tag:blogger.com,1999:blog-7785493.post6674683463810423448..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Latent admixture causes spurious serial founder effectDienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-7785493.post-49751799013398357052011-11-22T06:40:25.174+02:002011-11-22T06:40:25.174+02:00For some reason I thought mtDNA halpogroups A2, B2...For some reason I thought mtDNA halpogroups A2, B2, C1, D1, X2a were found both in NA and SA according to page 3 of this report. The are all Indigenous people.<br /><br />http://www.familytreedna.com/pdf/Fagundes-et-al.pdfDenise Neufeldhttps://www.blogger.com/profile/07801618253765424483noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-4153903598076478722011-09-26T00:42:33.756+03:002011-09-26T00:42:33.756+03:00"No. All thre are separate clades within R. N..."No. All thre are separate clades within R. None are more closely realated to each other than is any other R-derived haplogroup."<br /><br />yes, you confused D1 with D2 and I confused U and R.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-30207573252261298332011-09-25T03:39:57.054+03:002011-09-25T03:39:57.054+03:00"all the patterns you identified are very int..."all the patterns you identified are very interesting and not easy to explain". <br /><br />I think they are very easy to explain. <br /><br />"If we look at Y-DNA, hg C is found in the Americas, in Polynesia and in Australia". <br /><br />Three different basal groups. In order: C3 (same as NE Asia), C2 (same as Southern Wallacea) and C4(on its own). Therefore almost as ancient as the division between C and F. <br /><br />"If we look at mtDNA, America and Polynesia have hg B and Australia has hg P, all from the same clade U". <br /><br />No. All thre are separate clades within R. None are more closely realated to each other than is any other R-derived haplogroup. <br /><br />"No, we have D1 in America". <br /><br />Sorry. Can't remember where I got the idea that D2 was American. But according to Phylotree D1 is just one of 17 subclades of D4.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-11062739023352865592011-09-24T16:16:53.145+03:002011-09-24T16:16:53.145+03:00"And that is very inteesting in itself."..."And that is very inteesting in itself."<br /><br />Yes, Terry, all the patterns you identified are very interesting and not easy to explain. The mistake people are making is to try to explain the heterogeneous nature of the Amerindian population as a result of either multiple migrations or a random collecting effort on the part of a wandering Eurasian population that cherry picked Amerindian haplogroups a la carte from a wider menu of available lineages. IMO, the best way to interpret the data is that Amerindian and Old World populations share a deep common origin but have been evolving separately from each other for a very long time. Different selective pressures drove New World diversity down, while Old World diversity up resulting in the random preservation of certain lineages in one region and other in another region. This created an illusion of Amerindians being a subset of non-Amerindians.<br /><br />"But even then B failed to make much of an impression on New Guinea, and even less on Australia."<br /><br />If we look at Y-DNA, hg C is found in the Americas, in Polynesia and in Australia. If we look at mtDNA, America and Polynesia have hg B and Australia has hg P, all from the same clade U. <br /><br />"As I understand the situation we have D2"<br /><br />No, we have D1 in America.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-39407748637963775652011-09-22T07:33:51.585+03:002011-09-22T07:33:51.585+03:00"MtDNA M lineages are more frequent in SA&quo..."MtDNA M lineages are more frequent in SA". <br /><br />And that is very inteesting in itself. Haplogroups C and D have South America almost to themselves, so perhaps they were the first in. As I understand the situation we have D2, a member of the D4e1'5 haplogroup and C1 and C4c, from two separate subclades of the four within C. What is the geographic distribution of the American subclades within these groups? Related members of both haplogroups are widespread through South, East and Central Asia and are especially common in Northeast Asia, with more than 50% C in the Yukagir for example. D makes up a substantial proportion of the remainder. But neither haplogroup made it far into mainland SE Asia, and so failed to make it into New Guinea, Australia or out into the Pacific. <br /><br />"Overall, mtDNA N lineages are more frequent in NA than in SA. Out of them, hg X is exclusive to NA". <br /><br />Possibly a result of their being in the 'having been left behind' element of the population. Again the distribution of the American subclades would probably be revealing. American N haplogroups are just members of A2, one of the six subclades within A4, and B2, one of the two subclades within B4b. A is spread through Central Asia from the Volga east, via the Tibetan Plateau, to Northeast Asia although not as far north as C and D. Like the above haplogroups A made it to mainland SE Asia, but unlike them made it to the Philippines. But not beyond. <br /><br />When we look at B we see an altogether different pattern. B is almost circum-Pacific with B4a1a1a in Polynesia and B2, a clade within B4'b'd'e, in America. But even then B failed to make much of an impression on New Guinea, and even less on Australia.terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-80647960307245377752011-09-21T19:29:09.495+03:002011-09-21T19:29:09.495+03:00H&H do not refute the serial founder effects p...H&H do not refute the serial founder effects process in the Americas. Admixture has clouded the picture, but it has not completely erased evidence of other evolutionary processes. In fact, they show clearly that the pattern of gene-identity variation in the Americas is largely hierarchically patterned. Additionally, both authors have argued in favor of a serial founder effects process at the global level. Dienekes is right to urge caution in blindly assuming that the process is the only one that has shaped human genetic diversity. It is not. H&H have provided some insights into one of these processes. <br />One of the other posts is also right to point out that haploid genetic systems also provide some, albeit relatively weak, evidence for a serial founder effects process in the Americas. While haploid genetic data are relatively information-poor, they are required to sort out the details of the evolutionary process and its larger social and scientific meaning. <br />As to the pattern of admixture in the Americas, there is a large genetic and ethnographic literature supporting the admixture results in H&H (see also papers by Wang and colleagues, which inspired the analysis of H&H). <br />Lastly, we encourage the post citing Engelhardt and Stephens to read it and H&H more carefully. The latter clearly show that the discrete model underlying the STRUCTURE analysis is valid, and the former clearly explain why STRUCTURE is appropriate under this model.KLHhttps://www.blogger.com/profile/16519170542169707580noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-57421522274153942292011-09-20T17:58:38.171+03:002011-09-20T17:58:38.171+03:00I think this reasoning is wrong. Compare with this...I think this reasoning is wrong. Compare with this ADMIXTURE analysis: (http://www.nature.com/nature/journal/v463/n7282/fig_tab/nature08835_F3.html) Here you can see that what looks like "European" in e.g. the Na-Dene in the Structure analysis in the paper is actually primarily "East Asian". Even so that does not mean that it is due to East Asian admixture. Structure/admixture does not magically find 'true' populations, see for example Engelhardt and Stephens' paper in PloS genetics. Genetic drift (e.g. serial founder effects) can cause false signs of admixture such as the example of bottlenecked Southern American populations that characterise a certain 'cluster' just because they have such characteristic genetics. The effect of this on both PCA and Structure is the illusion of a gradient of ancestry that might just be a gradient in genetic similarity.poshttps://www.blogger.com/profile/08079946048638615709noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-6182121696260401132011-09-20T03:12:55.710+03:002011-09-20T03:12:55.710+03:00Andrew, Pacific coastal South America had millions...Andrew, Pacific coastal South America had millions of inhabitants, the natives there are less admixed than Mexicans because less Spaniards reached Peru, it was easier to emigrate to Mexico (it is easier to just cross the atlantic than crossing the atlantic, crossing the panama isthmus on a mule, and then going from Panama to Lima on a ship)<br /><br />And also, the natives of Peru and Bolivia survived better because of the reason mentioned before, there were less Spaniards to spread their diseases than in Mexico, and the natives in Peru and Bolivia lived in very high mountains in isolated villages, there was less contact. In Mexico the geography was much more similar to Spain, many mountains but not Andes like.<br /><br />Simply the dozens of thousands of Spaniards who moved to Peru in colonial times could not affect genetically the millions of natives who lived in the former Inca empire.<br /><br />In the USA you did not have any place with the population density of mexico, central america and the central andes of Peru, Ecuador and Bolivia.El Lurkerhttps://www.blogger.com/profile/13542765792516291356noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-5437417089138204262011-09-19T23:51:41.604+03:002011-09-19T23:51:41.604+03:00@Terry
What Andrew wrote makes no sense. Overall,...@Terry<br /><br />What Andrew wrote makes no sense. Overall, mtDNA N lineages are more frequent in NA than in SA. Out of them, hg X is exclusive to NA. MtDNA M lineages are more frequent in SA. There're no major mtDNA lineages that are only found in SA and not in NA, although there're Sa-specific sublineages. As far as Y-DNA is concerned, both hgs Q and C are found in NA and in SA. Hg C is more frequent in NA, hg Q is more frequent in SA, but hg C IS present in SA. They just recently detected hg C in Ecuador. http://www.ncbi.nlm.nih.gov/pubmed/20932815.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53649635715883726362011-09-18T05:53:51.328+03:002011-09-18T05:53:51.328+03:00"there are quite a few uniparental genes on b..."there are quite a few uniparental genes on both the Y-DNA and mtDNA side that are found in Native American populations in North America, but not South America, that could not possibly be a result of European admixture because they are derivative of uniparental markers that are almost entirely absent from Europe" <br /><br />I've recently become interested in American haplogroups through discussion with German, so I'm interested in what haplogroups those are. Can you elaborate please?terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-82546882107059647442011-09-17T18:01:59.182+03:002011-09-17T18:01:59.182+03:00I'm with Andrew. Surely there is the mystery ...I'm with Andrew. Surely there is the mystery of the X2a mtdna population (Kennewickians?) as well as the red-haired Spirit Cave corpses.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7785493.post-2893727412056889762011-09-17T15:28:10.781+03:002011-09-17T15:28:10.781+03:00Are the authors saying that European admixture int...Are the authors saying that European admixture into Canadian Indians is larger than in Mexican Indians? This is extremely hard to believe.sykes.1https://www.blogger.com/profile/10954672321945289871noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-5932693065074263882011-09-17T04:01:41.732+03:002011-09-17T04:01:41.732+03:00I'm skeptical because there are quite a few un...I'm skeptical because there are quite a few uniparental genes on both the Y-DNA and mtDNA side that are found in Native American populations in North America, but not South America, that could not possibly be a result of European admixture because they are derivative of uniparental markers that are almost entirely absent from Europe and in particular from the parts of Europe that were the source of early European admixture with Native American populations.<br /><br />It also begars the issue of why there isn't more latent European admixture in the Pacific coastal region of South America which had European colonial impacts long before they were present in North America.<br /><br />It is certainly no surprise that Native Americans believed to be "pure blooded" in fact have some latent European admixture, but the evidence for a serial founder effect from an Asian sourced population is too robust to be overcome by this fact.Andrew Oh-Willekehttps://www.blogger.com/profile/02537151821869153861noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-23505340724501500112011-09-17T03:52:31.717+03:002011-09-17T03:52:31.717+03:00Tree models are simple aristotelean categories as ...Tree models are simple aristotelean categories as seen through XIX classification systems. They may be valid on a macroevolutive context, to show the divergence of different spieces. But I think they are unsuitable for the study of current evoution inside a single species. Admixture is always possible and trees make it as if populations just split and never touch each other again.Andréshttps://www.blogger.com/profile/00708925743497933631noreply@blogger.com