Evolutionary models of metabolism, behaviour and personality

I explore the relationship between metabolism and personality by establishing how selection acts on metabolic rate and risk-taking in the context of a trade-off between energy and predation. Using a simple time budget model, I show that a high resting metabolic rate is not necessarily associated with a high daily energy expenditure. The metabolic rate that minimizes the time spent foraging does not maximize the net gain rate while foraging, and it is not always advantageous for animals to have a higher metabolic rate when food availability is high. A model based on minimizing the ratio of mortality rate to net gain rate is used to determine how a willingness to take risks should be correlated with metabolic rate. My results establish that it is not always advantageous for animals to take greater risks when metabolic rate is high. When foraging intensity and metabolic rate coevolve, I show that in a particular case different combinations of foraging intensity and metabolic rate can have equal fitness.     

The forward rate of binding of surface-tethered reactants: effect of relative motion between two surfaces

The reaction of molecules confined to two dimensions is of interest in cell adhesion, specifically for the reaction between cell surface receptors and substrate-bound ligand. We have developed a model to describe the overall rate of reaction of species that are bound to surfaces under relative motion, such that the Peclet number is order one or greater. The encounter rate between reactive species is calculated from solution of the two-dimensional convection-diffusion equation. The probability that each encounter will lead to binding depends on the intrinsic rate of reaction and the encounter duration. The encounter duration is obtained from the theory of first passage times. We find that the binding rate increases with relative velocity between the two surfaces, then reaches a plateau. This plateau indicates that the increase in the encounter rate is counterbalanced by the decrease in the encounter duration as the relative velocity increases. The binding rate is fully described by two dimensionless parameters, the Peclet number and the Damk?hler number. We use this model to explain data from the cell adhesion literature by incorporating these rate laws into "adhesive dynamics" simulations to model the binding of a cell to a surface under flow. Leukocytes are known to display a "shear threshold effect" when binding selectin-coated surfaces under shear flow, defined as an increase in bind rate with shear; this effect, as calculated here, is due to an increase in collisions between receptor and ligand with increasing shear. The model can be used to explain other published data on the effect of wall shear rate on the binding of cells to surfaces, specifically the mild decrease in binding within a fixed area with increasing shear rate.     

Positive correlation between evolutionary rate and recombination rate in Drosophila genes with male-biased expression

Previous studies have shown that genes that are expressed predominantly or exclusively in males tend to evolve rapidly in comparison to other genes. In most cases, however, it is unknown whether this rapid evolution is the result of increased positive (or sexual) selection on male-expressed traits or if it is due to a relaxation of selective constraints. To distinguish between these two possibilities, we analyzed the relationship between the nonsynonymous substitution rate (dN) and local recombination rate for 343 Drosophila genes that were classified as male, female, or nonsex biased in their expression. For the male-biased genes, a positive correlation between dN and recombination rate was observed. This can be explained by an increased rate of adaptive evolution in regions of higher recombination due to a reduction of Hill-Robertson interference. In contrast, the correlation between dN and recombination rate was negative for both female- and nonsex-biased genes, suggesting that these genes are primarily subject to purifying selection, which is expected to be less effective in regions of reduced recombination.     

Suppression of rpsL phenotypes by tuf mutations reveals a unique relationship between translation elongation and growth rate

We have found a simple relationship between bacterial growth rate and the translation elongation rate. Thus, for a set of defined ribosomal protein S12 mutations which reduce the efficiency of the ternary complex ribosome interaction (and restrict the frequency of translational errors) there is a linear relationship between growth rate and translation elongation rate. When these mutants are combined with defined EF-Tu mutants (which increase the probability of translational errors) both the elongation rate and growth rate reductions are reversed. The reductions and reversals are described by a unique linear relationship. We interpret this to mean that these two types of mutation exert opposing effects on the same molecular interaction. We suggest that this interaction is in the initial selection of the aminoacyl-tRNA on the ribosome. The slope of the relationship between translation elongation rate and growth rate, defined in per cent of the wild-type rates, is close to 1. Interestingly, the reversal of the elongation and growth phenotypes is Incomplete, suggesting that the ribosomal mutants have an additional defect which is not compensated for by the ternary complex interaction. Our results show that the efficiency of the ternary complex ribosome interaction limits the translation elongation rate, which in turn correlates with changes in exponential growth rate.     

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.      

On the constancy of cell division rate in the root meristem

This review examines under what circumstances the rate of cell division among cells of the root meristem is known to vary. First, methods are compared that have been used to quantify cell division rate. These can be grouped as being either cytological, in which the rate of accumulation of cells in a particular phase of the cell cycle is determined based on some form of cytological labeling, or kinematic, in which the rate of cell accumulation is determined from the net movement of cells. Then, evidence is reviewed as to whether cell division rates vary between different tissues or cell types, between different positions in the root, or finally between different environments. The evidence is consistent with cells dividing at a constant rate, and well documented examples where cell division rate changes substantially are rare. The constancy of cell division rate contrasts with the number of dividing cells, which varies extensively, and implies that a major point for cell cycle control is governing the exit from the proliferative state at the basal boundary of the meristem.     

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.     

Rainbow trout in seasonal environments: phenotypic trade‐offs across a gradient in winter duration

Survival through periods of resource scarcity depends on the balance between metabolic demands and energy storage. The opposing effects of predation and starvation mortality are predicted to result in trade‐offs between traits that optimize fitness during periods of resource plenty (e.g., during the growing season) and those that optimize fitness during periods of resource scarcity (e.g., during the winter). We conducted a common environment experiment with two genetically distinct strains of rainbow trout to investigate trade‐offs due to (1) the balance of growth and predation risk related to foraging rate during the growing season and (2) the allocation of energy to body size prior to the winter. Fry (age 0) from both strains were stocked into replicate natural lakes at low and high elevation that differed in winter duration (i.e., ice cover) by 59 days. Overwinter survival was lowest in the high‐elevation lakes for both strains. Activity rate and growth rate were highest at high elevation, but growing season survival did not differ between strains or between environments. Hence, we did not observe a trade‐off between growth and predation risk related to foraging rate. Growth rate also differed significantly between the strains across both environments, which suggests that growth rate is involved in local adaptation. There was not, however, a difference between strains or between environments in energy storage. Hence, we did not observe a trade‐off between growth and storage. Our findings suggest that intrinsic metabolic rate, which affects a trade‐off between growth rate and overwinter survival, may influence local adaptation in organisms that experience particularly harsh winter conditions (e.g., extended periods trapped beneath the ice in high‐elevation lakes) in some parts of their range.     

Relative rates of nuclear DNA evolution in human and Old World monkey lineages

Rates of substitution were compared between humans and Old World monkeys for sequences in or adjacent to 19 genes. The comparison of 21,299 sites in noncoding regions indicates that the substitution rate is approximately 43% greater in the Old World monkey lineage. However, 83% of the compared sites are in the region of the beta-globin gene family. Outside this region there is no consistent pattern of rate difference between the two lineages. Comparison of the coding regions of 16 genomically dispersed genes, involving 1,592 synonymous sites and 5,275 nonsynonymous sites, showed a faster rate of substitution in the human lineage at the nonsynonymous sites of the prion gene, but otherwise no evidence of rate difference between the two lineages. It is concluded that rate differences between these two lineages may be specific to certain regions of the genome rather than being a general phenomenon. This conclusion needs to be confirmed by comparison of a larger number of genomically dispersed sequences. It is, however, consistent with the results of DNA-DNA hybridization experiments, which show no difference in evolutionary rate between the two lineages.      

The Transpiration rate of Abies georgei and the Correlation with Enviromental Factors

The transpiration rate of Abies georgei (20 years) was determined at sample plots on subalpine in Northwest of Yunnan Province. The result of annual change shows that the rate is from lower to higher monthly. The transpiration rate reached maximum value of 195.88 mgH20·gdw-1·h-1 in July, then, it decreases gradually in a open-grown sample leaf of the current year. The phenomenon of “noon-rest” shows that the curve for day change of transpiration rate is the form of double peaks. Statistical analysis proves that the variance of transpiration rate is influenced mainly by the environmental factors, particularly by temperature, relative humidity and light intensity. The correlations between transpiration rate and temperature, light intensity are positive and that between transpiration rate and relative humidity is negative. The variances of the transpiration rate on the elevations are different. The transpiration rate decreases with the increase of elevation in the natural forest area. Change is less in whole day at high elevation and light wave too. The rate of transpiration in clear cut over area is higher than in the area under deep canopy of a subalpine natural forest, they are 186.15 and 123.97 respectively Lastly, the correlation between transpiration rate and environmental factors and plant setting are discussed in this paper.     

Protein protein interactions, evolutionary rate, abundance and age

Background

Does a relationship exist between a protein's evolutionary rate and its number of interactions? This relationship has been put forward many times, based on a biological premise that a highly interacting protein will be more restricted in its sequence changes. However, to date several studies have voiced conflicting views on the presence or absence of such a relationship.

Results

Here we perform a large scale study over multiple data sets in order to demonstrate that the major reason for conflict between previous studies is the use of different but overlapping datasets. We show that lack of correlation, between evolutionary rate and number of interactions in a data set is related to the error rate. We also demonstrate that the correlation is not an artifact of the underlying distributions of evolutionary distance and interactions and is therefore likely to be biologically relevant. Further to this, we consider the claim that the dependence is due to gene expression levels and find some supporting evidence. A strong and positive correlation between the number of interactions and the age of a protein is also observed and we show this relationship is independent of expression levels.

Conclusion

A correlation between number of interactions and evolutionary rate is observed but is dependent on the accuracy of the dataset being used. However it appears that the number of interactions a protein participates in depends more on the age of the protein than the rate at which it changes.     

Higher rate of tissue regeneration in polyploid asexual versus diploid sexual freshwater snails

Characterizing phenotypic differences between sexual and asexual organisms is a critical step towards understanding why sexual reproduction is so common. Because asexuals are often polyploid, understanding how ploidy influences phenotype is directly relevant to the study of sex and will provide key insights into the evolution of ploidy-level variation. The well-established association between genome size and cell cycle duration, evidence for a link between genome size and tissue regeneration rate and the growing body of research showing that ploidy influences growth rate and gene expression led us to hypothesize that healing and tissue regeneration might be affected by ploidy-level variation. We evaluated this hypothesis by measuring the rate of regeneration of antenna tissue of Potamopyrgus antipodarum, a New Zealand snail characterized by frequent coexistence between diploid sexuals and polyploid asexuals. Antennae of triploid and presumptive tetraploid asexuals regenerated more rapidly than the antennae of diploid sexuals, but regeneration rate did not differ between triploids and tetraploids. These results suggest either that ploidy elevation has nonlinear positive effects on tissue regeneration and/or that factors associated directly with reproductive mode affect regeneration rate more than ploidy level. The results of this study also indicate that the lower ploidy of sexual P. antipodarum is unlikely to confer advantages associated with more rapid regeneration.     

Neutral effect of recombination on base composition in Drosophila

Recombination is thought to have various evolutionary effects on genome evolution. In this study, we investigated the relationship between the base composition and recombination rate in the Drosophila melanogaster genome. Because of a current debate about the accuracy of the estimates of recombination rate in Drosophila, we used eight different measures of recombination rate from recent work. We confirmed that the G + C content of large introns and flanking regions is positively correlated with recombination rate, suggesting that recombination has a neutral effect on base composition in Drosophila. We also confirmed that this neutral effect of recombination is the main determinant of the correlation between synonymous codon usage bias and recombination rate in Drosophila.     

Phylogenetic signal, evolutionary process, and rate

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.     

The Correlation Between Recombination Rate and Dinucleotide Bias in Drosophila melanogaster

Revealing how recombination affects genomic sequence is of great significance to our understanding of genome evolution. The present paper focuses on the correlation between recombination rate and dinucleotide bias in Drosophila melanogaster genome. Our results show that the overall dinucleotide bias is positively correlated with recombination rate for genomic sequences including untranslated regions, introns, intergenic regions, and coding sequences. The correlation patterns of individual dinucleotide biases with recombination rate are presented. Possible mechanisms of interaction between recombination and dinucleotide bias are discussed. Our data indicate that there may be a genome-wide universal mechanism acting between recombination rate and dinucleotide bias, which is likely to be neighbor-dependent biased gene conversion.     

The response of isoprene emission rate and photosynthetic rate to photon flux and nitrogen supply in aspen and white oak trees

Isoprene is the primary biogenic hydrocarbon emitted from temperate deciduous forest ecosystems. The effects of varying photon flux density (PFD) and nitrogen growth regimes on rates of isoprene emission and net photosynthesis in potted aspen and white oak trees are reported. In both aspen and oak trees, whether rates were expressed on a leaf area or dry mass basis, (1) growth at higher PFD resulted in significantly higher rates of isoprene emission, than growth at lower PFD, (2) there is a significant positive relationship between isoprene emission rate and leaf nitrogen concentration in both sun and shade trees, and (3) there is a significant positive correlation between isoprene emission rate and photosynthetic rate in both sun and shade trees. The greater capacity for isoprene emission in sun leaves was due to both higher leaf mass per unit area and differences in the biochemical and/or physiological properties that influence isoprene emission. Positive correlations between isoprene emission rate and leaf nitrogen concentration support the existence of mechanisms that link leaf nitrogen status to isoprene synthase activity. Positive correlations between isoprene emission rate and photosynthesis rate support previous hypotheses that isoprene emission plays a role in protecting photosynthetic mechanisms during stress.     

The survival of mouse oocytes shows little or no correlation with the vitrification or freezing of the external medium,but the ability of the medium to vitrify is affected by its solute concentration and by the cooling rate

As survival of mouse oocytes subjected to vitrification depends far more on the warming rate than on the cooling rate, we wished to determine whether the lack of correlation between survival and cooling rate was mirrored by a lack of correlation between cooling rate and vitrification of the medium (EAFS), and between survival and the vitrification of the medium. The morphological and functional survival of the oocytes showed little or no relation to whether or not the EAFS medium vitrified or froze. We studied if the droplet size and the elapsed time (between placing the droplet on the Cryotop and the start of cooling) affects the result through modification of the cooling rate and solute concentration. Dehydration was rapid; consequently, the time between the placing the droplets into a Cryotop and cooling must be held to a minimum. The size of the EAFS droplet that is being cooled does not seem to affect vitrification. Finally, the degree to which samples of EAFS vitrify is firmly dependent on both its solute concentration and the cooling rate.     

The survival of mouse oocytes shows little or no correlation with the vitrification or freezing of the external medium,but the ability of the medium to vitrify is affected by its solute concentration and by the cooling rate

As survival of mouse oocytes subjected to vitrification depends far more on the warming rate than on the cooling rate, we wished to determine whether the lack of correlation between survival and cooling rate was mirrored by a lack of correlation between cooling rate and vitrification of the medium (EAFS), and between survival and the vitrification of the medium. The morphological and functional survival of the oocytes showed little or no relation to whether or not the EAFS medium vitrified or froze. We studied if the droplet size and the elapsed time (between placing the droplet on the Cryotop and the start of cooling) affects the result through modification of the cooling rate and solute concentration. Dehydration was rapid; consequently, the time between the placing the droplets into a Cryotop and cooling must be held to a minimum. The size of the EAFS droplet that is being cooled does not seem to affect vitrification. Finally, the degree to which samples of EAFS vitrify is firmly dependent on both its solute concentration and the cooling rate.     

Chemical decomposition of glutamine in cell culture media: effect of media type, pH, and serum concentration.

The chemical decomposition of glutamine to ammonia and pyrrolidonecarboxylic acid was studied at 37 degrees C in a pH range of 6.8-7.8 in different media preparations containing various amounts of fetal bovine serum. The media type influenced the decomposition rate, and the first-order rate constants increased with increasing pH values. The serum concentration had little or no effect on the decomposition rate. The importance of chemical decomposition of glutamine on the analysis of glutamine and ammonia metabolism was illustrated by an example of batch cultivation of a hybridoma cell line. The difference between the apparent uptake rate of glutamine and the actual uptake rate (which is corrected for the chemical decomposition) is shown to be as high as 200%. Similar discrepancy between the apparent and actual ammonia production rate is observed. Mathematical analysis was carried out to develop the relationship between the apparent and actual glutamine uptake and ammonia production rates. The analysis reveals that there are three important dimensionless parameter ratios that govern the difference between the apparent and actual glutamine uptake and ammonia production rates.     

Adaptive variation in growth rate: life history costs and consequences in the speckled wood butterfly,Pararge aegeria

An important assumption made in most lifehistory theory is that there is a trade-off between age and size at reproduction. This trade-off may, however, disappear if growth rate varies adaptively. The fact that individuals do not always grow at the maximum rate can only be understood if high growth rates carry a cost. This study investigates the presence and nature of such costs inPararge aegeria. Five females from two populations with known differences in life history (south Sweden and Maderia) were allowed to oviposit in the laboratory and their offspring were reared in environmental chambers under conditions leading to direct development. We measured several aspects of life history, including development times, pupal and adult weights, growth rate, female fecundity, longevity and larval starvation endurance. In both populations there seemed to be genetic variation in growth rate. There was no evidence for a trade-off between age and size at pupation. As predicted, larvae with high growth rates also lost weight at a relatively higher rate during starvation. High weight-loss rates were furthermore associated with a lower probability of surviving when food became available again. This is apparently the first physiological trade-off with growth rate that has been experimentally demonstrated. In both populations there were significant differences in growth rate between the sexes, but the populations differed in which sex was growing at the highest rate. In Sweden males had higher growth rates than females, whereas the reverse was true for Madeira. These patterns most likely reflect differences in selection for protandry, in turn caused by differences in seasonality between Sweden and Madeira. Together with the finding that males had shorter average longevity than females in the Swedish, but not in the Maderiran, population, this indicates that a lower adult quality also may be a cost of high growth rate. We argue that for the understanding of life history variation it is necessary to consider not only the two dimensions of age and size, but also to take into full account the triangular nature of the relationship between size, time and growth rate.