Characterization of Six Bacteriophages of Serratia liquefaciens CP6 Isolated from the Sugar Beet Phytosphere

Six phages (ΦCP6-1 to ΦCP6-6) that are commonly found in the phytosphere of sugar beet (Beta vulgaris var. Amethyst) were investigated, and their relative impacts on their host (Serratia liquefaciens CP6) were compared. There were fundamental differences between the two most abundant predators of CP6 (ΦCP6-1 and ΦCP6-4). Like ΦCP6-2 and ΦCP6-5, ΦCP6-1 belonged to the family Siphoviridae, while ΦCP6-4 exhibited the morphology of the family Podoviridae. The other phages were members of the family Myoviridae. DNA-DNA cross-hybridization revealed that ΦCP6-1 and ΦCP6-4 had little common DNA, although all of the other phages exhibited some genetic similarity. Like ΦCP6-2, ΦCP6-3, and ΦCP6-5, ΦCP6-1 was capable of forming a lysogenic association with its host, while ΦCP6-4 and ΦCP6-6 appeared to be entirely virulent. Single-step growth curve experiments revealed that ΦCP6-4 had a much shorter latent period and a smaller burst size than ΦCP6-1. Also, ΦCP6-1 could transduce a number of host chromosomal markers with transfer frequencies of 2.9 × 10⁻⁹ to 3.9 × 10⁻⁷, whereas ΦCP6-4 could not transduce S. liquefaciens CP6 genes. When viewed in the context of the strikingly different temporal niches of these phages, our data provide an insight into how bacteriophage interactions with their hosts might reflect the natural ecology of bacteriophages. Our data also illustrate how the potential for gene transfer changes over time in an environment that supports several different phages.     

Conformist learning in nine-spined sticklebacks' foraging decisions

Theoretical analyses have reported that in most circumstances where natural selection favours reliance on social learning, conformity (positive frequency-dependent social learning) is also favoured. These findings suggest that much animal social learning should involve a copy-the-majority strategy, yet there is currently surprisingly little evidence for conformist learning among animals. Here, we investigate this possibility in the nine-spined stickleback (Pungitius pungitius) by manipulating the number of demonstrator fish at two feeders, one rich and one poor, during a demonstration phase and evaluating how this affects the likelihood that the focal fish copy the demonstrators'' apparent choices. As predicted, we observed a significantly increased level of copying with increasing numbers of demonstrators at the richer of the two feeders, with copying increasing disproportionately, rather than linearly, with the proportion of demonstrators at the rich foraging patch. Control conditions with non-feeding demonstrators showed that this was not simply the result of a preference for shoaling with larger groups, implying that nine-spined sticklebacks copy in a conformist manner.     

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.     

Constraint and competition in assemblages: a cross-continental and modeling approach for ants

The mechanisms leading to structure in local assemblages are controversial. On the one hand, assemblage structure is thought to be the outcome of local interactions determined by the properties of species and their responses to the local environment. Alternatively, this structure has been shown to be an emergent property of assemblages of identical individuals or of random sampling of a regional assemblage. In ants at baits, a combination of environmental stress and interspecific competition is widely held to lead to a unimodal relationship between the abundance of dominant ants and species richness. It is thought that in comparatively adverse environments, both abundance and richness are low. As habitats become more favorable, abundance increases until the abundance of dominant ants is so high that they exclude those that are subordinate and so depress richness. Here we demonstrate empirically that this relationship is remarkably similar across three continents. Using a null model approach, we then show that the ascending part of the relationship is largely constrained to take this form not simply as a consequence of stress but also as a result of the shape of abundance frequency distributions. While the form of the species-abundance frequency distribution can also produce the descending part of the relationship, interspecific competition might lead to it too. Scatter about the relationship, which is generally not discussed in the literature, may well be a consequence of resource availability and environmental patchiness. Our results draw attention to the significance of regional processes in structuring ant assemblages.     

Effects of fine sediment inputs from a logging road on stream insect communities:a large-scale experimental approach in a Canadian headwater stream

A forest headwater stream was manipulated (logging road-crossing amended) to induce fine sediment inputs. Benthic inorganic sediment concentrations .particles 1.5–250 μm increased from a 2-year pre-disturbance average of about 800 g m^–2 to over 5000 g m^–2 that persisted for 3 years. Aquatic insect communities were examined over the 5-year study period in the manipulated and nearby reference streams. Overall, the effects of the fine sediment increases on aquatic insect communities were minimal. There were no significant effects of sedimentation on total aquatic insect abundance or biomass. An index of multivariate dispersion gave no evidence of community stress at the manipulated site. Multivariate ordination plots and time trends among univariate community metrics indicated only subtle changes in community structure. Among the univariate metrics (16 time series analyses in total), six gave evidence of a sediment impact on aquatic insect communities. Of those, the clearest indications of an effect were small reductions in diversity and richness of spring communities. These resulted from a significant decline in the proportion of spring shredders, accompanied by a significant increase in the percent Chironomidae. This large-scale experimental approach integrated the realism of a whole-stream study with the control of a manipulative study by including pre-manipulation measurements and excluding other confounding catchment disturbances. In this regard, it may provide a more realistic measure of benthic community level responses to sedimentation in streams at a magnitude associated with logging activity than many previous studies.     

Global patterns of geographic range size in birds

Large-scale patterns of spatial variation in species geographic range size are central to many fundamental questions in macroecology and conservation biology. However, the global nature of these patterns has remained contentious, since previous studies have been geographically restricted and/or based on small taxonomic groups. Here, using a database on the breeding distributions of birds, we report the first (to our knowledge) global maps of variation in species range sizes for an entire taxonomic class. We show that range area does not follow a simple latitudinal pattern. Instead, the smallest range areas are attained on islands, in mountainous areas, and largely in the southern hemisphere. In contrast, bird species richness peaks around the equator, and towards higher latitudes. Despite these profoundly different latitudinal patterns, spatially explicit models reveal a weak tendency for areas with high species richness to house species with significantly smaller median range area. Taken together, these results show that for birds many spatial patterns in range size described in geographically restricted analyses do not reflect global rules. It remains to be discovered whether global patterns in geographic range size are best interpreted in terms of geographical variation in species assemblage packing, or in the rates of speciation, extinction, and dispersal that ultimately underlie biodiversity.     

Lineage sorting in multihost parasites: Eidmanniella albescens and Fregatiella aurifasciata on seabirds from the Galapagos Islands

Parasites comprise a significant percentage of the biodiversity of the planet and are useful systems to test evolutionary and ecological hypotheses. In this study, we analyze the effect of host species identity and the immediate local species assemblage within mixed species colonies of nesting seabirds on patterns of genetic clustering within two species of multihost ectoparasitic lice. We use three genetic markers (one mitochondrial, COI, and two nuclear, EF1‐α and wingless) and maximum likelihood phylogenetic trees to test whether (1) parasites show lineage sorting based on their host species; and (2) switching of lineages to the alternate host species depends on the immediate local species assemblage of individual hosts within a colony. Specifically, we examine the genetic structure of two louse species: Eidmanniella albescens, infecting both Nazca (Sula granti) and blue‐footed boobies (Sula nebouxii), and Fregatiella aurifasciata, infecting both great (Fregata minor) and magnificent frigatebirds (Fregata magnificens). We found that host species identity was the only factor explaining the patterns of genetic structure in both parasites. In both cases, there is evident genetic differentiation depending on the host species. Thus, a revision of the taxonomy of these louse species is needed. One possible explanation of this pattern is extremely low louse migration rates between host species, perhaps influenced by fine‐scale spatial separation of host species within mixed colonies, and low parasite infrapopulation numbers.