Models for the diversification of life

The diversification of life through geological time a rise from presumably one species to many millions today. The diversification of marine families in the past 600 million years (Myr) appears to have followed two or three logistic curves, with equilibrium levels that lasted for up to 200 Myr. In contrast, continental organisms clearly show an exponential pattern of diversification, and although it is not clear whether the empirical diversification patterns are real or are artefacts of a poor fossil record, the latter explanation seems unlikely. Perhaps marine and continental organisms diversified in different ways, or perhaps the appearance of equilibrium patterns for marine organisms is an artefact of taxonomic structures.     

Temperature compensation of postsynaptic currents from the extraocular muscle of temperate teleost fishes

Miniature end plate currents were recorded from white inferior oblique extraocular muscle fibres of one temperate marine teleost (Aldrichetta forsteri, Family Mugilidae) and two temperate freshwater teleosts (Galaxias fasciatus, Family Galaxiidae and Oncorhynchus mykiss, Family Salmonidae). Miniature end plate currents were digitised and averaged over a temperature range of 5-25 degrees C. For each species, decay of miniature end plate currents was exponential and exhibited a strong temperature dependence. Lower temperatures resulted in prolonged decay phases, which decreased exponentially as a function of absolute temperature. Although values of the exponential time constant tau (tau) obtained for each species at 5 degrees C, 15 degrees C and 25 degrees C were significantly different, at any given temperature, there were no significant differences between tau values for the three species, despite differences in phylogeny (different families) and habitat (marine versus freshwater). At their normal temperature of 15 degrees C, mean values of tau for the three species ranged from 840 micros to 940 micros, and apparent activation energies ranged from -41 kJ mol(-1) deg(-1) to 50 kJ mol(-1) deg(-1). These observations confirm earlier reports that teleost miniature end plate currents are consistently shorter than those of other vertebrates.     

New perspectives for estimating body condition from mass/length data: the scaled mass index as an alternative method

Body condition is assumed to influence an animal's health and fitness. Various non‐destructive methods based on body mass and a measure of body length have been used as condition indices (CIs), but the dominant method amongst ecologists is currently the calculation of residuals from an ordinary least squares (OLS) regression of body mass against length. Recent studies of energy reserves in small mammals and starlings claimed to validate this method, although we argue that they did not include the most appropriate tests since they compared the CI with the absolute size of energy reserves. We present a novel CI (the ‘scaled mass index’) based on the central principle of scaling, with important methodological, biological and conceptual advantages. Through a reanalysis of data from small mammals, starlings and snakes, we show that the scaled mass index is a better indicator of the relative size of energy reserves and other body components than OLS residuals, performing better in all seven species and in 19 out of 20 analyses. We also present an empirical and theoretical comparison of the scaled mass index and OLS residuals as CIs. We argue that the scaled mass index is a useful new tool for ecologists.     

Tree-Structured Exponential Regression Modeling

A method for fitting piecewise exponential regression models to censored survival data is described. Stratification is performed recursively, using a combination of statistical tests and residual analysis. The splitting criterion employed in cross-validation is the average squared error of the residuals. The bootstrap is employed to keep the probability of a type I error (the error of discovering two or more strata when there is only one) of the method close to a predetermined value. The proposed method can thus also serve as a formal goodness-of-fit test for the exponential regression model. Real and simulated data are used for illustration.     

Model choice and influential cases for survival studies

Deletion diagnostics are developed for identifying observations that influence the estimates of regression parameters and the mixture parameter in the families of relative risk functions for failure time data. The diagnostic for the regression parameters is a generalization of Cain and Lange's (1984, Biometrics 40, 493-499) measure of individual influence. The generalizations of martingale residuals, Schoenfeld's partial residuals (1982, Biometrika 69, 239-241), and score residuals by Therneau, Grambsch, and Fleming (1990, Biometrika 77, 147-160) are also obtained. The influence of some observations on regression parameters can be drastically modified as the mixture parameter changes, even for a very small change. In addition, adding or deleting some observations might result in choosing different models. The diagnostics are applied to a family proposed by Guerrero and Johnson (1982, Biometrika 69, 309-314). One illustrative example is presented.     

The color of mass culture: spectral characteristics of a shallow water column through shade‐limited algal growth dynamics1

It is envisioned that mass algal cultivation for commercial biofuels production will entail the use of large raceway pond systems, which typically have shade‐limited photosynthetic growth within depths of 20–30 cm. The attenuation of light and spectral qualities of red, green, and blue wavelengths in a 20‐cm water column as a function of Chl‐a concentration during exponential and linear phases of growth dynamics for the marine diatom Thalassiosira pseudonana was examined under laboratory conditions. While photosynthetically available radiation (PAR) was in excess throughout the water column during the phase of exponential growth, PAR became rate limiting differently for red, green, and blue wavelengths during the phase of linear growth. The transition from exponential to linear growth occurred at 1–2 mg Chl‐a · L?1, whereby a scalar ~5 μmol photons · m?2 · s?1 at 20‐cm depth was found to occur as would be anticipated having the compensation point for where rates of photosynthesis and respiration are equal. During the phase of linear growth, red wavelengths became increasingly dominant at depth as Chl‐a concentrations increased, being contrary to the optical conditions for those natural bodies of water that forced the evolution of phytoplankton photosynthesis. It is hypothesized this dramatic difference in water column optics between natural and synthetic environments could influence a variety of biological reactions, importantly non‐photochemical quenching capacities, which could negatively impact crop yield.     

Phylogeny and paraphyly among tetrapod blood flukes (Digenea: Schistosomatidae and Spirorchiidae)

The blood flukes of turtles (Digenea: Spirorchiidae) and the blood flukes of crocodilians, birds and mammals (Digenea: Schistosomatidae) have long been considered as closely related, but distinct evolutionary lineages. Recent morphological and molecular studies have considered these families as sister taxa within the Schistosomatoidea. Representatives of both families have similar furcocercous cercariae and similar two-host life cycles, but have different definitive hosts, distinct reproductive patterns and different morphologies. Sequences including approximately 1800 bases of the small subunit ribosomal DNA and 1200 bases of the large subunit ribosomal DNA were generated from representatives of eight spirorchiid genera. These sequences were aligned with pre-existing sequences of Schistosomatidae and other representatives of the Diplostomida and analysed for phylogenetic signal using maximum parsimony and Bayesian inference. These analyses revealed that the Spirorchiidae is paraphyletic and that the turtle blood flukes are basal to the highly derived schistosomatids. Three genera of spirorchiids from marine turtles form a sister group to the Schistosomatidae and five genera of spirorchiids from freshwater turtles occupy basal positions in the phylogeny of tetrapod blood flukes. Marine turtles are considered to be derived from freshwater turtles and the results of the current study indicate that the spirorchiid parasites of marine turtles are similarly derived from a freshwater ancestor. The close relationship of the marine spirorchiids to schistosomatids and the basal position of the marine transmitted Austrobilharzia and Ornithobilharzia in the schistosomatid clade suggests that schistosomatids arose after a marine turtle blood fluke ancestor successfully colonised birds.     

Numerical bias estimation for mass spectrometric mass isotopomer analysis

Mass spectrometric (MS) isotopomer analysis has become a standard tool for investigating biological systems using stable isotopes. In particular, metabolic flux analysis uses mass isotopomers of metabolic products typically formed from ¹³C-labeled substrates to quantitate intracellular pathway fluxes. In the current work, we describe a model-driven method of numerical bias estimation regarding MS isotopomer analysis. Correct bias estimation is crucial for measuring statistical qualities of measurements and obtaining reliable fluxes. The model we developed for bias estimation corrects a priori unknown systematic errors unique for each individual mass isotopomer peak. For validation, we carried out both computational simulations and experimental measurements. From stochastic simulations, it was observed that carbon mass isotopomer distributions and measurement noise can be determined much more precisely only if signals are corrected for possible systematic errors. By removing the estimated background signals, the residuals resulting from experimental measurement and model expectation became consistent with normality, experimental variability was reduced, and data consistency was improved. The method is useful for obtaining systematic error-free data from ¹³C tracer experiments and can also be extended to other stable isotopes. As a result, the reliability of metabolic fluxes that are typically computed from mass isotopomer measurements is increased.     

Evolution of skull shape in carnivores 2. Additional modern carnivores

Fifteen functionally significant aspects of skull morphology were measured on skulls of 36 additional species of carnivores to complete a survey of skull shape in modern fissiped (land) carnivores that includes most of the living genera. The measurements were transformed to dimensionless variables based on the residuals from allometric equations, and were analysed singly and in a 10 variable principal components analysis. An initial study of 62 species of viverrids, canids, mustelids and felids had shown those families to be distinguished from each other by the functionally significant measurements. However, among the additional 36 species, some procyonids, ursids and mustelids display a range of diversity of skull morphology that overlaps that of the other families and diminishes the potential value of the measurements as taxonomic characters. Intraspecific variation is presented for 12 species, and is low enough to allow use of some features as species level diagnostic characters. The lack of correlation between diet and functionally significant aspects of skull morphology among omnivorous carnivores, and the absence of certain skull shapes among carnivores are discussed.     

Lipid content in 19 brackish and marine microalgae: influence of growth phase, salinity and temperature

Algal lipids provide essential fatty acids for higher trophic levels in the marine food web, and understanding the fatty acid composition in phytoplankton is critical for evaluating its value as a diet. Nineteen microalgal species, mainly originating from the Baltic Sea, covering major algal classes were grown in different growth conditions. Samples were taken during both the exponential and stationary growth phases and analysed regarding their fatty acid methyl esters and free fatty acids. Our results show that across all screened species, total fatty acids increased significantly from exponential to stationary growth phase. Furthermore, it was observed that warm-water species contained more lipids and differed in their lipid profile as compared with the cold-water species. Brackish water species also showed a slightly higher lipid content than the marine species, but their lipid profile was not significantly different. Plotting changes in lipids against changes in cell nitrogen revealed a significant dependency between decrease in cell nitrogen and increase in lipids across all tested species.     

Molecular phylogeny of a circum-global, diverse gastropod superfamily (Cerithioidea: Mollusca: Caenogastropoda): pushing the deepest phylogenetic limits of mitochondrial LSU rDNA sequences

The Cerithioidea is a very diverse group of gastropods with ca. 14 extant families and more than 200 genera occupying, and often dominating, marine, estuarine, and freshwater habitats. While the composition of Cerithioidea is now better understood due to recent anatomical and ultrastructural studies, the phylogenetic relationships among families remain chaotic. Morphology-based studies have provided conflicting views of relationships among families. We generated a phylogeny of cerithioideans based on mitochondrial large subunit rRNA and flanking tRNA gene sequences (total aligned data set 1873 bp). Nucleotide evidence and the presence of a unique pair of tRNA genes (i.e., threonine + glycine) between valine-mtLSU and the mtSSU rRNA gene support conclusions based on ultrastructural data that Vermetidae and Campanilidae are not Cerithioidea, certain anatomical similarities being due to convergent evolution. The molecular phylogeny shows support for the monophyly of the marine families Cerithiidae [corrected], Turritellidae, Batillariidae, Potamididae, and Scaliolidae as currently recognized. The phylogenetic data reveal that freshwater taxa evolved on three separate occasions; however, all three recognized freshwater families (Pleuroceridae, Melanopsidae, and Thiaridae) are polyphyletic. Mitochondrial rDNA sequences provide valuable data for testing the monophyly of cerithioidean [corrected] families and relationships within families, but fail to provide strong evidence for resolving relationships among families. It appears that the deepest phylogenetic limits for resolving caenogastropod relationships is less than about 245--241 mya, based on estimates of divergence derived from the fossil record.     

Manzamines

Manzamines are a unique class of β-carboline marine alkaloids with an unusual tetra- or pentacyclic system. These alkaloids have shown a variety of bioactivities against infectious diseases, cancer and inflammatory diseases. The greatest potential for the manzamine alkaloids appears to be against malaria, with improved potency relative to chloroquine and artemisinin. Over 80 manzamine-related alkaloids have been isolated from more than 16 species of marine sponges belonging to five families distributed from the Red Sea to Indonesia, which suggests a possible microbial origin for manzamine alkaloids. The current review summarizes marine literature, focusing on the biological activities of manzamines, the possible microbial origin of this class of compounds and the Red Sea as a possible source of manzamines from biosynthetic gene clusters of Red Sea microbes.     

New residuals for Cox regression and their application to outlier screening

The identification of individuals who 'died far too early' or 'lived far too long' as compared to their survival probabilities from a Cox regression can lead to the detection of new prognostic factors. Methods to identify outliers are generally based on residuals. For Cox regression, only deviance residuals have been considered for this purpose, but we show that these residuals are not very suitable. Instead, we develop and propose two new types of residuals: the suggested log-odds and normal deviate residuals are simple and intuitively appealing and their theoretical properties and empirical performance make them very suitable for outlier identification. Finally, various practical aspects of screening for individuals with outlying survival times are discussed by means of a cancer study example.     

Phylogenetic Studies in the Monocot Subclass Alismatidae: Evidence for a Reappraisal of the Aquatic Order Najadales

Within the angiosperm subclass Alismatidae (= superorder Alismatiflorae), contemporary taxonomists have often assigned the families Hydrocharitaceae and Najadaceae to different orders. The Najadaceae are presumably allied to a variety of aquatic families in the order Najadales, whereas the Hydrocharitaceae have been segregated as the order Hydrocharitales or placed within the order Alismatales. Analyses of DNA sequence data from the chloroplast gene rbcL, however, indicate that Najadaceae have a much closer phylogenetic relationship to Hydrocharitaceae than to families of the "Najadales" (Cymodoceaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae, Zosteraceae). This association supports previous studies based upon examination of floral structure and seed coat anatomy. The rbcL sequence data also indicate that the Zosteraceae and Potamogetonaceae are closely related families. The rbcL sequence of Zostera is actually more similar to that of Potamogeton richardsonii than is the sequence of the latter to a congener, Potamogeton amplifolius. The marine, dioecious, hydrophilous genus Zostera has acquired a number of distinctive adaptations, but probably diverged relatively rapidly from freshwater Potamogetonaceae. Molecular data place Ruppiaceae as a sister group to the marine Cymodoceaceae and do not support the commonly accepted merger of Ruppiaceae and Potamogetonaceae.     

Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments

Nine families of bivalve molluscs have undergone successful radiations in freshwater habitats, including three heterodont taxa: the Sphaeriidae, Corbiculidae, and Dreissenidae. Although the phylogenetic relationships of these freshwater heterodont families are controversial, most workers place the first two in the superfamily Corbiculoidea and assume that they represent a monophyletic grouping. We have tested competing phylogenetic hypotheses for the Corbiculoidea by constructing a representative molecular phylogeny, based on domains D1-D3 of the nuclear large subunit 28S rDNA, for 18 heterodont bivalves and for two oyster outgroup taxa. Our results do not support the monophyly of the Corbiculoidea and are consistent with the hypothesis that all three families of freshwater heterodonts represent independent colonization events by marine ancestors. Similarities in developmental mode specializations exhibited by some sphaeriids and corbiculids, such as sequential direct-developing broods, represent convergent adaptations to the freshwater environment. The corbiculid taxa form a clade with venerid and mactrid outgroups but we were not able to identify a putative marine outgroup for the sphaeriids.     

The End-Permian mass extinction: What really happened and did it matter?

Marine communities of the Paleozoic differ markedly from those of the post-Paleozoic, a dichotomy long recognized as the most fundamental change between the Cambrian metazoan radiation and the present. The end-Permian mass extinction of about 54% of marine families eliminated many of the groups that dominated Paleozoic communities. Correlative changes occurred in terrestrial vertebrate and plant communities, but there is no clear evidence that these changes are related to the marine extinction. The marine extinction occurred during a period of physical change, and a variety of extinction mechanisms have been proposed, most related to a major Late Permian marine regression or to climatic changes. Unfortunately, the regression has made it difficult to gather data on the rate, timing and pattern of extinction, and the available data exclude only a few hypotheses. Thus the largest mass extinction, and the one with the greatest evolutionary importance, is also the most poorly understood.     

The evolution of marine insects: phylogenetic, ecological and geographical aspects of species diversity in marine water striders

No other group of insects have been more successful in colonizing marine habitats than water striders and their allies (Heteroptera, Gerromorpha). More than 10% of the 1700 species of gerromorphan bugs are marine. Water striders have colonized the marine environment at least 14 times. The fossil records suggest that marine habitats were invaded by members of the families Veliidae and Gerridae earlier than 20-30 and 45 million years before present, respectively. Estuaries and mangrove swamps are undoubtedly the ancestral type of habitat, but water striders have diversified further in marine habitats including the surface of the open ocean (sea skaters. Halobates). Except for being obligatorily flightless, marine water striders are structurally very similar to their non-marine relatives. Physiological and behavioral rather than morphological specializations are likely to have been key innovations in the transition from limnic to marine habitats. The oldest and most species-rich clades originated in the Indo-West Pacific region. There are 3.5 times as many species of marine water striders in the Indo-West Pacific region than in the Atlantic/Caribbean/East Pacific region. This "diversity anomaly" is explained historically by region-specific differences in the origin and proliferation of clades, in paleoclimate and paleogeography, and in the propensity for dispersal between regions.