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Ancestral component bars (Structure, Admixture, etc.)
Topic Started: Mar 21 2012, 03:15 AM (859 Views)
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In this thread I will post ancestral components in form of bars, they are normally obtained by either the softwares Admixture or Structure.


Li et al. 2008

Recent genome-wide studies have been able to detect and quantify admixture like never before. Li et al. (2008), using more than 600,000 autosomal SNPs, identify seven global population clusters, including European, Middle Eastern and Central/South Asian.
Source: http://www.sciencemag.org/content/319/5866/1100.full.pdf
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Genetic Structure of Human populations

Rosenberg et al. 2002

Study : http://rosenberglab.bioinformatics.med.umich.edu/papers/popstruct.pdf

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Edited by Master, Sep 6 2012, 05:41 PM.
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Global Secondary Modes :

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Auton et al. :

Auton et al. [9] studied a sample of Greeks from Greece and Cyprus in a global context of 3,845 individuals based on about 450K SNPs. The results of the STRUCTURE analysis are shown below, with increasing number of clusters starting from K=2 (top row). The studied individuals from Greece (#15) and Cyprus (#9) appear unremarkable in this analysis. It is evident that, in comparison to worldwide populations, the studied Europeans are fairly homogeneous, composed primarily of the "red" component, with no apparent significant contributions from ancestral elements typical of other continental groups.
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Edited by Master, Mar 21 2012, 03:20 AM.
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Kopelman et al . 2009

Study Source : http://www.biomedcentral.com/content/pdf/1471-2156-10-80.pdf

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López Herráez et al. (2009) typed the same samples at close to 1 million SNPs and analyzed them in a Western Eurasian context, identifying a number of subclusters. This time, all of the European samples show some minor admixture. Among the Italians, Tuscany still has the most, and Sardinia has a bit too, but so does Lombardy (Bergamo), which is even farther north:

Study: http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0007888.g004&representation=PNG_M

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STRUCTURE :

Study : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852743/

Two different techniques were used: principal components analysis (PCA) , which find the most important dimensions summarizing the variability of the genetic data, and STRUCTURE a widely-used model-based clustering program, which assigns individuals to a number K of different clusters.
For each number of clusters (K), each cluster is assigned a color. Each individual from the studied populations corresponds to a vertical line, and consists in various proportions of the different clusters:

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Figure 1. Estimated population structure. Each individual is represented by a thin vertical line, which is partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters. Black lines separate individuals of different populations. Populations are labeled below the figure, with their regional affiliations above it. Ten structure runs at each K produced nearly identical individual membership coefficients, having pairwise similarity coefficients above 0.97, with the exceptions of comparisons involving four runs at K = 3 that separated East Asia instead of Eurasia, and one run at K = 6 that separated Karitiana instead of Kalash. The figure shown for a given K is based on the highest probability run at that K.

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Behar et al. 2010 : http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09103.html

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Edited by Master, May 19 2012, 05:36 PM.
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Genetic Landscape of Eurasia and “Admixture” in Uyghurs

Li et al. 2009 : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790568/

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