Did he screw-up ...Lazaridis latest Update Sept 2014 - SMH

[djoser-xyyman]

This is fascinating. Only Fig2 list Canary Islanders. No where in the remaining document list them.

Several things are disclosed in this new(sept 2014) report.

1. They are now admitting that there is a North-South cline vs a Near-East cline. I TOLD YOU SO!!!!. Neolithic Africans into Europe.

2. The Canary Islanders are the closest match to Early European Farmers(EEF) and Not Sardinians nor Near Easterners. DNATribes hinted as such in one of their early digest. Yet in their write up they state Sardinia. Did they mistakenly NOT remove the Bebers from that chart.


3. Interestingly they did not include other native North Africans. Why? They included North African Jews but NOT (or Arabs)the Berbers. I suspect they deleted Berbers and mistakenly forget to delete the Canary Berbers which is the closest match.
4. The AMY1(starch) genes was present in Europe and AMH long before the advent of agriculture. In fact hunter-gathers carry a high copy count. SO European scientists were BSing all along. Shows how their inferences are BS.



Someone tell me I am losing my mind. Correct me.

[djoser-xyyman]

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Ancient human genomes suggest three ancestral populations for present-day Europeans – Lazaridis et al Sep2014



reflect a strong bottleneck in Loschbour’s ancestors, as the genetic data show that he was not recently inbred (Extended Data Fig. 2). High copy numbers for the salivary amylase gene (AMY1) have been associated with a high starch diet12; our ancient genomes are consistent with the direction of this observation in that the Stuttgart farmer had the highest number of copies (16), whereas the ancient hunter-gatherers La Bran˜a (from Iberia)2,Motala12, and Loschbour had lower numbers (5, 6 and 13, respectively) (Supplementary Information section 7).We caution, however, that copy count in Loschbour is at the high end of present-day humans, showing that high copy counts of AMY1 cannot be accounted for entirely by selection since the switch to agriculture. Both Loschbour and Stuttgart had dark hair (.99% probability); and Loschbour, like La Bran˜a and Motala12, probably had blue OR light coloured eyes (.75%) whereas Stuttgart probably had brown eyes (.99% probability) (Supplementary Information section 8). Neither Loschbour nor La Bran˜a carries the skin-lightening allele in SLC24A5 that is homozygous in Stuttgart and nearly fixed in Europeans today2, but Motala12 carries at least one copy of the derived allele, showing that this allele was present in Europe before the advent of agriculture. We compared the ancient genomes to 2,345 present-day humans from 203 populations genotyped at 594,924 autosomal single nucleotide polymorphisms (SNPs)with the Human Origins array8 (Supplementary Information section 9) (Extended Data Table 1). We used ADMIXTURE13 to identify 59 ‘west Eurasian’ populations that cluster with Europe and the Near East (Supplementary Information section 9 and Extended Data Fig. 3). Principal component analysis (PCA)14 (Supplementary Information section 10) (Fig. 2) indicates a discontinuity between the Near East and Europe, with each showing north–south clines bridged only by a few populations of mainly Mediterranean origin.Weprojected15 the newly sequenced and previously published1–4 ancient genomes onto the first two principal components (PCs) (Fig. 2).

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[djoser-xyyman]

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And the pictures

[djoser-xyyman]

[djoser-xyyman]

www.nature.com/doifinder/10.1038/nature13673

[djoser-xyyman]

1.0 GENETIC MAKEUP OF EUROPEANS
• 18 Sep 2014
• Source: Eberhard Karls Universität, Tübingen

Quote:-------
Using the large dataset of present-day and ancient human data, the researchers were able to calculate the proportion of the ancestral components in present-day Europeans. "Nearly all Europeans have ancestry from all three ancestral groups," says Iosif Lazaridis from Harvard Medical School. "Differences between them are due to the relative proportions of ancestry. Northern Europeans have more hunter-gatherer ancestry—up to about fifty percent in Lithuanians—and Southern Europeans have more farmer ancestry." However, he cautions: "Even the early farmers themselves had some hunter-gatherer ancestry: They were not unmixed descendants of the original Near Eastern migrants that brought farming to Europe."

The researchers were also able to fit the genomic data of modern and ancient humans into a simplified genetic model to reconstruct the deep population history of modern humans outside Africa in the last 50,000 years. While the model suggests that present-day Europeans received contributions from at least three ancestral populations, it also suggests that Early Near Eastern farmers carried genetic material that FALLS OUTSIDE the typical non-African variation. “The finding of an ancient lineage that is present in Europeans and Near Easterners but not elsewhere in Eurasia was a major surprise of our study. It will be exciting to carry out further ancient DNA work to understand the archaeological cultures associated with the arrival of this ancestry,” says David Reich. “We are only starting to understand the complex genetic relationship of our ancestors,” adds Johannes Krause. “Only more genetic data from ancient human remains will allow us to disentagle our pre-historic past”.

[djoser-xyyman]

Through genetics - They have known for a long time that Africans (AMH) entered Europe NOT through the Levant but through Northern Africa and Southern Europe. They have been lying and/or just burying their heads in the sand like ostrich’s. Lying to themselves and to the world, the liars they are. Trying to convince themselves they are not a sub-set of recent North Africans who are in turn a sub-set of South Saharans. Using reverse psychology, trying to convince us North Africana are admixture of Europeans migrants and South Saharan Africans. They have been trying with all their might, media power and lies they are distantly related to Africans.

Pickerell corroborates what Lazaridis just authored in his Sep2014 study about 3 ancestry for modern Europeans. The lies are coming to end …maybe we can finally move on.

Here is what the infamous – Pickrell et al says.


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Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data -
Joseph K. Pickrell1*, Jonathan K. Pritchard1,2*
-DEC 2012


Two inferred edges were unexpected. First, perhaps the most surprising inference is that Cambodians trace about 16% of their ancestry to a population equally related to both Europeans and other East Asians (while the remaining 84% of their ancestry is related to other southeast Asians). This is partially consistent with clustering analyses, which indicate shared ancestry between Cambodians and central Asian populations [7]. To confirm that the Cambodians are admixed, we turned to less parameterized models. The predicted admixture event implies that allele frequencies in Cambodia are more similar to those in African populations than would be expected based on their East Asian ancestry. To test this, we used three-population tests [37]. We tested the trees [African, [Cambodian,Dai]] for evidence of admixture in the Cambodians (Methods). When using any African population, there is strong evidence of admixture (when using Yoruba, Z~{7:0 [p~1|10{12]; when using Mandenka, Z~{7:3 [p~1|10{12]; when using San, Z~{4:8 [p~8|10{7]). We conclude that the Cambodian population is the result of an admixture event involving a southeast Asian population related to the Dai and a Eurasian population only distantly related to those present in these data.
Finally, we infer an admixture edge from the Middle East (a population related to the Mozabite, a Berber population from northern Africa) to southern European populations (w~22%). This migration edge is the one edge that is not consistent across independent runs of TreeMix on these data (Figure S8). In particular, an alternative graph (albeit with lower likelihood) places the Mozabite as an admixture between southern Europe and Africa *****(RATHER ******than the Middle East and Africa), and does NOT include an edge from the middle East to southern Europe.

WE THUS HESITATE TO INTERPRET THIS RESULT, except to note that the relationship between northern African, the Middle East, and southern Europe involves complex patterns of gene flow that merit further investigation [43,57].



Discussion
In this paper, we have developed a unified model for inferring PATTERNS OF POPULATION SPLITS and mixtures from genome-wide allele frequency data. We have shown that this model is accurate in simulations, largely recapitulates the known relationships between well-studied human populations, and is able to identify new relationships between populations in both humans and dogs.



However, once population structure in a species has been identified, these methods((((((Insert by xyyman- ADMIXTURE AND STRUCTURE))))are not well-suited for describing how it arose, and are only indirectly informative about the historical relationships between different populations. The model developed in this paper is designed to more directly address these historical questions.


Methods
Graph estimation
As described in the Results, we developed an algorithm called TreeMix that uses the composite likelihood in Equation 28 to search for the maximum likelihood graph. Estimation involves two major steps. First, for a given graph topology, we need to find the maximum likelihood branch lengths and migration weights. Second, we need to search the space of possible graphs. First consider a given graph topology. We iterate between optimizing the branch lengths and weights. If the edge weights are known, the observed entries of the covariance matrix can be written down as an overdetermined system of linear equations (as in Equations 13–

[djoser-xyyman]

I missed this the first time around. There goes Jablonski’s nonsense theory on “ the food made them white”. Lighten of skin has NADA to do with agricultural diet. Nothing!!!

Quote:

reflect a strong bottleneck in Loschbour’s ancestors, as the genetic data show that he was not recently inbred (Extended Data Fig. 2). High copy numbers for the salivary amylase gene (AMY1) have been associated with a high starch diet12; our ancient genomes are consistent with the direction of this observation in that the Stuttgart farmer had the highest number of copies (16), whereas the ancient hunter-gatherers La Bran˜a (from Iberia)2,Motala12, and Loschbour had lower numbers (5, 6 and 13, respectively) (Supplementary Information section 7).We caution, however, that copy count in Loschbour is at the high end of present-day humans, showing that high copy counts of AMY1 cannot be accounted for entirely by selection since the switch to agriculture. Both Loschbour and Stuttgart had dark hair (.99% probability); and Loschbour, like La Bran˜a and Motala12, probably had blue OR light coloured eyes (.75%) whereas Stuttgart probably had brown eyes (.99% probability) (Supplementary Information section 8). Neither Loschbour nor La Bran˜a carries the skin-lightening allele in SLC24A5 that is homozygous in Stuttgart and nearly fixed in Europeans today2, but Motala12 carries at least one copy of the derived allele, showing that this allele was present in Europe before the advent of agriculture. We compared the ancient genomes to 2,345 present-day humans from 203 populations genotyped at 594,924 autosomal single nucleotide polymorphisms (SNPs)with the Human Origins array8 (Supplementary Information section 9) (Extended Data Table 1). We used ADMIXTURE13 to identify 59 ‘west Eurasian’ populations that cluster with Europe and the Near East (Supplementary Information section 9 and Extended Data Fig. 3). Principal component analysis (PCA)14 (Supplementary Information section 10) (Fig. 2) indicates a discontinuity between the Near East and Europe, with each showing north–south clines bridged only by a few populations of mainly Mediterranean origin.Weprojected15 the newly sequenced and previously published1–4 ancient genomes onto the first two principal components (PCs) (Fig. 2).

[zarahan]

Neither Loschbour nor La Bran˜a carries the skin-lightening allele in SLC24A5 that is homozygous in Stuttgart and nearly fixed in Europeans today2, but Motala12 carries at least one copy of the derived allele, showing that this allele was present in Europe before the advent of agriculture.

Need to pull & read the paper- not enough time these days, but are
they saying that said allele for skin-lightening was in place in
Europe before the advent of agriculture?

[djoser-xyyman]

That is exactly what they are saying. Not only that but the alleles for starch processing(AMY) was also in place BEFORE Agriculture.

But keep in mind what causes skin depigmentation is controversal. The popular belief is SLC24A5. 5 years ago the main gene was supposedly SLC45A2. In reality is may be cumulative per Kittles and Shriver. All link to the process (or interuption of the process) for making melanin via OCA2. (yes, Albinism).

Regardless. The bottomline is depigmentation is unrelated to Agriculture.