The stochastic community and the logistic-J distribution

A new formal model called the multispecies logistical (MSL) system produces species/abundance distributions that are compared statistically with those found in natural communities. The system, which is able to handle thousands of individuals from hundreds of species, iteratively selects random pairs of individuals and transfers a unit of biomass (or energy) between the respective species. Several elaborations of the model, including those with trophic compartments, appear to produce the same distribution. The theoretical distribution underlying the MSL system is a hyperbolic section, here called the logistic-J distribution. In the study reported here, the logistic-J distribution has been fitted to the species-abundance histograms of 125 randomly selected taxocoenoses. Since the overall chi square score of the logistic-J achieved near-optimality in this study, it cannot be distinguished statistically from the J-curves observed by field biologists. For comparison, the log-series distribution was given the same test and scored significantly higher (more poorly) than the mean logistic-J score. If there is a single, major distribution underlying natural communities, it is not the log-series distribution. Nor, owing to a mathematical error in its formulation, can it be the lognormal distribution. In the MSL system each species follows a “stochastic orbit” about the mean abundance producing, in consequence, the logistic-J distribution. Such orbits are produced by any system in which the probabilities of reproduction and death are approximately equal. Accordingly, the “stochastic communities hypothesis” is proposed here as the overall mechanism governing abundances in all natural communities. It is not a single mechanism, per se, but the net effect of all environmental influences.     

A neutral‐niche theory of nestedness in mutualistic networks

Recently, there has been a vigorous interest in community ecology about the structure of mutualistic networks and its importance for species persistence and coevolution. However, the mechanisms shaping mutualistic networks have been rarely explored. Here we extend for the first time the neutral theory of biodiversity to a multi trophic system. We focus on nestedness, a distinctive pattern of mutualistic community assembly showing two characteristics, namely, asymmetrical specialization (specialists interacting with generalists) and a generalist core (generalists interacting with generalists). We investigate the importance of relative species abundance (RSA) for the nested assembly of plant–animal mutualistic networks. Our results show that neutral mutualistic communities give rise to networks considerably more nested than real communities. RSA explains 60–70% of nested patterns in two real communities studied here, while 30–40% of nestedness is still unexplained. The nested pattern in real communities is better explained when we introduce interaction‐specific species traits such as forbidden links and intensity of dependence (relative importance of fruits for the diet of a frugivore) in our analysis. The fact that neutral mutualistic communities exhibit a perfectly nested structure and do not show a random or compartmentalized structure, underlines the importance of RSA in the assembly of mutualistic networks.     

Some nonstandard modeling techniques in theoretical biology

Three topics are surveyed. (1) The quasisteady-state assumption is a fundamental example of frequent instances in theoretical biology where advantage can be taken of the simultaneous existence of widely separated time scales. It is shown that appropriate scaling can provide a markedly sharper estimate of the range of validity of this approximation. (2) A new methodology for modelling dynamically changing networks is applied to simple morphogenesis in fungal colonies. A brief discussion is given of possible application to the complex polymerization and cross-linking that characterize cytoplasmic fibers. (3) It is shown that problems in ecology and immunology can be illuminated by considering nonlocal interactions (and hence integrodifferential equations) that generate patterns in “aspect space” or “shape space.”     

The emerging role of ICP-MS in proteomic analysis

Quantitative proteomics and absolute determination of proteins are topics of fast growing interest, since only the quantity of proteins or changes in their abundance reflect the status and extent of changes of a given biological system. Quantification of the desired proteins has been carried out by molecule specific MS techniques, but relative quantifications are commonplace so far even resorting to stable isotope labelling techniques such as ICAT and SILAC. In the last decade the idea of using element-selective mass spectrometric detection (e.g. ICP-MS instruments) to achieve absolute quantification has been realised and ICP-MS stands now as a new tool in the field of quantitative proteomics.In this review the emerging role of ICP-MS in protein and proteomic analysis is highlighted. The potential of ICP-MS methods and strategies for screening multiple heteroatoms (e.g. S, P, Se, metals) in proteins and their mixtures and extraordinary capabilities to tackle the problem of absolute protein quantifications, via heteroatom determinations, are discussed and illustrated. New avenues are also open derived from the use of ICP-MS for precise isotope abundance measurements in polyisotopic heteroatoms. The “heteroatom (isotope)-tagged proteomics” concept is focused on the use of naturally present element tags and also extended to any protein by resorting to bioconjugation reactions (i.e. labelling sought proteins and peptides with ICP-MS detectable heteroatoms). A major point of this review is displaying the possibilities of using a “hard” ion source, the ICP, to complement well-established “soft” ion sources for mass spectrometry to tackle present proteomic analysis.     

Behavioral inferences from Early Stone artifact assemblages: an experimental model

A methodological approach for assessing the nature and palaeographic distribution of early stone artifact assemblages is presented, modeled after an approach originally used for faunal analysis. By combining experimental replicative studies with careful analysis of Palaeolithic archaeological occurrences, it is potentially possible to reconstruct entire technological systems and to assess what stages of lithic reduction may be preferentially represented at high density artifact concentrations that we normally call archaeological “sites”, and what stages of reduction are found in lower density (“off site”) scatters.Based upon the results of this approach, alternative explanations for certain stages of lithic reduction being preferentially represented at a number of Plio-Pleistocene archaeological sites at Koobi Fora, Kenya are considered and evaluated with regard to early hominid organizational patterns. It appears that hominid stone technology was a relatively complex system by 1·9 to 1·4 million years B.P., involving significant transport and carrying of stone artifacts representing various stages of reduction and suggesting more foresight and planning than observed among extant nonhuman primates.The application of this approach to other Palaeolithic occurrences should enable anthropologists to obtain a better understanding of the organizational patterns of tool-making hominids throughout the course of human evolution.     

Linkage Rules for Plant–Pollinator Networks: Trait Complementarity or Exploitation Barriers?

Recent attempts to examine the biological processes responsible for the general characteristics of mutualistic networks focus on two types of explanations: nonmatching biological attributes of species that prevent the occurrence of certain interactions (“forbidden links”), arising from trait complementarity in mutualist networks (as compared to barriers to exploitation in antagonistic ones), and random interactions among individuals that are proportional to their abundances in the observed community (“neutrality hypothesis”). We explored the consequences that simple linkage rules based on the first two hypotheses (complementarity of traits versus barriers to exploitation) had on the topology of plant–pollination networks. Independent of the linkage rules used, the inclusion of a small set of traits (two to four) sufficed to account for the complex topological patterns observed in real-world networks. Optimal performance was achieved by a “mixed model” that combined rules that link plants and pollinators whose trait ranges overlap (“complementarity models”) and rules that link pollinators to flowers whose traits are below a pollinator-specific barrier value (“barrier models”). Deterrence of floral parasites (barrier model) is therefore at least as important as increasing pollination efficiency (complementarity model) in the evolutionary shaping of plant–pollinator networks.     

Testing the Generality of a Trophic-cascade Model for Plague

Climate may affect the dynamics of infectious diseases by shifting pathogen, vector, or host species abundance, population dynamics, or community interactions. Black-tailed prairie dogs (Cynomys ludovicianus) are highly susceptible to plague, yet little is known about factors that influence the dynamics of plague epizootics in prairie dogs. We investigated temporal patterns of plague occurrence in black-tailed prairie dogs to assess the generality of links between climate and plague occurrence found in previous analyses of human plague cases. We examined long-term data on climate and plague occurrence in prairie dog colonies within two study areas. Multiple regression analyses revealed that plague occurrence in prairie dogs was not associated with climatic variables in our Colorado study area. In contrast, plague occurrence was strongly associated with climatic variables in our Montana study area. The models with most support included a positive association with precipitation in April–July of the previous year, in addition to a positive association with the number of “warm” days and a negative association with the number of “hot” days in the same year as reported plague events. We conclude that the timing and magnitude of precipitation and temperature may affect plague occurrence in some geographic areas. The best climatic predictors of plague occurrence in prairie dogs within our Montana study area are quite similar to the best climatic predictors of human plague cases in the southwestern United States. This correspondence across regions and species suggests support for a (temperature-modulated) trophic-cascade model for plague, including climatic effects on rodent abundance, flea abundance, and pathogen transmission, at least in regions that experience strong climatic signals.     

Separating Macroecological Pattern and Process: Comparing Ecological,Economic, and Geological Systems

Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form (‘first-order effects’), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns (‘second-order effects’). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.     

Absolute Quantification of Endogenous Ras Isoform Abundance

Ras proteins are important signalling hubs situated near the top of networks controlling cell proliferation, differentiation and survival. Three almost identical isoforms, HRAS, KRAS and NRAS, are ubiquitously expressed yet have differing biological and oncogenic properties. In order to help understand the relative biological contributions of each isoform we have optimised a quantitative proteomics method for accurately measuring Ras isoform protein copy number per cell. The use of isotopic protein standards together with selected reaction monitoring for diagnostic peptides is sensitive, robust and suitable for application to sub-milligram quantities of lysates. We find that in a panel of isogenic SW48 colorectal cancer cells, endogenous Ras proteins are highly abundant with ≥260,000 total Ras protein copies per cell and the rank order of isoform abundance is KRAS>NRAS≥HRAS. A subset of oncogenic KRAS mutants exhibit increased total cellular Ras abundance and altered the ratio of mutant versus wild type KRAS protein. These data and methodology are significant because Ras protein copy number is required to parameterise models of signalling networks and informs interpretation of isoform-specific Ras functional data.     

Maternal-fetal interaction in the ABO system: a comparative analysis of healthy mothers and couples with recurrent spontaneous abortion suggests a protective effect of B incompatibility.

We investigated the possible differential effects of A and B blood group materno-fetal incompatibility on human fertility through a comparative analysis of couples with recurrent spontaneous abortion (RSA) and healthy mothers. ABO phenotype was determined in 5180 healthy mothers and their newborn babies from the population of Sassari (Sardinia) and in 1359 healthy puerperae (women who have just given birth) from the population of Rome. Mother-newborn joint ABO distribution in healthy mothers was compared with wife-husband joint ABO distribution in RSA couples. Distortions from expected distribution were evaluated by symmetry analysis. In both RSA couples and healthy mothers significant deviation from expected symmetry patterns were observed. Deviations in RSA are in the opposite direction to those observed in healthy puerperae. The most important difference observed concerned the symmetric joint phenotypes mother (women) A/infant (husband) B (B incompatible) and mother (women) B/infant (husband) A (A incompatible). A low number of B incompatible in RSA couples and a high number of B incompatible in healthy mothers was observed. The phenomenon is much more evident in women aged 24-28 years, a period of maximum fecundity. It is possible that the presence of anti-B immunoglobulin in the mother might have a protective effect against fetal loss in some cases of mother-infant ABO incompatibility.     

Evolution of early planktic foraminifers

The evolution of Mesozoic species of planktic foraminifers, particularly the succession of their morphotypes and the variation in their diversity and their abundance, is shown to be related to the adaptation of evolutionary strategy to fluctuations in the oceanic environment.During periods of stress (“oligotaxic period”) the more primitive species tend to invade the oceanic surface waters by means of r-selection. During stable “polytaxic” conditions, the same species engage in an adaptive radiation colonizing progressively deeper water through K-selection.The succession of morphotypes from the middle Jurassic to the end of the Cretaceous is compared with living planktic foraminifers and related to the biogeographic (cold arctic, warm equatorial faunas) and bathymetric distribution. A general model for the evolution of early planktic foraminifers is made with reference to the preceding observations, and in relation to the pattern of variation of trophic resources.     

Historical biogeography and speciation in the Neotropical highlands: Molecular phylogenetics of the jay genus Cyanolyca

Phylogenetic relationships were studied in the genus Cyanolyca, an assemblage of jays distributed from Mexico south to Bolivia. Given its fragmented distribution along the humid forests of the Neotropics, the genus Cyanolyca is a model group for exploring hypotheses on biogeography and speciation. Phylogenetic analyses were based on two mitochondrial and three nuclear loci; taxon sampling includes all species in the genus and most subspecies. Maximum parsimony, maximum likelihood, and Bayesian analyses produced trees that were congruent and highly robust at both terminal and deep nodes of the phylogeny. Cyanolyca comprises two major clades: one contains the Mesoamerican “dwarf” jays, and the other consists of two main groups—C. cucullata + C. pulchra and the “core” South American species. Prior hypotheses of relationships were explored statistically using Maximum Likelihood and Bayesian approaches. Dispersal-Vicariance analysis revealed the importance of the Northern Andes as a major center for biological diversification, and the effects of dispersal across the Panamanian Land Bridge in the composition of South American and Mesoamerican avifaunas. Phylogenetic patterns are highly congruent with an allopatric mode of speciation. Implications of these results are discussed in the context of the biogeography of Neotropical montane forests.     

Viruses and the microbial loop

The abundance of viral-like particles in marine ecosystems ranges from <104 ml^–1 to >10⁸ ml^–1. Their distribution in time and space parallels that of other biological parameters such as bacterial abundance and chlorophyll a. There is a lack of consensus between methods used to assess viral activity, i.e., rate of change in viral abundance (increase or decrease). The highest rates, 10–100 days^–1, are observed in experiments with short sampling intervals (0.2–2 h), while lower rates, on the order of 1 day^–1, are observed in experiments with longer sampling intervals (days). Few studies have been carried out, but viruses appear, at least in some cases, to have a significant impact on carbon and nutrient flow in microbial food webs. Viruses have also been demonstrated to exert a species specific control of both bacteria and phytoplankton populations in natural waters.     

Multistability in Large Scale Models of Brain Activity

Noise driven exploration of a brain network’s dynamic repertoire has been hypothesized to be causally involved in cognitive function, aging and neurodegeneration. The dynamic repertoire crucially depends on the network’s capacity to store patterns, as well as their stability. Here we systematically explore the capacity of networks derived from human connectomes to store attractor states, as well as various network mechanisms to control the brain’s dynamic repertoire. Using a deterministic graded response Hopfield model with connectome-based interactions, we reconstruct the system’s attractor space through a uniform sampling of the initial conditions. Large fixed-point attractor sets are obtained in the low temperature condition, with a bigger number of attractors than ever reported so far. Different variants of the initial model, including (i) a uniform activation threshold or (ii) a global negative feedback, produce a similarly robust multistability in a limited parameter range. A numerical analysis of the distribution of the attractors identifies spatially-segregated components, with a centro-medial core and several well-delineated regional patches. Those different modes share similarity with the fMRI independent components observed in the “resting state” condition. We demonstrate non-stationary behavior in noise-driven generalizations of the models, with different meta-stable attractors visited along the same time course. Only the model with a global dynamic density control is found to display robust and long-lasting non-stationarity with no tendency toward either overactivity or extinction. The best fit with empirical signals is observed at the edge of multistability, a parameter region that also corresponds to the highest entropy of the attractors.     

Evaluating the Arrhenius equation for developmental processes

The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi‐step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi‐step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and β‐galactosidase show non‐linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non‐uniform developmental scaling and propose that the observed departure from this law likely results more from non‐idealized individual steps rather than from the complexity of the system.     

Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis

Ciona intestinalis is a useful model organism to analyze chordate development and genetics. However, unlike vertebrates, it shares a unique mechanism called trans-splicing with lower eukaryotes. In the computational analysis of trans-splicing in C. intestinalis we report here, we discovered that although the amount of non-trans-spliced and trans-spliced genes is usually equivalent, the expression ratio between the two groups varies significantly with tissues and developmental stages. Among the seven tissues studied, the observed ratios ranged from 2.53 in “gonad” to 19.53 in “endostyle”, and during development they increased from 1.68 at the “egg” stage to 7.55 at the “juvenile” stage. We further hypothesize that this enrichment in trans-spliced mRNAs in early developmental stages might be related to the abundance of trans-spliced mRNAs in “gonad”. Our analysis indicates that in C. intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently.     

Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks

Attribution of biological robustness to the specific structural properties of a regulatory network is an important yet unsolved problem in systems biology. It is widely believed that the topological characteristics of a biological control network largely determine its dynamic behavior, yet the actual mechanism is still poorly understood. Here, we define a novel structural feature of biological networks, termed ‘regulation entropy’, to quantitatively assess the influence of network topology on the robustness of the systems. Using the cell-cycle control networks of the budding yeast (Saccharomyces cerevisiae) and the fission yeast (Schizosaccharomyces pombe) as examples, we first demonstrate the correlation of this quantity with the dynamic stability of biological control networks, and then we establish a significant association between this quantity and the structural stability of the networks. And we further substantiate the generality of this approach with a broad spectrum of biological and random networks. We conclude that the regulation entropy is an effective order parameter in evaluating the robustness of biological control networks. Our work suggests a novel connection between the topological feature and the dynamic property of biological regulatory networks.     

Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number

Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.     

Principles in the selection of inorganic elements by organisms — Application to molybdenum enzymes

Some basic principles were delineated with regard to the selection of inorganic elements by organisms; they are “basic fitness rule”, “abundance rule”, “efficiency rule” and “evolutionary pressure”. The basic fitness rule was then applied to the case of molybdenum, to show how inherently fit molybdenum is to the biological functions carried out by those enzymes dependent on it, including xanthine oxidase, sulfite oxidase, nitrate reductase and nitrogenase.