Computational protocol: Haplotype frequencies at the DRD2 locus in populations of the East European Plain

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Protocol publication

[…] The general strategy of statistical analysis was similar to that used in the work of Poloni et al. []. Allele frequencies, correspondence to Hardy-Weinberg equilibrium, and significance of linkage disequilibrium (P-values) were evaluated using Arlequin version 2.0 software . Linkage disequilibrium values (D') between polymorphic loci were calculated as suggested by Lewontin []. Frequencies of haplotypes were estimated from RFLP genotype data using the expectation-maximization algorithm of Excoffier and Slatkin [] implemented in Arlequin 2.0. Genetic affinities among populations were evaluated using coancestry coefficients, or linearized pairwise FST values [] calculated on the basis of allele or haplotype frequencies. Significance of genetic distances was tested using permutations [].Correlation of geographical and genetic distances was assessed using the Mantel test and XLSTAT version 2008.6.04 software (Addinsoft). Great circle geographical distances were calculated using the haversine formula; latitudes and longitudes were determined using Google Earth software. Multidimensional scaling (MDS) and cluster analysis with the unweighted pair-group average (UPGA) method were performed using STATISTICA version 6.0 . Statistical comparison of haplotype frequencies in population groups was performed using the Kolmogorov-Smirnov test implemented in XLSTAT. Differentiation between population groups defined by MDS and cluster analysis was estimated using the analysis-of-molecular-variance approach, AMOVA [], implemented in Arlequin 2.0. Conventional FST distances between haplotypes were used, i.e., all haplotypes were considered equidistant (a conservative scenario of pure drift). Significance of the genetic-structure indexes obtained with the AMOVA method was tested using a permutational procedure (1 × 106 permutations). […]

Pipeline specifications

Software tools Arlequin, Statistica
Applications Miscellaneous, Population genetic analysis
Organisms Homo sapiens