Evolution of Metamorphism in Thymidylate Synthases Within the Primate Lineages

Crystal structures of human thymidylate synthase (hTS) revealed that the protein exists in active and inactive conformations, defined by the position of a loop containing the active site nucleophile. TS is highly homologous among diverse species; however, the residue at position 163 (hTS) differs among species. Arginine at this position is predicted by structural modeling to enable conformational switching. Arginine or lysine is reported at this position in all mammals in the GenBank and Ensembl databases, with arginine reported in only primates. Sequence analysis of the TS gene of representative primates revealed that arginine occurs at this relative position in all primates except a representative of prosimians. Mutant human proteins were created with residues at position 163 that occur in TSs from prokaryotes and eukaryotes. Catalytic constants (k _cat) of mutant enzymes were 45–149% of hTS, with the lysine mutant (R163K) exhibiting the highest k _cat. The effect of lysine substitution on solution structure and on ligand binding was investigated. R163K exhibited higher intrinsic fluorescence, a more negative molar ellipticity, and higher dissociation constants (K _d) for ligands that modulate protein conformation than hTS. Temperature effects on intrinsic fluorescence and catalytic activity of hTS and R163K are consistent with proteins populating different conformational states. The data indicate that the enzyme with arginine at the position corresponding to 163 (hTS) evolved after the divergence of prosimians and simians and that substitution of lysine by arginine confers unique structural and functional properties to the enzyme expressed in simian primates.     

Time and space in the community structure of a species-rich limestone grassland

Abstract. The community structure of a species-rich grassland was investigated at a small spatial scale (0.001 m²), to determine whether evidence suggesting assembly rules could be found in temporal or spatial variation in either species richness or guild proportions. The community was alvar limestone grassland on the island of Öland, Sweden. Three sites were sampled: two lightly grazed, the other recently ungrazed. Plots with and without fertilizer were compared. Evidence was sought for restriction on the ability of species to co-occur within a limited spatial area. Restriction due to a limited number of niches available,‘niche limitation’, could be manifest as lower variance in quadrat richness than expected under a null model (i.e. RV_r, the ratio of observed: expected variance in richness, would be < 1.0). In several cases, RV_r values were significantly < 1.0, even using a patch model to allow for possible spatial variation in the environment. Low RV_r values were found only at the smallest square quadrat size, 10 cm². On Fertilized plots in the years immediately after application of fertilizer, low RV_r could not be demonstrated. Explanations of low RV_r other than niche limitation are considered, such as environmental heterogeneity (present and/or historical) and limitations to the co-occurrence of individual plant modules. Assembly rules based on guild membership were sought by looking at the variance across quadrats in the proportions of species from morphological guilds. An assembly rule would be seen as relatively constant proportion, estimated via RV_gp, the ratio of observed: expected variances in guild proportions. Significant guild proportionality was found in some cases. There was no evidence of guild proportionality in the years after the application of fertilizer. The significant effects in RV_r were more numerous than expected on a random basis, though not observed in every site in every year. Similar trends were seen in RV_gp. At the space/time scales examined, the species in a plant community may be constrained by assembly rules only intermittently, e.g. when resources are more limiting (Wiens 1977). Under this concept, when competition is relaxed, such as following fertilizer application, there is a temporary microhabitat ‘waterhole’ in which more species can coexist, and the assembly rules break down, at least temporarily whilst the species composition adjusts. There was some indication of a return to more deterministic community structure four years after fertilization commenced. Variants of van der Maarel's Carousel model were tested. A Niche-limited Carousel Model (i.e. a model in which there is some limitation in the number of species that can occupy a microsite) would imply restricted variation in richness through time for a single quadrat (temporal RV_r). Overall differences between years in species richness were demonstrated, and their effect removed; after this adjustment there was support for the Niche-limited Carousel Model. The extent of this limitation varied between sites. There were also consistent differences between quadrats in species richness. There was little evidence for constancy of guild proportions through time. The site that showed the strongest community structure in time and space, least year-to-year variation in mean species richness, and least response to fertilizer perturbation, is that on the shallowest soil. Possibly the thin soil results in greater resource limitation, supporting suggestions that assembly rules are stronger when resources are more limited.     

Accumulation of unusual sterile transcripts of TCRβ in mouse hybridoma, murine tumour and non-human primate marmoset tumour

Accumulation of immunoglobulin Ig RNA (from several loci viz., C_H, C_α, J_k-C_k and S_μ during Igμ isotype switching) in B cells and T cell receptor (TCR) RNAs (α, β andγ) in T cells of unusual sizes emanating from germline and rearranged genes were reported to accumulate in human and mouse (and murine too). The precise mechanism and function of these sterile RNA species are yet to be delineated. Similar accumulation of RNA species of unusual sizes were identified with DNA-RNA hybridization and isolation of cDNA employing with DNA and antibody probes in mouse hybridoma, murine tumour, non-human primate marmoset tumour and human leukemic cells.     

A model-independent test for the presence of regulatory equilibrium and non-random structure in island species trajectories

Aims To test a key prevision of the dynamic equilibrium theory of island biogeography, namely that changes in species numbers on islands over time (hereafter, species trajectories) are equilibrial, and to characterize aspects of the dynamical properties of species change over time using a model‐independent test. Methods We tested for regulatory equilibrium and non‐random structure in species numbers through time by comparing observed correlation coefficients at lag‐k for species trajectories from four true islands and two habitat islands. First, we estimated the shape of the autocorrelation function for each observed species trajectory by calculating correlation coefficients of the observed data between pairs of values N_t?k and N_t separated by lag‐k (k = 1, 2, …, N ? 1). Second, we tested the observed correlation coefficients at each lag against a distribution of correlation coefficients generated by randomly ordering observed numbers in the species trajectories. Results The patterns of autocorrelation functions for all but one of the observed species trajectories did not exhibit evidence of regulatory equilibrium, and, in fact, closely matched what would be expected from a non‐stationary or ‘random walk’ process. The majority of the correlation coefficients generated from the observed species trajectories did not deviate significantly from correlation coefficients produced by the randomized trajectories. However, there was strong evidence of unusual positive autocorrelation at small time lags for birds on islands measured annually (2‐ to 4‐year lags) and for arthropods on islands measured weekly (7‐ to 8‐week lags), suggesting some degree of structure in change in species richness over time. Main conclusions The autocorrelation function patterns for all but one of the observed species trajectories showed various forms of non‐stationarity. These types of patterns suggest that the numbers of species through time gradually wandered away from their initial sizes. Our model‐independent test of individual correlation coefficients revealed significant structure in the observed species trajectories. These trajectories appear to be non‐random at relatively short lag intervals, indicating a process with short memory.     

2 k contingency tables in ecology

Suppose observations are made on the presence or absence of k different species in N sampling units. Denote by s the number of species per sampling unit and let m₂ and Var(s) respectively be the observed variance of s and its expectation under the null hypothesis that all k species are independent. It is shown that the difference m₂—Var(s) is directly interpretable as a measure of the overall association among the species. Examples using field data are given and it is shown how the proposed measure of association may be used to judge: (i) whether some chosen group of species contributes markedly to the total amount of interdependence within a community; and (ii) whether some chosen group of species may be disregarded without affecting the result when ecological data are to be classified or ordinated.     

Energetically relevant predator–prey body mass ratios and their relationship with predator body size

Food web structure and dynamics depend on relationships between body sizes of predators and their prey. Species‐based and community‐wide estimates of preferred and realized predator–prey mass ratios (PPMR) are required inputs to size‐based size spectrum models of marine communities, food webs, and ecosystems. Here, we clarify differences between PPMR definitions in different size spectrum models, in particular differences between PPMR measurements weighting prey abundance in individual predators by biomass (r^bio) and numbers (r^num). We argue that the former weighting generates PPMR as usually conceptualized in equilibrium (static) size spectrum models while the latter usually applies to dynamic models. We use diet information from 170,689 individuals of 34 species of fish in Alaskan marine ecosystems to calculate both PPMR metrics. Using hierarchical models, we examine how explained variance in these metrics changed with predator body size, predator taxonomic resolution, and spatial resolution. In the hierarchical analysis, variance in both metrics emerged primarily at the species level and substantially less variance was associated with other (higher) taxonomic levels or with spatial resolution. This suggests that changes in species composition are the main drivers of community‐wide mean PPMR. At all levels of analysis, relationships between weighted mean r^bio or weighted mean r^num and predator mass tended to be dome‐shaped. Weighted mean r^num values, for species and community‐wide, were approximately an order of magnitude higher than weighted mean r^bio, reflecting the consistent numeric dominance of small prey in predator diets. As well as increasing understanding of the drivers of variation in PPMR and providing estimates of PPMR in the north Pacific Ocean, our results demonstrate that that r^bio or r^num, as well as their corresponding weighted means for any defined group of predators, are not directly substitutable. When developing equilibrium size‐based models based on bulk energy flux or comparing PPMR estimates derived from the relationship between body mass and trophic level with those based on diet analysis, weighted mean r^bio is a more appropriate measure of PPMR. When calibrating preference PPMR in dynamic size spectrum models then weighted mean r^num will be a more appropriate measure of PPMR.     

Merged mechanisms for hydride transfer from 1,4-dihydronicotinamides

Recent work on the reduction of heteroaromatic cations by 1,4-dihydronicotinamides and related reducing agents is reviewed. Extensive correlations are presented between the second-order rate constants (k₂) for these reactions and the second-order rate constants (k_OH) and equilibrium constants (pK_R⁺) for hydroxide ion attack on these cations. Close correlations of log k₂ with the electron affinities and one-electron reduction potentials of these cations are also presented. These relationships are considered in the context of a direct hydride transfer from donor to acceptor and also in terms of SET mechanisms which are also commonly discussed for such reactions. It is shown that the interpretation of these formal hydride transfer reactions in terms of an imbalanced development of electronic charge and C---H bond fission within the transition state species leads to a rational merging of the single-step hydride transfer mechanism and the SET mechanisms. The structures of the transition state species are expected to be highly variable and quite dependent upon the nature of the hydride donor and acceptor species, with considerable contribution from charge-transfer interactions. Such imbalanced transition state species are analyzed in terms of two different types of reaction coordinate diagrams and also in terms of the valence bond configuration mixing theory.     

On the relationships between absolute and allometric shell growth in unionid mussels (Bivalvia,Unionidae) from European Russia

The heuristic analysis of the relationship between the parameters of equations of linear (L. von Bertalanffy) and allometric shell growth was carried out on Unio pictorum (Linnaeus, 1758), U. tumidus Retzius, 1778, and U. crassus Retzius 1778 (Unionidae) from European Russia. Growth constants of the shell, k, were studied for length (k _L ), height (k _h ), and convexity (k _C ). It was shown that the ratios of growth constants (k _h /k _L , k _C /k _h , and k _C/k _L ) and parameter bfrom the allometric equations (h=aL ^b ;B=ah ^b ; C=aL ^b ) are connected by a strong negative correlation. If the b parameter is more than 1 (positive allometry), the growth constant relations are less than one, if b < 1 (negative allometry), the growth constant proportions are more than 1, and, in case when b is close to 1, (isometry), the growth constant proportions are also close to 1. All three types of allometric growth (isometry and both positive and negative allometry) are observed in the studied mussels.     

The Negative Binomial Distribution of Order k and Some of Its Properties

The negative binomial distribution of order k is introduced and briefly studied. First it is shown that it is a proper probability distribution. Then its probability generating function, mean and variance are derived. Finally it is shown that the number of trials until the rth kth consecutive success (r ≧ 1, k ≧ 1) in independent trials with constant success probability p (0 < p < 1) is distributed as negative binomial distribution of order k. The present paper generalizes results of SHANE (1973), PHILIPPOU and MUWAFI (1982), and PHILIPPOU, GEORGHIOU and PHILIPPOU (1982).     

Intramolecular electron transfer rate between active-site copper and TPQ in Arthrobacter globiformis amine oxidase

Copper amine oxidases catalyze the oxidative deamination of primary amines operating through a ping-pong bi bi mechanism, divided into reductive and oxidative half-reactions. Considerable debate still exists regarding the role of copper in the oxidative half-reaction, where O₂ is reduced to H₂O₂. Substrate-reduced amine oxidases display an equilibrium between a Cu(II) aminoquinol and a Cu(I) semiquinone, with the magnitude of the equilibrium constant being dependent upon the enzyme source. The initial electron transfer to dioxygen has been proposed to occur from either the reduced Cu(I) center or the reduced aminoquinol cofactor. In order for Cu(I) to be involved, it must be shown that the rate of electron transfer (k _ET) between the aminoquinol and Cu(II) is sufficiently rapid to place the Cu(I) semiquinone moiety on the mechanistic pathway. To further explore this issue, we measured the intramolecular electron transfer rate for the Cu(II) aminoquinol ⇆ Cu(I) semiquinone equilibrium in Arthrobacter globiformis amine oxidase (AGAO) by temperature-jump relaxation techniques. The results presented herein establish that k _ET is greater than the rate of catalysis (k _cat) for the preferred amine substrate β-phenylethylamine at three pH values, thereby permitting the Cu(I) semiquinone to be a viable catalytic intermediate during enzymatic reoxidation in this enzyme. The data show that k _ET is approximately equivalent at pH 6.2 and 7.2, being 2.5 times k _cat for these pH values. At pH 8.2, however, k _ET decreases, becoming comparable to k _cat. Potential reasons for the decreased k _ET at basic pH are presented. The implications of these results in light of a previously published study measuring reoxidation rates of substrate-reduced AGAO are also addressed.     

The spread of Hydramoeba infections in mixed hydra species systems

Summary The host-pathogen system, hydra and Hydramoeba hydroxena, was used as an experimental analog to explore properties of epizootics in mixed host species systems, and to determine the contribution of each host species to a measure of overall host community resistance. Epizootics of hydramoeba in systems of two host species were characterized by processes of enhancement and buffering of the infection where one host species is more resistant than the other. More complex host communities were constructed from four hydra species by varying the proportions of each. Community size and number of species were kept constant. Instantaneous infection rates and time infection reached a specific level were judged measures of community resistance or resilience. A Community Resistance Index(R _c ) was devised that associated an independent measure of the resistance of each component species in the system with the corresponding abundance of the species in the system. Experimental results indicated significant differences in infection rates and infection level time among the synthetic communities. R _c was found predictive of the behavior of the systems under pathogen stress and was considered a realistic measure of community resistance to stress. First order host species interactions were present during the infection process and lead to more complex enhancement processes involving transfer and accumulation of pathogen material. These interactions, however, were not of sufficient magnitude to render the positive R _c -community resistance regression insignificant.     

Numerical solutions of the Lamm equation. II. Equilibrium sedimentation

The Lamm equation has been solved numerically for conditions corresponding to equilibrium runs for a nonlinear concentration dependence of the form s/s₀ = (1 + kc)^?1. It is shown that the approach to equilibrium is very close to being exponential (in time) as in the case k = 0. We also compare results for the nonlinear case given above with results obtained for linear c-dependence of the form s/s₀ = 1 – kc. For relatively high speeds the time required to attain equilibrium may be greatly underestimated by use of the latter approximation. Finally, we present analytic approximations for the concentration distribution at equilibrium and as a function of time.     

Lack of prey switching and strong preference for mosquito prey by a temporary pond specialist predator

1. The strengths of trophic interactions within ecosystems can be mediated by complex mechanisms that require elucidation if researchers are to understand and predict population- and community-level stabilities. Where multiple prey types co-occur, prey switching (i.e. frequency-dependent predation) by predators may facilitate low-density prey refuge effects which promote coexistence. On the other hand, lack of switching and strong preferences by predators can strongly suppress prey populations, which is especially important considering vector species such as mosquitoes. 2. The present study quantifies prey switching and preference patterns of the temporary pond specialist copepod Lovenula raynerae towards larvae of the medically important Culex pipiens mosquito complex in the presence of different proportions of alternative Daphnia pulex prey. Further, it examines whether prey switching and preferences are contingent on the sex of the predator. 3. Lovenula raynerae exhibited a lack of prey switching and strong preference for larval mosquito prey overall, irrespective of predator sex. Also, when larval mosquitoes were available in higher proportions over daphniids, the strength of this positive selectivity increased. There was very little low-density refuge for mosquitoes where they were rare. 4. Lack of prey switching and strong preferences towards mosquitoes by predatory paradiaptomid copepods may enhance population-level regulation of disease vector mosquitoes that exploit temporary pond-style habitats. Accordingly, the conservation and promotion of these predators might enable better management of medically important species across landscapes.     

Hydraulic constraints on photosynthesis in subtropical evergreen broad leaf forest and pine woodland trees of the Florida Everglades

The relationship between water transport and photosynthesis represents the trade-off between carbon gain and water loss and was used to evaluate potential differences in water resource utilization among two dominant vegetation types of south Florida: subtropical evergreen broad leaf forests (hardwood hammocks) and pine woodlands (pine rocklands). We found consistent linear positive relationships between the quantum yield of photosystem II (ϕ _PSII), an index of photosynthetic capacity, and hydraulic conductivity per sapwood area (k _S) and per leaf area (k _L) across all species. The slope of the ϕ _PSII–k _S relationship was steeper for hardwood hammock than for pine rockland species. Mean ϕ _PSII was greater in pine rockland species and was greater for a given k _L than in hardwood hammock species. These results are consistent with previous observations demonstrating that pine rocklands tend to have better access to stable water sources than hardwood hammocks. We also found greater photosynthetic carbon isotope discrimination with increasing k _S and k _L in pine rockland species, but not in hardwood hammock species, suggesting increased stomatal conductance with increasing k _S and k _L, consistent with greater water availability in pine rockland habitats. Our study thus utilizes relationships between water transport and photosynthesis to evaluate hydraulic constraints on physiological function between two contrasting vegetation types with contrasting stability of water sources.     

PHENOTYPIC EVOLUTION BY NEUTRAL MUTATION

A general model is developed for predicting the genetic variance within populations and the rate of divergence of population mean phenotypes for quantitative traits under the joint operation of random sampling drift and mutation in the absence of selection. In addition to incorporating the dominance effects of mutant alleles, the model yields some insight into the effects of linkage and the mating system on the mutational production of quantitative-genetic variation. Despite these additional and potentially serious complications, it is found that, for small populations, the simple predictions obtained by previous investigators using additive-genetic models hold reasonably well. Even after accounting for dominance and linkage, the equilibrium level of genetic variance is unlikely to be much less than 2NV_m or to be more than 4NV_m, where N is the effective population size and V_m is the new variance from mutation appearing each generation. The rate of increase of the between-line variance per generation ultimately equals 2V_m regardless of population size, although the time to attain the asymptotic rate is proportional to N. Expressions are presented for the rate of approach to the equilibrium level of genetic variance and for the expected variance of the within-population and between-population genetic variances. The relevance of the derived model, which amounts to a generalization of the neutral theory to the phenotypic level, is discussed in the context of the detection of natural selection, the maintenance of pure lines for biomedical and agricultural purposes, the development of genetic conservation programs, and the design of indices of morphological distance between species.     

Interannual variation in effective number of breeders and estimation of effective population size in long‐lived iteroparous lake sturgeon (Acipenser fulvescens)

Quantifying interannual variation in effective adult breeding number (N_b) and relationships between N_b, effective population size (N_e), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long‐lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N_b and generational N_e using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N_b estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N_b across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced N_b relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N_b/N ratios (0.27–0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40‐fold difference in annual larval production across years (437–16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N_b/N. Estimates of N_e based on three single‐sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N_b. Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.     

A probability distribution model of small -scale species richness in plant communities

We devised a probability distribution model that best expressed species richness per quadrat in grassland communities, and clarified the mechanism by which the mean richness per quadrat was always larger than the variance among quadrats. Our model will aid in the understanding of community structures, and allow comparisons among different communities. The model was constructed based on relatively simple theoretical assumptions about the mechanisms in play in target communities. We assumed in the model that the number of species occurring in an actual quadrat, j, is the sum of “the fundamental number of species”, k (constant), and “a fluctuating number of species”, i (a Poisson variate with the mean of μ); that is, j = k + i, where i, j and k are non-negative integers. The probability that j species occur in a quadrat is given by a Poisson-like distribution (extended Poisson), with two parameters k and μ. The mean species richness in the probability distribution is expressed by λ (= k + μ), and the variance is λ − k. The proposed model afforded a good fit for the observed frequency distribution of species richness per quadrat. If even one species is common among many quadrats, the mean number of species per quadrat is greater than the variance. The greater the number of common species among quadrats is, the larger is the value of k, and then the more pronounced is the difference between the mean and the variance (although the variance does not change). We fitted the model to 55 datasets collected by ourselves from grasslands in various locations (Tibet, Inner Mongolia, Slovakia, or Japan), with varying quadrat size (0.25, 0.0625, or 0.01 m²), and under differing management status (various stocking densities).     

MATING SYSTEM AND GENETIC STRUCTURE OF THE DISTYLOUS TROPICAL TREE PSYCHOTRIA FAXLUCENS (RUBIACEAE)

The population genetics and mating system of the understory tropical rain forest tree Psychotria faxlucens were studied at two plots in Los Tuxtlas, Veracruz, México, on the Gulf of México coast. This species is distylous and is pollinated by moths, mainly small hawkmoths. The seeds are dispersed by gravity and by frugivorous birds. Controlled pollinations indicate that the trees are self-incompatible and that intramorph pollinations have lower compatibilities than intermorph pollinations. The pollen: ovule ratio is high, suggesting obligate xenogamy. Using electrophoretic allozyme methods we found that eight out of 20 loci were polymorphic (P = 0.400), the observed heterozygosity (H) was 0.198, and the mean expected heterozygosity (H) was 0.495, both relatively high values compared with that reported for tropical trees. The genetic differentiation between the two plots is low, as shown by the heterogeneity in allele frequencies and the F_st (mean F_st seedlings = 0.031, mean F_st adults = 0.026), although for some loci the plot differentiation is statistically significant. The studied populations are near Hardy-Weinberg proportions, both for seedlings (mean F = 0.128) and adults (mean F = 0.075). From the fixation rate, an indirect estimate of the outcrossing rate at equilibrium gave a mean of t = 0.898 for plot 1 and 0.685 for plot 2. Direct single loci and multiloci outcrossing rate estimates were generally not statistically different from 1.0.     

How to compare fluctuating asymmetry of different traits

Comparing fluctuating asymmetry (FA) between different traits can be difficult because traits vary at different scales. FA is generally quantified either as the variance of the difference between left and right (σ²_L?R) or the mean of the absolute value of this difference (μ_|R?L|). Corrections for scale differences are obtained by dividing by trait size mean. We show that a third index, one minus the correlation coefficient between left and right (1 ? r_L,R), is equivalent to σ²_L?R standardized by trait size variance. The indices are compared with Monte‐Carlo simulations. All achieve the expected correction for scale differences. High type I error rates (false indication of differences) occur only for σ²_L?R and μ_|R?L| if trait sizes close to or below 0 occur. 1 ? r_L,R with a bootstrap test has always low error rates. Recommendation of the index to be used should be based on whether standardization of FA by trait size mean or trait size variance is preferred. A survey of 36 traits in the Speckled Wood Butterfly (Pararge aegeria) indicated that σ²_L?R is slightly higher correlated to trait size variance than to trait size mean. Thus 1 ? r_L,R seems to be the superior index and should be reported when FA of different traits is compared.