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PubMed2004

SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.

SUMMARY: A Perl utility called SCANMS was written that operates on parametric bootstrap data generated by Hudson's simulator MS. SCANMS simulates sliding window analysis of Tajima's D or Fu and Li's D(*) or F(*) over the replicates and generates the empirical joint distribution of window minima and maxima. This distribution may then be used to calculate achieved significance values or significance cutoffs that account for multiple comparisons in sliding window analysis of real data. AVAILABILITY: SCANMS is available free of charge under the terms of the Academic Free License 2.0 and may be downloaded from http://www.lcb.uu.se/~dave/SCANMS

Algorithms↗
PubMed2002

Statistical properties of new neutrality tests against population growth.

A number of statistical tests for detecting population growth are described. We compared the statistical power of these tests with that of others available in the literature. The tests evaluated fall into three categories: those tests based on the distribution of the mutation frequencies, on the haplotype distribution, and on the mismatch distribution. We found that, for an extensive variety of cases, the most powerful tests for detecting population growth are Fu's F(S) test and the newly developed R(2) test. The behavior of the R(2) test is superior for small sample sizes, whereas F(S) is better for large sample sizes. We also show that some popular statistics based on the mismatch distribution are very conservative.

Computer Simulation↗
PubMed1986

Surnames in Sardinia. III. The spatial distribution of surnames for testing neutrality of genes.

1. A study on heterogeneity of males' surnames over time and space in the island of Sardinia was carried out using data from consanguineous marriages (1800-1970) and telephone directories (1978). 2. Variation of frequency of surnames over time is barely significant and 10 times lower than that over space, which is very highly significant. 3. For sufficiently frequent surnames the estimate of the Wahlund variance, calculated from chi 2 for heterogeneity in space, is independent of the frequency of a surname: this supplies evidence of neutrality in line with that obtained from the frequency distribution of surnames. 4. The Wahlund variance, W (also called FST), decreases regularly as the average size of the area considered (number of individuals per area, N) increases. The estimate of the parameter beta in the relation W = KN beta could be of interest for the study of population structure. 5. A correction factor of 1/4 must be made on the surnames' variance in consideration of their haploid unisexual transmission. 6. It is suggested that surnames could provide a baseline for estimating the value of Wahlund variance under random genetic drift and hence evaluating whether a gene behaves as selectively neutral. 7. The distribution of the Wahlund variances obtained from two sets of gene frequency data as compared with that obtained in comparable conditions for surnames in the same areas seems to show that most genes behave as neutral, with the exception of a few, with high W values, which presumably have been under different selection pressures in the area examined.

Consanguinity↗