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Results: 7

1.
Figure 7

Figure 7. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Frequency spectra of rs1385699 in CEPH-HGDP populations. rs1385699 is a non-synonymous SNP located in EDA2R. This image was downloaded from the UCSC Genome Browser Website [47].

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
2.
Figure 1

Figure 1. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Structure of the CEPH-HGDP Populations as estimated using frappe. Figures drawn using Distruct [45]. (a) Population structure estimated using 16,297 X chromosome SNP genotypes with K = 7. (b) Population structure estimated using 19,632 chromosome 16 SNP genotypes with K = 7.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
3.
Figure 6

Figure 6. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Change in haplotype heterozygosity between African agriculturists and East Asians. All sets of five consecutive X-linked SNPs were assembled into haplotypes. Haplotype heterozygosity was then calculated for all haplotypes in the Yoruba and the Han. The abscissa represents the chromosomal position of the center SNP while the ordinate gives the value of the Han heterozygosity as a proportion of the Yoruba heterozygosity (Han heterozygosity/Yoruba heterozygosity). The green data points represent haplotypes centered between 65 and 67 Mb and the blue data points represent haplotypes centered between 108.6 and 112.2 Mb.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
4.
Figure 5

Figure 5. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Previously implicated X-linked selection targets with elevated CLR, XP-EHH, or delta scores. Each row represents a particular delta comparison or a particular test as labeled. Each column represents a X-chromosomal region or locus that previous research has identified as being under selection. Colored boxes designate regions where elevated test scores were observed (see text and Materials and methods for details); blue boxes represent elevated CLR scores, red boxes represent elevated XP-EHH scores, and green boxes represent elevated delta values. Gray boxes denote regions where there are no scores for the corresponding test.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
5.
Figure 2

Figure 2. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Number of high-delta SNPs and regions represented by TA/EX values for the Yoruba-Han comparison. (a) The female proportion of the effective population size and the female proportion of migration were both varied over a range from 0.01 to 0.99. For each of the 9,800 possible pairs of these values, a list of TA/EX values was produced from the observed autosomal delta values for the Yoruba-Han. The color at a given point on the grid represents the number of high-delta SNPs out of 640,698 total SNPs found in this list. (b) The same as in (a), except that the color at a given point on the grid signifies the number of high-delta regions out of 13,395 total regions represented by each list of TA/EX delta values.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
6.
Figure 3

Figure 3. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Comparison of TA/EX and observed X-linked delta values. The female proportion of the effective population size and the female proportion of migration were both varied over a range from 0.01 to 0.99. For each of the 9,800 possible pairs of these values, a list of TA/EX delta values was produced from the observed autosomal delta values for the Yoruba-Han comparison. This list of TA/EX values was compared to the list of observed X-linked delta values using a two-sided Wilcoxon test. The color at a given point represents the resulting P-value of this comparison. Red locations on the grid represent Nf/N, mf/m value-pairs that produce sets of TA/EX delta values that significantly differ from the observed X-linked values; white and yellow regions on the grid represent Nf/N, mf/m value-pairs that produce TA/EX values that do not significantly differ from the observed X-linked values.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.
7.
Figure 4

Figure 4. From: Characterization of X-Linked SNP genotypic variation in globally distributed human populations.

Top ten regions for iHS, CLR, and XP-EHH scores and all high-delta regions. The numbers on the left side of each figure represent the beginning position of a region in megabases. Each chromosomal region is 400-kb in length. The letters across the top of each figure represent the eight continental regions: HG, hunter-gatherer; AA, African agriculturist; ME, Middle East; EU, Europe; CA, Central Asia; EA, East Asia; Oc, Oceania; Am, America. In the delta figure, the column labels represent the three population comparisons: YH, Yoruba-Han; YF, Yoruba-French; FH, French-Han. For iHS, CLR, and XP-EHH, each small column contains the numbers 1 to 10 denoting the top ten X-chromosomal regions for each particular test and continental group with the intensity of the color corresponding to the rank. For XP-EHH, the double line separating the African agriculturist column from the Middle East column signifies that the XP-EHH scores represented on the left side of the lines were calculated using East Asians as the reference sample while the scores represented on the right side of the lines were calculated using African agriculturists as the reference sample (Additional file 9). For delta, each blue shaded region contains either a high-delta SNP for the Yoruba-Han or Yoruba-French comparison, or a SNP with delta > 0.8 for the French-Han comparison.

Amanda M Casto, et al. Genome Biol. 2010;11(1):R10-R10.

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