Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a clade composed of all North American sequences plus a subset of Italian and French sequences. High genetic diversity in North America and the absence of genotypes diagnostic of the North American clade in the rest of Europe imply that southern Europe was colonized by immigration from North America; however, sequence divergence suggests that this colonization substantially pre-dated fisheries activities. Furthermore, the lack of southern European lineages in the rest of Europe, despite widespread rainbow trout farming, indicates that T. bryosalmonae is not transported through fisheries activities. This result strikingly contrasts with the commonness of fisheries-related introductions of other pathogens and parasites and indicates that fishes may be dead-end hosts. Our results also demonstrate that European strains of T. bryosalmonae infect and induce PKD in rainbow trout introduced to Europe.

Predators exert strong effects on ecological communities, particularly when they re‐occupy areas after decades of extirpation. Within species, such effects can vary over time and by sex and cascade across trophic levels. We used a space‐for‐time substitution to make foraging observations of sea otters (Enhydra lutris) across a gradient of reoccupation time (1–30 years), and nonmetric multidimensional scaling (nMDS) analysis to ask whether (a) sea otter niche space varies as a function of occupation time and (b) whether niche space varies by sex. We found that niche space varied among areas of different occupation times. Dietary niches at short occupation times were dominated by urchins (Mesocentrotus and Strongylocentrotus spp; >60% of diets) in open habitats at 10–40 m depths. At longer occupation times, niches were dominated by small clams (Veneroida; >30% diet), mussels (Mytilus spp; >20% diet), and crab (Decapoda; >10% diet) in shallow (<10 m) kelp habitats. Diet diversity was lowest (H′ = 1.46) but energy rich (~37 kcal/min) at the earliest occupied area and highest, but energy poor (H′ = 2.63, ~9 kcal/min) at the longest occupied area. A similar transition occurred through time at a recently occupied area. We found that niche space also differed between sexes, with bachelor males consuming large clams (>60%), and urchins (~25%) from deep waters (>40 m), and females and territorial males consuming smaller, varied prey from shallow waters (<10 m). Bachelor male diets were less diverse (H′ = 2.21) but more energy rich (~27 kcal/min) than territorial males (H′ = 2.54, ~13 kcal/min) and females (H′ = 2.74, ~11 kcal/min). Given recovering predators require adequate food and space, and the ecological interactions they elicit, we emphasize the importance of investigating niche space over the duration of recovery and considering sex‐based differences in these interactions.

Both black (Ursus americanus) and grizzly bears (U. arctos) are known to rub on trees and other objects, producing a network of repeatedly used and identifiable rub sites. In 2012, we used a resource selection function to evaluate hypothesized relationships between locations of 887 bear rubs in northwestern Montana, USA, and elevation, slope angle, density of open roads and distance from areas of heightened plant-productivity likely containing forage for bears. Slope and density of open roads were negatively correlated with rub presence. No other covariates were supported as explanatory variables. We also hypothesized that bear rubs would be more strongly associated with closed roads and developed trails than with game trails. The frequencies of bear rubs on 30 paired segments of developed tracks and game trails were not different. Our results suggest bear rubs may be associated with bear travel routes, and support their use as ''random'' sampling devices for non-invasive spatial capture-recapture population monitoring.

A general technique based on scoring scheme reweighting is proposed that can be used to speed up dynamic programming algorithms for a variety of pairwise sequence alignment problems. For the standard sequence alignment problem with an arbitrary gap penalty function, we show that a reweighted scoring scheme can be obtained by an efficient preprocessing step that computes a set of upper bounds on the score of the optimal alignment between pairs of suffixes of the sequences. A series of experiments on synthetic sequences and biological sequences indicate that our algorithm offers significant and robust speedup over the standard cubic-time dynamic programming algorithm. For sequences of length up to 2000 used in our experiments, the speedup factor ranges from 4 to more than 50. With a strong upper bound, a sub-cubic behavior in running time is also observed for all the tested situations.