Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics,small and large subunit rDNA sequences,and mitochondrial cox1

A matrix of 24 morphodevelopmental characters and an alignment of small subunit (SSU) and large subunit (LSU) rDNA nuclear and cox1 mitochondrial gene sequences (～4500 sites) were compiled from up to 12 phoronids including most named taxa, but probably constituting only a portion of worldwide diversity. Morphological data were analysed by weighted parsimony; sequence data by maximum and Bayesian likelihood, both with Phoronis ovalis as the local outgroup. Morphological and sequence‐based phylogenies were similar, but not fully congruent. Phoronid rDNAs were almost free from mutational saturation, but cox1 showed strong saturation unless distant outgroups and P. ovalis were omitted, suggesting that many phoronid divergences are old (≥100 Myr). rDNA divergence between named phoronid taxa is generally substantial, but Phoronopsis harmeri (from Vladivostock) and Phoronopsis viridis (from California) are genetically close enough to be conspecific. In another alignment, of 24 taxa, phoronid rDNAs were combined with data from brachiopods and distant (molluscan) outgroups. The relative ages of divergence between phoronids and their brachiopod sister‐groups, of the split between the P. ovalis and non‐ovalis lineages, and of other phoronid splits, were estimated from this alignment with a Bayesian lognormal uncorrelated molecular clock model. Although confidence limits (95% highest probability density) are wide, the results are compatible with an Early Cambrian split between phoronids and brachiopods and with the Upper Devonian latest age suggested for the P. ovalis/non‐ovalis split by the putative phoronid ichnofossil, Talpina. Most other ingroup splits appear to be ～50–200 Myr old. Inclusion of phoronids with brachiopods in the crown clade pan‐Brachiopoda suggests that a distinctive metamorphosis and absence of mineralization are ancestral phoronid apomorphies. Worldwide diversity and possible associations between character‐states and life‐history attributes deserve comprehensive further study.     

Fire tolerance of perennial grass tussocks in a savanna woodland

Grass populations in tropical savannas are highly resilient in relation to different fire regimes, but the mechanisms conferring such resilience have been poorly studied. Here we examine one such mechanism, high adult survival during fire, for three perennial grass species in an Australian savanna: Eriachne triseta Nees ex Steud, Eriachne avenacea R.Br and Chrysopogon latifolius S.T.Blake. The study examined survivorship after 3 years, at plots subject to experimental fire regimes (experiencing 0, 1, 2 or 3 fires over the study period) at the Territory Wildlife Park near Darwin in the Northern Territory, Australia. Mean survivorship was 79.9%, 64.3% and 62.0% for E. avenacea, E. triseta and C. latifolius respectively. For the two species of Eriachne, mean survivorship was highest (E. avenacea, 94.6%; E. triseta, 77.1%) in unburnt plots, whereas survivorship of C. latifolius was highest (71.7%) under highest fire frequency. However, variation in survivorship among fire regime treatments was not statistically significant for any of the study species. This negligible difference in survivorship among regimes points to fire tolerance (sprouting ability) as an important mechanism contributing to the resilience and persistence of perennial grasses in these savannas.     

New capabilities for Mycosphaerella graminicola research

Mycosphaerella graminicola is a major pathogen of wheat worldwide, causing Septoria leaf blotch disease. Targeted gene disruption in M. graminicola, by Agrobacterium tumefaciens‐mediated transformation, has become an established functional genomics tool for M. graminicola research in recent years. However, in order to advance research into this economically important pathogen, further functional genomics tools need to be developed. Here, we report three new capabilities for M. graminicola research: (i) two selectable markers have been shown to work robustly in M. graminicola, namely G418 and the fungicide carboxin; (ii) the generation of a strain of M. graminicola in which the KU70 (MUS‐51) homologue has been disrupted; in this strain, homologous recombination efficiencies increased to more than 95%, whilst maintaining wild‐type growth in vitro and full pathogenicity on wheat leaves; (iii) the ability to efficiently target and generate precise mutations of specific genes in the genomic context in M. graminicola. In addition, the insertion of the E198A mutation into the β‐tubulin gene (MgTUB1), conferring resistance to the fungicide benomyl, suggests that this mutant allele may provide an additional selectable marker. The collective use of these tools will permit further advancements in our knowledge of the biology and pathogenicity of this important plant pathogen.     

Separating physical disturbance and nutrient enrichment caused by Pacific salmon in stream ecosystems

1. Pacific salmon (Oncorhynchus spp.) deliver marine‐derived nutrients to the streams in which they spawn and die, and these resource subsidies can increase the abundance of stream biota. In strong contrast, physical disturbance from salmon spawning activity can reduce the abundance of benthic organisms. Previous experimental designs have not established the relative effects of these two contrasting processes on stream organisms during a salmon run. 2. We combined manipulative and observational field studies to assess the degree of nutrient enrichment, physical disturbance, and the net effect of salmon on the abundance of benthic periphyton. Related salmon‐mediated processes were also evaluated for benthic macroinvertebrates. Mesh exclosures (2 × 2 m plots) prevented salmon from disturbing areas of the stream channel, which were compared with areas to which salmon had access. Sampling was conducted both before and during the late‐summer spawning run of pink (O. gorbushca) and chum (O. keta) salmon. 3. Streamwater nitrogen and phosphorus concentrations increased sharply with the onset of the salmon run, and highly significant positive relationships were observed between the numbers of salmon present in the stream and these dissolved nutrients. Before the salmon run, periphyton biomass (as chlorophyll a) and total macroinvertebrate abundance were very similar between control and exclosure plots. During the salmon run, exclosures departed substantially from controls, suggesting significant disturbance imparted on benthic biota. 4. Comparing exclosures before and during the salmon run enabled us to estimate the effects of salmon in the absence of direct salmon disturbance. This ‘nutrient enrichment potential’ was significant for periphyton biomass, as was a related index for macroinvertebrate abundance (although enhanced invertebrate drift into exclosures during the salmon run could also have been important). Interestingly, however, the net effect of salmon, evaluated by comparing control plots before and during the salmon run, was relatively modest for both periphyton and macroinvertebrates, suggesting that nutrient enrichment effects were largely offset by disturbance. 5. Our results illustrate the importance of isolating the specific mechanisms via which organisms affect ecosystems, and indicate that the relative magnitude of salmon nutrient enrichment and benthic disturbance determines the net effect that these ecologically important fish have on stream ecosystems.     

Changes in Chloroplast DNA Levels during Growth of Spinach Leaves

In young spinach leaves, 1–4 mm long, 7–10% of thetotal DNA of the leaf was chloroplast (pt) DNA. Growth in theseleaves was mainly by cell division with plastid division keepingpace with cell division and maintaining about 10 plastids percell. About 1% of the leaf cells were formed in 4.0 mm leaves.Both cell division and cell expansion contribute to the nextstage of leaf growth, which was quantitatively the major periodof new cell formation, nuclear DNA synthesis and ptDNA synthesis.Relative to the nuclear DNA level ptDNA levels rose to 21% ofthe total DNA and chloroplast.plastome copy numbers from 1500to 5000 per cell while chloroplast numbers rose from 10 to 30per cell. In the final period of leaf growth, cell expansionwas the main determinant of growth and chloroplast number percell rose to 180. In contrast to young leaves, newly emergedcotyledons contained 20% of their DNA as ptDNA and, during cellexpansion, cell number per cotyledon doubled. On average, thecells became octoploid, and chloroplast numbers and plastomecopy numbers rose to 500 and 22 000 per cell respectively. Similarlevels of nuclear ploidy, chloroplast number and plastome copynumber were induced in the first leaf pair of spinach followingdecapitation. When senescence was induced in mature leaves byshading, no loss of nuclear or ptDNA occurred. Following theonset of leaf yellowing and a form of senescence induced bynitrogen deficiency in leaves which had not fully expanded,there was preferential loss of ptDNA which fell from 8200 to3700 plastome copies per cell over an 11 d period. Key words: Spinach, Chloroplast, DNA, Ploidy     

The Intra-cellular Localization of the Herbicide Diphenamid in Corn Root .Tip

The intra-cellalar localization of the herbicide N,N-dimethyl–2,2-diphenylacetamide (diphenamid) was examined in 10 mm root tips of corn seedlings (Zea mays L. cv. Shawnee). Experiments are described which culminate in the observation that a significant, measurable effect on root growth occurs within 12 hours after treatment with diphenamid. Corn seedlings were then treated with 14-C-diphenamid for 12 hours and the 10 mm root tips excised and homogenized. By use of differential centrifugation and gel filtration, the root homogenate was separated into fractions; as follows; cell wall, mitochondria, microsomal, protein and eluate. The highest concentration of the herbicide was found in the root tips. Furthermore, most of the radioactivity was found in the eluate. Results are discussed as to localization of diphenamid in the microsomal and protein fraction and possible mode of action.     

Implications of scale for patterns and processes in stream ecology

Abstract Although the scale-dependence of ecological patterns and processes is recognized by freshwater ecologists, current knowledge of scale effects is rudimentary and non-quantitative. We review issues of spatial and temporal scale in this paper to highlight conceptual problems relating to scale and some potential solutions. We present examples of how the spatial scale of a study influences observed patterns and their interpretation, and discuss how the size of an experimental arena influences the degree to which the dynamics of studied populations are influenced by exchange processes (immigration and emigration). The results of small-scale field experiments in streams will often be strongly influenced by the per capita exchange rates of organisms and differences in exchange rates may explain differences in the perceived effects of stream manipulations across scales. Spatial extent also influences the amount of spatial heterogeneity within a study site or arena, with important consequences for the outcome of predator-prey interactions. We suggest that changes in the availability of prey refuges may help explain why predator manipulations in streams appear to weaken as arena size increases. We also recommend that new techniques for decomposing and quantifying spatial heterogeneity be applied to characterize scale-dependent variation in freshwater systems. Lastly, we discuss the pitfalls of mismatching the temporal scale of experiments and models. Models incorporating spatial heterogeneity and the behaviour of organisms are needed to predict the short-term outcome of perturbations in streams, whereas models predicting long-term dynamics will need to integrate the impacts of episodic disturbance and all life history stages of organisms. In general, we recommend that freshwater ecologists undertake more multi-scale sampling and experimentation to examine patterns and processes at multiple scales, and make greater attempts to match the scales of their observations and experiments to the characteristic scales of the phenomena that they investigate.