tag:blogger.com,1999:blog-30238057828084122302024-03-09T15:46:44.736+01:00For what they were... we arePrehistory, Anthropology and GeneticsMajuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.comBlogger906125tag:blogger.com,1999:blog-3023805782808412230.post-64366184215500381572018-12-21T00:01:00.000+01:002018-12-21T00:01:05.490+01:00So long and thanks for all the fish<div style="text-align: justify;">
I've been procrastinating about this in vane hope of returning to my old animical self of being more interested in writing (and reading) about stuff that interests me but nope. It doesn't seem like I'm going back, so I feel it's pointless to keep open a blog (actually two) that I don't regularly or even irregularly update at all. Time to draw the curtain, sorry.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggn60MkDkOd5vHfvWHbLro-DYW9SlzZ4HsRdmDjMsxnsc4QETMlimOMb8dkY6GP49CprzX5js6BqYpP0p_exrU34rz8PvMpMME2X_uFV2xHeZQAsanREPJKzwq1PZprOf4Ni6dtqwOXxs/s1600/persiana.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="565" data-original-width="1003" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggn60MkDkOd5vHfvWHbLro-DYW9SlzZ4HsRdmDjMsxnsc4QETMlimOMb8dkY6GP49CprzX5js6BqYpP0p_exrU34rz8PvMpMME2X_uFV2xHeZQAsanREPJKzwq1PZprOf4Ni6dtqwOXxs/s640/persiana.jpeg" width="640" /></a></div>
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I will still occasionally write (in Castilian language basically) at my blog <a href="https://bagaudaberri.wordpress.com/" target="_blank">Bagauda</a> (Wordpress, where it's easier to control trolls and choose between pre-moderation or no moderation individually). </div>
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I considered opening a second WP blog in English but I don't feel energized enough at this point. If I do in the future, I will of course announce it here.</div>
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I will keep comments open for some weeks more but in a month or so I'll also close that because it's too much hassle. The blog will remain accessible as such "forever" (or for as long as Blogger maintains it) of course. </div>
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You can of course contact me by email if important at:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxUzjQD2kwNsFk3dOfWQfXldHYHwp2sAagHkIq7dperfB7LUPNXTEbgsK4A4dtsZLvd6xqVkKNt5TI0Ggpp2Gkna0giowEXl9d-cFX5MLzHRNQxQsl81Ee_YFTeKDnw3XfMRiZqGqndxI/s1600/email.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="25" data-original-width="163" height="61" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxUzjQD2kwNsFk3dOfWQfXldHYHwp2sAagHkIq7dperfB7LUPNXTEbgsK4A4dtsZLvd6xqVkKNt5TI0Ggpp2Gkna0giowEXl9d-cFX5MLzHRNQxQsl81Ee_YFTeKDnw3XfMRiZqGqndxI/s400/email.png" width="400" /></a></div>
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I'm also right now somewhat active at FB and YT under my legal (shortened) name Luis Aldamiz. But nothing too interesting going on there anyhow. Just comments and blah-blah, political discussions in FB, etc.</div>
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So, thanks for being there, thanks for your interest, your feedback, your collaborations in some cases, thanks to everyone (except to Chucky "I want to be your friend" the psychopatic troll of many names). </div>
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Enjoy the rest of your life, kids. Love and rage!</div>
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Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com33tag:blogger.com,1999:blog-3023805782808412230.post-42478830099367461622018-10-11T20:26:00.008+02:002020-12-31T15:16:09.570+01:00Major Guanche genetic influence in Puerto Ricans (guest article by Thierno)<div style="text-align: right;">
<span face=""arial" , "helvetica" , sans-serif"><span style="color: #990000;"><i>Guest article by <b>Thierno</b></i></span></span></div>
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<span face=""arial" , "helvetica" , sans-serif">A discussion on a study on Caribbean autosomal ancestry from 2013 by Andrés Moreno Estrada et al., "Reconstructing the Population Genetic History of the Caribbean,” was posted on this blog: </span></div>
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<span face=""arial" , "helvetica" , sans-serif"><a href="http://forwhattheywereweare.blogspot.com/2013/06/caribbean-autosomal-ancestry.html">http://forwhattheywereweare.blogspot.com/2013/06/caribbean-autosomal-ancestry.html</a></span></div>
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<span face=""arial" , "helvetica" , sans-serif">There were two important elements of information to consider from said post. </span></div>
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<span face=""arial" , "helvetica" , sans-serif">1) The ADMIXTURE graphs displayed a "black" component, largely found in Caribbean Admixed Latinos but only poorly represented in South Europe, which suggested a "recent" founder effect some 500 years ago. <span style="color: #990000;">[Note: "black" here refers to color coding of an autosomal component in Moreno 2013, not to Tropical African ancestry, that was color-coded as "green", please follow the link above for more details].</span></span></div>
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<span face=""arial" , "helvetica" , sans-serif">2) An interesting and informative discussion between a Puerto Rican named Charles, in search of his ancestry, and another blogger named Maju shed light on the little-known historical contribution of Canarian aboriginal Guanches (Berber) to the colonization of America. It is often referred to as the "Tributo de Sangre" (Blood Tribute).</span></div>
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<span face=""arial" , "helvetica" , sans-serif">They concluded that the "black" component which was displayed on the ADMIXTURE graphs of the study most likely had a North African origin, by way of Canarian aboriginal Guanche ancestry.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">This graph represents the stacked bar-plot of an unsupervised ADMIXTURE exercise which is aimed at studying the complex and intricate ancestral components of Puerto Ricans from Puerto Rico, based on samples that were collected from the 1000 Genomes panel.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">The choice of populations that are represented in these ADMIXTURE graphs was firstly made to account for the major, historically known contributors to the Puerto Rican population: Iberians, indigenous Caribbeans, and former African slaves who are, respectively, represented by the "Maya" and "Yoruba" samples. </span></div>
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<span face=""arial" , "helvetica" , sans-serif">Secondly, the presence of the merged North African samples in the dataset of these ADMIXTURE graphs serves as a formal test of comparison with the Iberian population in order to verify the aforementioned hypothesis.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">The graph for K=4 clearly shows the "light-blue" component, represented in the Puerto Rican (PUR) samples, in addition to their Iberian (red), “Maya-like” (green), and “Yoruba-like” (purple) contributions. </span></div>
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<span face=""arial" , "helvetica" , sans-serif">The "light-blue" component is largely restricted to the North African population and also mostly found in the Saharawi samples, making it a "Saharawi-like" component. In other words, it is the identifiable North African component of this ADMIXTURE exercise. </span></div>
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<span face=""arial" , "helvetica" , sans-serif">This finding contrasts with the typically much lower North African scores of Hispanic Caribbeans that are reported in commercial autosomal DNA tests. I suspect that the use of Mozabite samples as proxies for North African may conflate their Berber ancestral component with the Iberian ancestral side of their complex genetic makeup.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">I included Canarian samples because they still display a minor distinct variation of North African admixture relative to Iberians, although it is important to keep in mind that individuals from those samples, as well as present-day Canarians, are more similar to Iberians from an autosomal genetic standpoint. Moreover, studies that were done on Canarian autosomal DNA have shown disparities in the amount of Guanche (Berber) admixture among individuals who are located in different Islands of the archipelago. Canarians from La Gomera seem to have retained the most Guanche ancestry.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">Maju had a blog post about a paper on the estimates of Guanche or Berber genetic influence of Canarians here: </span></div>
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<a href="https://forwhattheywereweare.blogspot.com/2011/04/canarians-nw-africans-iberians-etc-from.html"><span face=""arial" , "helvetica" , sans-serif">https://forwhattheywereweare.blogspot.com/2011/04/canarians-nw-africans-iberians-etc-from.html</span></a></div>
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<span face=""arial" , "helvetica" , sans-serif">Hypotheses made in the recent past about a possible genetic link between Canarian aboriginal Guanches and Puerto Ricans, on the basis of the unknown role that the Canary Islands have played in the colonization of the Americas, are supported in these unsupervised ADMIXTURE runs. Hypothetically, they could have similar implications for some Admixed Latinos and specific Caribbean communities, but most notably for Hispanic Caribbeans.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">I am a person of Fula descent. I wasn't predisposed to experiment on this issue, in the sense that I have a different ethnic history. With the help of the software ADMIXTURE, I decided to use my autosomal data and compare it with publicly available datasets, which include populations that are compatible with my genetic history. In addition to my Fula-specific and West African ancestral components, which were similarly detected in the populations studied by Henn et al. in 2012, I also scored a North African percentage.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">I had noticed that my data matched up considerably with "New World" Afro-descendants but also, very intriguingly, with a large number of Hispanic Caribbeans.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">At first, I attributed it to the fact that West Africa was a region from which slaves were sent to the Americas.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">However, when I tried to identify what specific ancestral components I share with some of those Hispanic Caribbean matches, a common restricted Northwest African ancestry seemed to emerge as a pattern with several of them. After reading the blog-post of Maju on Caribbean autosomal ancestry - several years after he posted it - and the possible Northwest African hypothesis of Hispanic Caribbeans, I figured I would try to verify it and maybe, at the same time, manage to elucidate some of my questions.</span></div>
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<span style="color: #cc0000;"><span face=""arial" , "helvetica" , sans-serif">[</span></span><span face=""arial" , "helvetica" , sans-serif"><span style="color: #cc0000;"><i>Note </i>(</span></span><span face=""arial" , "helvetica" , sans-serif"><span style="color: #cc0000;"><span face=""arial" , "helvetica" , sans-serif"><span style="color: #cc0000;">update Dec-31-2020</span></span>)<i>: the sharing of this very drifted (PUR) component between the
complex admixed Puerto Rican samples and my sample is difficult to
interpret precisely, and from a historical standpoint, as the Lawson et
al. paper makes very clear (please see the last update from 2 years
ago). Comments below are clues for follow-up research.</i>]</span> <br /></span></div><div style="text-align: justify;"><span face=""arial" , "helvetica" , sans-serif"> </span></div><div style="text-align: justify;"><span face=""arial" , "helvetica" , sans-serif">The graph for K=5 indicates a green specific homogenization of the Puerto Rican samples (PUR) in comparison to the other populations, which suggests a recent founder effect that most likely took place over the past few centuries. </span></div>
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<span face=""arial" , "helvetica" , sans-serif">I would say that it indicates some complex genetic links between the Guanches and, possibly, other Northwest African populations.</span></div>
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<span face=""arial" , "helvetica" , sans-serif">I hope that these unsupervised ADMIXTURE exercises can be of help to those interested in the autosomal genetic links between Hispanic Caribbeans and Canarian aboriginal Guanches.</span></div>
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<i><span face=""arial" , "helvetica" , sans-serif">Thierno</span></i></div>
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<br /></div><br /><b>Appendix </b><br /> <br /> I used publicly available datasets to perform these ADMIXTURE exercises. <br /> <br /> The first one contains a combined dataset of populations from both the 1000 genome project and HGDP unrelated samples, for a total of 162,645 SNPs. It has been filtered and re-arranged by its contributors who are Peter Carbonetto and Amir Kermany. <br /> <br /> It belongs to the Ancestry DNA workshop on Github.com. <br /> <br /> All the repositories can be accessed here: <a href="https://www.blogger.com/#">https://github.com/Ancestry</a> <br /> <br /> It was publicly available until a year ago and was utilized during the Computational, Evolutionary and Human Genomics (CEHG) Symposium. <br /> <br /> The PUR (Puerto Ricans in Puerto Rico), IBS (Iberians from Iberia), the Maya and The Yoruba samples were selected from this dataset. <br /> <br /> The second dataset is from the Henn et al. study from 2012, “Genomic Ancestry of North Africans Supports Back-to-Africa Migrations.” It contains the North African samples that I used for the exercises. I merged them with the dataset that contains the PUR samples, and intersected 44,804 SNPs. <br /> <br /> This is the link to access it: <a href="https://www.blogger.com/#">http://biologiaevolutiva.org/dcomas/north-african-affy-6-0-data-henn-et-al-submitted/</a> <br /> <br /> The third dataset is from the Botigué et al. study from 2013, “Gene flow from North Africa contributes to differential human genetic diversity in Southern Europe.” <br /> <br /> It has Spain_S (Andalucians), Spain_NW (Galacians), and Canary Islanders. I also intersected 44,804 SNPs with the first and the main datasets. <br /> <br /> The link to access it is here: <a href="https://www.blogger.com/#">http://biologiaevolutiva.org/dcomas/north-african-affy-6-0-data-henn-et-al-submitted/</a> <br /> <br /> I used the software PLINK to update the physical and genetic positions of the SNPs from the second and third dataset, in order to properly merge them with the ones from the first dataset. I also made sure to merge only SNPs that were already found in the selected dataset (1000 genome and HGDP). <br /> <br /> Lastly, I intersected my personal data with the dataset (1000 genome and HGDP), for a total of 161,764 SNPs. <br /> <br /> The software ADMIXTURE was used to estimate ancestry. <br /> <br /> R was used to plot the estimates.<div style="text-align: justify;">
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I would like to briefly elaborate on the sampling strategy. The first ADMIXTURE runs that I produced contained additional continental European populations, as well as other West Asian samples. The display showing the distinctive ADMIXTURE coded colors between North African and European samples of the dataset appeared at higher K values, with their respective higher standard errors of the cross-validation error estimate.<br /><br />I had asked for Maju’s insight on admixture analyses in the past, as I was interested in how his posts on West African and Berber genetics related to my personal autosomal DNA. I did the same for this analysis. <br /><br />I followed Maju’s recommendations to limit the selection of the reference population to be analyzed to just 4: Iberians, West Africans, Mayans, and Northwest Africans. This resulted in the clear and distinctive display of Berber and Iberian components, starting at K=4 which has a lower standard error. I later added Canary Islander samples. <br /><br />Note: I have also been asked to replace Yoruba with Senegambian Mandinka samples to check for potential differences. This is something that I had already checked, but I didn't notice any difference in either the Berber percentage in Puerto Ricans or in their homogenization, which indicated a recent founder effect.<br /><br />Thierno<br />
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<b>Update March 14th 2019: </b><br /> <br /> After this article was posted last October, I received a lot of interesting feedback on the admixture analyses and suggestions for different ancestral contributions of Hispanic Caribbeans, both in private messages and in the comment section of this post/both publicly and privately. In light of this, I would like to go over some aspects of the analysis again. </div><div style="text-align: justify;"><br /> <br /> <b>A note of caution in the interpretation of estimates </b><br /> <br /> The estimates of the clusters from ADMIXTURE are not to be interpreted literally. The different ancestral k components are not “real” populations. They are designed to help identify differentiation between populations.</div><div style="text-align: justify;"><br /> Both supervised and unsupervised analyses will produce FSTs between the designated populations or between the clusters. They serve to evaluate “approximately” possible genetic variations. In this type of analysis, as we can observe in the graphs contained in this post, moderate amounts of the components that are less divergent from each other overlap across populations which share lower FSTs. Considering that FSTs between North Africans and West Eurasians is usually around 0.06, there will inevitably be a shared overlapping effect. As a result, it isn’t possible to obtain a very precise delineation between North African and Iberian samples. So, essentially, this is an evaluation of variation and not an accurate system of measurement. </div><div style="text-align: justify;"><br /> Intuitively, it seems that analyses which contain populations or clusters that are separated with higher FSTs will be more robust. It also seems that when FSTs fall below 0.05, the degree of differentiation in the displayed clusters is difficult to evaluate or make sense of. This may explain why analyses of intra-European/Mediterranean populations with FSTs that are around 0.01 are difficult to evaluate with ADMIXTURE. Other steps can be taken to mitigate the effects of linkage disequilibrium, as was the case for the dataset that was used for the analysis in this post. <br /> <br /> ADMIXTURE works better for recently admixed groups who derive their ancestry from distinct populations. For obvious historical reasons, African Americans and Hispanic Americans have recent ancestries that most admixture analyses can detect fairly well. <br /> Evidently, the total complexity and chaotic processes of ancient migrations which are not static, but rather dynamic cannot realistically be captured by ADMIXTURE. The complete reconstruction of such patterns on the basis of present-day populations would obviously be misleading. <br /> <br /> Daniel J. Lawson, Lucy van Dorp and Daniel Falush wrote a paper called, “A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots” (2018) in which they warned against some of the pitfalls of admixture analyses. <br /> <br /> While it’s not possible to make exact predictions from tools that are used in the field of population genetics, when interpreted correctly, some interesting information can still be extracted from various analyses.</div><div style="text-align: justify;"> <br /> Previous research on the possible Canarian legacy in America, including the examination of historical records, had been conducted prior to the publication of the Moreno et al. (2013) paper. With regard to the genetic affinity of the aboriginal inhabitants of the Canary Islands, a similar analysis was done more recently on the autosomal DNA of ancient Guanche samples that may have lived between the 7th and the 11th century and is discussed in a paper by Rodrı́guez-Varela et al. (2017). The authors conclude that a Northwest African-specific ancestry component makes up the majority of their autosomal ancestry, as well as other Berber populations from North Africa. Additionally, Y-DNA E1b-M81, which is found at high frequencies in Northwest Africa, was also detected in these samples.</div><div style="text-align: justify;"><br /> In the study from Arauna et al. (2016) on how “Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa,” the authors expressed doubts about the use of Mozabite samples as the sole proxy for North African genetic diversity. </div><div style="text-align: justify;"><br /> Considering that the paper from Moreno et al. didn’t have North African samples, the focus of this post was to explore potential variations by including Northwest African samples such as Moroccans and Saharawis. <br /> <br /> Naturally, to exactly what extent inhabitants of the Canary Islands – whose gene pool could have already been affected by the DNA of Iberian settlers - may have impacted the genetic pool of Hispanic Caribbeans is a question which would require further and more diversified analyses. <br /> <br /> <br /> <b>mtDNA L(xM,N) </b><br /> <br /> Several studies have reported mtDNA L(xM,N) among various Latin American communities. They strongly suggest recent African ancestry in the context of the recent colonization of the New World. The uncommon L(xM,N) lineages that have formed variant specific subclades which are not native to Africa but rather found in other continents or regions are extremely rare, it seems. <br /> <br /> In 2012 Cerezo et al. published a paper on subject which is titled, “Reconstructing ancient mitochondrial DNA links between Africa and Europe.” <br /> <br /> Another study, published by Ricardo Rodriguez-Varela and his colleagues, is called “Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.” <br /> <br /> More recently, a paper called “Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands” was published by Rosa Fregel with the mtDNA sequencing of 48 ancient individuals. Out of all of the L(xM,N) lineages that were analyzed, only the newly defined L3b1a12 was identified as a new Canarian-specific lineage. <br /> <br /> It appears that European and Canarian autochthonous mtDNAL(xM,N) lineages form subclades which correspond to specific mutations that are less likely to be found in Africa. <br /> <br /> In the case of Puerto Ricans, there was a project from National Geographic called “Genographic Project DNA Results Reveal Details of Puerto Rican History” (2014). After sampling 326 individuals from southeastern Puerto Rico and Vieques, they found that 80% of Puerto Rican men carry West Eurasian (or European) Y-DNA paternal lineages, while 60% of Puerto Ricans carry maternal lineages of Native American origin. This may shed some more light on the findings of Moreno et al., (2013), who wrote of the “Latin-European” component which seemed to indicate a founder effect. <br /> <br /> In contrast, it would be interesting for future research to sample Hispanic Caribbean communities where African ancestry may have been retained in higher proportions and, in the process, collect more mtDNA and Y-DNA. <br /> <br /> Thierno</div>
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Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com59tag:blogger.com,1999:blog-3023805782808412230.post-437549980591254802018-04-28T22:32:00.000+02:002018-04-28T22:32:18.415+02:00Video: Do genes make you fat?I don't usually deal with the medical aspects of genetics but this conference by Giles Yeo is so enticing and clarifying that I believe it deserves an entry here:<br />
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<br /><iframe allow="autoplay; encrypted-media" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/pOJYTMe_bp4?rel=0" width="560"></iframe></div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com101tag:blogger.com,1999:blog-3023805782808412230.post-48783612315244522072018-04-08T13:14:00.002+02:002018-04-09T03:16:55.516+02:00Luxmanda: a 3,000 years-old proto-Horner in Tanzania<div style="text-align: justify;">
I knew, more intuitively than rationally, that the Horner (Ethiopian, Somali, Eritrean) type of Afro-Eurasian admixture was very old but no idea it was so much. I knew that West Eurasian Upper Paleolithic had an impact on Africa (LSA) but I did not know it went so deep South nor that it had left such a massive legacy as ancient DNA reveals.</div>
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<div style="text-align: justify;">
<b>Pontus Skoglund et al.<i> Reconstructing Prehistoric African Population Structure</i>. Cell 2017</b> (<span style="color: #3d85c6;">open access</span>). DOI:<a href="https://doi.org/10.1016/j.cell.2017.08.049" target="_blank">10.1016/j.cell.2017.08.049</a></div>
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The data analysis speaks volumes by itself:<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit_EzPNCAfrqmVEBIAmBevSYUTEFm6ZLi6XZGVUj3zn-NA76xt3_OSIKdiSx5B_2gfQvyF35c4FnixqGtEDSIDQGvtTUWMhh3h7hgrAOjX1zXbAqZkWrxwrzoYKmTKszw9vXuBLMf6VQs/s1600/fig1.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="588" data-original-width="769" height="489" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit_EzPNCAfrqmVEBIAmBevSYUTEFm6ZLi6XZGVUj3zn-NA76xt3_OSIKdiSx5B_2gfQvyF35c4FnixqGtEDSIDQGvtTUWMhh3h7hgrAOjX1zXbAqZkWrxwrzoYKmTKszw9vXuBLMf6VQs/s640/fig1.jpeg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><h4>
<span class="label">Figure 1</span> - Overview of Ancient Genomes and African Population Structure</h4>
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</tbody></table>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh78aTKWm1mVkoeFrSxTSaA424kFwhDlXVQhKtwYwVcVp7rCwrNVGZZUxMxorDbUjocp5XkqgIFR904CwuvBrhx1-te2J-LFAE9iL8LnqBb9NhqwaHmN1UV3qNS9j0WM1ThYCUO3C-U_oY/s1600/fig2.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="585" data-original-width="769" height="486" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh78aTKWm1mVkoeFrSxTSaA424kFwhDlXVQhKtwYwVcVp7rCwrNVGZZUxMxorDbUjocp5XkqgIFR904CwuvBrhx1-te2J-LFAE9iL8LnqBb9NhqwaHmN1UV3qNS9j0WM1ThYCUO3C-U_oY/s640/fig2.jpeg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><b>Figure S2 - Ancient Individuals and African Population Structure</b></td></tr>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjf6leJcOw4rjBJ8kFpqimJIrXodAWiW7icPl1rUH21Qi6H1t1utes1ozKrjoT3ReaKtOTqzpGlGNGfuJD58TaNCOHMCeFyxFoKSsz3r-lJtdz2ITrIsyqwiEIBfC3Ex02ghgbVJA9yQsA/s1600/fig2.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="575" data-original-width="770" height="476" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjf6leJcOw4rjBJ8kFpqimJIrXodAWiW7icPl1rUH21Qi6H1t1utes1ozKrjoT3ReaKtOTqzpGlGNGfuJD58TaNCOHMCeFyxFoKSsz3r-lJtdz2ITrIsyqwiEIBfC3Ex02ghgbVJA9yQsA/s640/fig2.jpeg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><b>Figure 2 - Ancestral Components in Eastern and Southern Africa</b><br />
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We show bar plots with the proportions inferred for the best model for each target population. We used a model that inferred the ancestry of each target population as 1-source, 2-source, or 3-source mixture of a set of potential source populations.</td></tr>
</tbody></table>
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So much that I don't really know what else to say. Of course this is just a sample of what there is in the paper, read it. I'm sure there will be plenty of comments even if the study was published months ago.</div>
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Regarding <b>haploid DNA</b>, I don't see anything outstanding but, as I know there is generally quite a bit of interest, these are screenshots of the ancient lineages found (full data in the supp. materials of the study):</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix9P_gtRvr3MP_ejS4kguDblUykiXjTMHV3AJ50-EEsZMxOgltR3TwQ_vKFbkSnA5fD0QJkuRTjL0gUdbTSFDTU08ftNt_IreNlysyMHjZz4Hm7FTehFMFAAgwCmBkPw5UUs3rTjqEk9U/s1600/Y-DNA.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="152" data-original-width="437" height="111" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix9P_gtRvr3MP_ejS4kguDblUykiXjTMHV3AJ50-EEsZMxOgltR3TwQ_vKFbkSnA5fD0QJkuRTjL0gUdbTSFDTU08ftNt_IreNlysyMHjZz4Hm7FTehFMFAAgwCmBkPw5UUs3rTjqEk9U/s320/Y-DNA.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Ancient Y-DNA (screenshot)</td></tr>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxBC1ZjrpsPX0F4U2cjc5oatg5d97-Tu4XjosjCZknuw__aD599r2haPvRL5ujJeANcCl794ul0AiT95Q-BuQfDWoxuzLLN_dunxVb_WU348zb5Yq5UJjzUUxhSp6G91K4ci47MNghFJA/s1600/mtDNA.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="311" data-original-width="333" height="298" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxBC1ZjrpsPX0F4U2cjc5oatg5d97-Tu4XjosjCZknuw__aD599r2haPvRL5ujJeANcCl794ul0AiT95Q-BuQfDWoxuzLLN_dunxVb_WU348zb5Yq5UJjzUUxhSp6G91K4ci47MNghFJA/s320/mtDNA.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Ancient mtDNA (screenshot)</td></tr>
</tbody></table>
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Related: <a href="https://forwhattheywereweare.blogspot.com/2018/04/no-iberian-in-iberomaurusian.html" target="_blank"><i>No Iberian in Iberomaurusian</i></a>.<br />
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<div style="text-align: justify;">
<span style="color: #990000;"><b>Correction:</b> I first titled this "a 30,000 years-old...". That was a major error on my part and I apologize for any confusion it may have caused. Thanks to Capra Internetensis for spotting it.</span></div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com63tag:blogger.com,1999:blog-3023805782808412230.post-89084762455012218642018-04-08T12:35:00.000+02:002018-12-18T12:06:18.635+01:00No Iberian in Iberomaurusian<div style="text-align: justify;">
After almost a century of controversy on the matter, it seems that archaeogenetics solved the riddle. Not in the sense I thought it would but it did anyhow.</div>
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<div style="text-align: justify;">
<b><a href="doi:%2010.1126/science.aar8380" target="_blank">Marieke van de Loosdrecht et al., <i>Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations</i></a>. Science 2018</b> (<span style="color: red;">pay per view</span>). DOI:10.1126/science.aar8380 -- See also <a href="http://science.sciencemag.org/content/sci/suppl/2018/03/14/science.aar8380.DC1/aar8380_vandeLoosdrecht_SM.pdf" target="_blank">supplementary materials</a> (<span style="color: #38761d;">free </span>but hard to find). </div>
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Ancient DNA samples from Taforalt (Iberomaurusian or Oranian culture, Upper Paleolithic of North Africa) show no trace of Paleoeuropean ancestry (WHG), however they show strong affinity to West Asians of Palestinian type, showing also some significant amount of African Aboriginal ancestry, probably closer to East African Hadza and Sandawe and <a href="https://forwhattheywereweare.blogspot.com/2015/10/first-african-ancient-nuclear-dna.html" target="_blank">ancient Mota</a> than to West African types. The result is something roughly similar to <a href="https://en.wikipedia.org/wiki/Afar_people" target="_blank">Afars</a> but not quite the same in any case. </div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEbebtaO5JLMMXkJOmnA25R84MY3lDtfbpsJB6Ew6-cbHqT2QOGeIVIiUKBc01MPh6dbTJohL1_2THQdzkhqPH1hcwIyiP7_W0i6oqeF1dHPyopJOKiLVxPReAjuoM9g30cqNf8v9K2Rc/s1600/PCAsupp.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="709" data-original-width="569" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEbebtaO5JLMMXkJOmnA25R84MY3lDtfbpsJB6Ew6-cbHqT2QOGeIVIiUKBc01MPh6dbTJohL1_2THQdzkhqPH1hcwIyiP7_W0i6oqeF1dHPyopJOKiLVxPReAjuoM9g30cqNf8v9K2Rc/s640/PCAsupp.png" width="512" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fig. S8 - Taforalt individuals on the top PCs of present-day African, Near Eastern and South European populations. </td></tr>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSCMqtd511La4W9iUBfE9X8HhWbO7DYpTFA_TxBA05ithnrB1KFGLXJzQeTfad8eK2m3CjMksQeeF5Ntjiy7N9JJbM9WMTDUTF7ZbS5hoNmq72gDZO1uIw7TMxOhcZKZmKUae65fxhtJU/s1600/Admixturesupp.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="668" data-original-width="439" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSCMqtd511La4W9iUBfE9X8HhWbO7DYpTFA_TxBA05ithnrB1KFGLXJzQeTfad8eK2m3CjMksQeeF5Ntjiy7N9JJbM9WMTDUTF7ZbS5hoNmq72gDZO1uIw7TMxOhcZKZmKUae65fxhtJU/s640/Admixturesupp.png" width="420" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fig. S11 - ADMIXTURE results for a few informative K values.</td></tr>
</tbody></table>
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<div style="text-align: justify;">
So the conclusion must thus be that the Eurasian influence in North African Upper Paleolithic (call it Iberomaurusian, Oranian or my personal unorthodox preference: Taforaltian) arrived from West Asia with whichever intermediate stage in Egypt and Cyrenaica, where that influence is quite apparently much older in the archaeological record. This seems contradictory to the chronology of Taforaltian, with Western sites producing older radiocarbon dates but the genetic data seems overwhelming. </div>
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I must say I wish they would have contrasted with older (and <a href="https://forwhattheywereweare.blogspot.com/2016/05/large-paleoeuropean-dna-survey.html" target="_blank">available</a>) Paleoeuropean samples than WHG (Epipaleolithic) but I guess that some WHG influence would have shown up if there was some older European influx because the various Paleoeuropean layers are not disconnected. But it is still something someone should test, just in case. </div>
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<br />
<h4>
Haploid DNA</h4>
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The Taforalt sample was rich in <b>mtDNA U6a</b>, with also one instance of <b>M1b</b>: <br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhWTh4Efe2XhQSnCnCm-g6_UZgOcUueIN742H8o5lrJhMldpECQUFmAzJ94PGEXlp5qF22ngVt3IlsxU3I_4YBODerHE6IjSI2U06FLMGsJnGBdIe5kJMJXekbkjBQS-sPMlyyUBpH3ig/s1600/mtDNAtable.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="376" data-original-width="852" height="282" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhWTh4Efe2XhQSnCnCm-g6_UZgOcUueIN742H8o5lrJhMldpECQUFmAzJ94PGEXlp5qF22ngVt3IlsxU3I_4YBODerHE6IjSI2U06FLMGsJnGBdIe5kJMJXekbkjBQS-sPMlyyUBpH3ig/s640/mtDNAtable.png" width="640" /></a></div>
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<div style="text-align: justify;">
All six male samples carried Y-DNA E1b1b, with most of them being well defined as <b>E1b1b1a1-M78</b> (see table S16 for details).<br />
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<br />
Related: <a href="http://forwhattheywereweare.blogspot.com/2018/04/luxmanda-30000-years-old-proto-horner.html" target="_blank"><i>Luxmanda: a 3,000 years-old proto-Horner in Tanzania</i></a>. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com26tag:blogger.com,1999:blog-3023805782808412230.post-954885946052730862018-04-04T06:37:00.001+02:002018-04-04T23:33:05.021+02:00North African Neolithic was influenced by Europe... and European Chalcolithic by Iberian Neolithic<div style="text-align: justify;">
Or so it seems considering the data of Fregel et al., a study I have in my to-do list for some time and that I don't see cited often or ever at all.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Rosa Fregel et al., <i>Neolithization of North Africa involved the migration of people from both the Levant and Europe</i>. BioRxiv 2017 (pre-pub).</b> DOI:<a href="https://doi.org/10.1101/191569">10.1101/191569</a></div>
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The critical piece is probably this selection from Admixture results but which repeats over and over through the study with many more analyzed populations from all West Eurasia and North Africa:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnMbjH1aReiGokwQe3IcAVVGalm7uOiNUgdfLjL3TYXwp_3j7i49Lq7SlBwhQ6zDGiuqM7MjX_VKxvgbVZrRl6vHffFqOUuKbHzqPeztGrgSm1mWkzaTJDEjK-QW7yRXMktiiwRPgcDQg/s1600/Admixture1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="406" data-original-width="836" height="310" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnMbjH1aReiGokwQe3IcAVVGalm7uOiNUgdfLjL3TYXwp_3j7i49Lq7SlBwhQ6zDGiuqM7MjX_VKxvgbVZrRl6vHffFqOUuKbHzqPeztGrgSm1mWkzaTJDEjK-QW7yRXMktiiwRPgcDQg/s640/Admixture1.png" width="640" /></a></div>
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<div style="text-align: justify;">
We see how KEB (Morocco Neolithic) is a mix of European Neolithic intermediate between Iberia (purple) and Sardinian (blue) on one side and, on the other, something like Mozabites (not shown in this detail, cream). TOR is a new Neolithic sample from Andalusia.</div>
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Another ancient Moroccan sample IAM (pre-Neolithic, not shown here either) is fully cream-colored like mostly are modern Mozabites. </div>
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Interestingly we see for the first time the emergency of a purple-colored component that differentiates Iberian Early Neolithic from the rest (although this does not happen at lower K-values, so they are still related), a component that, in the MNChL (Middle Neolithic and Chalcolithic) period, somehow appears as dominant in Italy (no data for earlier times) and becomes quite dominant in Central Europe. </div>
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<div style="text-align: justify;">
This is intriguing to say the least. It must be said that modern Sardinians and Basques (these probably, not labeled) are low in the purple component, although less than other populations, and that somehow the Early Neolithic (blue) component made a comeback:</div>
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I do not want to over-interpret all this (autosomal genetics are not an exact science) but, judging on KEB, the purple component is not just a generic southern branch (Cardium Pottery) distinction but something specifically Iberian or Italo-Iberian. The matter needs more research but it is in any case very intriguing that the purple component seems to expand from Iberia or somewhere nearby (France?, Italy?) in the period leading to the Chalcolithic, a most critical one in the formation of the genetics of Europe.</div>
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There is a also a little hoard of DNAmt and Y-DNA, with G2a-M201 (in Europe), <span style="color: #660000;">E1b-L19* (in pre-Neolithic North Africa) and T-M184 (in Neolithic North Africa)</span> in the patrilineal side and quite a bit of varied K1a in the matrilineal one, as well as JT (also in both shores) and U6 and M1 in North Africa. </div>
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Worth reading and keeping in mind, no doubt.</div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com16tag:blogger.com,1999:blog-3023805782808412230.post-42075047908869916862018-03-31T08:41:00.000+02:002018-03-31T08:41:26.542+02:00Iberian genetic clusters<div style="text-align: justify;">
I've been the last two weeks or so chewing on this pre-pub and there's a point when no more chewing seems to be useful. So let's get to discuss it as well as possible.</div>
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<b>Clare Bycroft et al. <i>Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula</i>. BioRxiv 2018</b> (pre-pub. <a href="https://doi.org/10.1101/250191">DOI:10.1101/250191</a></div>
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The key finding is clustering of the populations of the Iberian Peninsula as in this map (locations for the Spanish state are precise, for Portugal unknown and located at random, also shadowing for Portugal is uniform for all the country):</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCXtlQqIZafSbE9TB5Dwaf20Wed1yRjzZLmykoOKIxV8x70Jxi1N8jRvYpHxjpd-JKQwoW4hCBKXlqNParHZLXoppXqCbn57pL8hA9LItGL7UB55xSBgv1g0EKqMopWbX4u2TD6WKsfLM/s1600/components.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="595" data-original-width="846" height="450" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCXtlQqIZafSbE9TB5Dwaf20Wed1yRjzZLmykoOKIxV8x70Jxi1N8jRvYpHxjpd-JKQwoW4hCBKXlqNParHZLXoppXqCbn57pL8hA9LItGL7UB55xSBgv1g0EKqMopWbX4u2TD6WKsfLM/s640/components.PNG" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Supp. Figure 1a </td></tr>
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The weirdest thing for me is that the Catalan-Alacant and Seville-León-Asturias cluster are strongly related in the cladogram. I'll discuss this below.</div>
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Another very weird feature is the presence of a group in Pontevedra province (Galicia) that is the most different of all, even more distinct than Basques. It is composed of many small highly endogamous subgroups. I do not have at the moment any explanation for this, honestly. </div>
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External influences: mostly "French"</h3>
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When factored as made up external populations, Iberians are mostly French (or something that approaches that label), although "mostly" varies from c. 60% in the West to c. 90% in Gipuzkoa. This pattern of "Frenchness" reminds that of the distribution R1b-S116. Correlation is not causation but it is still correlation and when R1b-S116 seems to stem from somewhere France and arrive to the Peninsula at least as early as the Bronze Age (or maybe before but still undetected, <a href="https://en.wikipedia.org/wiki/Terminus_post_quem" target="_blank"><i>terminus ante quem</i></a> at Los Lagos, as <a href="https://forwhattheywereweare.blogspot.com/2018/03/oldest-known-iberian-r1b-s116-and-df27.html" target="_blank">discussed recently</a>). </div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjk9z5qcZsB43vXTM7_wdRrDdjYJoEhtmVrsjlR4S3jPcAP6KByxyOT_H6IpUbEQ-eA-vtwX6LaOuvNtcjGvwIDLYnzVGCYpfkWah8KD10YoEXjiKliotWve591mNpJSV9R036SifYh6TY/s1600/France.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="394" data-original-width="445" height="352" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjk9z5qcZsB43vXTM7_wdRrDdjYJoEhtmVrsjlR4S3jPcAP6KByxyOT_H6IpUbEQ-eA-vtwX6LaOuvNtcjGvwIDLYnzVGCYpfkWah8KD10YoEXjiKliotWve591mNpJSV9R036SifYh6TY/s400/France.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Supp. Fig 5a</td></tr>
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The most affected population by this French influence are Basque1, which show no significant contribution from any other source (only very small from Italy1 and very tiny from North Morocco, see supp. fig. 7) but the authors say that (supp. info.):</div>
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<blockquote class="tr_bq">
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<span style="color: #0c343d;">Notably, the Basque-centred cluster has a markedly different profile from the rest. Firstly, it has much lower, or zero contributions from donor groups that contribute to all other clusters: Italy, NorthMorocco, and WesternSahara, and a very large contributionof 91% (88-93) from France. Additionally, the model fit for this cluster is strikingly less good than that for the other clusters (Supplementary Figure 4d), suggesting that Basque-like DNA is less well captured by the mixture of donor groups in this data set. Specifically the Basque share even more DNA with the French group than predicted by their mixture representation, <b>which might reflect, for example, that the DNA the Basque share with present-day French is only a subset of modern French ancestry. This pattern is seen for other Spanish groups also, but to a much lesser extent.</b></span></blockquote>
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-LfezYFLBd2NsjeXUjwXzUFyTGeBkzZnURawzReX47W4by6SPW5YskRnZgNNJg156MoFrgRhKKVqVAsJSUQFw7QW12CI2OIVAZ9e1n-ACnoImq_i3oqzj2itQQkeldrZw1-f0coSJJFI/s1600/modernity-source-area-1.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="608" data-original-width="500" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-LfezYFLBd2NsjeXUjwXzUFyTGeBkzZnURawzReX47W4by6SPW5YskRnZgNNJg156MoFrgRhKKVqVAsJSUQFw7QW12CI2OIVAZ9e1n-ACnoImq_i3oqzj2itQQkeldrZw1-f0coSJJFI/s320/modernity-source-area-1.jpg" width="262" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Area that demands urgent genetic research</td></tr>
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So it seems we may be dealing with some sort of "paleo-French" rather than modern Indoeuropeanized French. </div>
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<b>All genetic roads lead to France</b>, at least in Western Europe: it also happens <a href="https://www.nature.com/articles/s41598-017-17124-4" target="_blank">in Great Britain and Ireland</a>, and it is very apparent in the <a href="https://forwhattheywereweare.blogspot.com/2015/06/some-improved-knowledge-of-major-r1b.html" target="_blank">geographically sorted phylogeny of R1b-S116</a>. And is also this area where we see the earliest signs of mitochondrial DNA "modernity": in <a href="https://forwhattheywereweare.blogspot.com/2011/11/neolithic-basque-mtdna.html" target="_blank">Paternabidea</a> (Navarre) and <a href="https://forwhattheywereweare.blogspot.com/2015/05/neolithic-mtdna-from-seine-basin.html" target="_blank">Gurgy</a> (Burgundy), an area that demands much greater attention from genetic and archaeogenetic research than has received to this day. </div>
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The other major contributors are: <b>Italy </b>(mostly Italy1), with peaks of c. 20% and influencing mostly the South and Center, <b>North Morocco</b>, with peak of c. 10% in Portugal and a West and South distribution, and <b>Ireland</b>, with peak of c. 6% in Eastern Asturias and a broadly Western distribution. </div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" data-original-height="396" data-original-width="465" height="272" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRmLRr9xgzopCTysLdHRrpOHx6iPxBmRsHZQuhJcfKYLL1xlsv7QicUjZIBAeItl4olkJIhewqhUa-oERPsH5VaidGBQnN9g32iVKF5eNON9CN7o05fTjyHRWTbmQbhlhQNhkLGYmsadI/s320/Italy.png" style="margin-left: auto; margin-right: auto;" width="320" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Italian contribution (Italy1)</td></tr>
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRc7D4rogpK_kAuVW7WWqLpvtP8O-6pv_47gi9acAW099JkA_51NJTbXkswnvBQm04ODlt_hAF01LPCFn4THIJFCgNrJDtsm-A_u62O9rvw5udvirsFF5oi2Hz9oZxFL3OG518mdrREuE/s1600/NMorocco.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="394" data-original-width="457" height="171" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRc7D4rogpK_kAuVW7WWqLpvtP8O-6pv_47gi9acAW099JkA_51NJTbXkswnvBQm04ODlt_hAF01LPCFn4THIJFCgNrJDtsm-A_u62O9rvw5udvirsFF5oi2Hz9oZxFL3OG518mdrREuE/s200/NMorocco.png" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">North Morocco contribution</td></tr>
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEitwdBIptobaTIcSFGc1Z8cXjNBuD_KMU-lNBOdUuBp9mM2Z-A-e56gkzyEIl6HDydf1ZFjyBEL6fRhlLWqlJfaH0XWoTkFtky6piSuD3XYUs8eTx0FdEeDY52LqKAbdlOhX1oRxVvMIgE/s1600/Ireland.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="397" data-original-width="475" height="166" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEitwdBIptobaTIcSFGc1Z8cXjNBuD_KMU-lNBOdUuBp9mM2Z-A-e56gkzyEIl6HDydf1ZFjyBEL6fRhlLWqlJfaH0XWoTkFtky6piSuD3XYUs8eTx0FdEeDY52LqKAbdlOhX1oRxVvMIgE/s200/Ireland.png" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Ireland contribution</td></tr>
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What do exactly these <i>contributor </i>components mean? Hard to say, although part of the Italian and North Moroccan elements could well be related to historical episodes such as Roman and Muslim conquests. But only partly so,because the North African in Galicia just cannot be that high only from a Muslim conquest that was very limited in time, nor should we expect to be that much "Muslim" nor "Roman" in the remote and largely ignored area of modern Portugal: there must be more ancient origins, probably dating to the Neolithic, Chalcolithic or Bronze Age. </div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-r1OjOuhrYJsQE3lAx7w0n5CcJjHGX0eU9NrC33L0WgZqaMc8s6LPfLtdYN6jtrNF9TdTMTkxyEsmjGtzoWuFX-XUUzDpjp1ytKwrhX7Gv7bUfNFc0sx0meOT1v59LoHRwDb4PRa3Re8/s1600/WSahara.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="394" data-original-width="479" height="164" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-r1OjOuhrYJsQE3lAx7w0n5CcJjHGX0eU9NrC33L0WgZqaMc8s6LPfLtdYN6jtrNF9TdTMTkxyEsmjGtzoWuFX-XUUzDpjp1ytKwrhX7Gv7bUfNFc0sx0meOT1v59LoHRwDb4PRa3Re8/s200/WSahara.png" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">minor West Sahara contribution</td></tr>
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And in the case of the North African component we may have a guide in a minor West Saharan contribution (at right), which may well reflect an older and "purer" form of North Africanness and which is againcon centrated in Portugal and Galicia, with extension to parts of the Central Plateau but does not affect the South, the area where we should expect most of the Muslim period's genetic influence. </div>
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We cannot trace a line in Portugal because of the uncertainty of the geographic origins of the samples but we can do it within the boundaries of Spain and that line suggests that the Muslim genetic influence could be intense by the Southern third and maybe all the way to Zamora by the Western part but should not be relevant in Galicia nor Asturias nor (inferred, uncertain) much of Portugal. That in these areas, the North African element is peculiar and looks older than the Emirate/Caliphate of Cordoba. </div>
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Speculating on the possible origins of the Iberian clusters</h3>
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This part has given me a true headache. It is very hard to understand how these clusters formed and I will not pretend here that I have all the answers. The most strange of all is the affiliation of the Central-West and Eastern clusters. </div>
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The problem is not only the highly implausible relation between Asturias-León and West Andalusia, which the authors seem to believe product of historical colonization at the time of the Reconquista (13th century) but which makes no sense whatsoever because the Kingdom of Seville was never part of the barely autonomous Kindgom of León but an administrative division of Castile (of which León was by then just a dependency) and we should thus see at least some important influence of the Central (yellow triangles) cluster, which is dominant in Valladolid, Madrid and even the city (but not the countryside) of Burgos, and we do not see anything like that. </div>
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One possibility is of course that the components or some of them are not that real but I do not see any indication of that in the study, so, in wait of independent replication, I'll take them at face value. </div>
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So why then? I've been scratching my head until I could not think any further, I swear. </div>
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And this is my hypothesis, risky as it may be:</div>
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1. The essence of the split between the related <i>Spanish </i>components (excluding Galicians and Basques) and the Portuguese-Galician component could be at the Early Neolithic. When I mask the areas not or weakly affected by the Earliest Neolithic in the components map I get this:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZlPjX5YMMF48ZqyUgWYKeri3QkPD9rE8wi5ag4WK3ATk7ib0U5Aj5-jAjw4Yk_V5CRN1rYCSZAFBwj9mREuhtYI6p-wcFt9va98NjGFr6_TMnbMPkFugVYL9jDtgg0cgRUa9eGku2IwA/s1600/groupsmaskneolithic.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="494" data-original-width="674" height="468" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZlPjX5YMMF48ZqyUgWYKeri3QkPD9rE8wi5ag4WK3ATk7ib0U5Aj5-jAjw4Yk_V5CRN1rYCSZAFBwj9mREuhtYI6p-wcFt9va98NjGFr6_TMnbMPkFugVYL9jDtgg0cgRUa9eGku2IwA/s640/groupsmaskneolithic.png" width="640" /></a></div>
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... what seems to correspond odly too well to the first major split in the cladogram between the Portuguese-Galician (purple) component and the rest.</div>
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2. The expansion inwards may correlate with Chalcolithic and Bronze Age processes, which seem to be way too important everywhere and also in Iberia. So I used the Bell Beaker map I copied from Harrison (see <a href="https://forwhattheywereweare.blogspot.com/p/iberian-chalcolithic.html" target="_blank">here</a>) as cutoff for another mask (radius are relative to Bell Beaker density circles in the reference map):</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaGjQlDOuxchImyfA-CJrgNPhPZ3qxB0zNltB3mf0wsefzBcjm0p29cIh7fN5IRMYwEYwudtlreQgEJ7Qjn0HmfwwuHFO9zLF6r0FImprTw7-D5iDrjMAMug1M20Zw-kFet-l3cNPM5K4/s1600/grouopsmaskbeaker.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="494" data-original-width="674" height="467" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaGjQlDOuxchImyfA-CJrgNPhPZ3qxB0zNltB3mf0wsefzBcjm0p29cIh7fN5IRMYwEYwudtlreQgEJ7Qjn0HmfwwuHFO9zLF6r0FImprTw7-D5iDrjMAMug1M20Zw-kFet-l3cNPM5K4/s640/grouopsmaskbeaker.png" width="640" /></a></div>
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If so the split between the Central (yellow) and East (orange) groups (to which the brown and red and other groups are closely affiliated) could be related to this Bell Beaker period and derived Bronze Age cultures. The yellow or Central component could originate in Los Millares (Almería province) and spread northwards to Ciempozuelos (Madrid province) and from there to other areas with the Cogotas I culture of the Bronze Age. </div>
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The Purple (Western) component should be somehow related to Zambujal or Vila Nova de Sao Pedro (VNSP) culture of Portuguese Estremadura and spread northwards to tin-rich Galicia with the group of Montelavar already in the Bronze Age maybe.</div>
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The mysterious Red (Central-West) component could be related to some colonization of that area from the Bell Beaker dense area of Catalonia or the Denia district, or maybe even an older colonization, hard to say. What I know of that area in the late Prehistory is that it is ill-defined, partly for lack of research in the heavily farmed alluvial plain, and that it correlates with Southern Portugal but not fully, always showing a distinct personality, until it grows a clearly distinct personality in the Tartessian period, already in the Iron Age. It is also clear that the so-called <a href="https://en.wikipedia.org/wiki/V%C3%ADa_de_la_Plata" target="_blank">Silver Road</a> runs straight through that cluster and that it was important, and growingly so, in the Late Prehistory, having both commercial and religious significance and being clearly the main path of penetration of Phoenician influences inland, already in the proto-historical period. </div>
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While still caught with feeble pins, this Silver Road speculative explanation seems to make much better sense than the Reconquista hypothesis the paper appears to spouse and which I see nonsensical because the patterns observed are not as we could expect. </div>
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But of course it is always up to you to make up your own mind, I'm just offering some variant considerations that for me make some sense but that are by no means a well finished theory either, just better than the simplistic historical interpretation, which does not fit the facts too well. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com73tag:blogger.com,1999:blog-3023805782808412230.post-67742850538698969022018-03-31T04:45:00.000+02:002018-03-31T04:45:09.156+02:00A new genetics blog in Spanish<a href="https://wilhelmhgenealogy.files.wordpress.com/2018/03/finlandesasueca.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="701" data-original-width="688" height="200" src="https://wilhelmhgenealogy.files.wordpress.com/2018/03/finlandesasueca.png" width="196" /></a><br />
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<a href="https://wilhelmhgenealogy.wordpress.com/" target="_blank"><i><b>Wilhelm H > DNA and Genealogy</b></i></a>, by some guy called Wilhelm Halys, whom I know from Facebook. </div>
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His very <a href="https://wilhelmhgenealogy.wordpress.com/2018/03/30/endogamia-y-rootsfinder/" target="_blank">first post on endogamy using RootsFinder</a> seems very interesting, even if I have to admit I don't understand it well because I'm unfamiliar with this program. But that's good because it indicates novelty, fresheness and stuff to learn. </div>
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Hope you also find interesting, assuming you can read Spanish or use a translator.</div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com0tag:blogger.com,1999:blog-3023805782808412230.post-1417963226267834542018-03-25T15:35:00.000+02:002018-03-25T15:42:16.388+02:00A bit of satire<i>Disclaimer: this is a fictional work, any coincidence with reality is, well, coincidence... or something...</i><br />
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<span style="color: blue;">I told you years ago it would be like this. Having a nervous breakdown are we? Mwahahaha!<br /><br />Plenty of us in the Nordic Horde Party have also looked at this. It is settled.<br /><br />Iberia, the French samples we have, plus the British Neolithic samples tell us what the rest of France was like...</span><br />
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<span style="color: #990000;">So now France is part of Britain? I see, I see who's "losing it".</span><br />
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<span style="color: blue;">Game over!<br /> </span><br />
<span style="color: blue;">The megalithism stuff too. Forget it. Admit you didn't interpret stuff right.<br /><br />It is about you because...</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtha9DUkuxbNAMplhyphenhyphenKUqu76QBmIxeulHlTt0YUKnr1JNOHjNcFcF6ghptL2otrpL4cM_LFsJjpASARFpRFFecGinziRpH0sRx6Rz6GfINfN13EfWab2lQmtYiqB0aLisIxo1LP_vIo8Y/s1600/artzaina.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="198" data-original-width="302" height="131" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtha9DUkuxbNAMplhyphenhyphenKUqu76QBmIxeulHlTt0YUKnr1JNOHjNcFcF6ghptL2otrpL4cM_LFsJjpASARFpRFFecGinziRpH0sRx6Rz6GfINfN13EfWab2lQmtYiqB0aLisIxo1LP_vIo8Y/s200/artzaina.png" width="200" /></a></div>
<span style="color: #990000;">... because I'm stating the inconvenient truth, the obvious contradictions and limitations of the Pan-Indoeuropeanist ideology?</span><br />
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<span style="color: blue;">Do you only see the pictures or read the papers?</span><br />
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(Laughing) <span style="color: #990000;">I read cartoons only. Preferably manga with no text, all cries and extremely slow action designed to dumb down the newer generations.</span><br />
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<span style="color: blue;">But by all means, please keep the comedy rolling on.</span> <br />
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<span style="color: #990000;">Uh, alright. You want comedy, don't you? </span><br />
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<span id="goog_420172077"></span><span id="goog_420172078"></span><span style="color: blue;">Just be at peace with the fact your predictions based on modern DNA were wrong. And we the Nordic Horde Party has THE TRUTH. You can't fight against The Nordic Horde, just as Elcano could never even dream to circumnavigate the World on a rotten carrack.</span><br />
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<tr><td class="tr-caption" style="text-align: center;">J.S. Elcano, first person to sail around Earth</td></tr>
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(Elcano shows up from the Netherworld)<br />
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<span style="color: #741b47;">I did though!</span><br />
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<span style="color: #990000;">Thanks buddy for clarifying that. </span><br />
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(Elcano vanishes in a puff of smoke)<br />
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<span style="color: blue;">Just, deal with the facts: with our alternative facts!<br /><br />Everyone in Europe has Steppe ancestry. Basques too, Sardinians too, everyone belongs to the Nordic Horde, hierarchically organized by greater purity of Nordic Horde ancestry!</span><br />
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<span style="color: #990000;">... conveniently deformed by forced pseudoanalyses so the Brits and Germans retain top-dog position in your Nordicist revised hierarchy rather than being semi-Basque? I see...</span><br />
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<span style="color: blue;">... they also influenced the Basque despite the fact Basque speak a non-Indo European language. 20-30% contribution.</span><br />
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<span style="color: #990000;">Uh, <a href="https://forwhattheywereweare.blogspot.com/2018/03/oldest-known-iberian-r1b-s116-and-df27.html" target="_blank">here</a> it says zero contribution. And <a href="https://forwhattheywereweare.blogspot.com/2015/09/detailed-analysis-of-ancient-atapuerca.html" target="_blank">here</a> too, and <a href="https://forwhattheywereweare.blogspot.com/2015/06/alentoft-2015-more-ancient-dna-from.html" target="_blank">here</a>, and <a href="https://forwhattheywereweare.blogspot.com/2014/04/diversity-and-legacy-of-ancient.html" target="_blank">here</a>, and <a href="http://forwhattheywereweare.blogspot.com/2013/12/ancient-european-dna-and-some-debatable.html" target="_blank">here</a>...</span><br />
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<span style="color: blue;">Nein, nein, nein, Impossible!<br /><br />Is R1b Z2103 in Yamnaya not good enough for you?</span><br />
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<span style="color: #990000;">No. It's a very high distinct branch within M269 and has no direct relation with either S116 nor U106, nor their direct precursors, M412, etc.</span><br />
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<span style="color: blue;">Deny, deny, deny. Eventually you'll accept the truth.<br /><br />You're completely insane, but at the very least try and get the facts right. Our facts, our alternative facts!<br /><br />Ancient DNA will never prove you right. You will have to deal with this sooner or later. And if it does: we'll claim it is 'dubious', 'contaminated', whatever we need to impose our doctrine, because remember that a lie repeated one thousand times becomes truth, mwahahaha!</span><br />
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<span style="color: #990000;">Truth defends itself.</span><br />
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<span style="color: blue;">There's a new paper coming... I have connections, I know the future, mwahahaha! I'll enjoy seeing you try and squirm your way out of what you just said after you see the results.</span><br />
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<span style="color: #990000;">I heard that before and most of the time it was nothing like you imagined.</span><br />
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<span style="color: blue;">There's no getting away from it.</span><br />
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<span style="color: #990000;">OK, abracadabra, whatever, agur.</span><br />
<br />Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com26tag:blogger.com,1999:blog-3023805782808412230.post-82957491496238195602018-03-19T16:24:00.000+01:002018-05-02T15:58:33.420+02:00Quickie: the pre-Indoeuropean evolution of ancient Iberians: from 'Sardinian' to 'Basque'<div style="text-align: justify;">
This may be needed as transition between the ancient Iberian genetic data of Valdiosera and Günther that <a href="https://forwhattheywereweare.blogspot.com/2018/03/oldest-known-iberian-r1b-s116-and-df27.html" target="_blank">I discussed two days ago</a> and the modern Iberian genetic data that I'm planning to discuss very soon (just chewing on the data, because it is a bit perplexing in some aspects, but ref. <a href="https://www.biorxiv.org/content/early/2018/03/12/250191" target="_blank">Bycroft 2018</a> if you want to peek on it on your own). </div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrWmjWuXDFyQAlyp6UgT4acSyQ0_1N3TE9L1XvxTGeagSpMF5QVrKiLB1lbTCWAo982n9ihCc05jBc5XlKh6Tyj835XwwvDgfCPjxeGqRN93Hj9Xd02RzPPso00MV7AWjriIWZu9Kh2X4/s1600/PCAannotated.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="524" data-original-width="692" height="484" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrWmjWuXDFyQAlyp6UgT4acSyQ0_1N3TE9L1XvxTGeagSpMF5QVrKiLB1lbTCWAo982n9ihCc05jBc5XlKh6Tyj835XwwvDgfCPjxeGqRN93Hj9Xd02RzPPso00MV7AWjriIWZu9Kh2X4/s640/PCAannotated.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fig. 1B from <a href="https://doi.org/10.1073/pnas.1717762115" target="_blank">Valdiosera, Günther et al. 2018</a>, annotated by me.</td></tr>
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Just that: we see very clearly how ancient Iberians were at the beginning of Neolithic like modern Sardinians and by the time of Chalcolithic in some cases and at the Bronze Age everywhere, they had turned into something like modern Basques, i.e. more Paleoeuropean but not yet more Indoeuropean at all. </div>
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Modern Spaniards/Iberians seem to be mostly that Basque-like Bronze Age base plus some Indoeuropean admixture from either the continent (Celts surely) or Italy (Romans no doubt). </div>
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Maybe it is like stating the obvious but <i>the obvious</i> is not always obvious for everyone and understanding this will be handy when dealing with modern Iberian DNA and its structure. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com66tag:blogger.com,1999:blog-3023805782808412230.post-25678903686744344372018-03-17T12:11:00.004+01:002018-03-18T15:24:53.003+01:00Oldest known Iberian R1b-S116 (and DF27) is NOT at all Indoeuropean<div style="text-align: justify;">
This study is very interesting but it is very wrongly argued, maybe in an attempt to fit their findings with what has sadly become the mainstream current of "explanation" about the origins Y-DNA haplogroup R1b-S116 (also P312, etc.)</div>
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<b>Cristina Valdiosera, Thorsten Günther et al. <i>Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia</i>. PNAS 2018. </b><a href="https://doi.org/10.1073/pnas.1717762115">DOI:10.1073/pnas.1717762115</a></div>
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The issue is that they found the very first known carrier of R1b-S116 (and R1b-DF27, the main Iberian haplogroup) in an individual of the Bronze Age of Lower Rioja (Cueva de Los Lagos, Alhama de Cervera), belonging very clearly to the Central Iberian culture of Cogotas I, even if it is at its very northeast margin.</div>
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What is wrong? Well, the very title is wrong. It is nothing but an artifact produced by <b>forced</b> (<i>supervised</i>) results of Admixture within the simplistic 3-population model. Even then their result is in fact so weak that it immediately cried to me as "artifact" (<i>noise </i>or whatever you want to call it) and it is effectively nothing but that. </div>
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And to demonstrate it is as simple as digging into the supplementary materials and look at the <b>unsupervised </b>Admixture run (<a href="http://www.pnas.org/content/pnas/suppl/2018/03/07/1717762115.DCSupplemental/pnas.1717762115.sd03.pdf" target="_blank">dataset S03</a>), whose optimal columns (lowest CV scores) are K=16-19 (all four are optimal, what is fine with me but makes explanation and understanding a bit more dense). </div>
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As that unsupervised admixture is massive, with lots of global populations ancient and modern, I made a selection using only the four optimal K-values (K=16 to K=19, from left to right):</div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBwe8AQRzkaQhkc9sTcRYHF9j8MV7abwmiGhXfYLcJxqIADstiBHIlxmXGs7sSL4g3yQH1aKJEnirCsoI2BZWIq-2dzDZcXLBczJj5bkbwq370Oe6Itu0Ou29UDMVW4NYVQpHxH2LZtjk/s1600/valdiosera-admixture-selection.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1600" data-original-width="776" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBwe8AQRzkaQhkc9sTcRYHF9j8MV7abwmiGhXfYLcJxqIADstiBHIlxmXGs7sSL4g3yQH1aKJEnirCsoI2BZWIq-2dzDZcXLBczJj5bkbwq370Oe6Itu0Ou29UDMVW4NYVQpHxH2LZtjk/s640/valdiosera-admixture-selection.png" width="310" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><b>Click to expand</b> (labels at bottom are mine)</td></tr>
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And it is absolutely clear from K=16 to K=18 that there is not a speck of the Caucasus component which is absolutely universal in all the true Indoeuropean samples. There is a tiny speck of it in the K=19 column but there even Sardinians and some Anatolian Neolithic individuals have it at much greater values and thus cannot anymore be automatically interpreted as Indoeuropean marker, but just as extra Caucasus affinity present in some Neolithic-derived populations or individuals more than others since the very beginning of mainline (Vasconic) European Neolithic at the Aegean.</div>
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And this is it. Quod erat demonstrandum (Q.E.D): R1b-S116, at least in Iberia, has nothing to do with Indoeuropean expansion, nothing at all: it is absolutely clear that it is a pre-Indoeuropean thing. And it has been present in Lower Rioja since at least the Bronze Age. </div>
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Furthermore, when we look at the Central European Bell Beaker (Central BB) samples and compare them with their immediate chronological precursors of (definitely Indoeuropean) Corded Ware culture, we must admit that there is a decrease of the Caucasus component and an increase of the Vasconic Neolithic (light blue) element. This also speaks against the Indoeuropean "explanation" for the expansion of R1b-S116 into Central Europe, because the first known such ancient carriers are from the Bell Beaker period and not a moment earlier, and these clearly express an anti-Indoeuropean tendency in their autosomal genomes.</div>
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There is however a sizable Indoeuropean component in modern non-Basque Iberians, smaller than in most other European populations but very clear nevertheless. This must have arrived at later times: (1) with the Celts, who arrived to Catalonia at the end of the Bronze Age, later expanding into Central and Western Iberia, (2) with the Romans, (3) maybe also to some extent with the Germanic invaders of the late Roman period. None of these expansions seem particularly associated with R1b-S116, however <a href="http://www.cell.com/ajhg/fulltext/S0002-9297(08)00592-2" target="_blank">the c. 1% R1a and the c. 8% J2</a> (with plausible Italo-Roman origin) should be related to it, along with an assortment of other haplogroups. </div>
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For those willing to dig in the details, there is also a small treasure trove of other ancient Y-DNA, mostly I (which underlines the Paleoeuropean influence in Neolithic Iberia, regardless of whether this is local or was carried on from further East by the Neolithic settlers), as well as one instance of unspecific R1b, another of G and another of H.</div>
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Someone may ask, which is then the origin and means of expansion of R1b-S116, if not Indoeuropean? Good question to which I don't have yet a well defined answer. But my tentative explanation is that it should be related to two ultimately related processes within Western European "Neolithic" (Late Neolithic and Chalcolithic): </div>
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<li>The well documented phenomenon of increase, in most areas at least, of the Paleoeuropean component time passes, this may be to some extent because of simple absorption of local subneolithic "hunter-gatherers" but it probably also produced different subpopulations within the Western Neolithic and in some cases we do see these peripheral "Second Neolithic" groups expanding at the expense of the "First Neolithic" peoples. This is most clear in Central Europe with the expansion of <b>Funnelbeaker</b> cultures from, probably, Denmark and nearby areas of Low Germany. In fact <b>Michelsberg</b> culture and its close relative in France <b>Seine-Oise-Marne</b> basically wipe out the first farmers of LBK (Linear Pottery) at what I usually describe as the Chalcolithic but is often described as Middle or Late Neolithic in other sources. </li>
<li>Clearly <b>Bell Beaker</b> had something to do: we see their impact in Germany, Britain and Ireland and one could argue that Cogotas I is somehow derived from the Bell Beaker of Ciempozuelos, although in this I'm going to remain neutral and a bit skeptic until more evidence shows up. </li>
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But what seems very apparent tome is that R1b-S116 should have expanded from somewhere in France, probably towards the South. And we do need better genetic studies, including archaeogenetic ones, on the Hexagon before we can jump to conclusions. France is not the most affected area by Bell Beaker, so I am cautious about attributing too much weight to only Bell Beaker and I would rather think on a complex succession of expansions associated to various cultures. </div>
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Of great interest here should be the ill-known but fascinating <b>Artenacian culture</b>, which expanded in all West France and Belgium from a core at Dordogne before the BB period and coincident with the Corded Ware expansion in Central Europe. Like Bell Beaker folk, they were adept at bowmanship but their area is not densely affected by Bell Beaker later on (although there is indeed a scatter of findings). I do wonder if somehow Bell Beaker is derived from Artenac, even if it is clearly not the same thing. Food for thought.<br />
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<b>Update (March 18): small steppe-like noise appears in diverse Iberian samples since the Late Neolithic/Chalcolithic.</b><br />
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This has arisen in the discussion below (h/t to MZ): when the supervised (forced assignment to rigid three populations) is used, the appearance of "steppe" ancestry is found here and there also before the Bronze Age. As we see above, this is not real: it does not happen in the unsupervised model at all but mere "noise" or "artifact" produced by the excessive simplicity of the three populations model.<br />
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<div style="text-align: justify;">
This does not make the three populations model "wrong": it is still approximately right but "evidence" produced ONLY from rigidly applying this model is not evidence of anything, just a hint to be confirmed or rejected via wider analysis at best. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com42tag:blogger.com,1999:blog-3023805782808412230.post-78436141148022213062018-03-17T09:35:00.001+01:002018-03-17T09:35:35.020+01:00Most interesting video-conference on Luwians, Troy and the Sea Peoples<div style="text-align: justify;">
All archaeogenetics and no archaeology makes people go mad. So let's spice this a bit with this absolutely enticing video of a conference by Dr. Eberhard Zangger, which I have watched thrice already, twice tonight alone.</div>
<br />
<div style="text-align: center;">
<iframe allow="autoplay; encrypted-media" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/1DNyA90f_aw?rel=0" width="560"></iframe><br /></div>
<br />
<br />
<div style="text-align: justify;">
I love the general outline of the exposition even if I know some details, like the outline of Lower Troy are controversial. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
I also did pose the following questions as commentary to the video:</div>
<ol style="text-align: justify;">
<li>How can the professor be so sure that all ancient Western Anatolian
nations were Luwian and not from other diverse ethnicities? How that
they were the only ones in the last Sea Peoples' wave? Just the same
we see some non-Greeks in the Greek side of the Trojan war, I would
expect some non-Luwians in the Trojan side as well, assuming the Trojans
were Luwians and not Tyrsenians or something else. </li>
<li>What about the Phrygians who show up in Anatolia, West and East
(Armenians) after the Bronze Age collapse, out of nothing (they seem to
originate in an obscure Paeonian tribe, the Bryges)? Not a single
mention of them: I guess they would blurr the nice "Luwian" homogeneity. </li>
<li>What about the Greeks (Danaoi, Denesh) and their Pelasgian (Peleset,
Philistine) neighbors and often allies (Achilles himself and his
Myrmidons were that)? They seem also involved in that late Sea Peoples
wave and there is coincidence of cultural Hellenization (and not
Luwianization) of Cyprus precisely in that period of the late Sea
Peoples' attacks against Syria, Egypt and whatever else. Let's not
forget that the Egyptians speak of the foreign peoples making a
COALITION in their "islands", and I would say that this coalition
involved peoples from all the Aegean, and not just the Asian side of it
(although very good point about Evans' racism and his horrible influence
on Aegean studies). </li>
</ol>
<div style="text-align: justify;">
But please don't let my nit-pickiness wrong what I think is a great conference dealing with a topic that has been way too neglected and even purposely ignored. There is a lot of good stuff in the video.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
By the way, this is <a href="https://en.wikipedia.org/wiki/File:Luwian_Language_de.svg" target="_blank">the Wikipedia map of Luwian inscriptions</a> (unsure of what exactly the German legend says, "early" and "late" maybe?, but it's definitely about <a href="https://en.wikipedia.org/wiki/Luwian_language" target="_blank">Luwian</a> inscriptions):</div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://upload.wikimedia.org/wikipedia/commons/thumb/3/34/Luwian_Language_de.svg/638px-Luwian_Language_de.svg.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="599" data-original-width="638" src="https://upload.wikimedia.org/wikipedia/commons/thumb/3/34/Luwian_Language_de.svg/638px-Luwian_Language_de.svg.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Credit: Hendrik Tammen (CC-license)</td></tr>
</tbody></table>
<br />
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com8tag:blogger.com,1999:blog-3023805782808412230.post-5049240807870212932018-03-16T19:55:00.001+01:002018-03-16T19:55:55.777+01:00Ancient DNA from the Balkans <div style="text-align: justify;">
This study has been for several months around but I have not discussed until now and is well worth a mention. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Ian Mathieson et al., <i>The Genomic History Of Southeastern Europe</i>. BioRXiv (pre-pub) 2017.</b> <a href="https://doi.org/10.1101/135616">doi:10.1101/135616</a></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
There is a lot of ancient autosomal DNA from the region but it basically says one thing: everything was almost exactly as expected from archaeology. The Karanovo-Gumelnita people, famed for <a href="https://forwhattheywereweare.blogspot.com/2014/01/first-ever-bronze-was-smelt-in-balcans.html" target="_blank">inventing the Bronze Age a whole millenium earlier than anyone else</a>, and nearby related cultures, were within the mainstream (Vasconic) Neolithic genetic grouping. This changed however with the kurgan invasion expressed primarily in the Ezero culture, which I've been told should be considered direct precursors of Thracians. But the change is not something radical: more genetic affinity with the steppe is visible than before and more generalized through all samples. </div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRahCFje3V6g5ibmm_8XntAJK9_63oOFg0ka93e3BhcbTAYiUDrR2NB9BD9ncy4MjwoLoEYNn_4Ys3Achr1uYqYAShf8X4SFOOtidyQaQEz72-LTspoj8dMulKxZ8KyTgo0vJgyqtRQFg/s1600/MathiesonSEEAdmixture.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="350" data-original-width="1286" height="172" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRahCFje3V6g5ibmm_8XntAJK9_63oOFg0ka93e3BhcbTAYiUDrR2NB9BD9ncy4MjwoLoEYNn_4Ys3Achr1uYqYAShf8X4SFOOtidyQaQEz72-LTspoj8dMulKxZ8KyTgo0vJgyqtRQFg/s640/MathiesonSEEAdmixture.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fig. 1-D - <i>Supervised ADMIXTURE plot, modeling each ancient individual (one per row), as a mixture of <br />populations represented by clusters containing Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green).</i> (click to expand)</td></tr>
</tbody></table>
<br />
<br />
<div style="text-align: justify;">
Well, it is not exactly <i>everything </i>what is as expected, if we consider Polish Globular Amphorae
culture, which I would have expected to be at least somewhat steppary,
Indoeuropean, already but were not. Thus it seems I have to concede on
this culture and its precursors being still part of the Vasconic
Neolithic. This makes Indoeuropean penetration into Central-North Europe
a much more sudden episode and one directly tied to Corded Ware culture
and nothing else. It must have been perceived by its victims like a
massive catastrophe, because it was a huge area which they conquered and
to a large extent colonized in a very short span of time. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Lots of R1b in Epipaleolithic Balkans </b></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
Most interesting anyhow is the huge hoard of ancient Y-DNA R1b in the Iron Gates region (Lepenski Vir) before the Neolithic. This not only demonstrates, again, that this haplogroup is Paleoeuropean, at least in part, but, quite intriguingly makes earlier findings on modern data suggesting a possible origin or R1b-M269 in or near modern Serbia (<a href="http://leherensuge.blogspot.com/2010/05/finally-some-good-research-on-r1b1b2.html" target="_blank">Morelli 2010</a> and <a href="http://leherensuge.blogspot.com/2010/08/r1b1b2a1-is-almost-unique-of-west.html" target="_blank">Myres 2010</a>) at least somewhat plausible. However none of the Iron Gates R1b is described as R1b-M269 and in some cases it is excluded that it could be this sublineage. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
Thus the issue of the ultimate origins of this key lineage remains open, but let me underline that these Iron Gate individuals belonged to the WHG grouping, as did Villabruna (so far the oldest R1b carrier kown) and that they breach this way the assumed haplogroup homogeneity I2 conceived on merely Central and Northern European samples. Just as happened with mtDNA U haplogroup homogeneity when mtDNA H was detected by several independent studies of Iberian ancient DNA. It is normal to expect more diversity towards the south for several reasons but maybe the most critical of them is just average temperature, which makes the southern lands naturally more fertile (notably so for crops domesticated in the Middle East) and easier to inhabit. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
This trend was only broken in the Middle Ages when the heavy plough allowed the improved exploitation of deep Oceanic soils, being useless in the Mediterranean region of shallow soils however. It was only then when the center of European development moved from south to north, to Belgium specifically, where it remains till present day. So let's take Southern Europe a bit seriously, please. </div>
<br />Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com6tag:blogger.com,1999:blog-3023805782808412230.post-60052176187834405872018-03-16T18:43:00.000+01:002018-03-16T18:43:02.632+01:00Ancient genomes of SE Asia<div style="text-align: justify;">
Just a quick mention because I have such a long queue of stuff from Europe that I really have no time to look but very shallowly onto this study, which looks extremely interesting. Credit for the reference to Kristiina. </div>
<br />
<div style="text-align: justify;">
<b>Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter et al., <i>Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia</i>, BioRXiv (pre-pub) 2018.</b> <a href="https://doi.org/10.1101/278374">doi:10.1101/278374</a></div>
<br />
<blockquote class="tr_bq">
<div style="text-align: justify;">
<b><span style="color: #073763;">Abstract</span></b></div>
<div style="text-align: justify;">
<span style="color: #073763;"><br /></span></div>
<div style="text-align: justify;">
<span style="color: #073763;">Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. <b>We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations.</b> We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.</span></div>
</blockquote>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1_0xQcEoN19We7JkCUpNFQKPc0u66ZZwCjhgWdZGfDg79mTrKOyXO2VwPWkVTtbFsJ3WVZxl3-jGzg6tg-EAQ8BDcZX8cG-Rkj37ekIlCOg15cuAhu5WIl1oDOLK2dQj4WyMaz9zE7OI/s1600/SEAsiamodel.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="595" data-original-width="567" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1_0xQcEoN19We7JkCUpNFQKPc0u66ZZwCjhgWdZGfDg79mTrKOyXO2VwPWkVTtbFsJ3WVZxl3-jGzg6tg-EAQ8BDcZX8cG-Rkj37ekIlCOg15cuAhu5WIl1oDOLK2dQj4WyMaz9zE7OI/s1600/SEAsiamodel.PNG" /></a></div>
<br />Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com0tag:blogger.com,1999:blog-3023805782808412230.post-58038864364702188132018-03-02T05:43:00.000+01:002018-03-02T05:43:12.373+01:00Two big issues with Olalde 2018 (Indoeuropean Bell Beaker speculation)<div style="text-align: justify;">
"Just for being published in Nature it does not mean it is necessarily wrong" (popular saying).</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Iñigo Olalde et al., <i>The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe</i>.</b> <a href="https://doi.org/10.1101/135962" target="_blank">doi:10.1101/135962</a> (pre-pub version, no way I'm spending 1/3 of my monthly income on this, in case you're willing to waste your money, it's been recently published in Nature)</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Issue 1:</b> All comparisons are made between Anatolia Neolithic or other Early Neolithic in some cases and Yamna or Corded Ware. Late Neolithic is not used nor, critically, is Hunter-Gatherer populations or anything related. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
This means that everything will be much more Yamna-like than it should, just because Yamna are 50% HG, while Early Neolithic are very low in this component. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
This is very apparent in the PCA:</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWfxotPl3WlG7P5xecQXVkph-PQuIWsJ48-nbJJOhuoJqfiYqh-WHJaWGtW55bWBItNJ1CZ-5DcimqVgJscseYohyphenhyphenLE5qjDjIdEKwWC41Ct7L6qZ05WOCKkkiA4nq0YG214Puf2d_Nwx8/s1600/olaldePCAannotated.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="576" data-original-width="397" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWfxotPl3WlG7P5xecQXVkph-PQuIWsJ48-nbJJOhuoJqfiYqh-WHJaWGtW55bWBItNJ1CZ-5DcimqVgJscseYohyphenhyphenLE5qjDjIdEKwWC41Ct7L6qZ05WOCKkkiA4nq0YG214Puf2d_Nwx8/s1600/olaldePCAannotated.png" /></a></div>
<br />
<br />
<div style="text-align: justify;">
It's junk-in: junk-out.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Issue 2:</b> there is a huge sampling gap precisely where <a href="https://forwhattheywereweare.blogspot.com/2015/05/neolithic-mtdna-from-seine-basin.html" target="_blank">ancient mtDNA</a> (and <a href="http://forwhattheywereweare.blogspot.com/2015/06/some-improved-knowledge-of-major-r1b.html" target="_blank">modern Y-DNA</a>) tells us that the origin of the modern West-Central European genetics should be: in France and nearby areas like the Basque Country, West Germany. Sure: they sample some Eastern French sites but see "issue 1" above.</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPWNqfPBF7vs4hrEFLPkgKxwYw3y26LasPCTbmQb9ODai6cMvPaLKaE7qoP-2T4WAcs38gFobUDbV3nEmKlc0LX2jZlMmnZYbC-dMF37QM18XNGev4jAPvVTiM8R8eEbbzqMqLHOafvK4/s1600/olaldegap.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="461" data-original-width="513" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPWNqfPBF7vs4hrEFLPkgKxwYw3y26LasPCTbmQb9ODai6cMvPaLKaE7qoP-2T4WAcs38gFobUDbV3nEmKlc0LX2jZlMmnZYbC-dMF37QM18XNGev4jAPvVTiM8R8eEbbzqMqLHOafvK4/s1600/olaldegap.png" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
<br />
Nuff said.Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com97tag:blogger.com,1999:blog-3023805782808412230.post-22903170144983336082018-02-21T21:17:00.000+01:002018-02-21T21:29:43.449+01:00Caribbean Taino ancient DNA still alive in admixed populations<div style="text-align: justify;">
Taino Native Americans also had a very high genetic diversity, comparable to other continental large native populations such as Andeans or Amazonians, what speaks of high mobility in the Caribbean islands before European colonization.<br />
<br />
The mitochondrial lineage B2 was sequenced, although it is today rare in the region. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Hannes Schroeder et al., <i>Origins and genetic legacies of the Caribbean Taino. PNAS 2018</i>. </b>DOI:<a href="https://doi.org/10.1073/pnas.1716839115" target="_blank">10.1073/pnas.1716839115</a></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
</div>
<blockquote class="tr_bq">
<div style="text-align: justify;">
<span style="color: #073763;">The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.</span></div>
</blockquote>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.pnas.org/content/pnas/early/2018/02/13/1716839115/F2.large.jpg?width=800&height=600&carousel=1" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.pnas.org/content/pnas/early/2018/02/13/1716839115/F2.large.jpg?width=800&height=600&carousel=1" data-original-height="747" data-original-width="800" height="371" width="400" /></a></td></tr>
<tr align="justify"><td class="tr-caption"><span style="color: #073763;"><b><span class="fig-label">Fig. 2.</span></b></span><br />
<div class="first-child" id="p-15">
<span style="color: #073763;">Taino demography. Total estimated length of genomic ROH for the Taino and the Clovis genome (<a class="xref-bibr" href="http://www.pnas.org/content/early/2018/02/13/1716839115#ref-13" id="xref-ref-13-4">13</a>) and selected Native American and Siberian genomes (<a class="xref-bibr" href="http://www.pnas.org/content/early/2018/02/13/1716839115#ref-15" id="xref-ref-15-3">15</a>, <a class="xref-bibr" href="http://www.pnas.org/content/early/2018/02/13/1716839115#ref-31" id="xref-ref-31-2">31</a>, <a class="xref-bibr" href="http://www.pnas.org/content/early/2018/02/13/1716839115#ref-32" id="xref-ref-32-2">32</a>)
in a series of length categories. ROH distributions for modern
individuals have been condensed into population-level silhouettes (<a class="in-nw" href="http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1716839115/-/DCSupplemental"><i>SI Appendix</i>, section 14</a>).</span></div>
</td></tr>
</tbody></table>
<br />Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com0tag:blogger.com,1999:blog-3023805782808412230.post-8616960536665656522018-02-17T00:11:00.001+01:002018-02-17T00:11:58.766+01:00Ironworks the Iron Age style: the true thing done again by Burkinabe elders for the sake of historical document<div style="text-align: justify;">
This is a truly fascinating film, made by the people of Burkina Faso documenting their own, now vanishing tradition of iron smelting and forging, done again for the sake of historical documentation by the elders who used to do it decades ago (and some youngsters helping too) reproducing all the steps: from charcoal making and iron ore mining and selection, to the construction of the furnaces, the smelting of ore and finally tool-making itself. I cannot recommend it more wholeheartedly:</div>
<br />
<div style="text-align: center;">
<br /><iframe allow="autoplay; encrypted-media" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/ereJcjDAKLM?rel=0" width="560"></iframe></div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com2tag:blogger.com,1999:blog-3023805782808412230.post-42108933753364253172018-02-17T00:02:00.000+01:002018-02-17T00:02:14.283+01:00Obsidian exchange in Neolithic Sicily and Sardinia (video)<div style="text-align: justify;">
Thanks to <i>Theasparagus </i>for noticing this quite interesting video-lesson on quite obviously seagoing peoples of the Central Mediterranean and their journeys to distant volcanic islands to obtain the valuable obsidian (sharper than a scalpel) and also to the mainland to trade it for whatever goods.</div>
<br />
<div style="text-align: center;">
<br /><iframe allow="autoplay; encrypted-media" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/5f4IdasDkK8?rel=0" width="560"></iframe></div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com2tag:blogger.com,1999:blog-3023805782808412230.post-82236846302766123602018-02-14T00:15:00.000+01:002018-02-14T00:15:51.114+01:00Dystruct versus Admixture<div style="text-align: justify;">
Not really able yet to discern if this is an alternative way ahead for autosomal archaeogenetics or just another dead end. But it does seem interesting enough to mention here in any case.<br />
<br />
It may be very important in the deciphering of the so-called "ANE" ghostly genetic influence.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b>Tyler A. Joseph & Itsik Pe'er. <i>Inference of population structure from ancient DNA.</i> bioRXiv 2018 (pre-pub). <a href="https://doi.org/10.1101/261131" target="_blank">DOI:10.1101/261131</a></b> </div>
<br />
<div style="text-align: justify;">
<blockquote class="tr_bq">
<span style="font-size: x-small;"><span style="color: #073763;">Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.</span></span></blockquote>
</div>
<br />
<br />
<div style="text-align: justify;">
Still digesting this one but I do find very intriguing that they claim that Dystruct has much less <i>time-entropy</i> than ADMIXTURE (i.e. the relation between ancient and modern populations seems to be better identified) and that, using this method they get that the Samara (proto-Indoeuropean) population becomes much more clearly related to Kostenki-14 (a Gravettian hunter-gatherer from the Don area) and that the Paleo-Siberian "ANE" individuals form then their own distinct cluster with very limited impact in Europe (but much larger in parts of Asia (not labeled: South Asia?). This Kostenki-Samara "orange" component keeps influencing Western Indoeuropeans (Corded Ware, Unetice) but at markedly decreasing frequencies of "purity". </div>
<div style="text-align: justify;">
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However the first admixture of Corded Ware is not with earlier farmers (mostly "green") but with some sort of late "hunter-gatherer" population ("brown" or "maroon" component. Only after the backlash of Bell Beaker, which in Central Europe appears as a mix of Neolithic peoples, Indoeuropeans and maybe even more of that mysterious extra HG element, we see some "return of the farmers", which clearly persists in Unetice.</div>
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In general, modern Europeans are (fig.5a, not shown here) quite "greener" than Unetice and some populations (I'm guessing Sardinians and Basques, no labels provided) have zero "orange" (IE) component, which ranges (my visual estimate) between 9% and 27% otherwise.</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9GZhZnIV_dzaCgAW-ZWwbanLphjJ9fNm2fDfh4XMTivdjme7YJR7HHlYAtT4awnil_5kZss0ifiJmyU-B-3xlq5UnD3HFv_mI3Ri8Bq4u022SslssHmGvZswr7XYJ60YjYirti0AQDJ4/s1600/DystructAncients.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="597" data-original-width="1085" height="352" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9GZhZnIV_dzaCgAW-ZWwbanLphjJ9fNm2fDfh4XMTivdjme7YJR7HHlYAtT4awnil_5kZss0ifiJmyU-B-3xlq5UnD3HFv_mI3Ri8Bq4u022SslssHmGvZswr7XYJ60YjYirti0AQDJ4/s640/DystructAncients.png" width="640" /></a></td></tr>
<tr align="justify"><td class="tr-caption" style="text-align: center;">Fig.5-b (click to expand): Ancestry estimates for 92 ancient samples. The three leftmost samples are the Pleistocene hunter-gatherers. In Dystruct, late Neolithic samples and beyond present as a mixture of hunter-gatherers, Yamnaya steppe herders,and early Neolithic samples, matching supported historical migrations of steppe herders into Eastern and Western Europe.</td></tr>
</tbody></table>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com7tag:blogger.com,1999:blog-3023805782808412230.post-69038226694231989802018-02-13T23:34:00.001+01:002018-02-14T00:16:41.218+01:00Scandinavian hunter-gatherers had double west-east origins<div style="text-align: justify;">
SHG origins' mystery solved? What about possible Norwegian "EHG-like" genetic influences into Atlantic Europe?</div>
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<b>Torsten Günther, Helena Malmström, Emma Svensson, Ayça Omrak et al. <i>Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation</i>. bioRXiv 2017 (pre-pub). <a href="https://doi.org/10.1101/164400" target="_blank">DOI:10.1101/164400</a></b></div>
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<blockquote class="tr_bq">
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<span style="color: #073763;">Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans.</span></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="height: 529px; margin-left: auto; margin-right: auto; text-align: center; width: 442px;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAQMaALGILXGivtPAxMW01A-XDHZITtBvyHSGLnzKSVpgzqYhF2mUdRh-tbUQWvnXPaiO3ubdor_hJpCsY-bvl4ESwxr49_MOlrtk_DyaQpLHnKfxyoRAwmW1iKeW0S-LscJWLzF9BmhY/s1600/Scandinavia.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="314" data-original-width="286" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAQMaALGILXGivtPAxMW01A-XDHZITtBvyHSGLnzKSVpgzqYhF2mUdRh-tbUQWvnXPaiO3ubdor_hJpCsY-bvl4ESwxr49_MOlrtk_DyaQpLHnKfxyoRAwmW1iKeW0S-LscJWLzF9BmhY/s400/Scandinavia.png" width="363" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fig. 1:<br />
<div style="text-align: justify;">
Mesolithic samples and their genetic affinities – (A) Map of the Mesolithic European samples used in this study. The pie charts show the model-based [16,17] estimates of genetic ancestry for each SHG individual. The map also displays the ice sheet covering Scandinavia 10,000 BP (most credible (solid line) and maximum extend (dashed line) following [10]). Newly sequenced sites are shown in bold and italics, SF11 is excluded from this map due to its low coverage (0.1x). Additional European EHG and WHG individuals used in this study derive from sites outside this map (...)</div>
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Intriguingly, Swedish Epipaleolithic peoples (SHG) have the light skin variant in the gene SLC45A2, variant that is now uniformly spread through all Europe and accounts for 15% of the skin color variance in <a href="https://forwhattheywereweare.blogspot.com/2013/04/eye-and-skin-pigmentation-genetics-cape.html" target="_blank">a key Cape Verde study</a> and that was so far attributed solely (or almost solely) to Neolithic farmers (among which it was fixated and who had indeed a very large genetic impact in the European subcontinent). They also have the blue eyes allele, as Western Hunter-Gatherers did. However, if we are to follow, Günther's explanations in <a href="https://tgnthr.wordpress.com/2017/10/19/genomics-of-mesolithic-scandinavians-on-youtube/" target="_blank">this video</a>, the variance of looks in Epipaleolithic Scandinavia was greater than in present day. </div>
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PS- Legend says that when my namesake Fray Luis de León returned to his classroom after five years imprisoned by the Inquisition, he began his class with these words: "As we were saying yesterday..."</div>
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Expect less lengthy articles because I really want to use this blog as open notebook, and not spend so much time following news and dissecting them thoroughly, so my style may become a bit more telegraphic. </div>
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I also don't know for how long I will be able to continue blogging, as my personal economic situation is bad and worsening and you never know when police may come and arrest you for saying "fuck the king" or whatever other quite reasonable opinion. We live very troubled times and I'm personally quite bad at <i>winning</i>. </div>
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<div style="text-align: justify;">
Also my apologies in advance if I fail to quickly approve comments. I usually check my email once per day or so but sometimes I just forget. Please, be patient if that happens: I only censor fascism, racism, sexism and homophobia (and those individuals who have managed to really get on my nerves, and they know who they are). Sadly I have to keep pre-moderating all comments, else the lonely troll will get away with his abuses.</div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com3tag:blogger.com,1999:blog-3023805782808412230.post-59540845032202773502017-02-04T09:39:00.001+01:002017-02-04T09:39:31.107+01:00The patrilineage R1b-DF27 in North Iberia<div style="text-align: justify;">
Just weeks ago a new study on Northern Iberian Y-DNA, focused specifically on R1b-DF27, was published. It covers Asturias, Cantabria, Basque Country and Aragon, finding greater diversity in the Basque Country and Cantabria and lower in Aragon and Asturias.</div>
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<div style="text-align: justify;">
<b>Patricia Villaescusa et al., <i>Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain</i>. FSI-Genetics 2017. <span style="color: red;">Pay per view</span> → <a href="http://dx.doi.org/10.1016/j.fsigen.2016.12.013" target="_blank">LINK</a></b> [doi:10.1016/j.fsigen.2016.12.013]</div>
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<blockquote class="tr_bq">
<b><span style="color: #073763;">Abstract</span></b><br />
<span style="color: #073763;"><br /></span>
<span style="color: #073763;">The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27. Our results reveal frequencies over 35% of DF27 haplogroup in the four North Iberian populations analyzed and high frequencies for its subhaplogroups. Considering the low frequency of DF27 and its sublineages in most populations outside of the Iberian Peninsula, this haplogroup seems to have geographical significance; thus, indicating a possible Iberian patrilineal origin of vestiges bearing this haplogroup. The dataset presented here contributes with new data to better understand the complex genetic variability of the Y chromosome in the Iberian Peninsula, that can be applied in Forensic Genetics.</span></blockquote>
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The study, quite conveniently, differentiates between "native Basques" (those whose patrilineal ancestors lived in the Basque Country for at least the last three generations) and "resident Basques" (those whose recent patrilineal ancestors immigrated, mostly from NW Iberia).</div>
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R1b-DF27 is one of four major R1b sublineages in Western Europe and one of the three "brothers" that can be tracked to an origin somewhere in what is now Southern France, most likely, i.e. together they form part of R1b-S116. The fourth lineage would be, naturally, R1b-U106, "brother" of S116 and found typically around the North Sea. It is the one with the southernmost distribution, being very dominant in Iberia and among Basques. Probably it is also important in all the south of modern France but clear data is missing as of now.</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzsJ8O6O-50zJBGk4fHOJV1WDgJloxCS7wB0SibQeuATUKQaY6SYdLeLQW119DbxPlG2GLTRB4k-Ck-E9QEj_dP3dQIi0Q85wktra9lOMfKC3NGAnrUuk8490OtTFtbhcah-8yLrXuaxY/s1600/EuropeanR1b.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzsJ8O6O-50zJBGk4fHOJV1WDgJloxCS7wB0SibQeuATUKQaY6SYdLeLQW119DbxPlG2GLTRB4k-Ck-E9QEj_dP3dQIi0Q85wktra9lOMfKC3NGAnrUuk8490OtTFtbhcah-8yLrXuaxY/s1600/EuropeanR1b.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Reconstructed spread of R1b to Western Europe and within it (dates objectively unknown so far, own work)</td></tr>
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This is the key data table of the study, showing the frequency of the various sublineages of R1b-DF27 ("*" means "others", so "DF27", without asterisk, means "all DF27" and "DF27*" means instead "remaining DF27 after exclusion of the other mentioned subclades")<i><b>:</b></i></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiceMxiszjmCnmI7gB2cCfpxCZFQ3CyxdtnzFMFbcfnMDN-v8JYvucwk5sSmsxOAYTKnPqw2qJIdMSjBUZJp9Df92r2Wo5PnTTQCpiAmXo3lNvmQfOrAAvVbtpC-WZC0keJrOUOtgmgk8g/s1600/Villaescusa-table1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="119" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiceMxiszjmCnmI7gB2cCfpxCZFQ3CyxdtnzFMFbcfnMDN-v8JYvucwk5sSmsxOAYTKnPqw2qJIdMSjBUZJp9Df92r2Wo5PnTTQCpiAmXo3lNvmQfOrAAvVbtpC-WZC0keJrOUOtgmgk8g/s640/Villaescusa-table1.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Click to expand (frequencies are absolute, relative to whole sample)</td></tr>
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It is also worth sticking this other graph, which shows (top right) the (SNP-based) true phylogeny of the haplogroup R1b-DF27 and, complementarily, the (somewhat messy) haplotype structure based on a limited number of short tandem repeats (STR), in which only Z220 appears clearly defined:</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdDY49aTflMnauv8LGqbJSlFzLSmpa-1D9Kl7ugdM-OaubHAgQeYsOswaI5rHx-aCP_HDrgALsnCIgQd9NgGJ6-6S-e_LvhXRx3KuQSHoUFJsAWzD5-VfXj9xRxI6LF7dz_Li8XoxS2xM/s1600/Villaescusa-fig3.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="408" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdDY49aTflMnauv8LGqbJSlFzLSmpa-1D9Kl7ugdM-OaubHAgQeYsOswaI5rHx-aCP_HDrgALsnCIgQd9NgGJ6-6S-e_LvhXRx3KuQSHoUFJsAWzD5-VfXj9xRxI6LF7dz_Li8XoxS2xM/s640/Villaescusa-fig3.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Click to expand</td></tr>
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The study is very limited in its scope but it does show that there is a very high diversity for this lineage among Basques. This however does not necessarily indicate that Basques are the direct origin: much more data from the rest of Iberia and very especially from France is required before we can jump to any conclusion. Based on the limited data we have, I am of the opinion that the lineage did not originate in Iberia most likely but rather in what is now Southern France, migrating southwards via the two natural corridors: the Basque Country and Catalonia. </div>
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Sadly enough we just do not have enough modern data, much less ancient one, in order to issue a definitive judgment on the matter. However the overall pattern of distribution of R1b-S116 strongly suggest a "Southern French" origin, not just for "Iberian" DF27 but also for the other two "brother" lineages: "Alpine" U152 and "North Atlantic" M529. </div>
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The big question is how and when did this expansion took place. A "South French" origin was much easier to explain when the Paleolithic continuity model seemed reasonable, however recent ancient DNA findings strongly suggest that the Neolithic and Chalcolithic saw major population changes in much of Europe until stabilization was achieved -- exact patterns vary on specific regions: in some cases this does not happen until the Bronze Age, in others, like the Basque Country and quite possibly the Atlantic parts of France, it may have happened much earlier, even as soon as the early Neolithic. </div>
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So my best recipe for an explanation is that we have to look very carefully at what happened in Western Europe, particularly towards the Atlantic Ocean in that "transitional" period, when not just large cultural phenomena like Dolmenic Megalithism or later also Bell Beaker manifested in quite expansive and dynamic manner but also a dearth of smaller cultures were the actual social or ethnic pieces making them possible. For example it is plausible that Michelsberg culture (originating in Lower Rhineland apparently and swiftly replacing the early Neolithic LBK culture in Germany, North France and nearby areas) could be involved in the expansion southwards of R1b-U106 and other traits of the modern genetic pools we observe. Another culture well worth taking a look at is the Artenac culture, which expanded from Dordogne towards the North up to Belgium soon after the Michelsberg/SOM era. Rather than one single and sudden expansion of a well defined population, it seems to me that we are before a jigsaw puzzle of several cultures and several chronologies, related maybe but not exactly the same. </div>
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See also:<br />
<ul>
<li><div class="post-title entry-title" itemprop="name">
<i><a href="http://forwhattheywereweare.blogspot.com/2015/06/some-improved-knowledge-of-major-r1b.html" target="_blank">Some improved knowledge of major R1b sublineage S116</a></i></div>
</li>
<li><div class="post-title entry-title" itemprop="name">
<i><a href="http://forwhattheywereweare.blogspot.com/2016/01/basque-r1b-df27.html" target="_blank">Basque R1b-DF27</a></i></div>
</li>
<li><div class="post-title entry-title" itemprop="name">
<i><a href="http://forwhattheywereweare.blogspot.com/2012/03/basque-and-gascon-y-dna-survey.html" target="_blank">Basque and Gascon Y-DNA survey</a></i> (DF27 was not yet described but the imprecise data is still quite suggestive of its strong presence among Gascons, sublineage Z196 was reported anyhow)</div>
</li>
</ul>
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Thanks once again to Jean Lohizun.Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com77tag:blogger.com,1999:blog-3023805782808412230.post-79165470208545812412017-01-09T23:43:00.001+01:002017-01-09T23:43:13.120+01:00Extensive ancient Iberian mtDNA analysis<div style="text-align: justify;">
A very interesting thesis on Iberian ancient mitochondrial DNA is available (found via <a href="https://bellbeakerblogger.blogspot.com/2016/12/once-upon-time-in-west-dna-roth-2016.html" target="_blank">Bell Beaker Blogger</a>):</div>
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<b>Christina Roth, <i>Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula</i>. University of Mainz (thesis), 2016. <span style="color: #38761d;">Freely available</span> → <a href="https://publications.ub.uni-mainz.de/theses/frontdoor.php?source_opus=100000815&la=en" target="_blank">LINK</a></b></div>
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As all theses, it is very extensive, and I can only make some comments here (space and time are always too limited, you know), hoping to grasp the most interesting aspects of it.</div>
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First of all Roth finds that Iberian hunter-gatherers (HGW in the paper) were not quite like Central European ones (HGC), at least not in the mtDNA. Instead, in this aspect the Central European hunter-gatherers were closer to Eastern European ones (HGE), as well as to the Pitted Ware late subneolithic population of Gotland.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi3MyIvboUvm_-HYcuDpfhBFZQ2YI2Kpz3luulNs-6DWrxXQJoVpctaUmrkesK12L-SEEm6YzGU6mGJt8hFLPU55GGGNlSOR2m5uiqLYhsnXj70FmJZOV4kuaIGczM1C0xTl7ZdbTiu3-E/s1600/map-HGs-haplogroups.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="449" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi3MyIvboUvm_-HYcuDpfhBFZQ2YI2Kpz3luulNs-6DWrxXQJoVpctaUmrkesK12L-SEEm6YzGU6mGJt8hFLPU55GGGNlSOR2m5uiqLYhsnXj70FmJZOV4kuaIGczM1C0xTl7ZdbTiu3-E/s640/map-HGs-haplogroups.png" width="640" /></a></div>
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<br />
<h3>
<b>Iberia-only mtDNA analysis</b></h3>
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<div style="text-align: justify;">
This will be a recurrent issue along the analysis she makes. But let's focus on Iberia by the moment. Notice that she does not just use her own data but also from many other sources, including some unpublished materials, this makes a bit difficult to follow all the details, so I feel I can only focus on the statistical analysis she makes and which is the core of the thesis.</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjL1KMQPaO21Pg7bXWgMsPnJ4yKT3-sYJIz6wjFqFr6N60WuGvzXFIlLg9T1PhUf_WKgGNjwdUI0mBNJJVZExnYjF0VzpvYxGwSde521-uoyH9EqszwmCGCFMf1k_m5-pcT_A9qu8pZayE/s1600/PCA-annotated.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="428" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjL1KMQPaO21Pg7bXWgMsPnJ4yKT3-sYJIz6wjFqFr6N60WuGvzXFIlLg9T1PhUf_WKgGNjwdUI0mBNJJVZExnYjF0VzpvYxGwSde521-uoyH9EqszwmCGCFMf1k_m5-pcT_A9qu8pZayE/s640/PCA-annotated.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Annotated by me, because I found the abbreviations quite hard to follow</td></tr>
</tbody></table>
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The general overview is confirmed, with minor variations, in the cluster analysis (which I also took the liberty of annotating, but take my notes for what they are: mere scribbling on the margin in an attempt to better understand the data, nothing else):</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtlMCKlvoVJNOwN4bqqn0NlESuX6dRrMjhF6h5LiyKhzPk4PtPPWSvYr7E3BRcLIIVQnectoqfuVeS1f2DS6n9je6yW4l2R5CtYRc_U0I3W4JJKr7Kvh-ltKInPMt8rlQp-Ck2-GXU10E/s1600/clusters-fig17-annotated.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="346" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtlMCKlvoVJNOwN4bqqn0NlESuX6dRrMjhF6h5LiyKhzPk4PtPPWSvYr7E3BRcLIIVQnectoqfuVeS1f2DS6n9je6yW4l2R5CtYRc_U0I3W4JJKr7Kvh-ltKInPMt8rlQp-Ck2-GXU10E/s640/clusters-fig17-annotated.png" width="640" /></a></div>
<span id="goog_1169461091"></span><span id="goog_1169461092"></span><br />
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Particular care not to take the arrows of my notes too seriously: they are just conceptual, a very loose sequencing of the available data for a very tentative visualization of it. If it helps you, cool, else ignore please.</div>
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In any case, it seems clear cluster 2 is more influenced by hunter-gatherer genetics and that, with the data available in this study, we reach the end of the timeline within it in the following regions: Upper Ebro and Basque Country (data up to Late Neolithic but see <a href="http://forwhattheywereweare.blogspot.com/2013/09/basque-and-other-european-origins.html" target="_blank">my own 2013 compilation for a longer period</a>), Southern Iberia (up to Chalcolithic) Southeast and Northeast, this one after originally being in the "more Neolithic" cluster 1 (in fact the author does argue for Catalonia as main "gate" for Neolithic genetics into Iberia on light of the available data, which does not include another important "gate", the SE one, for lack of data for the early period). </div>
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Inversely, cluster 1 is more influenced by "farmer" genetics, first detected in the Northeast (Catalonia and nearby areas of Aragon) but then also affecting the Northern Plateau and the West (Central Portugal). This last is very important because it is here where a key civilizational hub, the oldest known civilization of the Atlantic shores, emerged in the Chalcolithic, playing a key role in the wider Megalithic and Bell Beaker phenomena. I have at times speculated that it might be the origin of "modernity" in Western European genetic pools but on light of this data I have to recant, the origin should be elsewhere, probably in/around what is now France (and therefore it's not likely to be directly related to Bell Beaker, except maybe in the islands, but rather to Michelsberg/SOM, Artenacian and such -- always in wait of more data, just a cautious hypothesis). </div>
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Finally the farmer-leaning cluster reaches the Southern Plateau, near Madrid, what suggests a N→S move of the then-forming Cogotas I herder culture, rather than the opposite. </div>
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What we do see is not inconsistent with modern Iberian genetics anyhow: while Central Europe seem to have seen an increase of "hunter-gatherer" genetics along time, in Iberia the main tendency is the opposite: an increase of "farmer" genetics and further dilution of the aboriginal genetic pool. There is however at least one clear exception in the Northeast and that is also consistent with modern Iberian genetics. Some regions (south, southeast and the totally unknown northwest) have only fragmentary sequences here, so unclear, although the final tendency, up to the Bronze Age, is to cluster 2b (i.e. mixed but rather tending to "hunter-gatherer" genetics).</div>
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To finish with the Iberia-only bloc, notice that these are the lineages found among early Iberian farmers by region (in color those haplogroups associated to the arrival of Neolithic per the available data):</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHgJIqhJpEjyUyjHjBoUAPg03JPz2aZ0ciYMhX3ki1beJk6cqGQBySfpCBBEcd1fj1FMutyr86i9z9jddqea80f0H7pU5cjl7Ae4XFTTX0fzEh_kFi2LZpm12vJ_fRzdcuMW5LKWhgzno/s1600/map-ENeo-Hgs.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="464" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHgJIqhJpEjyUyjHjBoUAPg03JPz2aZ0ciYMhX3ki1beJk6cqGQBySfpCBBEcd1fj1FMutyr86i9z9jddqea80f0H7pU5cjl7Ae4XFTTX0fzEh_kFi2LZpm12vJ_fRzdcuMW5LKWhgzno/s640/map-ENeo-Hgs.png" width="640" /></a></div>
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Notice how the pool in the Northern region is quite modern-like, not yet exactly as it is locally today but it would pass quite unnoticed in a map of Europe.</div>
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<h3>
<b>Iberia and the rest of Europe</b></h3>
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What about the pan-European context (with the usual huge blanks in France, Britain, etc.)? Quite interesting as well:</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRJw6klBhpwTJPY6alb-uXyCcPTzLA2nGq2dtQKKi7pv80vZcVpJyM0cHSCM0s_w2C-v8oI2YTv3CMQwN4O3wDQwNKyW3GiUNeUKjxupzlS9-_Ixq1GKD5PzrNlEe-sCcCN_5UdDXiDIw/s1600/PCA-Europe-annotated.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="430" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRJw6klBhpwTJPY6alb-uXyCcPTzLA2nGq2dtQKKi7pv80vZcVpJyM0cHSCM0s_w2C-v8oI2YTv3CMQwN4O3wDQwNKyW3GiUNeUKjxupzlS9-_Ixq1GKD5PzrNlEe-sCcCN_5UdDXiDIw/s640/PCA-Europe-annotated.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Annotated by Maju on fig. 23 (click to enlarge)</td></tr>
</tbody></table>
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As mentioned before, the Iberian hunter gatherers (HGW) appear clearly distinct from their Central and Eastern cousins in the mtDNA analysis. And with all this Iberian dataset it becomes apparent that there seem to be two "zones of admixture": one for Iberians and another for Central Europeans, the difference being on which aborigines they mix with. </div>
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Notice that it is not possible to differentiate here between local Central European and intrusive Eastern European admixture, as both aboriginal hunter-gatherer populations appear closely related in all analyses (maybe an artifact of the sampling strategy or maybe actually relevant, can't say). </div>
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It also caught my eye that a German site (Blätterhöhle, Westfalia, famed because farmer and hunter-gatherers living side by side were located there some years ago), clusters intensely with Iberian hunter-gatherers and related populations. I have to research more on this matter (which I had ignored so far) but I suspect it may be very relevant, because we could get an even longer <i>chain</i> of early "modern" mtDNA pools, adding this site to Paternabidea (Navarre) and Gurgy (Burgundy), spanning a long stretch of Western Europe, an area quite neglected by archaeogenetics so far, it must be said.</div>
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It is also worth mentioning that UC (which I believe stands for Unetice
Culture) pulls the "Central European zone of admixture" in the PCA
downwards, with a polarity of its own, a polarity that should probably
be considered as specifically Indoeuropean. </div>
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The cluster analysis confirms much of what I just said above, not annotated for a change:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmNv8E1HeVvkk1aoeoPq5G8yW_osFxNc9spV53Q5b2WkfWRGF8rINgz_f_aqia2EU2m5u9s3F34WjbyL7SkH-clQAD44ugcHrtO8kTHD4PHGcwvg0qEYGBTCbd3j9S5a4qUQX-laA35oI/s1600/Europe-clusters.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="378" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmNv8E1HeVvkk1aoeoPq5G8yW_osFxNc9spV53Q5b2WkfWRGF8rINgz_f_aqia2EU2m5u9s3F34WjbyL7SkH-clQAD44ugcHrtO8kTHD4PHGcwvg0qEYGBTCbd3j9S5a4qUQX-laA35oI/s640/Europe-clusters.png" width="640" /></a></div>
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We see very clearly here a larger cluster more influenced by "farmer" genetics and a smaller one that includes all pre-Neolithic aborigines, plus two populations already post-Neolithic but clearly identifiable as at least largely aboriginal (PWC and BLA), plus a subcluster of Neolithic Iberians, from the North (NSE and EVN) and the West (CPE). </div>
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The author notices that: <span style="color: #073763;"><i>Bernburg (BEC) and Funnel Beaker (FBC) samples (...) show almost no significant differences to any Iberian group, except to the Early Neolithic of Northern Spain (NSE) and Chalcolithic of East Spain (ESC)</i></span>. Hard to interpret but worth noticing, no doubt. </div>
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And there is a lot more in the thesis but I can only review so much, so take a look and tell me and the World if I'm missing something of relevance or you feel I'm misinterpreting something or whatever. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com23tag:blogger.com,1999:blog-3023805782808412230.post-16052236885056915872017-01-01T23:17:00.001+01:002017-01-01T23:17:24.656+01:00Chad's Eurasian genetic input similar to that in Ethiopia<div style="text-align: right;">
<span style="color: #cc0000;"><i>Quickies</i></span></div>
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<b>Marc Haber et al. <i>Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations</i>. AJHG 2016. <span style="color: #3d85c6;">Open access</span> → <a href="http://dx.doi.org/10.1016/j.ajhg.2016.10.012" target="_blank">LINK</a></b><span style="font-size: x-small;"> [doi:10.1016/j.ajhg.2016.10.012]</span><br />
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<blockquote class="tr_bq">
<b><span style="color: #073763;">Summary</span></b><br />
<span style="color: #073763;"><br /></span>
<span style="color: #073763;">Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.</span></blockquote>
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Worth a read no doubt but careful, careful, careful with their chronological guesstimates. Their starting point is the assumption (once and again demonstrated all kinds of WRONG) of:</div>
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Eurasians and Africans diverged around 60,000–80,000 ya and subsequently had different patterns of population-size changes: in particular, compared with Africans, the Eurasian population experienced a sharp decrease in size ∼60,000 ya.</div>
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So add around 65-70% (x1.7) to all dates, else you are bound to fall in the pit of molecular-clock-o-logical self-complacent pseudoscience. So where it reads c. 6-7 Ka for the first migration (R1b-related), it should be 10,000 years ago (which is the actual dating of Afroasiatic expansion by most accounts, with origin not exactly in "Eurasia" but rather in or near Sudan, where those Eurasian lineages, R1b and J1, had since long before most likely), and when they say 3 Ka ago, it's probably 5000 years ago, within the context of Neolithic inflows possibly: 3000 years ago was already well into Ancient Egypt and peoples just did not cross it without proper paperwork anymore, actually 3000 years ago is the Bronze Age collapse and Egypt, Lower Egypt specifically, fell to Africans, to Libyans and other Berbers known as Meshwesh (Amazigh, probably from modern Tunisia) to be precise. </div>
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Dr. Haber: time to update your clock, it just doesn't work, and you are confusing people to no avail. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com37tag:blogger.com,1999:blog-3023805782808412230.post-22793283393210971232017-01-01T18:46:00.000+01:002017-01-01T18:46:21.409+01:00Forests burnt in Ice Age Europe<div style="text-align: right;">
<span style="color: #cc0000;"><i>Quickies</i></span></div>
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<b>Jed O. Kaplan et al., <i>Large Scale Anthropogenic Reduction of Forest Cover in Last Glacial Maximum Europe</i>. PLoS ONE 2016. <span style="color: #0b5394;">Open access</span> → <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166726" target="_blank">LINK</a></b> [doi:10.1371/journal.pone.0166726]</div>
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<blockquote class="tr_bq">
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<span style="color: #073763;"><b>Abstract</b></span></div>
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<span style="color: #073763;"><br />
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<span style="color: #073763;">Reconstructions of the vegetation of Europe during the Last Glacial Maximum (LGM) are an enigma. Pollen-based analyses have suggested that Europe was largely covered by steppe and tundra, and forests persisted only in small refugia. Climate-vegetation model simulations on the other hand have consistently suggested that broad areas of Europe would have been suitable for forest, even in the depths of the last glaciation. Here we reconcile models with data by demonstrating that the highly mobile groups of hunter-gatherers that inhabited Europe at the LGM could have substantially reduced forest cover through the ignition of wildfires. Similar to hunter-gatherers of the more recent past, <b>Upper Paleolithic humans were masters of the use of fire, and preferred inhabiting semi-open landscapes to facilitate foraging, hunting and travel</b>. Incorporating human agency into a dynamic vegetation-fire model and simulating forest cover shows that even small increases in wildfire frequency over natural background levels resulted in <b>large changes in the forested area of Europe</b>, in part because trees were already stressed by low atmospheric CO2 concentrations and the cold, dry, and highly variable climate. <b>Our results suggest that the impact of humans on the glacial landscape of Europe may be one of the earliest large-scale anthropogenic modifications of the earth system</b>.</span></div>
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Not sure what to think, really. In any case the data they manage and share with us is very much worth taking a look at. <br />
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<br />Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com1tag:blogger.com,1999:blog-3023805782808412230.post-83140133750947307172017-01-01T18:26:00.001+01:002017-01-01T18:26:46.591+01:00Reconstructing Sardinian population history<div style="text-align: justify;">
A very interesting pre-pub study, dealing with Sardinian genetics in great sub-national detail but also within the wider European and Mediterranean context, became available in the last weeks. I won't probably be able to make justice to it here, so please take a look yourselves.</div>
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<b>Charleston W.K. Chiang et al., <i>Population history of the Sardinian people inferred from whole-genome sequencing</i>. BioRXiv 2016. <span style="color: #3d85c6;">Open access pre-pub</span> → <a href="http://biorxiv.org/content/early/2016/12/07/092148" target="_blank">LINK</a></b> [doi:10.1101/092148]</div>
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<blockquote class="tr_bq">
<b><span style="color: #073763;">Abstract</span></b><br />
<span style="color: #073763;"><br /></span>
<div style="text-align: justify;">
<span style="color: #073763;">The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find <b>the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations.</b> <b>Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. </b>These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.</span></div>
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The authors call to some question the extreme simplicity of the three populations model of Lazaridis and subsequent studies. They do not flatly reject it but it seems that the lack of nuance bothers them a lot, as it does to me. This is quite clear when they find once and again Sardinian-Basque lines of relationship without going through Italian, Spaniard or French intermediaries, also when they face the issue of the largest Y-DNA haplogroups in the island, I2a1a (M26, almost exclusively a Sardinian and Pyrenean haplogroup) and R1b1a2 (M269), which are not typically associated with Neolithic farmers, suggesting that there is more to Neolithic settlement than meets the eye in the too simplistic three populations' model. They even seem to consider if Paleolithic peoples from Sardinia itself or maybe some other locations contributed heavily to what they feel is a sex-biased genetic pool. </div>
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They do confirm that Sardinians have both strong "Neolithic" (Stuttgart) and "Paleolithic" (Lochsbour) ancestry and no (negative even) "Steppe" (Yamnaya) one, although this last is truer for the most isolated sub-populations than for the more cosmopolitan ones. </div>
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They also estimate that Sardinians have been generally isolated from the rest of Europeans for some 330 generations, what reads as approx. 9900 years, i.e. since the very early Neolithic settlement of the island. We would actually have to reduce that time span a bit but within reason, else it becomes Epipaleolithic in fact, what is most unlikely. Alternatively, as the main comparison is Northern Europe, this date could refer to the branching out of Painted-Linear (continental) and Impressed-Cardium (maritime) Neolithic cultures in the Aegean or the Balcans. </div>
Majuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.com0