Interspecific variation in life history relates to antipredator decisions by marine mesopredators on temperate reefs

As upper-level predatory fishes become overfished, mesopredators rise to become the new 'top' predators of over-exploited marine communities. To gain insight into ensuing mechanisms that might alter indirect species interactions, we examined how behavioural responses to an upper-level predatory fish might differ between mesopredator species with different life histories. In rocky reefs of the northeast Pacific Ocean, adult lingcod (Ophiodon elongatus) are upper-level predators that use a sit-and-wait hunting mode. Reef mesopredators that are prey to adult lingcod include kelp greenling (Hexagrammos decagrammus), younger lingcod, copper rockfish (Sebastes caurinus) and quillback rockfish (S. maliger). Across these mesopredators species, longevity and age at maturity increases and, consequently, the annual proportion of lifetime reproductive output decreases in the order just listed. Therefore, we hypothesized that the level of risk taken to acquire resources would vary interspecifically in that same order. During field experiments we manipulated predation risk with a model adult lingcod and used fixed video cameras to quantify interactions between mesopredators and tethered prey (Pandalus shrimps). We predicted that the probabilities of inspecting and attacking tethered prey would rank from highest to lowest and the timing of these behaviours would rank from earliest to latest as follows: kelp greenling, lingcod, copper rockfish, and quillback rockfish. We also predicted that responses to the model lingcod, such as avoidance of interactions with tethered prey, would rank from weakest to strongest in the same order. Results were consistent with our predictions suggesting that, despite occupying similar trophic levels, longer-lived mesopredators with late maturity have stronger antipredator responses and therefore experience lower foraging rates in the presence of predators than mesopredators with faster life histories. The corollary is that the fishery removal of top predators, which relaxes predation risk, could potentially lead to stronger increases in foraging rates for mesopredators with slower life histories.     

Satiation in Collection of Myrmecochorous Diaspores by Colonies of <Emphasis Type="Italic">Aphaenogaster rudis</Emphasis> (Formicidae: Myrmicinae) in Central Ohio,USA

When ants are dispersing seeds (myrmecochory), cessation of foraging can be as important as recruitment in determining dispersal success. We studied food collection by Aphaenogaster rudis from experimental depots by monitoring temporal variation and preference in food removal (diaspores of Asarum canadense and Sanguinaria canadensis and larvae of Tenebrio obscurus). Removal of diaspores, but not insect larvae, declined to nearly zero over the scale of hours. Satiation extended over the scale of days for diaspores. Extensive collection of larvae inhibited future collection of diaspores, but the converse was not observed. Increasing distance from the nest reduced removal of diaspores, but not of food bodies isolated from diaspores. Removal rates for diaspores were uncorrelated with the number of workers or brood in a colony.     

Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.