When is the Wilcoxon-Mann-Whitney procedure a test of location? Implications for effect-size measures.

The Wilcoxon-Mann-Whitney procedure is invariant under monotone transformations but its use as a test of location or shift is said not to be so. It tests location only under the shift model, the assumption of parallel cumulative distribution functions (cdfs). We show that infinitely many monotone transformations of the measured variable produce parallel cdfs, so long as the original cdfs intersect nowhere or everywhere. Thus there are infinitely many effect sizes measured as shifts of medians, invalidating the notion that there is one true shift parameter and thereby rendering any single estimate dubious. Measuring effect size using the probability of superiority alleviates this difficulty.

Genomic variation in cline shape across a hybrid zone.

Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome-scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well-defined categories of locus types (e.g., neutral vs. highly selected). Our multi-locus analysis reveals cross-genomic variation in selective constraints on gene flow and locus-specific flexibility in the permeability of the interspecies membrane.

The effect of marker choice on estimated levels of introgression across an avian (Pipridae: Manacus) hybrid zone.

Hybrid zones are often characterized by narrow, coincident clines for diverse traits, suggesting that little introgression occurs across them. However, this pattern may result from a bias in focussing on traits that are diagnostic of parental populations. Such choice of highly differentiated traits may cause us to overlook differential introgression in nondiagnostic traits and to distort our perception of hybrid zones. We tested this hypothesis in an avian hybrid zone by comparing cline structure in two sets of molecular markers: isozyme and restriction fragment length polymorphism markers chosen for differentiation between parental forms, and microsatellite markers chosen for polymorphism. Two cline-fitting methods showed that cline centre positions of microsatellite alleles were more variable than those of isozyme and restriction fragment length polymorphism markers, and several were significantly shifted from those of the diagnostic markers. Cline widths of microsatellite alleles were also variable and two- to eightfold wider than those of the diagnostic markers. These patterns are consistent with the idea that markers chosen for differentiation are more likely to be under purifying selection, and studies focussed on these markers will underestimate overall introgression across hybrid zones. Our results suggest that neutral and positively selected alleles may introgress freely across many hybrid zones without altering perceived boundaries between hybridizing forms.

Methods for comparing sources of strand compositional asymmetry in microbial chromosomes.

Significant compositional biases in bacterial chromosomes have been explained by replication- and transcription-coupled repair mechanisms, the latter causing GC skew to indicate the direction of replication when gene polarity is correspondingly entrained. Correlations between indicators of replication direction, skew, and transcription polarity are computed for the complete nucleotide sequences of 20 microbial chromosomes and interpreted through statistical tests. A second quantitative method, previously applied to the first complete draft of the Escherichia coli K12 genome, characterizes the sequences by average skew and net skew due to replication. These methods generally agree in finding the coexistence of replication- and translation-coupled effects and in identifying atypical sequences in which one influence is clearly dominant. The replication-dominated class is exemplified by two chlamydial sequences and the transcription-dominated class by three archaea. The preference for leading-strand transcription in two mycoplasmas is stronger than the skew implies. These concordant methods provide an objective framework for comparing sources of strand compositional asymmetry and interpreting skew diagrams.

Pervasive properties of the genomic signature.

BACKGROUND: The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the causes and the functional significance of this phenomenon could be illuminated by determining if it persists on smaller scales. The profile is computed from the base step "odds ratios" that compare dinucleotide frequencies to those expected under the assumption of stochastic equilibrium (thorough shuffling). Analysis is carried out on 22 sequences, representing 19 species and comprised of about 53 million bases all together, to assess stability of the signature in windows ranging in size from 50 kilobases down to 125 bases. RESULTS: Dinucleotide relative abundance distance from the global signature is computed locally for all non-overlapping windows on each sequence. These distances are log-normally distributed with nearly constant variance and with means that tend to zero slower than reciprocal square root of window size. The mean distance within genomes is larger for protist, plant, and human chromosomes, and smaller for archaea, bacteria, and yeast, for any window size. CONCLUSIONS: The imprint of the global signature is locally pervasive on all scales considered in the sequences (either genomes or chromosomes) that were scanned.

THE DUAL ROLE OF SELECTION AND EVOLUTIONARY HISTORY AS REFLECTED IN GENETIC CORRELATIONS.

The patterns of genetic correlations between a series of eye and antenna characters were compared among two sets of spring-dwelling and cave-dwelling populations of Gammarus minus. The two sets of populations originate from different drainages and represent two separate invasions of cave habitats from surface-dwelling populations. Matrix correlations, using permutation tests, indicated significant correlations both between populations in the same basin and from the same habitat. The technique of biplot, which allows for the simultaneous consideration of relationships between different genetic correlations and different populations, was used to further analyze the correlation structure. A rank-3 biplot indicated that spring and cave populations were largely differentiated by eye-antennal correlations, whereas basins were differentiated by both eye-antennal and antennal-antennal correlations. Eye-antennal correlations, which are likely to be subject to selection, were most similar within habitats, which are likely to have similar selective regimes.