Is there variation in crossover interference levels among chromosomes from human males?

We demonstrate that recent data from human males are consistent with constant interference levels among chromosomes under the two-pathway model, whereas inappropriately fitting shape parameters of Gamma distributions to immunofluorescent interfoci distances observed on finite chromosomes generates false interpretations of higher levels of interference on shorter chromosomes. We provide appropriate statistical methodology.

Individual, sexual, seasonal, and temporal variation in the amount of sagebrush lizard scent marks.

Although many animals deposit scent marks, previous studies have focused almost entirely on rodents or on the chemical structure of the signal. Here, we study the quantity and temporal pattern of chemical deposition by the territorial sagebrush lizard Sceloporus graciosus, measuring both femoral pore and fecal deposits. Specifically, we tested whether variation in deposition is a good cue of individual and sexual identity and/or whether it is more closely associated with body size and reproductive state, indicators of physiological condition. The results support the latter hypothesis. We found that although the amount of fluid deposited on a single perch (rarely quantified in mammals) carries little information on individual or sexual identity, it reflects the physiological condition and reproductive state of individual lizards and is replenished on a roughly weekly cycle, potentially providing additional information on the producer's activity level. The amount of deposition may thus provide important information to chemical receivers making mate choice and territorial defense decisions. The results further suggest that seasonal increases in gland production allow lizards to mark more sites rather than to influence the quality of the signal on a single perch.

Crossover interference in humans.

Crossing-over between homologous chromosomes facilitates proper disjunction of chromosomes during meiosis I. In many organisms, gene functions that are essential to crossing-over also facilitate the intimate chromosome pairing called "synapsis." Many organisms--including budding yeast, humans, zebrafish, Drosophila, and Arabidopsis--regulate the distribution of crossovers, so that, most of the time, each chromosome bundle gets at least one crossover while the mean number of crossovers per chromosome remains modest. This regulation is obtained through crossover interference. Recent evidence suggests that the organisms that use recombination functions to achieve synapsis have two classes of crossovers, only one of which is subject to interference. We statistically test this two-pathway hypothesis in the CEPH data and find evidence to support the two-pathway hypothesis in humans.

Crossover interference in Arabidopsis.

The crossover distribution in meiotic tetrads of Arabidopsis thaliana differs from those previously described for Drosophila and Neurospora. Whereas a chi-square distribution with an even number of degrees of freedom provides a good fit for the latter organisms, the fit for Arabidopsis was substantially improved by assuming an additional set of crossovers sprinkled, at random, among those distributed as per chi square. This result is compatible with the view that Arabidopsis has two pathways for meiotic crossing over, only one of which is subject to interference. The results further suggest that Arabidopsis meiosis has >10 times as many double-strand breaks as crossovers.

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known.

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.