Fluctuating Mutation Bias and the Evolution of Base Composition in Drosophila

The idea that the pattern of point mutation in Drosophila has remained constant during the evolution of the genus has recently been challenged. A study of the nucleotide composition focused on the Drosophila saltans group has evidenced unsuspected nucleotide composition differences among lineages. Compositional differences are associated with an accelerated rate of amino acid replacement in functionally less constrained regions. Here we reassess this issue from a different perspective. Adopting a maximum-likelihood estimation approach, we focus on the different predictions that mutation and selection make about the nonsynonymous-to-synonymous rate ratio. We investigate two gene regions, alcohol dehydrogenase (Adh) and xanthine dehydrogenase (Xdh), using a balanced data set that comprises representatives from the melangaster, obscura, saltans, and willistoni groups. We also consider representatives of the Hawaiian picture-winged group. These Hawaiian species are known to have experienced repeated bottlenecks and are included as a reference for comparison. Our results confirm patterns previously detected. The branch ancestral to the fast-evolving willistoni/saltans lineage, where most of the change in GC content has occurred, exhibits an excess of synonymous substitutions. The shift in mutation bias has affected the extent of the rate variation among sites in Xdh. Received: 4 May 1999 / Accepted: 26 July 1999     

Evolutionary Lability of Context-Dependent Codon Bias in Bacteria

In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered. Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably between genomes. Received: 6 May 1999 / Accepted: 29 October 1999     

Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes

To understand the process and mechanism of protein evolution, it is important to know what types of amino acid substitutions are more likely to be under selection and what types are mostly neutral. An amino acid substitution can be classified as either conservative or radical, depending on whether it involves a change in a certain physicochemical property of the amino acid. Assuming Kimura's two-parameter model of nucleotide substitution, I present a method for computing the numbers of conservative and radical nonsynonymous (amino acid altering) nucleotide substitutions per site and estimate these rates for 47 nuclear genes from mammals. The results are as follows. (1) The average radical/conservative rate ratio is 0.81 for charge changes, 0.85 for polarity changes, and 0.49 when both polarity and volume changes are considered. (2) The radical/conservative rate ratio is positively correlated with the nonsynonymous/synonymous rate ratio for charge changes or when both polarity and volume changes are considered. (3) Both the conservative/synonymous rate ratio and the radical/synonymous rate ratio are lower in the rodent lineage than in the primate or artiodactyl lineage, suggesting more intense purifying selection in the rodent lineage, for both conservative and radical nonsynonymous substitutions. (4) Neglecting transition/transversion bias would cause an underestimation of both radical and conservative rates and the ratio thereof. (5) Transversions induce more dramatic genetic alternations than transitions in that transversions produce more amino acid altering changes and among which, more radical changes. Received: 6 April 1999 / Accepted: 16 August 1999     

Testing for differences in survival with delayed ascertainment

During the interim stages of most large-scale clinical trials, knowledge that a patient is alive or dead is usually not up-to-date. This is due to the pattern of patient visits to hospitals as well as the administrative set-up used by the study to obtain information on vital status. On a two-armed study, if the process of ascertaining vital status is not the same in both treatment groups, then the standard method of testing based on the logrank statistic may not be applicable. Instead, an ad hoc modification to the logrank test, which artificially truncates follow-up prior to the time of analysis, is often used. These approaches have not been formally addressed in the literature. In the early stages of a clinical trial, severe bias or loss of power may result. For this situation, we propose a class of test statistics that extends the usual class of U statistics. Asymptotic normality is derived by reformulating the statistics in terms of counting processes and employing the theory of U statistics along with martingale techniques. For early interim analyses, a numerical study indicates that the new tests can be more powerful than the current practice when differential ascertainment is present. To illustrate the potential loss of information when lagging follow-up to control for ascertainment delays, we reanalyze an AIDS clinical trial with the truncated logrank and the new statistics.     

A meta-analysis of case-control and cohort studies with interval-censored exposure data: application to chorionic villus sampling

Chorionic villus sampling (CVS) is a valued method of prenatal diagnosis that is often preferred over amniocentesis because it can be performed earlier, but which has also raised concern over a possible association with increased risk of terminal transverse limb deficiency (TTLD). We present and apply a meta-analytic method for estimating a combined dose-response effect from a series of case-control and cohort studies in which the exposure variable is interval-censored. Assuming coarsening at random for the interval-censoring, and calling upon the familiar result of Cornfield to pool case-control and cohort information on the association between a rare binary outcome and a multilevel exposure variable, we form a likelihood-based model to assess the effect of gestational age at the time of CVS on the presence or absence of a rare birth defect. Effect estimates are computed with a variant of the EM algorithm termed the method of weights, which enables the use of standard weighted regression software. Our findings suggest that CVS exposure at early gestational age leads to an increased risk of TTLD.     

Evolutionarily Conserved Optimization of Amino Acid Biosynthesis

The “cognate bias hypothesis” states that early in evolutionary history the biosynthetic enzymes for amino acid x gradually lost residues of x, thereby reducing the threshold for deleterious effects of x scarcity. The resulting reduction in cognate amino acid composition of the enzymes comprising a particular amino acid biosynthetic pathway is predicted to confer a selective growth advantage on cells. Bioinformatic evidence from protein-sequence data of two bacterial species previously demonstrated reduced cognate bias in amino acid biosynthetic pathways. Here we show that cognate bias in amino acid biosynthesis is present in the other domains of life—Archaebacteria and Eukaryota. We also observe evolutionarily conserved underrepresentations (e.g., glycine in methionine biosynthesis) and overrepresentations (e.g., tryptophan in asparagine biosynthesis) of amino acids in noncognate biosynthetic pathways, which can be explained by secondary amino acid metabolism. Additionally, we experimentally validate the cognate bias hypothesis using the yeast Saccharomyces cerevisiae. Specifically, we show that the degree to which growth declines following amino acid deprivation is negatively correlated with the degree to which an amino acid is underrepresented in the enzymes that comprise its cognate biosynthetic pathway. Moreover, we demonstrate that cognate fold representation is more predictive of growth advantage than a host of other potential growth-limiting factors, including an amino acid’s metabolic cost or its intracellular concentration and compartmental distribution. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. Niles Lehman Ethan O. Perlstein and Benjamin L. de Bivort contributed equally to this work.     

Are All Global Positioning System Collars Created Equal? Correcting Habitat-Induced Bias Using Three Brands in the Central Canadian Rockies

Abstract: Global positioning system (GPS) collars are changing the face of wildlife research, yet they still possess biases such as habitat-induced fix-rate bias, which is a serious concern for habitat selection studies. We studied GPS bias in the Central Canadian Rockies, a critical area for wildlife conservation, to provide a statistical approach to correct GPS habitat bias for habitat selection studies using GPS collars. To model GPS habitat bias we deployed 11 different collars from 3 brands of GPS collars (Advanced Telemetry Systems [ATS], Asanti, MN; LOTEK Engineering Ltd., Newmarket, ON, Canada; and Televilt, Lindesberg, Sweden) in a random-stratified design at 86 sites across habitat and topographic conditions. We modeled the probability of obtaining a successful location, P_FIX, as a function of habitat, topography, and collar brand using mixed-effects logistic regression in an information theoretic approach. For LOTEK collars, we also investigated the effect of 8 and 12 GPS channels on fix rate. The ATS collars had the highest overall fix rates (97.4%), followed by LOTEK 12 channel (94.5%), LOTEK 8 channel (85.6%), and Televilt (82.3%). Sufficient model selection uncertainty existed to warrant model averaging for logistic regression P_FIX models. Collar brand influenced fix rate in all P_FIX models: fix rates for ATS and LOTEK 12 channel were not statistically different, whereas LOTEK 8 channel receivers had intermediate fix rates, and Televilt had the lowest. Fix rate was reduced in aspen stands, closed coniferous stands, and sites in narrow mountainous valleys but was higher on upper mountain slopes. Slight discrepancies between fix rates from field trials and observed species fix rates (wolf [Canis lupus] and elk [Cervus elaphus]) suggest uncorrected behavioral or movement-induced bias similar to other recent studies. Regardless, the strong habitat-induced bias in GPS fix rates confirms that in our study area habitat effects are critical, especially for poorer performance brands. Based on previous studies of effects of the amount of bias on inferences, our results suggest correction for GPS bias should be mandatory for Televilt collars in the Canadian Rockies, optional for LOTEK (dependent on the no. of channels), and unnecessary for ATS. Thus, our GPS bias model will be useful to researchers using GPS collars on a variety of species throughout the Rocky Mountain cordillera.     

Changes in obesity-related attitudes in women seeking weight reduction

Objective: To examine changes in obesity‐related attitudes in a sample of obese women who participated in either dieting or non‐dieting interventions. Research Methods and Procedures: A total of 123 obese women were randomly assigned to one of three weight control programs: meal replacement diet, balanced deficit diet, or a non‐dieting program. (The first two groups were combined as a single dieting condition.) Participants completed questionnaires (at baseline, Week 20, and Week 40) to assess beliefs and attitudes about obesity, along with measures of self‐esteem, depression, and body image. Results: At Weeks 20 and 40, participants in the non‐dieting condition reported significantly less negativity about obesity than those in the dieting group. Women in the dieting condition did not report an increase in negative attitudes toward obesity, despite losing significantly more weight than non‐dieting participants. Both groups experienced improvements in self‐esteem, body image, and depressive symptoms. Improvement in self‐esteem was associated with a reduction in negativity about obesity and with improvements in body image. Discussion: The non‐dieting program produced greater reductions in negative attitudes toward obesity than the dieting intervention. Dieting (with successful weight loss), however, did not result in greater negativity toward obesity. Non‐dieting programs seem to be useful in obese women for improving self‐esteem, body image, and internalized negative attitudes about obesity.     

Predicting feed intake and feed efficiency in lactating dairy cows using digesta marker techniques

Direct measurement of individual animal dry matter intake (DMI) remains a fundamental challenge to assessing dairy feed efficiency (FE). Digesta marker, is currently the most used indirect technique for estimating DMI in production animals. In this meta-analysis we evaluated the performance of marker-based estimates against direct or observed measurements and developed equations for the prediction of FE (g energy-corrected milk (ECM)/kg DMI). Data were taken from 29 change-over studies consisting of 416 cow-within period observations. Most studies used more than one digesta marker. So, for each observed measurement of DMI, faecal dry matter output (FDMO) and apparent total tract dry matter digestibility (DMD), there was one or more corresponding marker estimate. There were 924, 409 and 846 observations for estimated FDMO (eFDMO), estimated apparent total tract DMD (eDMD) and estimated DMI (eDMI), respectively. The experimental diets were based mainly on grass silage, with soya bean or rapeseed meal as protein supplements and cereal grains or by-products as energy supplements. Across all diets, average forage to concentrate ratio on a dry matter (DM) basis was 59 : 41. Variance component and repeatability estimates of observed and marker estimations were determined using random factors in mixed procedures of SAS. Between-cow CV in observed FDMO, DMD and DMI was, 10.3, 1.69 and 8.04, respectively. Overall, the repeatability estimates of observed variables were greater than their corresponding marker-based estimates of repeatability. Regression of observed measurements on marker-based estimates gave good relationships (R²=0.87, 0.68, 0.74 and 0.74, relative prediction error =10.9%, 6.5%, 15.4% and 18.7%for FDMO, DMD, DMI and FE predictions, respectively). Despite this, the mean and slope biases were statistically significant (P<0.001) for all regressions. More than half of the errors in all regressions were due to mean and slope biases (52.4% 87.4%, 82.9% and 85.8% for FDMO, DMD, DMI and FE, respectively), whereas the contributions of random errors were small. Based on residual variance, the best model for predicting FE developed from the dataset was FE (g ECM/kg DMI)=1179(±54.1) +38.2(±2.05)×ECM(kg/day)−0.64(±0.051)×BW (kg)−75.6(±4.39)×eFDMO (kg/day). Although eDMD was positively related to FE, it only showed a tendency to reduce the residual variance. Despite inaccuracy in marker procedures, eFDMO from external markers provided a reliable determination for FE measurement. However, DMD estimated by internal markers did not improve prediction of FE, probably reflecting small variability.