Contrasting root associated fungi of three common oak-woodland plant species based on molecular identification: host specificity or non-specific amplification?

An increasingly popular approach used to identify arbuscular mycorrhizal (AM) fungi in planta is to amplify a portion of AM fungal small subunit ribosomal DNA (SSU-rDNA) from whole root DNA extractions using the primer pair AM1-NS31, followed by cloning and sequencing. We used this approach to study the AM fungal community composition of three common oak-woodland plant species: a grass (Cynosurus echinatus), blue oak (Quercus douglasii), and a forb (Torilis arvensis). Significant diversity of AM fungi were found in the roots of C. echinatus, which is consistent with previous studies demonstrating a high degree of AM fungal diversity from the roots of various hosts. In contrast, clones from Q. douglasii and T. arvensis were primarily from non-AM fungi of diverse origins within the Ascomycota and Basidiomycota. This work demonstrates that caution must be taken when using this molecular approach to determine in planta AM fungal diversity if non-sequence based methods such as terminal restriction fragment length polymorphisms, denaturing gradient gel electrophoresis, or temperature gradient gel electrophoresis are used.     

Oligomycin inhibition of phosphate uptake and ATP labeling in excised maize roots

ATP labeling by newly absorbed ³²P in excised maize roots was reduced 34% by the presence of oligomycin during a 4-min uptake period with no reduction in rate of phosphorus absorption. Longer exposure to oligomycin, during pretreatment periods or longer uptake periods, reduced phosphorus absorption and further reduced ATP synthesis. In these tissues it appears that oligomycin inhibits ATP production at the mitochondria, that ATP is the energy source for phosphorus uptake at the plasmalemma, and that a depletion in the ATP supply causes a reduced rate of uptake.     

Common Cuckoo Cuculus canorus and host behaviour at Reed Warbler Acrocephalus scirpaceus nests

This study is based on continuous video recordings made at 53 Reed Warbler Acrocephalus scirpaceus nests each day during the laying period. Egg-laying by the Common Cuckoo Cuculus canorus was recorded in 14 (26.4%) of these nests. By analysing the activity of the host birds around and at the nest, we found that this is probably not the only cue used by the Common Cuckoo when locating suitable nests to parasitize. Furthermore, in most cases there was no significant difference between the length of time the host birds spent at the nest in the morning and afternoon, thus providing little support for the hypothesis that the Common Cuckoo lays in the afternoon because it is less likely to be seen by the nest owners then. Parasitized Reed Warblers rejected the Common Cuckoo egg more frequently when they observed the parasite at their nests. However, contrary to what should be expected, most Common Cuckoos laid their eggs in the presence of the host(s), and in general their egg-laying behaviour (for example duration of stay at the nest) was less secretive than described earlier. When partially depredating host clutches, Cuckoos showed the same behavioural pattern at parasitized and unparasitized nests, indicating that the latter may act as a potential reserve for egg-laying.     

Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.      

Molecular homology and DNA hybridization

Summary We reviewed the concept of homology, which can broadly be defined as a correspondence between characteristics that is caused by continuity of information (Van Valen 1982). The concept applies widely in molecular biology when correspondence is taken to mean a genetic relationship resulting from a unique heritable modification of a feature at some previous point in time. Such correspodence can be established for features within a single organism as well as between organisms, making paralogy a valid form of molecular homology under this definition. Molecular homology can be recognized at a variety of organizational levels, which are intedependent. For example, the recognition of homology at the site level involves a statement of homology at the sequence level, and vice versa. This hierarchy, the potential for nonhomologous identity at the site level, and such processes as sequence transposition combine to yield a molecular equivalent to complex structural homology at the anatomical level. As a result, statements of homology between heritable units can involve a valid sense of percent homology.We analyzed DNA hybridization with respect to the problems of recognizing homology and using it in phylogenetic inference. Under a model requiring continuous divergence among compared sequences, DNA hybridization distances embed evolutionary hierarchy, and groups inferred using pairwise methods of tree reconstruction are based on underlying patterns of apomorphic homology. Thus, symplesiomorphic homology will not confound DNA hybridization phylogenies. However, nonhomologous identities that act like apomorphic homologies can lead to inaccurate reconstructions. The main difference between methods of phylogenetic analysis of DNA sequences is that parsimony methods permit hypotheses of nonhomology, whereas distance methods do not.This article was presented at the C.S.E.O.L. Conference on DNA-DNA Hybridization and Evolution, Lake Arrowhead, California, May 11–14, 1989     

Biotransformation of monoaromatic and chlorinated hydrocarbons at an aviation gasoline spill site

A shallow water table aquifer under the U.S. Coast Guard Air Station at Traverse City, MI, has acclimated to the aerobic and anaerobic transformation of monoaromatic hydrocarbons (BTX) released from an aviation gasoline spill. The aquifer also exhibits reductive dechlorination of a chlorinated solvent spill adjacent to the aviation gasoline spill. The groundwater is buffered near neutrality. The aviation gasoline plume is methanogenic and the aquifer contains enough iron minerals to support significant iron solubilization. Field evidence of both aerobic and anaerobic biotransformation of monoaromatics was confirmed by laboratory studies of aquifer material obtained from the site. In the laboratory studies, the removal of the monoaromatics in the anaerobic material was rapid and compared favorably with removal in aerobic material. The kinetics of anaerobic removal of monoaromatics in the laboratory were similar to the kinetics at field scale in the aquifer. Biotransformation of the chlorinated solvents was not observed until late in the study, when daughter products from reductive dechlorination of the chlorinated solvents were identified by GC/MS.     

Demographic costs of inbreeding revealed by sex-specific genetic rescue effects

Background  

Inbreeding can slow population growth and elevate extinction risk. A small number of unrelated immigrants to an inbred population can substantially reduce inbreeding and improve fitness, but little attention has been paid to the sex-specific effects of immigrants on such "genetic rescue". We conducted two subsequent experiments to investigate demographic consequences of inbreeding and genetic rescue in guppies.