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Ancient Egyptian DNA from 1300BC to 426 AD
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[QUOTE]Originally posted by Doug M: [QB] [QUOTE]Originally posted by Swenet: [qb] Doug, I know you want to talk about your 22ky old "farmers" that don't exist. But (pre)dynastic Egyptians had [URL=http://s10.postimg.org/w4jqr4ig9/24_5_2014_22_22_45.png]this purple component you keep running away from[/URL]. Care to explain what it is without running away? [/qb][/QUOTE]So just say you don't agree that the folks of Wadi Kubbaniya were proto farmers then. I can't comment on some snippet of something without the report or study it originates from. And again, I don't have a PROBLEM with some "Eurasian" DNA being in Africa at any time period. The issue I have is with it being called EEF. As posted, they are lumping together a whole bunch of different DNA lineages together as EEF. They are inconsistent in that definition across various authors. I prefer to call it Eurasian. Period. Technically the populations in the Levantine region and Anatolia aren't "EEF". EEF is a reference to the DOWNSTREAM populations in Europe who are a mixture of those folks from Anatolia and the Levant who carried what they call "Basal Eurasian". And again as I keep saying this whole scheme is about coming up with a set of nomenclature that MASKS (REMOVES and HIDES) the African component from all these groups. That is the whole point. [QUOTE] [b]The findings from Raghavan et al. (43) discussed above suggested the existence of an ancient North Eurasian (ANE) population, with affinities to both Native Americans and Europeans. In a related study, Lazaridis et al. (51) obtained high-coverage genomes from an ancient Western European hunter-gatherer (found near Loschbour, Luxembourg) and an ancient Central European farmer (found near Stuttgart, Germany), and proposed a three-way mixture model of European origins. According to this model, the Loschbour individual belonged to the original modern human occupants of Europe, called Western hunter-gatherers (WHG). The ancestors of this population mixed with a basal Eurasian population coming from the Near East during the Neolithic to produce a population called Early European farmers (EEF), which likely brought agriculture into the region. This is the population to which the Stuttgart and Ötzi individuals belonged. Afterward, a third wave of migration from the Pontic steppe introduced the ANE ancestry component into the region.[/b] In the past year, the number of Eurasian aDNA genomes has exploded from less than a dozen to over a hundred (4, 5, 52). Insights from whole-genome shotgun sequence data (5) as well as SNP capture data (4) have helped refine previous theories. For example, Haak et al. (4) showed that the Yamnaya—an Early Bronze Age population from the Pontic Steppe—contained ∼50% ANE ancestry. Haak et al. argued that a population stemming from this source may have been the one responsible for bringing ANE ancestry into Eastern and Central Europe via a massive westward migration 4,500 y ago (the “Corded Ware” culture), and might therefore have been responsible for importing horses and Indo-European languages. Moreover, Allentoft et al. (5) found that people living in the Altai Mountains in Russia until 4,500 y ago (the Afanasievo culture) shared close genetic affinities with the Yamnaya, which could explain why Indo-European languages are also spoken in central Asia. Haak et al. (4) also detected a resurgence of WHG ancestry immediately before the Yamnaya immigration into Europe (6,000–5,000 y ago) and placed a date on the first Near-Eastern migration of early farmers in the early Neolithic at 8,000–9,000 y ago. Additionally, Jones et al. (53) showed that the other half of the Yamnaya ancestry came from a fourth source population: the “Caucasus hunter-gatherers” (CHG), who split from the WHG ∼45,000 y ago and from the EEF ∼25,000 y ago. [b]At present, it appears that western Eurasian populations are mixtures of four ancestral sources (ANE, EEF, WHG, CHG). Nevertheless, given the changes in our understanding of European history that come with each new group of fossils sequenced, it seems likely that the current models will soon be superseded.[/b] [/QUOTE] http://www.pnas.org/content/113/23/6380.full Note that two of these populations the ANE and EEF SHOULD have high levels of African DNA lineages. But by using these composite labels as a reference for multiple DNA lineages it is easy to mask out that there was an African presence in Eurasia from the very beginning and that this presence continued right through to the present day. Because the way they are saying it, Africans suddenly stopped migrating out of Africa 60,000 years ago. Using their own words, the whole point of all these studies is to mask out any African populations. Hence: [QUOTE] Admixture proportions for Stuttgart in the absence of a Near Eastern ancient genome. We used Loschbour and BedouinB as surrogates for ‘unknown hunter-gatherer’ and Near Eastern (NE) farmer populations that contributed to Stuttgart (Supplementary Information section 13). Ancient Near Eastern ancestry in Stuttgart is estimated by the f4 ratio 8,15 f4 (Outgroup, X;Loschbour,Stuttgart) /f4 (Outgroup, X ;Loschbour, NE). [b]A complication is that BedouinB is a mixture of NE and African ancestry. We therefore subtracted the effects of African ancestry using estimates of the BedouinB African admixture proportion from ADMIXTURE (Supplemen-tary Information section 9) or ALDER 68.[/b] [b]Admixture graph modelling. We used ADMIXTUREGRAPH (version 3110) to model population relationships between Loschbour, Stuttgart, Onge, and Karitiana using Mbuti as an African outgroup.[/b] We assessed model fit using a block jackknife of differences between estimated and fitted f statistics for the set of included populations (we expressed the fit as a Z score). We determined that a model failed if j Z j . 3 for at least one f statistic. A basic tree model failed and we manually amended the model to test all possible models with a single admixture event, which also failed. Further manual amendment to include 2 admixture events resulted in 8 successful models, only one of which could be amended to also fit MA1 as an additional constraint. We successfully fit both the Iceman and LaBrana into this model as simple clades and Motala12 as a two-way mixture. We also fit present-day west Eurasians as clades, two-way mixtures, or three-way mixtures in this basic model, achieving a successful fit for a larger number of European populations ( n = 26) as three-way mixtures.We estimated the individualadmixture proportionsfromthe fittedmodel parameters. To test if fitted parameters for different populations are consistent with each other, we jointly fit all pairs of populations A and B by modifying ADMIXTUREGRAPH to add a large constant (10,000) to the variance term f3 (A0, A, B). By doing this, we can safely ignore recent gene flow within Europe that affects statistics that include both A and B . Ancestry estimates from f4 ratios. [b]We estimate EEF ancestry using the f4 ratio 8,15 f4 (Mbuti, Onge; Loschbour, European)/ f 4 (Mbuti, Onge; Loschbour, Stuttgart) , which produces consistent results with ADMIXTUREGRAPH (Supplementary Informa- tion section 14). We use f4 (Stuttgart,Loschbour; Onge MA1)/ f 4 (Mbuti, MA1; Onge, Loschbour) to estimate Basal Eurasian admixture into Stuttgart. We use f4 (Stuttgart, Loschbour; Onge Karitiana) / f 4 (Stuttgart, Loschbour; Onge MA1) to estimate ANE mixture in Karitiana (Fig. 4). We use f 4 ( Test ,Stuttgart;Karitiana,Onge)/f 4 (MA1, Stutt- gart; Karitiana, Onge) to lower bound ANE m ixture into north Caucasian populations.[/b] MixMapper analysis. We carried out MixMapper 2.0 (ref. 7) analysis, a semi-supervised admixture graph fitting technique. First, we infer a scaffold tree of populations without strong evidence of mixture relative to each other (Mbuti, Onge, Loschbour and MA1). [b]We do not include European populations in the scaffold as all had significantly negative f3 statistics indicating admixture[/b]. We then ran MixMapper to infer the relatedness of the other ancient and present day samples, fitting them onto the scaffold as two- or three-way mixtures. The uncertainty in all parameter estimates is measured by block bootstrap resampling of the SNP set (100 replicates with 50 blocks). TreeMix analysis. [b]We applied TreeMix 21 to Loschbour, Stuttgart, Motala12, and MA1 (ref. 3), LaBrana and the Iceman1 , along with the present-day samples of Karitiana, Onge and Mbuti. We restricted the analysis to 265,521 Human Origins array sites after excluding any SNPs where there were no-calls in any of the studied individuals. The tree was rooted with Mbuti and standard errors were estimated using blocks of 500 SNPs. We repeated the analysis on whole-genome sequence data, rooting with chimp and replacing Onge with Dai as we did not have Onge whole genome.[/b] sequence data 55 .Wevariedthenumberofmigrationevents( m)between0and5. Inferring admixture proportions with minimal modelling assumptions. We devised a method to infer ancestry proportions from three ancestral populations (EEF, WHG, and ANE) without strong phylogenetic assumptions (Supplementary Information section 17). We rely on 15 ‘non-west Eurasian’ outgroups and study f 4 ( European, Stuttgart; O 1 ,O 2) which is expectedtoequal ab f 4 (Loschbour, Stuttgart; O 1 ,O 2) 1 a ( 1 2 b) f 4 (MA1,Stuttgart; O 1 ,O 2)if European has1 2 a ancestry from EEF and b ,1 2 b ancestry from WHG and ANE respectively. This defines a system of 15 2 ~ 105 equationswithunknowns ab , a (1 2 b), which we solve with least squares implemented in the function lsfit in R to obtain estimates of a and b . We repeated this computation 22 times dropping one chromosome at a time 20 to obtain block jackknife 67 estimates of the ancestry proportions and standard errors, with block size equal to the number of SNPs per chromosome. We assessed consistency of the inferred admixture proportions with those derived from the ADMIXTUREGRAPH model based on the number of standard errors between the two (Extended Data Table 1). Haplotype-based analyses. We used RefinedIBD from BEAGLE 4 27 with the set- tings ibdtrim 5 20 and ibdwindow 5 25 to identify identity-by-descent (IBD) tracts: genomic segments or recently shared ancestry between Loschbour and Stuttgart and populations from the POPRES data set 69 . We kept all IBD tracts spanning at least 0.5 centimorgans (cM) and with a LOD score . 3 (Supplementary Informa- tionsection18).We alsousedChromoPainter 29 tostudy haplotype sharingbetween Loschbour and Stuttgart and present-day West Eurasian populations (SI19). We identified 495,357 SNPs that were complete in all individuals and phased the data using Beagle 4 (ref. 27) with parameters phase-its 5 50 and impute-its 5 10. We did not keep sites with missing data to avoid imputing modern alleles into the ancient individuals. We used both unlinked (-k 1000) and linked modes (estimating -n and -Mby sampling 10% of individuals). We combined ChromoPainter output for chro- mosomes 1–22 using ChromoCombine 29 . We carried out a PCA of the co-ancestry matrix using fineSTRUCTURE 29 . 31. Delsate, D., Guinet, J.-M. & Saverwyns, S. De l’ocr[/b][/QUOTE] http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets_files/2014_Nature_Lazaridis_EuropeThreeAncestries.pdf Of course the reason for masking the African ancestry, according to them, is to understand the ancient ancestral populations involved in the development of European populations purely within Europe, but the problem is that IN REAL LIFE, African DNA is part of the development of European populations going all the way back to the beginning. EEF, ANE and WHG are all similarly affected by MASKING out the African component in order to understand intra-European gene flow. As for the development of farming itself, it is already widely documented that it was BEHAVIORS related to subsistence strategies that laid the basis for the development of farming. And there are various evidences of this both IN and OUTSIDE Africa, not ironically many of the sites outside Africa being in the nearby Levant. I don't see that as a coincidence. [QUOTE] Abstract Use-wear analysis of five glossed flint blades found at Ohalo II, a 23,000-years-old fisher-hunter-gatherers’ camp on the shore of the Sea of Galilee, Northern Israel, provides the earliest evidence for the use of composite cereal harvesting tools. The wear traces indicate that tools were used for harvesting near-ripe semi-green wild cereals, shortly before grains are ripe and disperse naturally. The studied tools were not used intensively, and they reflect two harvesting modes: flint knives held by hand and inserts hafted in a handle. The finds shed new light on cereal harvesting techniques some 8,000 years before the Natufian and 12,000 years before the establishment of sedentary farming communities in the Near East. Furthermore, the new finds accord well with evidence for the earliest ever cereal cultivation at the site and the use of stone-made grinding implements.[/QUOTE] http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167151 [QUOTE] Ohalo II is located 5.5 miles (9 km) south of the modern city of Tiberias, and was discovered in 1989 when the level of the lake plummeted. Excavations at the site exposed six brush hut dwellings, a human grave, copious and well-preserved remains of both animal and plant foods, beads from the Mediterranean Sea, as well as evidence of flint tool manufacture and use. “The plant remains from the site were unusually well-preserved because of being charred and then covered by sediment and water which sealed them in low-oxygen conditions,” said Prof Ehud Weiss of Bar-Ilan University in Ramat-Gan, Israel, team leader and senior author of a paper published in the journal PLoS ONE. “Due to this, it was possible to recover an extensive amount of information on the site and its inhabitants – which made this a uniquely preserved site, and therefore one of the best archaeological examples worldwide of hunter-gatherers’ way of life. Here we see evidence of repeated sowing and harvesting of later domesticated cereals.” In the Ohalo II dwellings was a particularly rich assemblage of some 150,000 plant remains, showing that the residents gathered over 140 different plant species from the surrounding environment. Among these, the archaeologists identified edible cereals – such as wild emmer, wild barley, and wild oats. These cereals were mixed with 13 species of so-called proto-weeds – ancestors of the modern-day weeds known to flourish in cultivated, single-crop fields – indicating that they grew and were subsequently unintentionally gathered together. “Because weeds thrive in cultivated fields and disturbed soils, a significant presence of weeds in archaeobotanical assemblages retrieved from Neolithic sites and settlements of later age is widely considered an indicator of systematic cultivation,” said co-author Prof Marcelo Sternberg of Tel Aviv University. The archaeologists also found a grinding slab – a stone tool with which cereal starch granules were extracted – as well as a distribution of seeds around this tool, reflecting that the cereal grains were processed into flour. This flour was probably used to make dough, maybe by baking it on an installation of flat stones, found just outside one of the shelters. Until now, scientists believed farming was invented 12,000 years ago in the Cradle of Civilization – Iraq, the Levant, parts of Turkey and Iran – an area that was home to some of the earliest known human civilizations. The researchers’ discovery offers the first evidence that trial plant cultivation began far earlier – some 23,000 years ago. “While full-scale agriculture did not develop until much later, our study shows that trial cultivation began far earlier than previously believed, and gives us reason to rethink our ancestors’ capabilities. Those early ancestors were more clever and more skilled than we knew,” Prof Sternberg said.[/QUOTE] http://www.sci-news.com/archaeology/science-farming-ohalo-ii-israel-03052.html And of course Wadi Kubbaniyah also follows the same pattern. [URL=https://books.google.com/books?id=mtOhAwAAQBAJ&pg=PA165&lpg=PA165&dq=wadi+kubbaniya&source=bl&ots=0Hh3f0mpPF&sig=jjKgjLFDQUMtBwi6IJIm0o3cwQ4&hl=en&sa=X&ved=0ahUKEwjZhsXu66PTAhXIQCYKHdRdBuAQ6AEIczAQ#v=onepage&q=wadi%20kubbaniya&f=false]https://books.google.com/books?id=mtOhAwAAQBAJ&pg=PA165&lpg=PA165&dq=wadi+kubbaniya&source=bl&ots=0Hh3f0mpPF&sig=jjKgjLFDQUMtBwi6IJIm0o3cwQ4&hl=en&sa=X&ved=0ahUKEwjZhsXu66PTAhXIQCY KHdRdBuAQ6AEIczAQ#v=onepage&q=wadi%20kubbaniya&f=false[/URL] Not to mention other sites also found in Europe: https://www.newscientist.com/article/dn28139-stone-age-people-were-making-porridge-32000-years-ago/ So the idea of Africans grinding wild grains 100,000 years ago is not far fetched and neither is the idea that this "survival toolkit" migrated out of Africa along with modern humans. [IMG]https://upload.wikimedia.org/wikipedia/commons/thumb/5/54/Pilon.jpg/794px-Pilon.jpg[/IMG] https://en.wikipedia.org/wiki/File:Pilon.jpg [/QB][/QUOTE]
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