Performance of the cyclic autumnal moth,<Emphasis Type="Italic"> Epirrita autumnata</Emphasis>, in relation to birch mast seeding

The mast depression hypothesis has been put forward to explain the 9- to 10-year population cycle of the autumnal moth (Epirrita autumnata; Lepidoptera: Geometridae) in northern Fennoscandia. We analysed long-term data from Finnish Lapland in order to evaluate the critical assumption of the mast depression hypothesis: that better individual performance of herbivores, followed by high annual growth rate of populations, occurs in the year following mast seeding of the host, the mountain birch ( Betula pubescens ssp. czerepanovii). Since mast seeding has been suggested to occur at the expense of chemical defence against herbivores, we bioassayed the quality of birch leaves from the same trees by means of yearly growth trials with autumnal moth larvae. We also measured the size of wild adults as a determinant of potential fecundity of the species in different years. The relative growth rate of larvae was poorer in post-mast years compared to other years, rather than better as assumed by the hypothesis. Conversely, a slight indication of the increase in potential fecundity was observed due to the somewhat larger adult size in post-mast years. Population growth rate estimates, however, showed that the increase in fecundity would have to be much higher to facilitate population increase towards a cyclic peak with outbreak density. Accordingly, our two data sets do not support the assumption of a higher annual growth rate in autumnal moth populations subsequent to mast seeding of the host, thereby contradicting the predictions of the mast depression hypothesis. Temperatures, when indexed by the North Atlantic Oscillation and accumulated thermal sums, were observed to correlate with the abundance or rate of population change of the autumnal moth. The factors underlying the regular population cycles of the autumnal moth, however, remain unidentified. Overall, we suggest that the causal agents in cyclic insect population dynamics should be clarified by field experimentation, since trophic interactions are complex and are further modified by abiotic factors such as climate.     

Reduction in size and fecundity of the autumnal moth, <Emphasis Type="Italic">Epirrita autumnata</Emphasis>, in the increase phase of a population cycle

Increasing fecundity with increasing density has been observed for many cyclic herbivore populations, including some forest Lepidoptera. We monitored population density, body size and reproductive capacity of the cyclic lepidopteran, the autumnal moth (Epirrita autumnata, Geometridae), from the early increase phase to the devastating outbreak density in northernmost Norway. Larval density of the species increased exponentially from 1998 to 2002 and remained at the outbreak level also in 2003. Within the same period, the body size and fecundity of individuals reduced as analysed from several parallel datasets on larvae, pupae and adults. In another study area in northernmost Finland, the density increase of the autumnal moth was moderate only, and true outbreak density was not attained during the study. Despite that, a reduction was again detected in the size and fecundity of individuals. Possible factors responsible for the reduced size and fecundity of individuals in the Norwegian population were quantitative shortage of foliage, rapid and delayed inducible resistances of the host, mountain birch (Betula pubescens ssp. czerepanovii), as well as crowding-induced responses of larvae. These factors likely acted in concert, although non-delayed responses to the density were emphasized. Our findings did not support the hypotheses of climatic release, inducible susceptibility of the host tree and mast depression (i.e. lowered chemical defence of the host tree after its mast seeding) as promoters of the fecundity-based density increase of the autumnal moth, since the reduced fecundity in relation to increased density was strongly against the predictions of these hypotheses. Therefore, we suggest that the density increase of autumnal moth populations is promoted by high survival rather than exceptionally high fecundity.     

Efficient estimation of emission probabilities in profile hidden Markov models

MOTIVATION: Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that the conserved amino acids are not emphasized, but signal and noise are treated equally. For this reason, the number of estimated emission parameters is often enormous. Focusing the analysis on conserved residues only should increase the accuracy of sequence database search. RESULTS: We address this issue with a new method for efficient emission probability (EEP) estimation, in which amino acids are divided into effective and ineffective residues at each conserved alignment position. A practical study with 20 protein families demonstrated that the EEP method is capable of detecting family members from other proteins with sensitivity of 98% and specificity of 99% on the average, even if the number of free emission parameters was decreased to 15% of the original. In the database search for TIM barrel sequences, EEP recognizes the family members nearly as accurately as HMMER or Blast, but the number of false positive sequences was significantly less than that obtained with the other methods. AVAILABILITY: The algorithms written in C language are available on request from the authors.     

Optimization of a Bifidobacterium longum production process

Bifidobacteria are used as probiotics mainly in the dairy industry as cell suspensions or as freeze-dried additives. So far there have been no reports on a thorough investigation on factors influencing the production process or a statistical approach to the optimization thereof. A 2(8-4) fractional factorial design was used in determining the critical parameters influencing bioreactor cultivations of Bifidobacterium longum ATCC 15707. Glucose, yeast extract and l-cysteine concentrations were found critical for the cultivation of this strain. Glucose and yeast extract concentrations were further studied together with temperature in a three factor central composite design. The optimized cultivation conditions were temperature 40 degrees C, yeast extract concentration 35 gl(-1) and glucose concentration 20 gl(-1). Freeze-drying of frozen cell suspensions of B. longum was studied first in controlled temperatures and thereafter with temperature programming experiments. The results were statistically evaluated. A temperature program with a 2 h temperature gradient from -10 to 0 degrees C, a 10 h temperature gradient from 0 to +10 degrees C and a 12 h temperature hold at +10 degrees C was found best for the freeze-drying process. Temperature programming reduced drying times by over 50% and improved the product activity by over 160%.     

Predator-induced synchrony in population oscillations of coexisting small mammal species

Comprehensive analyses of long-term (1977-2003) small-mammal abundance data from western Finland showed that populations of Microtus voles (field voles M. agrestis and sibling voles M. rossiaemeridionalis) voles, bank (Clethrionomys glareolus) and common shrews (Sorex araneus) fluctuated synchronously in 3 year population cycles. Time-series analyses indicated that interspecific synchrony is influenced strongly by density-dependent processes. Synchrony among Microtus and bank voles appeared additionally to be influenced by density-independent processes. To test whether interspecific synchronization through density-dependent processes is caused by predation, we experimentally reduced the densities of the main predators of small mammals in four large agricultural areas, and compared small mammal abundances in these to those in four control areas (2.5-3 km(2)) through a 3 year small-mammal population cycle. Predator reduction increased densities of the main prey species, Microtus voles, in all phases of the population cycle, while bank voles, the most important alternative prey of predators, responded positively only in the low and the increase phase. Manipulation also increased the autumn densities of water voles (Arvicola terrestris) in the increase phase of the cycle. No treatment effects were detected for common shrews or mice. Our results are in accordance with the alternative prey hypothesis, by which predators successively reduce the densities of both main and alternative prey species after the peak phase of small-mammal population cycles, thus inducing a synchronous low phase.     

Birds help plants: a meta-analysis of top-down trophic cascades caused by avian predators

The tritrophic interactions between plants, herbivores and avian predators are complex and prone to trophic cascades. We conducted a meta-analysis of original articles that have studied birds as predators of invertebrate herbivores, to compare top-down trophic cascades with different plant responses from different environments and climatic areas. Our search found 29 suitable articles, with a total of 81 separate experimental study set-ups. The meta-analysis revealed that plants benefited from the presence of birds. A significant reduction was observed in the level of leaf damage and plant mortality. The presence of birds also positively affected the amount of plant biomass, whereas effects on plant growth were negligible. There were no differences in the effects between agricultural and natural environments. Similarly, plants performed better in all climatic areas (tropical, temperate and boreal) when birds were present. Moreover, both mature plants and saplings gained benefits from the presence of birds. Our results show that birds cause top-down trophic cascades and thus they play an integral role in ecosystems.     

Does application of methyl jasmonate to birch mimic herbivory and attract insectivorous birds in nature?

Earlier studies have suggested that insectivorous birds, similar to invertebrate predators and parasitoids, may be guided by herbivore-induced plant volatiles (HIPVs) to damaged, herbivore-rich trees. Recent studies have also shown that birds use olfaction more than previously thought, underlying the potential for HIPVs to be sensed by insectivorous birds and utilised during foraging for prey. The HIPV production in plants is mediated, at least partly, by the jasmonic acid signalling pathway, and similar HIPVs to those induced by herbivores can often be induced by exposing plants to methyl jasmonate (MeJa). We studied the effects of MeJa on volatile emission and bird attraction using mature mountain birches (Betula pubescens ssp. czerepanovii) under natural conditions in northern Finland. Experimental trees were assigned to four treatment groups: herbivore-damaged [autumnal moth (Epirrita autumnata)], higher dose of MeJa (30 mM), lower dose of MeJa (15 mM) and control. All trees had three branches covered with mesh bags, but there were larvae inside the bags only of the herbivore-damage treatment. Bird predation rate was monitored with artificial plasticine larvae which were checked daily for peck marks. Birds most often pecked the larvae in the herbivore-damaged trees, but the attractiveness of MeJa-treated trees did not differ from the control. High within-treatment variation in systemic HIPV emissions probably masked MeJa treatment effects. The bird predation rate was high in birches that emitted large amounts of α-pinene. Thus, α-pinene may be one cue used by birds to find herbivore-rich birches.     

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays

Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.