Comparative analysis of phylogenetic and fishing effects in life history patterns of teleost fishes

The effects of fishing on life history traits and life history strategies of teleost fishes are analysed by a new comparative method that splits traits into an allometric part (size effect), an autoregressive phylogenetic component, and an environmental component (fishing effect). Both intra- and inter-specific variation of age and size at maturity, fecundity, adult size and egg size are analysed by comparing 84 populations of 49 species submitted to various fishing pressures. Two axes of life history diversification are found among teleosts. One is the well-known slow-fast continuum separating short-lived and early maturing species (like Clupeiformes) from longer-lived species that mature late relative to their size and spawn larger eggs (like salmonids or Scorpaeniformes). An additional strategy involves the schedule of resource allocation to growth and reproduction. Indeterminate growth allows higher teleosts (e.g. Gadiformes) to reach a large size while maturing early and laying small eggs. Increasing fishing pressure decreases age at maturity and egg size, and increases fecundity at maturity, the slope of the fecundity-length relationship and relative size at maturity. These compensations for higher adult mortality differ among life history strategies. Indeterminate growth is associated with a greater flexibility in resource allocation to growth and reproduction that facilitates greater resilience to fishing mortality.     

Markers for hypersensitive response and senescence show distinct patterns of expression

Controlled cellular suicide is an important process that can be observed in various organs during plant development. From the generation of proper sexual organs in monoecious plants to the hypersensitive response (HR) that occurs during incompatible pathogen interactions, programmed cell death (PCD) can be readily observed. Although several biochemical and morphological parameters have been described for various types of cell death in plants, the relationships existing between those different types of PCD events remain unclear. In this work, we set out to examine if two early molecular markers of HR cell death (HIN1 and HSR203J) as well as a senescence marker (SAG12) are coordinately induced during these processes. Our result indicates that although there is evidence of some cross-talk between both cell death pathways, spatial and temporal characteristics of activation for these markers during hypersensitive response and senescence are distinct. These observations indicate that these markers are relatively specific for different cell death programs. Interestingly, they also revealed that a senescence-like process seems to be triggered at the periphery of the HR necrotic lesion. This suggests that cells committed to die during the HR might release a signal able to induce senescence in the neighboring cells. This phenomenon could correspond to the establishment of a second barrier against pathogens. Lastly, we used those cell death markers to better characterize cell death induced by copper and we showed that this abiotic induced cell death presents similarities with HR cell death.     

Cholesterol-dependent separation of the beta2-adrenergic receptor from its partners determines signaling efficacy: insight into nanoscale organization of signal transduction

Determining the role of lipid raft nanodomains in G protein-coupled receptor signaling remains fraught by the lack of assays directly monitoring rafts in native membranes. We thus combined extensive biochemical and pharmacological approaches to a nanoscale strategy based on bioluminescence resonance energy transfer (BRET) to assess the spatial and functional influence of cholesterol-rich liquid-ordered lipid nanodomains on beta(2) adrenergic receptor (beta(2)AR) signaling. The data revealed that whereas beta(2)AR did not partition within liquid-ordered lipid phase, a pool of G protein and adenylyl cyclase (AC) were sequestered in these domains. Destabilization of the liquid-ordered phase by cholesterol depletion led to a lateral redistribution of Galpha(s) and AC that favored interactions between the receptor and its signaling partners as assessed by BRET. This resulted in an increased basal and agonist-promoted beta(2)AR-stimulated cAMP production that was partially dampened as a result of constitutive protein kinase A-dependent phosphorylation and desensitization of the receptor. This restraining influence of nanodomains on beta(2)AR signaling was further substantiated by showing that liquid-ordered lipid phase stabilization using caveolin overexpression or increasing membrane cholesterol amount led to an inhibition of beta(2)AR-associated signaling. Given the emerging concept that clustering of receptors and effectors into signaling platforms contributes to the efficacy and selectivity of signal transduction, our results support a model whereby cholesterol-promoted liquid-ordered lipid phase-embedding G(s) and AC allows their lateral separation from the receptor, thus restraining the basal activity and controlling responsiveness of beta(2)AR signaling machinery within larger signaling platforms.     

Impact of myxomatosis in relation to local persistence in wild rabbit populations: the role of waning immunity and the reproductive period

Many diseases are less severe when they are contracted in early life. For highly lethal diseases, such as myxomatosis in rabbits, getting infected early in life can represent the best chance for an individual to survive the disease. For myxomatosis, early infections are attenuated by maternal antibodies. This may lead to the immunisation of the host, preventing the subsequent development of the lethal form of the disease. But early infection of young individuals requires specific demographic and epidemiological contexts, such as a high transmission rate of the pathogen agent. To investigate other factors involved in the impact of such diseases, we have built a stochastic model of a rabbit metapopulation infected by myxomatosis. We show that the impact of the pathogen agent can be reduced by early infections only when the agent has a long local persistence time and/or when the host subpopulations are highly connected. The length of the reproductive period and the duration of acquired immunity are also important factors influencing the persistence of the pathogen and thus, the impact of the disease. Besides confirming the role of classical factors in the persistence of a pathogen agent, such as the size of the subpopulation or the degree of connectivity, our results highlight novel factors that can modulate the impact of diseases whose severity increase with age.     

Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable?

Rao has developed quadratic entropy to measure diversity in a set of entities divided up among a fixed set of categories. This index depends on a chosen matrix of dissimilarities among categories and a frequency distribution of these categories. With certain choices of dissimilarities, this index could be maximized over all frequency distributions by eliminating several categories. This unexpected result is radically opposite to those obtained with usual diversity indices. We demonstrate that the elimination of categories to maximize the quadratic entropy depends on mathematical properties of the chosen dissimilarities. In particular, when quadratic entropy is applied to ultrametric dissimilarities, all categories are retained in order to reach its maximal value. Three examples, varying from simple one-dimensional to ultrametric dissimilarity matrices, are provided. We conclude that, as far as diversity measurement is concerned, quadratic entropy is most relevant when applied to ultrametric dissimilarities.     

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.     

True versus false parasite interactions: a robust method to take risk factors into account and its application to feline viruses

Background

Multiple infections are common in natural host populations and interspecific parasite interactions are therefore likely within a host individual. As they may seriously impact the circulation of certain parasites and the emergence and management of infectious diseases, their study is essential. In the field, detecting parasite interactions is rendered difficult by the fact that a large number of co-infected individuals may also be observed when two parasites share common risk factors. To correct for these “false interactions”, methods accounting for parasite risk factors must be used.

Methodology/Principal Findings

In the present paper we propose such a method for presence-absence data (i.e., serology). Our method enables the calculation of the expected frequencies of single and double infected individuals under the independence hypothesis, before comparing them to the observed ones using the chi-square statistic. The method is termed “the corrected chi-square.” Its robustness was compared to a pre-existing method based on logistic regression and the corrected chi-square proved to be much more robust for small sample sizes. Since the logistic regression approach is easier to implement, we propose as a rule of thumb to use the latter when the ratio between the sample size and the number of parameters is above ten. Applied to serological data for four viruses infecting cats, the approach revealed pairwise interactions between the Feline Herpesvirus, Parvovirus and Calicivirus, whereas the infection by FIV, the feline equivalent of HIV, did not modify the risk of infection by any of these viruses.

Conclusions/Significance

This work therefore points out possible interactions that can be further investigated in experimental conditions and, by providing a user-friendly R program and a tutorial example, offers new opportunities for animal and human epidemiologists to detect interactions of interest in the field, a crucial step in the challenge of multiple infections.     

Linkage conservation of homologous esterase loci in fish (Cyprinodontoidei: Poeciliidae)

Homologies among esterase isozymes in fish in the poeciliid genera Poeciliopsis and Xiphophorus are proposed. Esterase homologies are based on their tissue distributions and inhibition and substrate properties. The five esterases include two carboxylesterases, one eserine sulfate-sensitive esterase, and two esterases resistant to inhibition, one of which reacts only with acetate esters. Linkage studies in Poeciliopsis monacha indicate that the loci encoding the two carboxylesterases are linked to each other and to the locus for eye-specific lactate dehydrogenase. Comparisons of the linkage reported here with earlier studies in Xiphophorus suggest that there is a large region of linkage homology in the genetic maps of Poeciliopsis and Xiphophorus.This work was supported by grants from the National Science Foundation (DEB76-19285) to R. C. Vrijenhoek and the Charles and Johanna Busch Fund to R. C. Vrijenhoek and N. H. Hart. J. F. L. and P. J. P. were supported by U.S. Public Health Service Genetics Training Grant GM07129-04.