Kidd Lab

Department of Genetics, Yale University

Phenylalanine Hydroxylase Haplotypes

Schematic of the four sites studied
Haplotype frequencies for 29 populations
Average haplotype frequencies by "continent"
Xi coefficient of overall disequilibrium for 30 populations
Principal components analysis of populations

Figure 1. Schematic map of four restriction site polymorphisms at the PAH locus. The numbered boxes correspond to the first nine of the 13 exons. Relative spacing is the best estimate from multiple sources.

© 1999 Kenneth K. Kidd, Yale University. All rights reserved.
This figure may be reproduced for classroom use only.

Figure 2. Frequencies of the eight most frequent PAH haplotypes for each of 29 populations as color-coded stacked bars. The haplotypes are coded as follows: "1" indicates site absent, "2" indicates site present for the sites ordered as in Figure 1. The vertical lines at the right show the geographical groupings used in Figure 3: Africa, Europe and South West Asia, East Asia, Melanesia, Siberia, North America, South America.

© 1999 Kenneth K. Kidd, Yale University. All rights reserved.
This figure may be reproduced for classroom use only.

Figure 3. Average frequencies of the eight most frequent haplotypes by geographic region. The averages are based on data in ALFRED with the number of populations averaged for each region given at the right margin. Melanesia and Siberia have only one population each, Nasioi and Yakut, respectively.

© 1999 Kenneth K. Kidd, Yale University. All rights reserved.
This figure may be reproduced for classroom use only.

Figure 4. Overall linkage disequilibrium as the Xi coefficient for the four-site PAH haplotype in 30 populations. The Xi coefficient is a permutation-based statistic defined in Zhao et al. (1999). Coefficients are given for each population ordered left to right in the same order as top to bottom in Figure 2 except the value for Samaritans is inserted as the 7th (3rd "European") population. Geographic groupings are the same as in Figure 3 and are indicated across the top and botton; M. = Melanesia (Nasioi), S. = Siberia (Yakut). All values are statistically significant at p<.001 except for the Yoruba at p = .002.

Figure 5. Principal components analysis of 30 populations based on PAH haplotype frequency data. African populations are represented by circles, European and Southwest Asian populations by squares, East Asian populations by triangles, American Native populations by X's, the Melanesian population by a plus, and the Siberian population by a diamond. These first two prinicpal components account for 68.6% of the variance.

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