Measures of response agreement for qualitative data: Some generalizations and alternatives.

A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

/pdf/a-new-statistic-for-detecting-genetic-differentiation-46ry2wfo8f.pdf

A new statistic for detecting genetic differentiation.

High-frequency P element loss in Drosophila is homolog dependent.

A fundamental task in data analysis is understanding the differences between several contrasting groups. These groups can represent different classes of objects, such as male or female students, or the same group over time, e.g. freshman students in 1993 through 1998. We present the problem of mining contrast sets: conjunctions of attributes and values that differ meaningfully in their distribution across groups. We provide a search algorithm for mining contrast sets with pruning rules that drastically reduce the computational complexity. Once the contrast sets are found, we post-process the results to present a subset that are surprising to the user given what we have already shown. We explicitly control the probability of Type I error (false positives) and guarantee a maximum error rate for the entire analysis by using Bonferroni corrections.

Detecting Group Differences: Mining Contrast Sets

Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant nonrandom associations between closely or completely linked polymorphic neutral loci in a population of constant size at equilibrium under mutation and genetic drift. In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid. This result is illustrated by the analysis of mitochondrial DNA sequence data from humans. In comparing all pairs of informative sites, fewer than 5% of the pairs show significant disequilibrium in Sardinians, which have apparently undergone rapid population growth, while 20% to 30% in !Kung and Pygmies, which apparently have not undergone rapid growth, show significance. The extent of linkage disequilibrium in a population is closely related to the gene genealogies of the loci examined, with "star-like" genealogies making significant linkage disequilibrium unlikely.

/pdf/linkage-disequilibrium-in-growing-and-stable-populations-1m9q8jqj75.pdf

Linkage disequilibrium in growing and stable populations

SUMMARY A Monte Carlo investigation of 2 X n tables with fixed marginals has been performed. The results of the Monte Carlo distribution show that the probability of Type I error given by the conventional x2 test is in general conservative for 5 or more degrees of freedom even when expectations of successes are very small in each

R. C. Lewontin

Papers

The robustness of homogeneity tests in 2 x n tables.