Inferring natural selection operating on conservative and radical substitution at single amino acid sites

Natural selection operating on amino acid substitution at single amino acid sites can be detected by comparing the rates of synonymous (r(S)) and nonsynonymous (r(N)) nucleotide substitution at single codon sites. Amino acid substitutions can be classified as conservative or radical according to whether they retain the properties of the substituted amino acid. Here methods for comparing the rates of conservative (r(C)) and radical (r(R)) nonsynonymous substitution with r(S) at single codon sites were developed to detect natural selection operating on these substitutions at single amino acid sites. A method for comparing r(C) and r(R) at single codon sites was also developed to detect biases toward these substitutions at single amino acid sites. Charge was used as the property of the amino acids. In a computer simulation, false-positive rates of these methods were always < 5%, unless termination sites were included in the computation of the numbers of sites and estimates of transition/transversion rate ratio were highly biased. The frequency of detection of natural selection operating on conservative substitution was almost independent of the presence of natural selection operating on radical substitution, and vice versa. Natural selection operating specifically on conservative and radical substitution was detected more efficiently by comparing r(S) with r(C) and r(S) with r(R) than by comparing r(S) with r(N). These methods also appeared to be robust against the occurrence of recombination during evolution. In an analysis of class I human leukocyte antigen, negative selection operating on conservative substitution, but not positive selection operating on radical substitution, was observed at some of the codon sites with r(R) > r(C), suggesting that r(R) > r(C) may not necessarily be an indicator of positive selection operating on radical substitution.     

Human cationic amino acid transporters are not affected by direct nitros(yl)ation

Amino Acids - A direct inhibiting effect of NO on the function of CAT-1 and -2A has been postulated to occur via nitrosylation of cysteine residues in the transporters. Neither the NO donor SNAP...     

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection

One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to relatively weak selective constraints and so may, to a first approximation, be regarded as neutral. Synonymous sites are also interdigitated with nonsynonymous sites and so are affected equally by genomic context and demographic factors. Hence a comparison of levels of polymorphism and divergence between synonymous sites and amino acid replacement sites in a gene is potentially informative about the magnitude of selective forces associated with amino acid replacements. We have analyzed 56 genes in which polymorphism data from D. simulans are compared with divergence from a reference strain of D. melanogaster. The framework of the analysis is Bayesian and assumes that the distribution of selective effects (Malthusian fitnesses) is Gaussian with a mean that differs for each gene. In such a model, the average scaled selection intensity (gamma = N(e)s) of amino acid replacements eligible to become polymorphic or fixed is -7.31, and the standard deviation of selective effects within each locus is 6.79 (assuming homoscedasticity across loci). For newly arising mutations of this type that occur in autosomal or X-linked genes, the average proportion of beneficial mutations is 19.7%. Among the amino acid polymorphisms in the sample, the expected average proportion of beneficial mutations is 47.7%, and among amino acid replacements that become fixed the average proportion of beneficial mutations is 94.3%. The average scaled selection intensity of fixed mutations is +5.1. The presence of positive selection is pervasive with the single exception of kl-5, a Y-linked fertility gene. We find no evidence that a significant fraction of fixed amino acid replacements is neutral or nearly neutral or that positive selection drives amino acid replacements at only a subset of the loci. These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed.     

Why kin and group selection models may not be enough to explain human other-regarding behaviour

Models of kin or group selection usually feature only one possible fitness transfer. The phenotypes are either to make this transfer or not to make it and for any given fitness transfer, Hamilton's rule predicts which of the two phenotypes will spread. In this article we allow for the possibility that different individuals or different generations face similar, but not necessarily identical possibilities for fitness transfers. In this setting, phenotypes are preference relations, which concisely specify behaviour for a range of possible fitness transfers (rather than being a specification for only one particular situation an animal or human can be in). For this more general set-up, we find that only preference relations that are linear in fitnesses can be explained using models of kin selection and that the same applies to a large class of group selection models. This provides a new implication of hierarchical selection models that could in principle falsify them, even if relatedness--or a parameter for assortativeness--is unknown. The empirical evidence for humans suggests that hierarchical selection models alone are not enough to explain their other-regarding or altruistic behaviour.     

Accuracy and power of bayes prediction of amino acid sites under positive selection

Bayes prediction quantifies uncertainty by assigning posterior probabilities. It was used to identify amino acids in a protein under recurrent diversifying selection indicated by higher nonsynonymous (d(N)) than synonymous (d(S)) substitution rates or by omega = d(N)/d(S) > 1. Parameters were estimated by maximum likelihood under a codon substitution model that assumed several classes of sites with different omega ratios. The Bayes theorem was used to calculate the posterior probabilities of each site falling into these site classes. Here, we evaluate the performance of Bayes prediction of amino acids under positive selection by computer simulation. We measured the accuracy by the proportion of predicted sites that were truly under selection and the power by the proportion of true positively selected sites that were predicted by the method. The accuracy was slightly better for longer sequences, whereas the power was largely unaffected by the increase in sequence length. Both accuracy and power were higher for medium or highly diverged sequences than for similar sequences. We found that accuracy and power were unacceptably low when data contained only a few highly similar sequences. However, sampling a large number of lineages improved the performance substantially. Even for very similar sequences, accuracy and power can be high if over 100 taxa are used in the analysis. We make the following recommendations: (1) prediction of positive selection sites is not feasible for a few closely related sequences; (2) using a large number of lineages is the best way to improve the accuracy and power of the prediction; and (3) multiple models of heterogeneous selective pressures among sites should be applied in real data analysis.     

Stimulation of insulin release by glyceraldehyde may not be similar to glucose

Glyceraldehyde (GA) has been used to study insulin secretion for decades and it is widely assumed that beta-cell metabolism of GA after its phosphorylation by triokinase is similar to metabolism of glucose; that is metabolism through distal glycolysis and oxidation in mitochondria. New data supported by existing information indicate that this is true for only a small amount of GA's metabolism and also suggest why GA is toxic. GA is metabolized at 10-20% the rate of glucose in pancreatic islets, even though GA is a more potent insulin secretagogue. GA also inhibits glucose metabolism to CO2 out of proportion to its ability to replace glucose as a fuel. This study is the first to measure methylglyoxal (MG) in beta-cells and shows that GA causes large increases in MG in INS-1 cells and d-lactate in islets but MG does not mediate GA-induced insulin release. GA severely lowers NAD(P) and increases NAD(P)H in islets. High NADH combined with GA's metabolism to CO2 may initially hyperstimulate insulin release, but a low cytosolic NAD/NADH ratio will block glycolysis at glyceraldehyde phosphate (GAP) dehydrogenase and divert GAP toward MG and D-lactate formation. Accumulation of D-lactate and 1-phosphoglycerate may explain why GA makes the beta-cell acidic. Reduction of both GA and MG by abundant beta-cell aldehyde reductases will lower the cytosolic NADPH/NADP ratio, which is normally high.     

Signals and behavioural responses are not coupled in males: aggression affected by replacement of an evolutionarily lost colour signal

Male Sceloporus virgatus lack the blue abdominal patches which are used during aggressive encounters in other Sceloporus lizards. Herein we report that, despite having lost this signal, males have retained a behavioural response to experimentally restored blue abdominal patches. We tested two adaptive hypotheses: selection acted primarily upon signallers or selection acted upon both signallers and receivers. The first predicts that only the signal is lost and that male interactions should be affected by the restoration of blue patches. The latter predicts that both the signal and behavioural response are lost and the display of the restored blue patches should have no effect on male-male interactions. We compared the behaviour of receivers in paired encounters where one male (signaller) had blue-painted abdominal patches to a set of trials where both males had white-painted abdomens, unmanipulated abdomens or a novel-painted pattern. The receivers of the blue-painted signal were more likely to display submissive behaviour. The receivers in either the unmanipulated, white-painted or novel-painted signal trials were more likely to display neutral behaviour. These results support the hypothesis that receivers have retained a behavioural response and selection has acted primarily on the signaller. We believe this is the first documentation of males responding to an evolutionarily lost signal in conspecific males.     

A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection

The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.

What maintains genetic variation remains an unresolved mystery. This study describes the development of a new test and its application to human population genomic data, suggesting that natural selection may have a much more important role than previously thought, with hundreds of non-synonymous polymorphisms subject to balancing selection.     

Resistance and tolerance to herbivory in Salix cordata are affected by different environmental factors

Abstract.  1. Effects of sand burial and nutrients on the ability of sand-dune willow ( Salix cordata ) to tolerate or resist herbivory by the beetle Altica subplicata were evaluated in field experiments.
2. To assess tolerance, all combinations of sand burial (none, 50%), nutrients (presence, absence), and beetles (presence, absence) were applied to caged plants and growth responses to herbivory were measured. Sand burial increased plant growth rate, but decreased S. cordata 's tolerance to herbivory. Although nutrients increased growth, tolerance to herbivory was unaffected.
3. To assess resistance, plants were exposed to all combinations of sand burial and nutrients, and then to natural beetle colonisation. The presence of nutrients, but not sand burial, significantly increased the percentage of plants with beetles, for both adults and larvae. This decreased resistance to beetles of plants grown with added nutrients occurred only in the absence of sand burial.
4. The performance and preference of beetles were examined in laboratory experiments. Larvae developed faster and had increased pupation success on plants with nutrients added. Beetles also showed a marginally significant feeding preference for leaves grown with added nutrients. Thus, S. cordata tolerance to herbivory was affected by sand burial, whereas resistance, preference, and performance were affected by nutrient level.     

Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.

The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different evolutionary models and generally more reliable than that by likelihood-based methods. In contrast, the results obtained by likelihood-based methods depend on the models and on the initial parameter values used. It is sometimes difficult to obtain the maximum likelihood estimates of parameters for a given model, and the results obtained may be false negatives or false positives depending on the initial parameter values. It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths of the phylogenetic tree are relatively small.     

Plant functional traits differ in adaptability and are predicted to be differentially affected by climate change

1. Climate change is testing the resilience of forests worldwide pushing physiological tolerance to climatic extremes. Plant functional traits have been shown to be adapted to climate and have evolved patterns of trait correlations (similar patterns of distribution) and coordinations (mechanistic trade‐off). We predicted that traits would differentiate between populations associated with climatic gradients, suggestive of adaptive variation, and correlated traits would adapt to future climate scenarios in similar ways.
2. We measured genetically determined trait variation and described patterns of correlation for seven traits: photochemical reflectance index (PRI), normalized difference vegetation index (NDVI), leaf size (LS), specific leaf area (SLA), δ¹³C (integrated water‐use efficiency, WUE), nitrogen concentration (N_CONC), and wood density (WD). All measures were conducted in an experimental plantation on 960 trees sourced from 12 populations of a key forest canopy species in southwestern Australia.
3. Significant differences were found between populations for all traits. Narrow‐sense heritability was significant for five traits (0.15–0.21), indicating that natural selection can drive differentiation; however, SLA (0.08) and PRI (0.11) were not significantly heritable. Generalized additive models predicted trait values across the landscape for current and future climatic conditions (>90% variance). The percent change differed markedly among traits between current and future predictions (differing as little as 1.5% (δ¹³C) or as much as 30% (PRI)). Some trait correlations were predicted to break down in the future (SLA:N_CONC, δ¹³C:PRI, and N_CONC:WD).
4. Synthesis: Our results suggest that traits have contrasting genotypic patterns and will be subjected to different climate selection pressures, which may lower the working optimum for functional traits. Further, traits are independently associated with different climate factors, indicating that some trait correlations may be disrupted in the future. Genetic constraints and trait correlations may limit the ability for functional traits to adapt to climate change.

     

Specific amino acid substitutions are not required for transformation by v-myb of avian myeloblastosis virus.

The protein product of the v-myb oncogene of avian myeloblastosis virus, p48v-myb, differs structurally in several ways from its normal cellular homolog, p75c-myb. We demonstrated that the 11 specific amino acid substitutions found in two independent molecular clones of this virus were not required for the transformation of myeloblasts by v-myb.     

Hematopoiesis and thymic apoptosis are not affected by the loss of Cdk2

Cell cycle regulation is essential for proper homeostasis of hematopoietic cells. Cdk2 is a major regulator of S phase entry, is activated by mitogenic cytokines, and has been suggested to be involved in antigen-induced apoptosis of T lymphocytes. The role of Cdk2 in hematopoietic cells and apoptosis in vivo has not yet been addressed. To determine whether Cdk2 plays a role in these cells, we performed multiple analyses of bone marrow cells, thymocytes, and splenocytes from Cdk2 knockout mice. We found that Cdk2 is not required in vivo to induce apoptosis in lymphocytes, a result that differs from previous pharmacological in vitro studies. Furthermore, thymocyte maturation was not affected by the lack of Cdk2. We then analyzed the hematopoietic stem cell compartment and found similar proportions of stem cells and progenitors in Cdk2(-)(/)(-) and wild-type animals. Knockouts of Cdk2 inhibitors (p21, p27) affect stem cell renewal, but a competitive graft experiment indicated that renewal and multilineage differentiation are normal in the absence of Cdk2. Finally, we stimulated T lymphocytes or macrophages to induce proliferation and observed normal reactivation of Cdk2(-)(/)(-) quiescent cells. Our results indicate that Cdk2 is not required for proliferation and differentiation of hematopoietic cells in vivo, although in vitro analyses consider Cdk2 to be a major player in proliferation and apoptosis in these cells and a potential target for therapy.     

The sharing of amino acid short spans by ancestrally unrelated proteins may be the result of ubiquitous alpha and beta secondary structures

Short homologies are often found when genetically unrelated proteins are compared but it is not known whether the rate at which they occur is or not above randomness. Comparing 190 pairs of unrelated proteins enable us to show that the frequency at which pairs of unrelated proteins share little spans of amino acids is compatible with chance.However, it appears that those short homologies are mainly located within protein subregions of identical secondary structure: the frequency at which pairs of unrelated proteins exhibit related spans of amino acids inside subregions of identical secondary structure is far above randomness. Those data suggest that the sharing of related spans of amino acids by genetically unrelated proteins could result from structural constraints imposed by the α or β secondary structures.     

Mating success and oviposition of a butterfly are not affected by non-lethal tissue sampling

Non-lethal methods of tissue sampling are increasingly used for genetic studies of insect species and the effects of this approach have long been assumed to be minimal. Tissue removal has the potential to influence insect reproductive behaviours such as mate recognition, courtship or oviposition but the effects of non-lethal sampling on reproductive success have not been widely and adequately tested. Here, we test potential effects of both wing-clipping and leg removal on reproductive behaviours of the cabbage white butterfly (Pieris rapae). We conducted a total of 93 male and 59 female mating trials, and found no significant differences in mating success between treated (i.e., tissue removed) and control individuals in either sex. We also monitored the number and location of eggs laid by 58 females. We found no significant differences in egg-laying behaviour among leg removed and control individuals. Power analysis indicated that we had sufficient statistical power to detect moderate effects of treatment on both mating and oviposition. Our study provides the most comprehensive examination to date of the effects of non-lethal sampling on reproductive behaviours in a butterfly/insect species, and supports the contention that tissue sampling is non-detrimental. To fully comprehend the general impacts of tissue sampling on butterfly reproductive behaviour however, additional similar studies need to be conducted on a variety of species with differing mating behaviours. Only through meta-analysis, may it be possible to detect more subtle effects of tissue removal which cannot be revealed within a single study due to sample size limitations.     

Dietary fat-induced changes in protein and carbohydrate selection are not explained by alterations in neuronal membrane fatty acid composition

We previously showed changes in protein and carbohydrate selection in response to qualitative differences in dietary fat. Alterations in macronutrient selection were specifically related to changes in dietary saturated fat, but not to relative or absolute differences in dietary essential fatty acids. Three experiments were conducted to determine if changes in specific fatty acids in bulk phase neural membranes were associated with differences in macronutrient selection. For each experiment, specific fatty acid profiles were achieved by blending dietary fat sources. Rats consumed 20% (w/w) fat diets varying only in their fatty acid composition. After 2 weeks, rats were challenged with a selection paradigm. Each experiment showed a significant effect of dietary fat on neural membrane fatty acid composition (p less than 0.05) and alterations in individual fatty acids were correlated with changes in dietary fatty acids (p less than 0.05). However, dietary fat had no consistent effect with respect to which particular neural membrane fatty acids were modified, and there was no correlation between changes in specific membrane fatty acids and macronutrient selection. These findings suggest that alteration of specific fatty acids in bulk phase neural membranes do not mediate macronutrient selection behavior.     

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Background  

In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner.     

Sprint and vertical jump performances are not affected by six weeks of static hamstring stretching

The purpose of this study was to investigate whether 6 weeks of static hamstring stretching effects range of motion (ROM), sprint, and vertical jump performances in athletes. Twenty-one healthy division III women's track and field athletes participated in the study. Subjects were tested for bilateral knee ROM; 55-m sprint time; and vertical jump height before, at 3 weeks, and after the 6-week flexibility program. Subjects were randomly assigned to treatment and control groups and warmed up with a 10-minute jog on a track before a hamstring stretching protocol. The stretching protocol consisted of four repetitions held for 45 seconds, 4 days per week. Four variables (left and right leg ROM, 55-m sprint time, vertical jump) were analyzed using a repeated-measures analysis of variance design. No significant differences (P < or = 0.05) were found with any of the four variables between the stretching and control groups. Six weeks of a static hamstring stretching protocol did not improve knee ROM or sprint and vertical jump performances in women track and field athletes. The use of static stretching should be restricted to post practice or competition because of the detrimental effects reported throughout the literature. Based on the current investigation, it does not seem that chronic static stretching has a positive or negative impact on athletic performance. Thus, the efficacy of utilizing this practice is questionable and requires further investigation.