Trait-mediated indirect interactions in a marine intertidal system as quantified by functional responses

Studies of trait-mediated indirect interactions (TMIIs) typically focus on effects higher predators have on per capita consumption by intermediate consumers of a third, basal prey resource. TMIIs are usually evidenced by changes in feeding rates of intermediate consumers and/or differences in densities of this third species. However, understanding and predicting effects of TMIIs on population stability of such basal species requires examination of the type and magnitude of the functional responses exhibited towards them. Here, in a marine intertidal system consisting of a higher-order fish predator, the shanny Lipophrys pholis, an intermediate predator, the amphipod Echinogammarus marinus, and a basal prey resource, the isopod Jaera nordmanni, we detected TMIIs, demonstrating the importance of habitat complexity in such interactions, by deriving functional responses and exploring consequences for prey population stability. Echinogammarus marinus reacted to fish predator diet cues by reducing activity, a typical anti-predator response, but did not alter habitat use. Basal prey, Jaera nordmanni, did not respond to fish diet cues with respect to activity, distribution or aggregation behaviour. Echinogammarus marinus exhibited type II functional responses towards J. nordmanni in simple habitat, but type III functional responses in complex habitat. However, while predator cue decreased the magnitude of the type II functional response in simple habitat, it increased the magnitude of the type III functional response in complex habitat. These findings indicate that, in simple habitats, TMIIs may drive down consumption rates within type II responses, however, this interaction may remain de-stabilising for prey populations. Conversely, in complex habitats, TMIIs may strengthen regulatory influences of intermediate consumers on prey populations, whilst potentially maintaining prey population stability. We thus highlight that TMIIs can have unexpected and complex ramifications throughout communities, but can be unravelled by considering effects on intermediate predator functional response types and magnitudes.

Phenotypic plasticity affects the response of a sexually selected trait to anthropogenic noise

Sexually selected traits are shaped by an interaction between sexual selection and other natural selection pressures in the environment. However, there is little understanding of how recent anthropogenic environmental change affects the elaboration of sexually selected traits. Most sexually selected traits are complex displays comprising multiple components that interact in a functional way, thereby affecting overall trait expression. To understand how environmental change may shape the expression of sexually selected traits, we have to consider not only (i) the phenotypic plasticity of individual components of traits but also their (ii) phenotypic integration, that is, the correlations among trait components, as well as (iii) plasticity integration, that is, the correlations among the plasticities of trait components. Here, we show that background noise is a considerable pressure in shaping a sexually selected multicomponent acoustic signal, bird song. We compared singing behavior of European robins (Erithacus rubecula) in territories that differed in levels of anthropogenic noise and conducted noise-exposure experiments to test if behavioral plasticity caused immediate changes in song components, for example, minimum frequency, song complexity, and song length. We found that song components differed in their plasticity to background noise and that plasticity integration between components may further restrict the elaboration of song. Thus, the altered expression of song components under noise exposure leads to increased phenotypic integration, which is linked with reduced song complexity. Our findings demonstrate that plasticity integration restricts the elaboration of a sexually selected trait, which raises the question of how changing environments may modify sexual selection.

Trait assembly in plant assemblages and its modulation by productivity and disturbance

Understanding how communities assemble is a key challenge in ecology. Conflicting hypotheses suggest that plant traits within communities should show divergence to reflect strategies to reduce competition or convergence to reflect strong selection for the environmental conditions operating. Further hypotheses suggest that plant traits related to productivity show convergence within communities, but those related to disturbance show divergence. Data on functional diversity (FD ) of 12 traits from 30 communities ranging from arable fields, mown and grazed grasslands to moorland and woodland were employed to test this using randomisations tests and correlation and regression analysis. No traits showed consistent significant convergence or divergence in functional diversity. When correlated to measures of the environment, the most common pattern was for functional diversity to decline (7 out of 12 traits) and the degree of convergence (7 out of 12 traits) to increase as the levels of productivity (measured as primary productivity, soil nitrogen release and vegetation C:N) and disturbance increased. Convergence or a relationship between functional diversity and the environment was not seen for a number of important traits, such as LDMC and SLA, which are considered as key predictors of ecosystem function. The analysis indicates that taking into account functional diversity within a system may be a necessary part of predicting the relationship between plant traits and ecosystem function, and that this may be of particular importance within less productive and less disturbed systems. © 2011 Springer-Verlag.

Trait directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass Holcus lanatus

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate toler- ance in wild grass Holcus lanatus genotypes screened from the same habitat.

De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide poly- morphism (SNP) calling were conducted on RNA extracted from H.lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (P) and phosphorus-treated (P+) genovars of tolerant (T) and nontoler- ant (N) phenotypes were mapped to this reference transcriptome.

Heatmaps of the gene expression data showed strong clustering of each P+/P treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA- binding protein and transposable elements.

A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP pro- files, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.

Predator cue studies reveal strong trait-mediated effects in communities despite variation in experimental designs

Nonconsumptive or trait-mediated effects of predators on their prey often outweigh density-mediated interactions where predators consume prey. For instance, predator presence can alter prey behaviour, physiology, morphology and/or development. Despite a burgeoning literature, our ability to identify general patterns in prey behavioural responses may be influenced by the inconsistent methodologies of predator cue experiments used to assess trait-mediated effects. We therefore conducted a meta-analysis to highlight variables (e.g. water type, predator husbandry, exposure time) that may influence invertebrate prey's behavioural responses to fish predator cues. This revealed that changes in prey activity and refuge use were remarkably consistent overall, despite wide differences in experimental methodologies. Our meta-analysis shows that invertebrates altered their behaviour to predator cues of both fish that were fed the focal invertebrate and those that were fed other prey types, which suggests that invertebrates were not responding to specific diet information in the fish cues. Invertebrates also altered their behaviour regardless of predator cue addition regimes and fish satiation levels. Cue intensity and exposure time did not have significant effects on invertebrate behaviour. We also highlight that potentially confounding factors, such as parasitism, were rarely recorded in sufficient detail to assess the magnitude of their effects. By examining the likelihood of detecting trait-mediated effects under large variations in experimental design, our study demonstrates that trait-mediated effects are likely to have pervasive and powerful influences in nature.

Identification of quantitative trait loci for rice grain element composition on an arsenic impacted soil:Influence of flowering time on genetic loci

Elements in grain crops such as iron, zinc and selenium are essential in the human diet, whereas elements such as arsenic are potentially toxic to humans. This study aims to identify quantitative trait loci (QTLs) for trace elements in rice grain. A field experiment was conducted in an arsenic enriched field site in Qiyang, China using the Bala x Azucena mapping population grown under standard field conditions. Grains were subjected to elemental analysis by inductively coupled plasma mass spectroscopy. QTLs were detected for the elemental composition within the rice grains, including for iron and selenium, which have previously been detected in this population grown at another location, indicating the stability of these QTLs. A correlation was observed between flowering time and a number of the element concentrations in grains, which was also revealed as co-localisation between flowering time QTLs and grain element QTLs. Unravelling the environmental conditions that influence the grain ionome appears to be complex, but from the results in this study one of the major factors which controls the accumulation of elements within the grain is flowering time.

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.