Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

A large trophic quilt

Plants and invertebrate herbivores are major constituents of terrestrial food webs. Identifying component species and tracing their interactions in highly diverse communities are a monumental task. Novotny et al. 2010 present the first broad conspectus of herbivore–plant interactions in a forest in Papua New Guinea. In more than 15 years, nearly 7000 feeding links were traced between about 200 plants and 1500 insect herbivores. Although staggering, these figures might represent only 15% of the total herbivore richness and interaction diversity in that lowland forest. Standardized comparisons also showed distinctive specialization and diversification patterns in different feeding guilds, restricting the possibility of using any single guild as surrogate for the entire assemblage.     

Monitoring of trophic chains

In the paper simple trophic chains of the type resource-producer-primary consumer are considered. For an analysis of the dynamic state monitoring of this system, the concept of observability of mathematical systems theory is proposed. Using a linearization method of non-linear observation systems, biologically interpretable sufficient conditions are obtained to guarantee local observability. The latter means that based on the dynamic observation of a single component, the state of the whole system can be uniquely recovered, at least near a positive equilibrium.     

Beyond trophic morphology: stable isotopes reveal ubiquitous versatility in marine turtle trophic ecology

The idea that interspecific variation in trophic morphology among closely related species effectively permits resource partitioning has driven research on ecological radiation since Darwin first described variation in beak morphology among Geospiza. Marine turtles comprise an ecological radiation in which interspecific differences in trophic morphology have similarly been implicated as a pathway to ecopartition the marine realm, in both extant and extinct species. Because marine turtles are charismatic flagship species of conservation concern, their trophic ecology has been studied intensively using stable isotope analyses to gain insights into habitat use and diet, principally to inform conservation management. This legion of studies provides an unparalleled opportunity to examine ecological partitioning across numerous hierarchical levels that heretofore has not been applied to any other ecological radiation. Our contribution aims to provide a quantitative analysis of interspecific variation and a comprehensive review of intraspecific variation in trophic ecology across different hierarchical levels marshalling insights about realised trophic ecology derived from stable isotopes. We reviewed 113 stable isotope studies, mostly involving single species, and conducted a meta‐analysis of data from adults to elucidate differences in trophic ecology among species. Our study reveals a more intricate hierarchy of ecopartitioning by marine turtles than previously recognised based on trophic morphology and dietary analyses. We found strong statistical support for interspecific partitioning, as well as a continuum of intraspecific trophic sub‐specialisation in most species across several hierarchical levels. This ubiquity of trophic specialisation across many hierarchical levels exposes a far more complex view of trophic ecology and resource‐axis exploitation than suggested by species diversity alone. Not only do species segregate along many widely understood axes such as body size, macrohabitat, and trophic morphology but the general pattern revealed by isotopic studies is one of microhabitat segregation and variation in foraging behaviour within species, within populations, and among individuals. These findings are highly relevant to conservation management because they imply ecological non‐exchangeability, which introduces a new dimension beyond that of genetic stocks which drives current conservation planning. Perhaps the most remarkable finding from our data synthesis is that four of six marine turtle species forage across several trophic levels. This pattern is unlike that seen in other large marine predators, which forage at a single trophic level according to stable isotopes. This finding affirms suggestions that marine turtles are robust sentinels of ocean health and likely stabilise marine food webs. This insight has broader significance for studies of marine food webs and trophic ecology of large marine predators. Beyond insights concerning marine turtle ecology and conservation, our findings also have broader implications for the study of ecological radiations. Particularly, the unrecognised complexity of ecopartitioning beyond that predicted by trophic morphology suggests that this dominant approach in adaptive radiation research likely underestimates the degree of resource overlap and that interspecific disparities in trophic morphology may often over‐predict the degree of realised ecopartitioning. Hence, our findings suggest that stable isotopes can profitably be applied to study other ecological radiations and may reveal trophic variation beyond that reflected by trophic morphology.     

Competition between phenotypes

Summary We present two models for phenotypic-dependent interspecific competition. In both cases the survivorship of individuals of one population depends on the entire phenotypic distribution of the other species. The first model considers a continuously varying metric trait, with assortative or random mating; the second model examines a character controlled by two alleles at a single locus. Pursuing the notion that each population maximizes its mean fitness we define a vector-optimum strategy using the concepts of cooperative and competitive optima. It is found that the dynamical constraints placed on the equations of motion by Mendelian genetics often prevent a population from evolving to a strategic optimum. However, for the single locus case with complete dominance, the competitive optimum always coincides with some dynamical equilibrium on the Hardy-Weinberg manifold.     

Murine catalase phenotypes

An examination of three inbred strains of mice differing with respect to liver and kidney catalase activity reveals two distinct genetic factors controlling the level of liver catalase activity. The first genetic factor controls the catalytic activity of the enzyme. Specific activity of purified enzyme from C57BL/6 and C57BL/Ha strains is 60% of that of the DBA/2 strain. The second factor controls the content of liver catalase. Liver catalase of C57BL/Ha is degraded in vivo at a rate one half that of liver catalase of DBA/2 and C57BL/6, resulting in the accumulation of twice as many catalase molecules in C57BL/Ha. The factor affecting turnover of catalase is apparently specific for catalase of liver since no differences exist in kidney catalase levels between C57BL/Ha and C57BL/6. Furthermore, this factor does not appear to alter the metabolism of total liver protein since no substantial difference in the turnover rate of liver protein is observed among the strains. It is particularly significant that the genetic factor affecting the amount of liver catalase does so by altering the rate of catalase degradation rather than the rate of synthesis, confirming the previously published report of Rechcigl and Heston (1967). Thus, these studies emphasize that the quantity of an enzyme in animal cells is a balance between the rate of synthesis and the rate of degradation of the enzyme.This paper was presented at a symposium entitled Genetic Control of Mammalian Metabolism held at The Jackson Laboratory, Bar Harbor, Maine, June 30–July 2, 1969. The symposium was supported in part by an allocation from NIH General Research Support Grant FR 05545 from the Division of Research Resources to The Jackson Laboratory.This investigation was supported by USPHS Research Grant GM 14931 from the Division of General Medical Sciences, and Grants PF-373 and P-427 from the American Cancer Society.     

Rotifer occurrence and trophic degree

Information on the distribution of planktic, periphytic and benthic rotifers from diverse waters in south and central Sweden was analysed for details on relationships to the trophic degree. Three factors were combined in order to get an estimation of the trophic degree: tot-P-content, electrolytic conductivity and content of dry matter. Indicators of oligotrophic and eutrophic environments are enumerated. As far as the planktic species are concerned, the results are largely compatible with those of earlier investigations (while the non-planktic forms were previously less known in this respect). Some eutrophy indicators have been reported as typical of saprobic environments.     

The evolution of trophic structure

The trophic relationships of an ecological community were represented by digital individuals consuming resources or prey within a simulated ecosystem and producing offspring that may differ from their parents. When individuals meet, a few simple rules are used to decide the outcome of their interaction. Trophically complex systems persist for long periods of time even in finite communities, provided that the strength of predator-prey interaction is sufficient to repay the cost of maintenance. The topology of the food web and important system-level attributes such as overall productivity follow from the rules of engagement: that is, the macroscopic properties of the ecosystem follow from the microscopic attributes of individuals, without the need to invoke the emergence of novel processes at the level of the whole system. Evolutionarily stable webs exist only when the pool of available species is small. If the pool is large, or speciation is allowed, species composition changes continually, while overall community properties are maintained. Ecologically separate and topologically different source webs based on the same pool of resources usually coexist for long periods of time, through negative frequency-dependent selection at the level of the source web as a whole. Thus, the evolved food web of species-rich communities is a highly dynamic structure with continual species turnover. It both imposes selection on each species and itself responds to selection, but selection does not necessarily maximize stability, productivity or any other community property.     

Eco-evolutionary trophic dynamics: loss of top predators drives trophic evolution and ecology of prey

Ecosystems are being altered on a global scale by the extirpation of top predators. The ecological effects of predator removal have been investigated widely; however, predator removal can also change natural selection acting on prey, resulting in contemporary evolution. Here we tested the role of predator removal on the contemporary evolution of trophic traits in prey. We utilized a historical introduction experiment where Trinidadian guppies (Poecilia reticulata) were relocated from a site with predatory fishes to a site lacking predators. To assess the trophic consequences of predator release, we linked individual morphology (cranial, jaw, and body) to foraging performance. Our results show that predator release caused an increase in guppy density and a "sharpening" of guppy trophic traits, which enhanced food consumption rates. Predator release appears to have shifted natural selection away from predator escape ability and towards resource acquisition ability. Related diet and mesocosm studies suggest that this shift enhances the impact of guppies on lower trophic levels in a fashion nuanced by the omnivorous feeding ecology of the species. We conclude that extirpation of top predators may commonly select for enhanced feeding performance in prey, with important cascading consequences for communities and ecosystems.     

Application of trophic transfer efficiency and age structure in the trophic analysis of fossil assemblages

We evaluate onshore-offshore trends in age-frequency distributions and trophic transfer efficiencies using 11 modern death assemblages off the Texas coast. Trophic transfer efficiencies within trophic levels offer little insight over that achieved by a size-frequency distribution. Production/biomass ratios will always be 1 in the fossil record. Within trophic-level estimates of paleogrowth efficiency, the ratio of paleoproduction to paleoingestion (Pⁱ_glt/Iⁱ_lt where i indicates the i^th trophic level and lt indicates the time-averaged value) follow the expected ecological trend precisely in that paleogrowth efficiency is consistently higher in primary consumers than in predators in all 11 death assemblages. Paleoutilization efficiency, the ratio of predator paleoingestion to prey paleoproduction, I²_lt^°/P¹_glt^°, may provide information on the degree of bias in the preservation of primary (1 °) and secondary (2 °) consumer trophic groups. I²_lt^°/P¹_glt^° fell below 0.1 in most cold-seep and bay assemblages, indicating a large surplus of primary consumers. In sharp contrast, I²_lt^°/P¹_glt^°     

Morphological drivers of trophic cascades

Worldwide, local anthropogenic extinctions have recently been reported to induce trophic cascades, defined as perturbations of top consumers that propagate along food chains down to primary producers. This focus on the effects of top‐consumer extinction (i.e. of species presence) ignores potential cascading effects of the rapid morphological changes that may precede extinction. Here, we show in an experimental, three‐level food chain including medaka fish, herbivorous zooplankton and unicellular algae that varying body length of a single fish from large (36.3 mm) to small (11.5 mm) induced a stronger trophic cascade than varying an average‐sized (23.8 mm) fish from being present to absent. The strength of fish predation on zooplankton scaled quasi linearly (not with a power exponent) with fish body length and associated gape width, suggesting that the resultant trophic cascade was morphology (not metabolism)‐dependent. The effect of fish body length was stronger on phyto‐ than on zooplankton, because large‐sized fish had the unique ability to suppress large‐sized herbivores, which in turn had high grazing capacities. Hence, our results show that consumer body size, by setting diet breadth, can both drive and magnify the strength of trophic cascades. In contrast, fish body shape had no significant effect on fish predatory performances when its allometric component (the effect of size on shape) was removed. In the wild, human‐induced body downsizing of top consumers is widespread, and mitigating the resultant perturbations to ecosystem function and services will require a paradigm shift from preserving species presence towards preserving species size structure.     

Leading indicators of trophic cascades

Regime shifts are large, long-lasting changes in ecosystems. They are often hard to predict but may have leading indicators which are detectable in advance. Potential leading indicators include wider swings in dynamics of key ecosystem variables, slower return rates after perturbation and shift of variance towards lower frequencies. We evaluated these indicators using a food web model calibrated to long-term whole-lake experiments. We investigated whether impending regime shifts driven by gradual increase in exploitation of the top predator can create signals that cascade through food webs and be discerned in phytoplankton. Substantial changes in standard deviations, return rates and spectra occurred near the switch point, even two trophic levels removed from the regime shift in fishes. Signals of regime shift can be detected well in advance, if the driver of the regime shift changes much more slowly than the dynamics of key ecosystem variables which can be sampled frequently enough to measure the indicators. However, the regime shift may occur long after the driver has passed the critical point, because of very slow transient dynamics near the critical point. Thus, the ecosystem can be poised for regime shift by the time the signal is discernible. Field tests are needed to evaluate these indicators.     

Phylogenetic analysis of trophic associations

Ecologists frequently collect data on the patterns of association between adjacent trophic levels in the form of binary or quantitative food webs. Here, we develop statistical methods to estimate the roles of consumer and resource phylogenies in explaining patterns of consumer-resource association. We use these methods to ask whether closely related consumer species are more likely to attack the same resource species and whether closely related resource species are more likely to be attacked by the same consumer species. We then show how to use estimates of phylogenetic signals to predict novel consumer-resource associations solely from the phylogenetic position of species for which no other (or only partial) data are available. Finally, we show how to combine phylogenetic information with information about species' ecological characteristics and life-history traits to estimate the effects of species traits on consumer-resource associations while accounting for phylogenies. We illustrate these techniques using a food web comprising species of parasitoids, leaf-mining moths, and their host plants.     

Bioaccumulation and trophic dilution of human pharmaceuticals across trophic positions of an effluent-dependent wadeable stream

Though pharmaceuticals are increasingly observed in a variety of organisms from coastal and inland aquatic systems, trophic transfer of pharmaceuticals in aquatic food webs have not been reported. In this study, bioaccumulation of select pharmaceuticals was investigated in a lower order effluent-dependent stream in central Texas, USA, using isotope dilution liquid chromatography–tandem mass spectrometry (MS). A fish plasma model, initially developed from laboratory studies, was tested to examine observed versus predicted internal dose of select pharmaceuticals. Pharmaceuticals accumulated to higher concentrations in invertebrates relative to fish; elevated concentrations of the antidepressant sertraline and its primary metabolite desmethylsertraline were observed in the Asian clam, Corbicula fluminea, and two unionid mussel species. Trophic positions were determined from stable isotopes (δ¹⁵N and δ¹³C) collected by isotope ratio-MS; a Bayesian mixing model was then used to estimate diet contributions towards top fish predators. Because diphenhydramine and carbamazepine were the only target compounds detected in all species examined, trophic magnification factors (TMFs) were derived to evaluate potential trophic transfer of both compounds. TMFs for diphenhydramine (0.38) and carbamazepine (1.17) indicated neither compound experienced trophic magnification, which suggests that inhalational and not dietary exposure represented the primary route of uptake by fish in this effluent-dependent stream.     

Addressing the trophic status in urban ponds: An evaluation of current trophic state indexes

Ponds are generally understudied. Quality problems in urban freshwaters can arise from eutrophication, and trophic status classification gives information related to their ecological situation. Ponds may strongly differ from larger lakes for which most current trophic status classification methods have been developed. This paper seeks to compare and contrast the suitability of six trophic status indexes (TSI) and OECD trophic classifications system currently used to evaluate the eutrophication level of urban ponds in the Subtropical region. The trophic status was evaluated based on total phosphorus (TP), soluble reactive phosphorus (SRP), total nitrogen (TN) and phytoplankton chlorophyll a (Chl a) in 12 ponds placed in different cities from the Pampean region (Argentina), in the warm and cold seasons. Our results demonstrate that there was no relationship between pond size (0.08–2.45 ha) and trophic status. TSIs estimated with Chl a showed significant differences between seasons and the range oligotrophic-hypertrophic of trophism was encountered. Conversely, TSIs estimated with nutrient concentrations (TP, SRP, TN) did not. The pond's classification in trophic levels fell in the eutrophic-hypertrophic extreme, and only considering TN/TP broadened the trophic range. No relationship was encountered between Chl a and P; however, Chl a and TN/TP were positively correlated during the warm season. Lower trophic levels regarding TSI (Chl a) were generally associated with a dense floating-macrophyte cover. We suggest that the TSI considered should correspond to the latitudinal region in which the ponds are located. Our results indicate that it appears restrictive to consider only P contents in ponds to assess eutrophication. Under the proposed framework, the key issues for the study of pond trophic classification will be to include not only P but N concentrations and TN/TP. Also, phytoplankton Chl a concentration jointly with floating macrophytes biomass/coverage should be considered as diagnosis parameters.