Rigorous conditions for food-web intervality in high-dimensional trophic niche spaces

Food webs represent trophic (feeding) interactions in ecosystems. Since the late 1970s, it has been recognized that food-webs have a surprisingly close relationship to interval graphs. One interpretation of food-web intervality is that trophic niche space is low-dimensional, meaning that the trophic character of a species can be expressed by a single or at most a few quantitative traits. In a companion paper we demonstrated, by simulating a minimal food-web model, that food webs are also expected to be interval when niche-space is high-dimensional. Here we characterize the fundamental mechanisms underlying this phenomenon by proving a set of rigorous conditions for food-web intervality in high-dimensional niche spaces. Our results apply to a large class of food-web models, including the special case previously studied numerically.

Food-web structure in low- and high-dimensional trophic niche spaces

A question central to modelling and, ultimately, managing food webs concerns the dimensionality of trophic niche space, that is, the number of independent traits relevant for determining consumer-resource links. Food-web topologies can often be interpreted by assuming resource traits to be specified by points along a line and each consumer's diet to be given by resources contained in an interval on this line. This phenomenon, called intervality, has been known for 30 years and is widely acknowledged to indicate that trophic niche space is close to one-dimensional. We show that the degrees of intervality observed in nature can be reproduced in arbitrary-dimensional trophic niche spaces, provided that the processes of evolutionary diversification and adaptation are taken into account. Contrary to expectations, intervality is least pronounced at intermediate dimensions and steadily improves towards lower- and higher-dimensional trophic niche spaces.

Regenerative Medicine and New Labour Life Science Policy: Rhetorics of Success, Narratives of Sustainability and Survival

Advances in stem cell science and tissue engineering are being turned into applications and products through a novel medical paradigm known as regenerative medicine. This paper begins by examining the vulnerabilities and risks encountered by the regenerative medicine industry during a pivotal moment in its scientific infancy: the 2000s. Under the auspices of New Labour, British medical scientists and life science innovation firms associated with regenerative medicine, received demonstrative rhetorical pledges of support, aligned with the publication of a number of government initiated reports presaged by Bioscience 2015: Improving National Health, Increasing National Wealth. The Department of Health and the Department of Trade and Industry (and its successors) held industry consultations to determine the best means by which innovative bioscience cultures might be promoted and sustained in Britain. Bioscience 2015 encapsulates the first chapter of this sustainability narrative. By 2009, the tone of this storyline had changed to one of survivability. In the second part of the paper, we explore the ministerial interpretation of the ‘bioscience discussion cycle’ that embodies this narrative of expectation, using a computer-aided content analysis programme. Our analysis notes that the ministerial interpretation of these reports has continued to place key emphasis upon the distinctive and exceptional characteristics of the life science industries, such as their ability to perpetuate innovations in regenerative medicine and the optimism this portends – even though many of the economic expectations associated with this industry have remained unfulfilled.

Macroecological patterns and niche structure in a new marine food web

The integration of detailed information on feeding interactions with measures of abundance and body mass of individuals provides a powerful platform for understanding ecosystem organisation. Metabolism and, by proxy, body mass constrain the flux, turnover and storage of energy and biomass in food webs. Here, we present the first food web data for Lough Hyne, a species rich Irish Sea Lough. Through the application of individual-and size-based analysis of the abundance-body mass relationship, we tested predictions derived from the metabolic theory of ecology. We found that individual body mass constrained the flux of biomass and determined its distribution within the food web. Body mass was also an important determinant of diet width and niche overlap, and predator diets were nested hierarchically, such that diet width increased with body mass. We applied a novel measure of predator-prey biomass flux which revealed that most interactions in Lough Hyne were weak, whereas only a few were strong. Further, the patterning of interaction strength between prey sharing a common predator revealed that strong interactions were nearly always coupled with weak interactions. Our findings illustrate that important insights into the organisation, structure and stability of ecosystems can be achieved through the theoretical exploration of detailed empirical data.

Determining trophic niche width: An experimental test of the stable isotope approach

Determining the trophic niche width of an animal population and the relative degree to which a generalist population consists of dietary specialists are long-standing problems of ecology. It has been proposed that the variance of stable isotope values in consumer tissues could be used to quantify trophic niche width of consumer populations. However, this promising idea has not yet been rigorously tested. By conducting controlled laboratory experiments using model consumer populations (Daphnia sp., Crustacea) with controlled diets, we investigated the effect of individual- and population-level specialisation and generalism on consumer d C mean and variance values. While our experimental data follow general expectations, we extend current qualitative models to quantitative predictions of the dependence of isotopic variance on dietary correlation time, a measure for the typical time over which a consumer changes its diet. This quantitative approach allows us to pinpoint possible procedural pitfalls and critical sources of measurement uncertainty. Our results show that the stable isotope approach represents a powerful method for estimating trophic niche widths, especially when taking the quantitative concept of dietary correlation time into account. © 2012 The Authors.

Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation

Background: Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the species genomes were subsequently published. In this study, we performed comparative genomics on eight strains of Cronobacter, including six that we sequenced (representing six of the seven species) and two previously published, closed genomes.

Results: We identified and characterized the features associated with the core and pan genome of the genus Cronobacter in an attempt to understand the evolution of these bacteria and the genetic content of each species. We identified 84 genomic regions that are present in two or more Cronobacter genomes, along with 45 unique genomic regions. Many potentially horizontally transferred genes, such as lysogenic prophages, were also identified. Most notable among these were several type six secretion system gene clusters, transposons that carried tellurium, copper and/or silver resistance genes, and a novel integrative conjugative element.

Conclusions: Cronobacter have diverged into two clusters, one consisting of C. dublinensis and C. muytjensii (Cdub-Cmuy) and the other comprised of C. sakazakii, C. malonaticus, C. universalis, and C. turicensis, (Csak-Cmal-Cuni-Ctur) from the most recent common ancestral species. While several genetic determinants for plant-association and human virulence could be found in the core genome of Cronobacter, the four Cdub-Cmuy clade genomes contained several accessory genomic regions important for survival in a plant-associated environmental niche, while the Csak-Cmal-Cuni-Ctur clade genomes harbored numerous virulence-related genetic traits.

Environmental filtering vs. resource-based niche partitioning in diverse soil animal assemblages

Terrestrial invertebrates constitute most of described animal biodiversity and soil is a major reservoir of this diversity. In the classical attempt to understand the processes supporting biodiversity, ecologists are currently seeking to unravel the differential roles of environmental filtering and competition for resources in niche partitioning processes: these processes are in principle distinct although they may act simultaneously, interact at multiple spatial and temporal scales, and are often confounded in studies of soil communities. We used a novel combination of methods based on stable isotopes and trait analysis to resolve these processes in diverse oribatid mite assemblages at spatial
scales at which competition for resources could in principle be a major driver. We also used a null model approach based on a general neutral model of beta diversity. A large and significant fraction of community variation was explainable in terms of linear and periodic spatial structures in the distribution of organic C, N and soil structure: species were clearly arranged along an environmental, spatially structured gradient. However, competition related trait differences did not map onto the distances separating species along the environmental gradient and neutral models provided a satisfying approximation of beta diversity patterns. The results represent the first robust evidence
that in very diverse soil arthropod assemblages resource-based niche partitioning plays a minor role while environmental filtering remains a fundamental driver of species distribution.

Site Distribution at the Edge of the Palaeolithic World: A Nutritional Niche Approach

This paper presents data from the English Channel area of Britain and Northern France on the spatial distribution of Lower to early Middle Palaeolithic pre-MIS5 interglacial sites which are used to test the contention that the pattern of the richest sites is a real archaeological distribution and not of taphonomic origin. These sites show a marked concentration in the middle-lower reaches of river valleys with most being upstream of, but close to, estimated interglacial tidal limits. A plant and animal database derived from Middle-Late Pleistocene sites in the region is used to estimate the potentially edible foods and their distribution in the typically undulating landscape of the region. This is then converted into the potential availability of macronutrients (proteins, carbohydrates, fats) and selected micronutrients. The floodplain is shown to be the optimum location in the nutritional landscape (nutriscape). In addition to both absolute and seasonal macronutrient advantages the floodplains could have provided foods rich in key micronutrients, which are linked to better health, the maintenance of fertility and minimization of infant mortality. Such places may have been seen as ‘good (or healthy) places’ explaining the high number of artefacts accumulated by repeated visitation over long periods of time and possible occupation. The distribution of these sites reflects the richest aquatic and wetland successional habitats along valley floors. Such locations would have provided foods rich in a wide range of nutrients, importantly including those in short supply at these latitudes. When combined with other benefits, the high nutrient diversity made these locations the optimal niche in northwest European mixed temperate woodland environments. It is argued here that the use of these nutritionally advantageous locations as nodal or central points facilitated a healthy variant of the Palaeolithic diet which permitted habitation at the edge of these hominins’ range.