MC conjecture for most of its corpus)<br />2. Testing of such predictions experimentally (the MCH has never gone through this)<br />3. Refinement, including independent replication<br /><br /><i>Bizarre, because you dismiss the molecular clock as a tool on one hand, then cling to it with the other</i>. <br /><br />As I said before I don't fully dismiss the MCH, I just take it for what it is: an unconfirmed fashionable hypothesis. I know of the severe limitations of using the SNP tree for MC analysis but I also know that a more or less random sample of the actual SNPs is already there for the longer and best studied branches. And I know that when you claim (on mere hypothetical unconfirmed grounds, worse: on your personal radical reading of such feeble premises) that a 4% of the sample suddenly appeared in less than 1% of the time, looks suspicious. <br /><br />It's not my sole objection, if you bothered reading.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-33575691289974882712009-10-06T03:31:10.055+03:002009-10-06T03:31:10.055+03:00Obviously I can't agree with you in this: I wa...<i>Obviously I can't agree with you in this: I want to look at the whole picture and not allow the tree of my obsessions to hide the forest behind it. MC estimates alone cannot prove anything.</i><br /><br />We may be at an impasse, because you discard data and the scientific method as implausible because they don't fit your preconceptions. That is no way to carry on a discussion.<br /><br />But before I abandon you, let me warn you once more to abandon any attempt to use the ISOGG tree as a molecular clock. That you do so belies your grasp of the subject, I'm afraid, and risks leading other poor souls down the same path.<br /><br />That you reference "the very apparent period of calm that lies between R1b1b2a1-L51 and R1b1b2a1a-L11, by mere SNP count" is sadly bizarre. Sad, because it is completely wrong. Bizarre, because you dismiss the molecular clock as a tool on one hand, then cling to it with the other.<br /><br />VVVincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-72801364768450333722009-10-06T03:04:09.128+03:002009-10-06T03:04:09.128+03:00I wouldn't have thought that such rigor demand...<i>I wouldn't have thought that such rigor demanded justification</i>. <br /><br />You present conjectural stuff as proven and that demands a justification... or rather proof. <br /><br /><i>That's just flim-flam. The molecular clock is "generally accepted" practice in the field of population genetics, without doubt</i>. <br /><br />But is not demonstrated in any consistent way. Lobotomy and electroshock was "generally accepted practice" not so long ago in the field of psychiatric medicine. That is a commonplace (maybe for lack of better means or maybe for intellectual laziness and academic inertia) means absolutely nothing about it being true. <br /><br />C-14 is a valid datation method but before it was accepted, maybe in a less credulous age, it had to be satisfactorily proven. Even after that, it has needed of some significative refinements anyhow to reach the quite decent calibrated dates we have now. But first of all it was confirmed in its efficiency, would it be a mere statistical conjecture as the MC, it would have never been accepted. <br /><br />I'd like some clear evidence of MC really working as it's claimed before it is presented as evidence of anything else. But some people seem to prefer to put the cart before the horses and to "prove" hypothesis on the results of equations based on other hypothesis. That I call credulity. <br /><br />I accept, with due reservations, the MC as a method of conjectural estimation but I cannot accept it as proof of anything that is against other logical elements present. I cannot just accept it on its own regardless of everything else. <br /><br /><i>... but there is nothing "theoretical" about observing a genome mutate from father to son</i>.<br /><br />I have absolutely no problem with that part. But the accumulative processes in the haploid genome hardly have to do anything with that raw mutation rate. They are much more dependent on demographic factors than anything else.<br /><br />In a sense we are in agreement: we agree that the raw mutation rate cannot be used in all circumstances. But you claim that it can be used in some circumstances, while I instead think that such claim is highly conjectural and contradictory. I rather think that with an expanding population and the raw mutation rate, no fixation can ever happen. <br /><br />For example, you are using a computer simulation (by definition highly imperfect) that is concieved to reproduce a very simplified hunter-gathering model, to justify the same process happening within a farming context, where the population figures should be 10 or 100 times higher at least. And you are not even including by any means the dual nature of European Neolithic waves, which should have caused not one but at least two different founder effects. <br /><br />For example, you are simply discarding a lot of contradictory evidence from the presence of other haplogroups that do fit much better with the Neolithic waves structure, like E1b1b1 and J2b. Or, for example, you are ignoring the very apparent period of calm that lies between R1b1b2a1-L51 and R1b1b2a1a-L11, by mere SNP count. <br /><br />How come, for example, the Neolithic wave, that is an East to West movement, produces links between SW and NW Europe, axis that is clearly perpendicular to the double Neolithic path?<br /><br />You may not be yet aware but it has been known these days that <a href="http://rspb.royalsocietypublishing.org/content/early/2009/09/25/rspb.2009.1422.full" rel="nofollow">small mammals like shrews and voles also have their own "Celtic fringe"</a> in Great Britain, in a very much parallel way to that of humans. The human "Celtic fringe" is not just defined by extremely high R1b but also by other genetic factors like very high Rh-, factors that you prefer to ignore. <br /><br />For you there seems to be nothing else that conjectural MC estimates. And these are for you enough evidence to discard everything else. <br /><br />Obviously I can't agree with you in this: I want to look at the whole picture and not allow the tree of my obsessions to hide the forest behind it. MC estimates alone cannot prove anything.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-91774850355124047192009-10-06T01:48:29.751+03:002009-10-06T01:48:29.751+03:00"I am assuming they were somewhere in the tre..."I am assuming they were somewhere in the tree, in fact in the Eurasian Y(xA,B) branch. Could be wrong but is a reasonable thought". <br /><br />Only because it fits your pre-existing beliefs. I agree it could be, but not necessarily so. <br /><br />Vincent. That link you provided on waves is most interesting. I've always maintained that individual genes move through populations effectively in a wave. <br /><br />A short digression from the direction you and Maju are going: I have a problem with the author's Rh data. He (or rather an author he quotes) claims the original was Dce, but it seems this claim is based primarily on the fact that this version is predominant in Africa, and it is then presumed all modern human genes originated there. <br /><br />We know from animal and poultry breeding that mutations are much more likely to give rise to recessive genes than to dominant genes. This is just as well because we all have at least one allele that would be very disadvantageous if we had a double dose. Therefore my guess would be that the original Rh gene would have been DCE, never mind that we don't find it today. However the author mentions that dCE, a single mutation from DCE, is still around though very rare. Another single mutation DcE is found in Siberia. <br /><br />The next single mutation DCe is found in SE Asia and Oceania. The African version, Dce, requires another mutation from either this version or from the Siberian DcE, so is probably not the original version. The other mutation from DCe, dCe, is present today but again described by the author as being a minor haplogroup. The Rh- gene, dce, could derive from either dCe or Dce, depends on where the first is most commonly found.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-21997164725739538282009-10-05T22:18:07.935+03:002009-10-05T22:18:07.935+03:00But that's mere circular reasoning: to justify...<i>But that's mere circular reasoning: to justify a TRMCA estimate you use a TRMCA estimate. It's not valid evidence. </i><br /><br />I am not trying to "justify" anything other than using the best data and methods for the task at hand. I wouldn't have thought that such rigor demanded justification.<br /><br /><i>And MCH has not been proven in any way like C14 or other generally accepted datation methods have been once and again. It's just a theoretical construct.</i><br /><br />That's just flim-flam. The molecular clock is "generally accepted" practice in the field of population genetics, without doubt. <br /><br />And C-14 dating is no less a "theoretical construct" than the molecular clock is. Or, said more directly, both are equally real. C-14 dating may be both more accurate and more precise than STR based dating or Y-SNP based dating, but there is nothing "theoretical" about observing a genome mutate from father to son.<br /><br />VVVincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57941238719031041572009-10-05T21:49:31.861+03:002009-10-05T21:49:31.861+03:00For starters, the cases are more different than yo...<i>For starters, the cases are more different than you concede. R1b1b2 has a TMRCA of less than 8,000 years while Y-Adam lived more like 150,000 years ago. Don't let yourself fall again into the weak thinking of using the known SNPs as a clock</i>. <br /><br />But that's mere circular reasoning: to justify a TRMCA estimate you use a TRMCA estimate. It's not valid evidence. <br /><br />All the rest you say is very interesting but only applies within the MC paradigm. And MCH has not been proven in any way like C14 or other generally accepted datation methods have been once and again. It's just a theoretical construct.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63312349348648543602009-10-05T20:38:00.207+03:002009-10-05T20:38:00.207+03:00But we are talking of something only some 5 times ...<i>But we are talking of something only some 5 times longer (I mean: the "most derived" R1b branch has, from the R1b node, about 1/5 of the whole length when we count from the absolute human root), if we attend to known SNPs. It's a room and a house what we're comparing here: the difference is not that big - or does not look that way at least. </i><br /><br />For starters, the cases are more different than you concede. R1b1b2 has a TMRCA of less than 8,000 years while Y-Adam lived more like 150,000 years ago. Don't let yourself fall again into the weak thinking of using the known SNPs as a clock.<br /><br />And the thing you must aim to avoid is mentioned in the paper: mutational saturation. Saturation refers to the effect of constraints on allele range, which cause variance to accumulate non-linearly with time. In other words, it is what causes a marker to have different degrees of "clockiness" when compared over different lengths of time.<br /><br />Some STRs that work perfectly well as a clock for short time frames (say, 100 generations) are horrible clocks for longer time frames (say, 1000 generations) and completely unreliable at even longer time frames (say, 5000 generations).<br /><br />So STRs are great for estimating short periods of time. They "tick" quickly, so you can measure small numbers of generations with a small number of markers. With greater numbers of generations, saturation starts to kick in and their performance as clocks deteriorates.<br /><br />SNPs are great for estimating long periods of time. You need a huge number of them if you want any precision, but each SNP "ticks" so slowly that saturation is hardly a concern at al.<br /><br />Want to estimate TMRCA of R1b1b2? 50 to 100 medium-fast STRs should do the trick.<br /><br />Want to estimate TMRCA of Y-Adam? Dump the medium-fast STRs and find 50 to 100 really slow ones, or else sequence 100k bp of SNPs.<br /><br />VVVincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-4104141103369607472009-10-05T19:21:03.653+03:002009-10-05T19:21:03.653+03:00Erratum: "or rather a racial variant" sh...Erratum: "or rather a racial variant" should read "or rather a <b>radical</b> variant".Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-21973081028389449992009-10-05T19:19:16.575+03:002009-10-05T19:19:16.575+03:00Someone from the extinct Yugoslavia wrote: "...Someone from the extinct Yugoslavia wrote: "be two to agree is not to be two to be right". <br /><br />Linkage disequilibrium between the Y-DNA and culture, WTF? What culture, btw? I only see generalist claims all based on the MCH (or rather an extremist version of it) and little preshistorical knowledge. Stones and bones are still more real than fuzzy equations and computer models. <br /><br /><i>Aren't you making an assumption here? You're assuming that the 100,000 year old humans in Asia possessed modern haplogroups</i>. <br /><br />I am assuming they were somewhere in the tree, in fact in the Eurasian Y(xA,B) branch. Could be wrong but is a reasonable thought if you do not begin with the MC straight away. Alternatively they went extinct. <br /><br /><i>And Dienekes has reminded us often enough that haplogroups can easily be replaced</i>. <br /><br />That's his opinion. Just that. I don't see Dienekes as any teacher but as someone who shares interests with me, even if from a very different viewpoint often. <br /><br /><i>Who said anything about "bind faith"? Not me, for sure</i>. <br /><br />Obviously it was me - and I assume all the responsability, of course. When you build all the explanations based on a badly tested hypothesis (or rather a racial variant of it, much more controversial), instead of using a wider array of data, when you, rather shockingly, claim things are that way based only on that very feeble theoretical basis, I call that faith. The MC is not C-14 by any means but you treat them the same way. <br /><br />It's not essentially different than when someone claims that Earth is 4000 years old based "on the Bible" only without much or any contrast with other more relevant data. <br /><br />I think most scientists are much more cautious when dealing with these. They do not make bold claims based only on TRMCA educated hunches: they wisely just state them and let us and other scientists judge. But in a more "commoner" layer of the debate some people have gone too far in this line and are at just a mere step away from worshipping MCH estimates. <br /><br />And I wonder how much of this has to do with the business of selling genetic tests and promising "accurate results" that should also sound familiar (i.e. recent and not remotely prehistoric and rather trivial) to customers. <br /><br /><i>I already said that using intraclade variance to estimate TMRCAs where drift is big factor is unwise</i>. <br /><br />We can agree on that. The problem is that I understand that this applies to all lineages that are widespread: that non-drifted lineages are all private or at most moderately extended. That there is impossible to explain things like R1b or whatever of the like without a brutal drift at various stages prior to R1b1b2a1a1 expansion. <br /><br /><i>The tool I [use] to measure the width of a room may be very different from the tool you use to measure the width of an ocean</i>.<br /><br />Absolutely. But we are talking of something only some 5 times longer (I mean: the "most derived" R1b branch has, from the R1b node, about 1/5 of the whole length when we count from the absolute human root), if we attend to known SNPs. It's a room and a house what we're comparing here: the difference is not that big - or does not look that way at least. <br /><br /><i>Or better yet, use SNPs</i>. <br /><br />Hmmm... ok. But if I can use SNPs to measure the house why can't I use them to measure the room? It's all in meters after all.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-89393810442445150932009-10-05T16:55:53.013+03:002009-10-05T16:55:53.013+03:00But you can't just go with the MC hypothesis a...<i>But you can't just go with the MC hypothesis and blind faith and claim that what looks like a valley is a highly sloped mountain. </i><br />Who said anything about "bind faith"? Not me, for sure. We use the best data and the best methods, and keep looking for ways to get better. In fact, that's the whole point of the paper this post is about.<br /><br /><i>Plus, yeah, what's the TRMCA of "Adam" with your system? </i><br /><br />I already said that using intraclade variance to estimate TMRCAs where drift is big factor is unwise. This surely applies to questions of Y-Adam.<br /><br />But, assuming you cared so much about this that you persisted anyway. Think this through. The tool I you to measure the width of a room may be very different from the tool you use to measure the width of an ocean. <br /><br />There is nothing incongruous about that, so why should you be shocked to find that the right tool for estimating the TMRCA of a R1b1b2 may not be identical to the right tool for estimating the TMRCA of the entire Y-chromosome phylogeny?<br /><br />Again, that's a crucial take-away from the current paper: if you pick the appropriate markers for your task in the first place, you won't have to do all the "evolutionary effective" correction BS in the first place. Don't use dinucleotide or trinucleotide STRs for dating Y-Adam. Pick as many pentnuclelotide and hexanucleotide markers as you can find and work from there. Or better yet, use SNPs.<br /><br />VVVincenthttps://www.blogger.com/profile/00008012554198066886noreply@blogger.com