Fear factor: prey habitat selection and its consequences in a predation risk landscape

Predation risk influences prey use of space. However, little is known about how predation risk influences breeding habitat selection and the fitness consequences of these decisions. The nest sites of central-place foraging predators may spatially anchor predation risk in the landscape. We explored how the spatial dispersion of avian predator nests influenced prey territory location and fitness related measures. We placed 249 nest boxes for migrant pied flycatchers Ficedula hypoleuca , at distances between 10 and 630 m, around seven different sparrowhawk nests Accipiter nisus . After closely monitoring flycatcher nests we found that flycatcher arrival dates, nest box occupation rates and clutch size showed a unimodal relationship with distance from sparrowhawk nests. This relationship suggested an optimal territory location at intermediate distances between 330 and 430 m from sparrowhawk nests. Furthermore, pied flycatcher nestling quantity and quality increased linearly with distance from sparrowhawk nests. These fitness related measures were between 4 and 26% larger in flycatcher nestlings raised far from, relative to those raised nearby, sparrowhawk nests. Our results suggest that breeding sparrowhawk affected both flycatcher habitat selection and reproductive success. We propose that nesting predators create predictable spatial variation in predation risk for both adult prey and possibly their nests, to which prey individuals are able to adaptively respond. Recognising predictable spatial variation in perceived predation risk may be fundamental for a proper understanding of predator-prey interactions and indeed prey species interactions.     

Local modification of benthic flow environments by suspension-feeding stream insects

Larval black flies often exhibit spatially aggregated distributions, and individuals within patches can potentially reduce the supply of suspended food particles to downstream neighbors by modifying local flow characteristics. We used hot-film anemometry to quantify the magnitude and spatial extent of flow modifications downstream from feeding Simulium vittatum larvae in a laboratory flume, and to determine whether temporal patterns of flow variation are related to movements of the larval feeding appendages. Mean velocity 1 mm downstream from feeding larvae was reduced by 75%, and the percent reduction in velocity diminished asymptotically with downstream distance. Reduced velocities were evident as much as 60 mm downstream from, and 3 mm to either side of, larvae. Turbulence intensity (i.e., the SD of the velocity time series) was generally higher in this region relative to control flow conditions. Three results demonstrate the major contribution of the larval feeding appendages (i.e., labral fans) to such flow modification. First, there was a minimal reduction in mean velocity 5 mm downstream from non-feeding larvae (i.e., with closed labral fans), whereas mean velocity at the same location was reduced markedly when larvae were feeding. Second, the power spectrum of the velocity time series exhibited greatest power at frequencies that corresponded to the frequency of labral fan motions. Third, fan flick times accounted for most of the variance in the velocity power spectrum. The large local flow modifications that we documented have potentially important consequences for the feeding performance and growth of individuals located within larval aggregations, and are likely to influence behavioral interactions and spacing patterns.     

Gene Conversion in the Evolution of Both the H-2 and Qa Class I Genes of the Murine Major Histocompatibility Complex

In order to better understand the role of gene conversion in the evolution of the class I gene family of the major histocompatibility complex (MHC), we have used a computer algorithm to detect clustered sequence similarities among 24 class I DNA sequences from the H-2, Qa, and Tla regions of the murine MHC. Thirty-four statistically significant clusters were detected; individual analysis of the clusters suggested at least 25 past gene conversion or recombination events. These clusters are comparable in size to the conversions observed in the spontaneously occurring H-2K(bm) and H-2K(km2) mutations, and are distributed throughout all exons of the class I gene. Thus, gene conversion does not appear to be restricted to the regions of the class I gene encoding their antigen-presentation function. Moreover, both the highly polymorphic H-2 loci and the relatively monomorphic Qa and Tla loci appear to have participated as donors and recipients in conversion events. If gene conversion is not limited to the highly polymorphic loci of the MHC, then another factor, presumably natural selection, must be responsible for maintaining the observed differences in level of variation.     

Communal farmers of Namibia appreciate vultures and the ecosystem services they provide

Ecosystem services are cited as one of the many reasons for conserving declining vulture populations in Africa. We aimed to explore how communal farmers in Namibia perceive vultures and the ecosystem services they provide, with special focus on cultural and regulating ecosystem services. We surveyed 361 households across Namibia’s communal farmlands and found that over two-thirds of households liked vultures and found them useful, stating that they were harmless and useful for locating dead livestock. The minority of households who disliked vultures believed that they were killing their livestock. Poisoning was the main cause of vulture mortalities reported by farmers. While poisoning appears to be a concern for vultures in the communal farmlands, it appears that cultural use of vulture body parts is a minimal threat. We found that few farmers knew of cultural beliefs about vultures or uses for body parts; most farmers believed these beliefs and practices to be outdated. It is further promising that communal farmers have an overall positive perception of vultures. This highlights the potential for communal conservancies to bring attention to vulture conservation in their constituencies.     

Transcriptional profiling of inductive mesenchyme to identify molecules involved in prostate development and disease

Background  

The mesenchymal compartment plays a key role in organogenesis, and cells within the mesenchyme/stroma are a source of potent molecules that control epithelia during development and tumorigenesis. We used serial analysis of gene expression (SAGE) to profile a key subset of prostatic mesenchyme that regulates prostate development and is enriched for growth-regulatory molecules.     

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Background  

Rare genomic changes (RGCs) that are thought to comprise derived shared characters of individual clades are becoming an increasingly important class of markers in genome-wide phylogenetic studies. Recently, we proposed a new type of RGCs designated RGC_CAMs (after Conserved Amino acids-Multiple substitutions) that were inferred using genome-wide identification of amino acid replacements that were: i) located in unambiguously aligned regions of orthologous genes, ii) shared by two or more taxa in positions that contain a different, conserved amino acid in a much broader range of taxa, and iii) require two or three nucleotide substitutions. When applied to animal phylogeny, the RGC_CAM approach supported the coelomate clade that unites deuterostomes with arthropods as opposed to the ecdysozoan (molting animals) clade. However, a non-negligible level of homoplasy was detected.     

Multipoint approximations of identity-by-descent probabilities for accurate linkage analysis of distantly related individuals

We propose an analytical approximation method for the estimation of multipoint identity by descent (IBD) probabilities in pedigrees containing a moderate number of distantly related individuals. We show that in large pedigrees where cases are related through untyped ancestors only, it is possible to formulate the hidden Markov model of the Lander-Green algorithm in terms of the IBD configurations of the cases. We use a first-order Markov approximation to model the changes in this IBD-configuration variable along the chromosome. In simulated and real data sets, we demonstrate that estimates of parametric and nonparametric linkage statistics based on the first-order Markov approximation are accurate. The computation time is exponential in the number of cases instead of in the number of meioses separating the cases. We have implemented our approach in the computer program ALADIN (accurate linkage analysis of distantly related individuals). ALADIN can be applied to general pedigrees and marker types and has the ability to model marker-marker linkage disequilibrium with a clustered-markers approach. Using ALADIN is straightforward: It requires no parameters to be specified and accepts standard input files.     

A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407

In most cases, Escherichia coli exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic E. coli (ETEC) is the predominant cause of E. coli-mediated diarrhea in the developing world and is responsible for a significant portion of pediatric deaths. In this study, we determined the complete genomic sequence of E. coli {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407, a prototypical strain of enterotoxigenic E. coli, which reproducibly elicits diarrhea in human volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains, revealing that the chromosome is closely related to that of the nonpathogenic commensal strain E. coli HS and to those of the laboratory strains E. coli K-12 and C. Furthermore, these analyses demonstrated that there were no chromosomally encoded factors unique to any sequenced ETEC strains. Comparison of the E. coli {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407 plasmids with those from several ETEC strains revealed that the plasmids had a mosaic structure but that several loci were conserved among ETEC strains. This study provides a genetic context for the vast amount of experimental and epidemiological data that have been published.Current dogma suggests the Gram-negative motile bacterium Escherichia coli colonizes the infant gut within hours of birth and establishes itself as the predominant facultative anaerobe of the colon for the remainder of life (3, 59). While the majority of E. coli strains maintain this harmless existence, some strains have adopted a pathogenic lifestyle. Contemporary tenets suggest that pathogenic strains of E. coli have acquired genetic elements that encode virulence factors and enable the organism to cause disease (12). The large repertoire of virulence factors enables E. coli to cause a variety of clinical manifestations, including intestinal infections mediating diarrhea and extraintestinal infections, such as urinary tract infections, septicemia, and meningitis. Based on clinical manifestation of disease, the repertoire of virulence factors, epidemiology, and phylogenetic profiles, the strains causing intestinal infections can be divided into six separate pathotypes, viz., enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), diffuse adhering E. coli (DAEC), and enterotoxigenic E. coli (ETEC) (33, 35, 39).ETEC is responsible for the majority of E. coli-mediated cases of human diarrhea worldwide. It is particularly prevalent among children in developing countries, where sanitation and clean supplies of drinking water are inadequate, and in travelers to such regions. It is estimated that there are 200 million incidences of ETEC infection annually, resulting in hundreds of thousands of deaths in children under the age of 5 (55, 64). The essential determinants of ETEC virulence are traditionally considered to be colonization of the host small-intestinal epithelium via plasmid-encoded colonization factors (CFs) and subsequent release of plasmid-encoded heat-stable (ST) and/or heat-labile (LT) enterotoxins that induce a net secretory state leading to profuse watery diarrhea (20, 62). More recently, additional plasmid-encoded factors have been implicated in the pathogenesis of ETEC, namely, the EatA serine protease autotransporter (SPATE) and the EtpA protein, which acts as an intermediate in the adhesion between bacterial flagella and host cells (23, 32, 42, 46). Furthermore, a number of chromosomal factors are thought to be involved in virulence, e.g., the invasin Tia; the TibA adhesin/invasin; and LeoA, a GTPase with unknown function (14, 21, 22). E. coli {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407 is considered a prototypical ETEC strain; it expresses colonization factor antigen 1 (CFA/I) and the heat-stable and heat labile toxins. Loss of a 94.8-kb plasmid encoding CFA/I and a gene for ST enterotoxin from E. coli strain {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407 leads to reduced ability to cause diarrhea (17).Here, we report the complete genome sequence and virulence factor repertoire of the prototypical ETEC strain {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407 and the nucleotide sequence and gene repertoire of the plasmids from ETEC strain E1392/75, and we describe a novel conserved secretion system associated with the sequenced ETEC strains.