Adaptive evolution and effective population size in wild house mice

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ～ 25,000-120,000), M. m. domesticus (N(e) ～ 58,000-200,000), and M. m. castaneus (N(e) ～ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.     

Detection of drug binding to DNA by hydroxyl radical footprinting. Relationship of distamycin binding sites to DNA structure and positioned nucleosomes on 5S RNA genes of Xenopus.

We report the use of hydroxyl radical footprinting to analyze the interaction of distamycin and actinomycin with the 5S ribosomal RNA genes of Xenopus. There is a qualitative difference in the hydroxyl radical footprints of the two drugs. Distamycin gives a conventional (albeit high-resolution) footprint, while actinomycin does not protect DNA from hydroxyl radical attack, but instead induces discrete sites of hyperreactivity. We find concentration-dependent changes in the locations of distamycin binding sites on the somatic 5S gene of Xenopus borealis. A high-affinity site, containing a G.C base pair, is replaced at higher levels of bound drug by a periodic array of different lower affinity sites that coincide with the places where the minor groove of the DNA would face in toward a nucleosome core that is known to bind to the same sequence. These results suggest that distamycin recognizes potential binding sites more by the shape of the DNA than by the specific sequence that is contained in the site and that structures of many sequences are deformable to a shape that allows drug binding. We discuss the utility of hydroxyl radical footprinting of distamycin for investigating the underlying structure of DNA.     

Effect of naloxone on gonadotrophin secretion at various stages of development in the ewe lamb

Spring-born crossbred ewe lambs were raised in a natural photoperiod and saline (N = 6) or naloxone (1 mg/kg) in saline (N = 6) was injected (i.m.) every 2 h for 6 h at 5, 10 and 15 weeks of age and for 8 h at 20, 25 and 30 weeks of age. Blood samples were taken every 12 min during treatment periods. Naloxone had no effect on time to first oestrus (controls 235 +/- 6 days, naloxone 242 +/- 7 days). Mean serum LH concentrations and LH pulse frequency were elevated by naloxone in ewe lambs at 20, 25, and 30 weeks of age (P less than 0.05). The only FSH response to naloxone was a depression of mean serum concentrations at 30 weeks of age (P less than 0.05). LH pulse amplitude was elevated at 5 weeks of age in all ewe lambs and declined thereafter to a nadir at 30 weeks of age in control, but not in naloxone-treated animals (P less than 0.05). LH pulse frequency was elevated at 10 weeks of age in control ewe lambs and in all animals at 30 weeks of age (P less than 0.05). FSH pulse frequency declined from 5 weeks of age in control ewe lambs (P less than 0.05), with very few pulses noted in 25- and 30-week-old animals. We conclude that (1) opioidergic suppression of LH, but not FSH, secretion developed at 20 weeks of age in the growing ewe lambs used in the present study, with no obvious change in suppression before the onset of first oestrus: (2) pulsatile FSH secretion occurred in the young ewe lamb but was lost as the lamb matured: (3) attainment of sexual maturity was preceded by an elevation in LH pulse frequency.     

Cladistics and the land plants: A response to Robinson

The reconstruction of phylogenetic relationships should be based not on belief but on an explicit and logical analysis of all available characters. Hennigian phylogenetic systematics (cladistics) provides a framework for evaluating putative homologies characterizing particular hierarchical levels, determining relationships of taxa sharing congruent patterns of homologies, and constructing a classification based on this information. Fossils can and should be included in the analysis if enough of the relevant characters are preserved; this is not currently possible for early land plants because of the fragmentary fossil record. To avoid circularity, adaptive and functional considerations should be addressed only after a phylogenetic hypothesis based on patterns on patterns of shared homologies is available.     

THE RECONSTRUCTION OF ANCESTRAL CHARACTER STATES

The problem of error in the phylogenetic reconstruction of ancestral character states is explored by developing the model of Frumhoff and Reeve (1994). Information about the evolutionary rate of change within a character is inferred from the distribution of its character states on a known phylogeny, and this information is used to impose confidence limits on the error associated with ancestral state inference. Ancestral state inference is found to be remarkably robust under the model assumptions for a wide range of parameter values; however, the probability of error increases when the number of species within a clade is small and/or state-transition probabilities are strongly skewed in favor of the non-ancestral state. The rationale for expecting such a skew, a hypothesis of parallelism, is shown to rely on assumptions of low rates of change in at least two phylogenetically inherited characters: the tendency to occupy a particular ecological niche and the tendency to respond in a particular way to selection. A means for judging the relative likelihoods of parallelism vs. straightforward homology as explanations for a given character-state distribution is suggested. General problems with the model are discussed, as are methods for making it more realistic.     

Heterogeneity in Rates of Recombination across the Mouse Genome

If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.     

A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data

Drosophila melanogaster belongs to a closely related group of eight species collectively known as the melanogaster subgroup; all are native to sub-Saharan Africa and islands off the east coast of Africa. The phylogenetic relationships of most species in this subgroup have been well documented; however, the three most closely related species, D. simulans, D. sechellia, and D. mauritiana, have remained problematic from a phylogenetic standpoint as no data set has unambiguously resolved them. We present new DNA sequence data on the nullo and Serendipity-alpha genes and combine them with all available nuclear DNA sequence data; the total data encompass 12 genes and the ITS of rDNA. A methodological problem arose because nine of the genes had information on intraspecific polymorphisms in at least one species. We explored the effect of inclusion/exclusion of polymorphic sites and found that it had very little effect on phylogenetic inferences, due largely to the fact that 82% of polymorphisms are autapomorphies (unique to one species). We have also reanalyzed our previous DNA-DNA hybridization data with a bootstrap procedure. The combined sequence data set and the DNA-DNA hybridization data strongly support the sister status of the two island species, D. sechellia and D. mauritiana. This at least partially resolves what had been a paradox of parallel evolution in these two species.      

Reliability of Task-Based fMRI for Preoperative Planning: A Test-Retest Study in Brain Tumor Patients and Healthy Controls

Background

Functional magnetic resonance imaging (fMRI) continues to develop as a clinical tool for patients with brain cancer, offering data that may directly influence surgical decisions. Unfortunately, routine integration of preoperative fMRI has been limited by concerns about reliability. Many pertinent studies have been undertaken involving healthy controls, but work involving brain tumor patients has been limited. To develop fMRI fully as a clinical tool, it will be critical to examine these reliability issues among patients with brain tumors. The present work is the first to extensively characterize differences in activation map quality between brain tumor patients and healthy controls, including the effects of tumor grade and the chosen behavioral testing paradigm on reliability outcomes.

Method

Test-retest data were collected for a group of low-grade (n = 6) and high-grade glioma (n = 6) patients, and for matched healthy controls (n = 12), who performed motor and language tasks during a single fMRI session. Reliability was characterized by the spatial overlap and displacement of brain activity clusters, BOLD signal stability, and the laterality index. Significance testing was performed to assess differences in reliability between the patients and controls, and low-grade and high-grade patients; as well as between different fMRI testing paradigms.

Results

There were few significant differences in fMRI reliability measures between patients and controls. Reliability was significantly lower when comparing high-grade tumor patients to controls, or to low-grade tumor patients. The motor task produced more reliable activation patterns than the language tasks, as did the rhyming task in comparison to the phonemic fluency task.

Conclusion

In low-grade glioma patients, fMRI data are as reliable as healthy control subjects. For high-grade glioma patients, further investigation is required to determine the underlying causes of reduced reliability. To maximize reliability outcomes, testing paradigms should be carefully selected to generate robust activation patterns.