Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.      

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Phylogenetic analysis supports horizontal transfer of P transposable elements

Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from a number of different analyses are highly consistent and reveal a P-element phylogeny that contradicts the phylogeny of the species. At least three instances of horizontal transfer are necessary to explain this incongruence, but other explanations cannot be ruled out at this time.      

Degradabflity and phenolic components of cell walls of wheat in relation to susceptibility to Puccinia striiforntis

Cell walls of tips and bases of laminae of flag leaves from 11 cultivars of winter wheat of varying susceptibility to Puccinia striiforntis yellow rust) were compared by examining their phenolic components released by treatment with a commercial cellulase. Isolated cell walls of both susceptible and resistant cultivars released water-soluble carbohydrate esters of phenolic acids, the major acid detected being trans-ferulic. There was no relationship between the amount of phenolic esters released by cellulase and susceptibility to yellow rust. The leaf lamina tips, which were much more susceptible to yellow rust than the corresponding bases, had lower cell wall contents than the bases and their walls were more degradable by cellulase. Examination of transverse sections of leaf laminae of cv. Little Joss showed that cells whose walls contained phenolic groups that gave a red colour reaction with p-nitrobenzene diazonium tetrafluoroborate, occupied a larger area of leaf lamina bases than of the tips. A greater percentage of the abaxial epidermal cells of the bases, compared with the tips, had walls that gave this red colour reaction. We suggest that the presence of phenolic groups in these walls may be related to the greater resistance of the bases to P. striiforntis.     

A less-than-annual breeding cycle in a pair of African Bat Hawks Machaeramphus alcinus

This cycle differs from the known situation in rural Bat Hawks which lay annually mainly during September and October. These probably take advantage of easily-caught pregnant female bats in September/October in order to attain breeding condition, whereas fledgling Bat Hawks take advantage of recently independent but naive juvenile bats in January/February. The relative dearth of bats in rural areas outside this period may account for the regular annual breeding of Bat Hawks at the time of greatest prey availability.     

Quantitative Assessment of Bacterial Adhesion to Eukaryotic Cells of Human Origin

An in vitro system to measure the adhesion of bacteria to human, eukaryotic cells was devised. Adhesion indices for test strains of bacteria could be calculated. Significant differences were then observed between various strains of Escherichia coli from a variety of sources, in their ability to adhere. The possible applications of the test, especially for the routine screening of bacteria for adhesion and for inhibitors of attachment, were considered.