Fine-scale adaptation in a clonal sea anemone

Local adaptation in response to fine-scale spatial heterogeneity is well documented in terrestrial ecosystems. In contrast, in marine environments local adaptation has rarely been documented or rigorously explored. This may reflect real or anticipated effects of genetic homogenization, resulting from widespread dispersal in the sea. However, evolutionary theory predicts that for the many benthic species with complex life histories that include both sexual and asexual phases, each parental habitat patch should become dominated by the fittest and most competitive clones. In this study we used genotypic mapping to show that within headlands, clones of the sea anemone Actinia tenebrosa show restricted distributions to specific habitats despite the potential for more widespread dispersal. On these same shores we used reciprocal transplant experiments that revealed strikingly better performance of clones within their natal rather than foreign habitats as judged by survivorship, asexual fecundity, and growth. These findings highlight the importance of selection for fine-scale environmental adaptation in marine taxa and imply that the genotypic structure of populations reflects extensive periods of interclonal competition and site-specific selection.

Asexual reproduction does not produce clonal populations of the brooding coral Pocillopora damicornis on the Great Barrier Reef, Australia

We have investigated the relationship between genotypic diversity, the mode of production of brooded larvae and disturbance in a range of reef habitats, in order to resolve the disparity between the reproductive mode and population structure reported for the brooding coral Pocillopora damicornis. Within 14 sites across six habitats, the ratio of the observed (G o) to the expected (G e) genotypic diversity ranged from 69 to 100% of that expected for random mating. At three other sites in two habitats the G o /G e ranged from 35 to 53%. Two of these sites were recently bleached, suggesting that asexual recruitment may be favoured after disturbance. Nevertheless, our data suggest that brooded larvae, from each of five habitats surveyed, were asexually produced. While clonal recruitment may be important in disturbed habitats, the lack of clonality detected, both in this and earlier surveys of 40 other sites, implies that a disturbance is normally insufficient to explain this species’ continued investment in clonal reproduction.

Spectral element model updating for damage identification using clonal selection algorithm

A spectral element model updating procedure is presented to identify damage in a structure using Guided wave propagation results. Two damage spectral elements (DSE1 and DSE2) are developed to model the local (cracks in reinforcement bar) and global (debonding between reinforcement bar and concrete) damage in one-dimensional homogeneous and composite waveguide, respectively. Transfer matrix method is adopted to assemble the stiffness matrix of multiple spectral elements. In order to solve the inverse problem, clonal selection algorithm is used for the optimization calculations. Two displacement-based functions and two frequency-based functions are used as objective functions in this study. Numerical simulations of wave propagation in a bare steel bar and in a reinforcement bar without and with various assumed damage scenarios are carried out. Numerically simulated data are then used to identify local and global damage of the steel rebar and the concrete-steel interface using the proposed method. Results show that local damage is easy to be identified by using any considered objective function with the proposed method while only using the wavelet energy-based objective function gives reliable identification of global damage. The method is then extended to identify multiple damages in a structure. To further verify the proposed method, experiments of wave propagation in a rectangular steel bar before and after damage are conducted. The proposed method is used to update the structural model for damage identification. The results demonstrate the capability of the proposed method in identifying cracks in steel bars based on measured wave propagation data.

The effect of herbivores on genotypic diversity in a clonal aquatic plant

In clonal plants, vegetative parts may outcompete seeds in the absence of disturbance, limiting the build-up of genotypic diversity through repeated seedling recruitment (RSR). Herbivory may provide disturbance and trigger establishment of strong colonizers (seeds) at the expense of strong competitors (clonal propagules). In the clonal aquatic fennel pondweed Potamogeton pectinatus, two distinct herbivore guilds may modify the dynamics of propagation. In winter, Bewick's swans may deplete patches of tubers, promoting seedling establishment in spring. In summer, seed consumption by waterfowl can reduce the density of viable seeds but grazing may also reduce tuber production and hence facilitate seedling establishment. This study is among the first to experimentally test herbivore impact on plant genotypic diversity. We assess the separate and combined effects of both herbivore guilds on genotypic diversity and structure of fennel pondweed beds. Using microsatellites, we genotyped P. pectinatus from an exclosure experiment and assessed the contribution of herbivory, dispersal and sexual reproduction to the population genetic structure. Despite the predominance of clonal propagation in P. pectinatus, we found considerable genotypic diversity. Within the experimental blocks, kinship among genets decreased with geographic distance, clearly identifying a role for RSR in the maintenance of genotypic diversity within the fennel pondweed beds. However, over a period of five years, none of the herbivory treatments affected genotypic diversity. Hence, sexual reproduction on a local scale is important in this putatively clonal plant and possibly sufficient to ensure a relatively high genotypic diversity even in the absence of herbivores. Although we cannot preclude a role of herbivory in shaping genotypic diversity of a clonal plant, after five years of exclusion of the two investigated herbivore guilds no measurable effect on genotypic diversity was detected. © 2014 The Authors.

Fine-scale patterns of genetic variation in a widespread clonal seagrass species

Seagrasses are ecosystem engineers that offer important habitat for a large number of species and provide a range of ecosystem services. Many seagrass ecosystems are dominated by a single species, with research showing that genotypic diversity at fine spatial scales plays an important role in maintaining a range of ecosystem functions. However, for most seagrass species, information on fine-scale patterns of genetic variation in natural populations is lacking. In this study, we use a hierarchical sampling design to determine the levels of genetic and genotypic diversity at different spatial scales (centimeters, meters, kilometers) in the Australian seagrass Zostera muelleri. Our analysis shows that at fine spatial scales (<1 m), levels of genotypic diversity are relatively low (R(Plots) = 0.37 ± 0.06 SE), although there is some intermingling of genotypes. At the site (10’s m) and meadow location (km) scale, we found higher levels of genotypic diversity (R(sites) = 0.79 ± 0.04 SE; R(Locations) = 0.78 ± 0.04 SE). We found some sharing of genotypes between sites within meadows, but no sharing of genotypes between meadow locations. We also detected a high level of genetic structuring between meadow locations (FST = 0.278). Taken together, our results indicate that both sexual and asexual reproductions are important in maintaining meadows of Z. muelleri. The dominant mechanism of asexual reproduction appears to occur via localized rhizome extension, although the sharing of a limited number of genotypes over the scale of 10’s of meters could also result from the localized dispersal and recruitment of fragments. The large number of unique genotypes at the meadow scale indicates that sexual reproduction is important in maintaining these populations, while the high level of genetic structuring suggests little gene flow and connectivity between our study sites. These results imply that recovery from disturbances will occur through both sexual and asexual regeneration, but the limited connectivity at the landscape scale implies that recovery at meadow-scale losses is likely to be limited.

Methicillin-susceptible Staphylococcus aureus endocarditis isolates are associated with clonal complex 30 genotype and a distinct repertoire of enterotoxins and adhesins.

BACKGROUND: Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity. METHODS: IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes. RESULTS: 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P < .05 for all). CONCLUSIONS: MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study.

An immune network approach for web document clustering

The human immune system provides inspiration for solving a wide range of innovative problems. In this paper, we propse an immune network based approach for web document clustering. All the immune cells in the network competitively recognize the antigens (web documents) which are presented to the network one by one. The interaction between immune cells and an antigen leads to an augment of the network through the clonal selection and somatic mutation of the stimulated immune cells, while the interaction among immune cells results in a network compression. The structure of the immune network is well maintained by learning and self-regularity. We use a public web document data set to test the effectiveness of our method and compare it with other approaches. The experimental results demonstrate that the most striking advantage of immune-based data clustering is its adaptation in dynamic environment and the capability of finding new clusters automatically.

Laboratory enhanced surveillance for meningococcal disease in Victoria

Objective: To describe the epidemiological and microbiological characteristics and notification patterns of invasive meningococcal disease (IMD) in Victoria between 1990 and 1999.

Methods: Cases of IMD occurring between 1990 and 1995 identified in any of three databases were combined, matching where possible. Statistical modelling provided estimates of cases missing from all datasets. Notification sources for 1999 and 2000 cases were identified. Cases identified from notification and laboratory results provided the data to describe IMD epidemiology between 1990 and 1999.

Results: Between 1990 and 1995, 479 cases of IMD were identified. Three individual datasets each identified between 62 and 82% of cases and 47% of cases were identified in all three datasets. Statistical modelling estimated that between 37 and 83 additional cases were not identified by any dataset. Serogroup B and C strains caused 63 and 33% of culture-positive cases, respectively, with a substantial rise in serogroup C cases in 1999. Epidemiological characteristics remained relatively constant between 1990 and 1998, but an increase in patient age was seen in cases with serogroup C disease in 1999. In addition to three clonal strains seen elsewhere, an additional strain was identified that was unique to Victoria. Since January 1999, only 72% of notifications have come from treating doctors.

Conclusions: Meningococcal disease is of increasing public health significance in Victoria. Laboratory enhanced notification has improved case identification and detailed microbiological information has improved our understanding of the changing epidemiology of this disease. Collaboration with laboratories and other agencies, active investigation of putative cases and microbiological monitoring are important elements in supporting public health decisions about the control of IMD.

Learning to detect texture objects by artificial immune approaches

This paper introduces a novel method to detect texture objects from satellite images. First, a hierarchical strategy is developed to extract texture objects according to their roughness. Then, an artificial immune approach is presented to automatically generate segmentation thresholds and texture filters, which are used in the hierarchical strategy. In this approach, texture objects are regarded as antigens, and texture object filters and segmentation thresholds are regarded as antibodies. The clonal selection algorithm inspired by human immune system is employed to evolve antibodies. The population of antibodies is iteratively evaluated according to a statistical performance index corresponding to object detection ability, and evolves into the optimal antibody using the evolution principles of the clonal selection. Experimental results of texture object detection on satellite images are presented to illustrate the merit and feasibility of the proposed method.

Do reproductive tactics vary with habitat heterogeneity in the intertidal sea anemone Actinia tenebrosa?

Cnidarians display a diverse range of reproductive tactics including sexual and asexual modes of reproduction. Although few studies have looked for intraspecific variation in reproductive tactics, flexible expression of such life-history traits may be favoured in species that occupy a range of habitats. We tested this in the sea anemone Actinia tenebrosa by comparing cycles of reproductive activity and the mode of production of brooded larvae in local populations occupying boulder fields and stable rock platforms. We determined the mode of production of broods from eight rock platforms (separated by up to 1600 km) and two boulder shores on the south east coast of Australia using a combination of allozyme data and four newly characterised microsatellite markers.

We determined seasonal patterns of brooding and gonad development by monthly dissection of 15–30 adults from each of two boulder fields and two stable platforms. Previous genetic studies have shown that populations of A. tenebrosa on rock platforms can be highly clonal, whereas anemones on more heterogeneous boulder habitats display levels of genotypic diversity similar to that expected for sexual reproduction. We genotyped a total of 221 juveniles from 37 brooding adults including 11 broods and 80 juveniles from boulder shores. We did not detect any evidence of sexual production of broods. All brooded juveniles displayed identical multi-locus genotypes to their brood parent irrespective of habitat of origin or location, including 28 broods (200 juveniles) that were heterozygous at one or more locus. Similarly, we found that temporal patterns of gonad formation and brooding were consistent across habitats and locations. We detected 346 mature males, 234 non-reproductive or immature individuals, and no mature females within a total of 580 dissected individuals. These data suggest that the reproductive tactics of A. tenebrosa are essentially fixed and that variation in the genotypic diversity of populations may reflect variation in factors such as the input of sexually derived planktonically dispersed recruits or post-settlement processes. However, the apparent lack of females paradoxically implies that sexual reproduction, and hence recruitment, must be rare or no longer possible within some populations, and highlights the need for long-term studies of these populations.

Tracking phenotypically and functionally distinct T cell subsets via T cell repertoire diversity

Antigen-specific T cell receptors (TCRs) recognise complexes of immunogenic peptides (p) and major histocompatibility complex (MHC) glycoproteins. Responding T cell populations show profiles of preferred usage (or bias) toward one or few TCRβ chains. Such skewing is also observed, though less commonly, in TCRα chain usage. The extent and character of clonal diversity within individual, antigen-specific T cell sets can be established by sequence analysis of the TCRVβ and/or TCRVα CDR3 loops. The present review provides examples of such TCR repertoires in prominent responses to acute and persistent viruses. The determining role of structural constraints and antigen dose is discussed, as is the way that functionally and phenotypically distinct populations can be defined at the clonal level. In addition, clonal dissection of “high” versus “low” avidity, or “central” versus “effector” memory sets provides insights into how these antigen specific T cell responses are generated and maintained. As TCR diversity potentially influences both the protective capacity of CD8+ T cells and the subversion of immune control that leads to viral escape, analysing the spectrum of TCR selection and maintenance has implications for improving the functional efficacy of T cell responsiveness and effector function.

Consequences of immunodominant epitope deletion for minor influenza virus-specific CD8+-T-cell responses

The extent to which CD8+ T cells specific for other antigens expand to compensate for the mutational loss of the prominent DbNP366 and DbPA224 epitopes has been investigated using H1N1 and H3N2 influenza A viruses modified by reverse genetics. Significantly increased numbers of CD8+ KbPB1703+ , CD8+ KbNS2114+, and CD8+ DbPB1-F262+ T cells were found in the spleen and in the inflammatory population recovered by bronchoalveolar lavage from mice that were first given the -NP-PA H1N1 virus intraperitoneally and then challenged intranasally with the homologous H3N2 virus. The effect was less consistent when this prime-boost protocol was reversed. Also, though the quality of the response measured by cytokine staining showed some evidence of modification when these minor CD8+-T-cell populations were forced to play a more prominent part, the effects were relatively small and no consistent pattern emerged. The magnitude of the enhanced clonal expansion following secondary challenge suggested that the prime-boost with the -NP-PA viruses gave a response overall that was little different in magnitude from that following comparable exposure to the unmanipulated viruses. This was indeed shown to be the case when the total response was measured by ELISPOT analysis with virus-infected cells as stimulators. More surprisingly, the same effect was seen following primary challenge, though individual analysis of the CD8+ KbPB1703+ , CD8+ KbNS2114+, and CD8+ DbPB1-F262+ sets gave no indication of compensatory expansion. A possible explanation is that novel, as yet undetected epitopes emerge following primary exposure to the -NP-PA deletion viruses. These findings have implications for both natural infections and vaccines.

Design earthquake ground motion prediction for Perth metropolitan area with microtremor measurements for site characterization

Perth is the largest city in Western Australia and home to three-quarters of the state's residents. In recent decades, there have been a lot of earthquake activities just east of Perth in an area known as the South-West Seismic Zone. Previous numerical results of site response analyses based on limited available geology information for PMA indicated that Perth Basin might amplify the bedrock motion by more than 10 times at some frequencies and at some sites. Hence, more detailed studies on site characterization and amplification are necessary. The microtremor method using spatial autocorrelation (SPAC) processing is a useful tool for gaining thickness and shear wave velocity (SWV) of sediments and has been adopted in many previous studies. In this study, the response spectrum of rock site corresponding to the 475-year return period for PMA is defined according to the probabilistic seismic hazard analysis (PSHA) based on the latest ground motion attenuation model of Southwest Western Australia. Site characterization in PMA is performed using two microtremor measurements, namely SPAC technique and H/V method. The clonal selection algorithm (CSA) is introduced to perform direct inversion of SPAC curves to determine the soil profiles of representative PMA sites investigated in this study. Using the simulated bedrock motion as input, the responses of the soil sites are estimated using numerical method based on the shear-wave velocity vs. depth profiles determined from the SPAC technique. The response spectrum of the earthquake ground motion on surface of each site is derived from the numerical results of the site response analysis, and compared with the respective design spectrum defined in the Australian Earthquake Loading Code. The comparison shows that the code spectra are conservative in the short period range, but may slightly underestimate the response spectrum at some long period range.

Compensatory growth in an aquatic plant mediates exploitative competition between seasonally tied herbivores

The degree to which vertebrate herbivores exploitatively compete for the same food plant may depend on the level of compensatory plant growth. Such compensation is higher when there is reduced density-dependent competition in plants after herbivore damage. Whether there is relief from competition may largely be determined by the life-history stage of plants under herbivory. Such stage-specific compensation may apply to seasonal herbivory on the clonal aquatic plant sago pondweed (Potamogeton pectinatus L.). It winters in sediments of shallow lakes as tubers that are foraged upon by Bewick's Swans (Cygnus columbianus bewickii Yarrell), whereas aboveground biomass in summer is mostly consumed by ducks, coots, and Mute Swans. Here, tuber predation may be compensated due to diminished negative density dependence in the next growth season. However, we expected lower compensation to summer herbivory by waterfowl and fish as density of aboveground biomass in summer is closely related to photosynthetic carbon fixation. In a factorial exclosure study we simultaneously investigated (1) the effect of summer herbivory on aboveground biomass and autumn tuber biomass and (2) the effect of tuber predation in autumn on aboveground biomass and tuber biomass a year later. Summer herbivory strongly influenced belowground tuber biomass in autumn, limiting food availability to Bewick's Swans. In contrast, tuber predation in autumn by Bewick's Swans had a limited and variable effect on P. pectinatus biomass in the following growth season. Whereas relief from negative density dependence largely eliminates effects of belowground herbivory by swans, aboveground herbivory in summer limits both above- and belowground plant biomass. Hence, there was an asymmetry in exploitative competition, with herbivores in summer reducing food availability for belowground herbivores in autumn, but not the other way around.