tag:blogger.com,1999:blog-3427954556695420515.post2038681107996377260..comments2024-02-22T00:36:40.647+02:00Comments on Kalevan ja Untamon geenit: Achilles’ heel of admixture analyses. Maurihttp://www.blogger.com/profile/03670078523265515878noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-3427954556695420515.post-19958258694901893322015-04-04T22:55:18.674+03:002015-04-04T22:55:18.674+03:00I'll do it as a separate text with no connecti...I'll do it as a separate text with no connection to our discussion, but the focus will be the same.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-56926234669511316902015-04-04T22:11:17.014+03:002015-04-04T22:11:17.014+03:00Maju, I'll write a blog update about this issu...Maju, I'll write a blog update about this issue quoting Haak's results and some relevant admixture analysis. This is very interesting and wouldn't get coverage here as a comment. It is also difficult to add necessary quotes here. I need original studies to demonstrate more.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-2241041689305321362015-04-04T17:45:40.649+03:002015-04-04T17:45:40.649+03:00And then on your latest comment:
"ancient au...And then on your latest comment:<br /><br />"ancient autosomal references vs modern uniparental genes - match"<br /><br />Do they? I don't see how can you compare them in any obvious way.<br /><br />Also the Yamna influence seems very important on the autosomal aspect but not at all on the mtDNA aspect (Y-DNA is argued but probably not either). Inversely the Chalcolithic haploid influence seems to span from the West but the only Atlantic reference genome that we have so far, Gökhem does not work well with it. <br /><br />So I do not see how they "match" in any simple way. But no doubt this is largely for lack of enough ancient samples. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-1631681356825911322015-04-04T17:41:01.606+03:002015-04-04T17:41:01.606+03:00I reproduce here the original commentary for the r...I reproduce here the original commentary for the record:<br /><br /><i>I do agree that haploid lineages do not have to correlate in any obvious way (or even in any way at all) with autosomal (recombinant) genetics and I think that what you attempt to convey makes sense, even if it's not too clearly explained: if we look at our modern rather small intra-European differences, everyone ancient is likely to be an oddball, almost exotic (that's what you mean, right?)<br /><br />However I have to strongly question your claim: "mtDna H is usually connected to ancient farmer populations, to the first farmers in Europe". That is simply not true.<br /><br />The oldest mtDNA H in Europe (it has been just made public) is a from a Paleolithic woman from Cantabria (Iberian Peninsula). Additionally mtDNA H has been unmistakably detected in other two Cantabrian Magdalenian samples (100%), in one Epipaleolithic Basque sample (33%), in one Epipaleolithic Karelian sample (11%) and in one transitional Meso-Neolithic sample from Franchthi cave (Greece). There are other less confirmed (HVS-I only) data suggesting also loads of mtDNA H in Epipaleolithic Portugal (Chandler 2005), Late UP Arif (North Morocco), late UP Andalusia, UP Britain and Gravettian Russia (Sunghir). In other words, mtDNA H was very possibly scattered everywhere in Europe except apparently in the north-central region.<br /><br />On the other hand Early Neolithic peoples were very low in their mtDNA H frequencies, much less than some UP populations apparently and certainly less than modern levels, with just around 25% of this lineage. It is true that mtDNA expands first (but not last) in Central Europe with the arrival of Danubian Neolithic but it's also true that this expansion cannot account at all with the formation of the modern mtDNA pool in that part of Europe, very particularly because its frequency of H is very low yet. See this.<br /><br />So for me mtDNA H was irregularly scattered among European hunter-gatherers, with populations ranging from near 0% (Central and North Europe) to near 100% (some parts of Iberia at the very least). Some of it was picked by early European farmers on their way to Central and Western Europe but a large part of it was actually distributed with the so-called hunter-gatherer backflow in the Chalcolithic, probably in relation to Megalithism and maybe also Bell Beaker. </i>Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-68470514139614298402015-04-04T13:22:04.790+03:002015-04-04T13:22:04.790+03:00So keeping it simple
ancient autosomal reference...So keeping it simple <br /><br />ancient autosomal references vs modern uniparental genes - match<br />modern autosomal references vs modern uniparental genes - don't match<br /><br /><br />For what reason admixture tests done using present-day autosomal reference data show conflicting results with present-day uniparental genes and similar conflict is not present when we use ancient autosomal reference data? If there is any explanation it probably could also be proved by some scientifically acceptable way. It is not enough to assume that "it happens because ancient genomes are different than modern ones" because without any scientific understanding we can't make conclusions about history!Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-28608489733852071412015-04-04T10:33:25.302+03:002015-04-04T10:33:25.302+03:00Maju, I apologize that I deleted your oiginal comm...Maju, I apologize that I deleted your oiginal comment during publishing it. Luckily I was able to c/p and didn't lose it totally.<br /><br />You are likely right, I have not followed attentively the discussion about uniparental genes. But my idea was not just it, I tried to understand differences between admixture analyses made using ancient and present day samples. Even mentioning just mtDna H was only indicative, this same phenomenon can be noticed with many other unipoarental groups when compared to admixtures made by ancient and present day samples. The H was only an example and if I was wrong as to its history, don't throw out the baby with the bath water.<br /><br />I also do agree that there is differences between ancient and modern autosomal, but my questions was: is this difference partly (sometimes mostly) caused by failed tests, being no real. I think that it is caused by formal admixture tests which act like a described in my text. The context between uniparental and autosomal genes is rather complex in along history, I realize it. But just look Haak et al. 2015 results on page 122 and notice that those result are much better in line with uniparental genes. Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-3427954556695420515.post-53407025328050552032015-04-04T10:26:51.471+03:002015-04-04T10:26:51.471+03:00Maju4. huhtikuuta 2015 0.25
I do agree that haplo...Maju4. huhtikuuta 2015 0.25<br /><br />I do agree that haploid lineages do not have to correlate in any obvious way (or even in any way at all) with autosomal (recombinant) genetics and I think that what you attempt to convey makes sense, even if it's not too clearly explained: if we look at our modern rather small intra-European differences, everyone ancient is likely to be an oddball, almost exotic (that's what you mean, right?)<br /><br />However I have to strongly question your claim: "mtDna H is usually connected to ancient farmer populations, to the first farmers in Europe". That is simply not true.<br /><br />The oldest mtDNA H in Europe (it has been just made public) is a from a Paleolithic woman from Cantabria (Iberian Peninsula). Additionally mtDNA H has been unmistakably detected in other two Cantabrian Magdalenian samples (100%), in one Epipaleolithic Basque sample (33%), in one Epipaleolithic Karelian sample (11%) and in one transitional Meso-Neolithic sample from Franchthi cave (Greece). There are other less confirmed (HVS-I only) data suggesting also loads of mtDNA H in Epipaleolithic Portugal (Chandler 2005), Late UP Arif (North Morocco), late UP Andalusia, UP Britain and Gravettian Russia (Sunghir). In other words, mtDNA H was very possibly scattered everywhere in Europe except apparently in the north-central region.<br /><br />On the other hand Early Neolithic peoples were very low in their mtDNA H frequencies, much less than some UP populations apparently and certainly less than modern levels, with just around 25% of this lineage. It is true that mtDNA expands first (but not last) in Central Europe with the arrival of Danubian Neolithic but it's also true that this expansion cannot account at all with the formation of the modern mtDNA pool in that part of Europe, very particularly because its frequency of H is very low yet. See this.<br /><br />So for me mtDNA H was irregularly scattered among European hunter-gatherers, with populations ranging from near 0% (Central and North Europe) to near 100% (some parts of Iberia at the very least). Some of it was picked by early European farmers on their way to Central and Western Europe but a large part of it was actually distributed with the so-called hunter-gatherer backflow in the Chalcolithic, probably in relation to Megalithism and maybe also Bell Beaker.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.com