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PubMedDate not supplied

Genes that affect morphogenesis of the murine mandible. Recombinant-inbred strain analysis.

The CXB set of recombinant inbred mouse strains provided an opportunity to observe the effects of reassorted subsets of genes on the shape of the mandible. The distances between 12 landmarks in all paired combinations were calculated to evaluate genetic control in small regions. The genetic relationships between interlandmark distances revealed genes to have most of their effects in localized regions, and the greater heritabilities usually to apply to those distances between adjacent landmarks. Interrelationships between measurements are usually explicable on a developmental basis. It is proposed that genes of this sort bring about the changes seen in organ shape during evolution. A model plan for the organization of gene activation during morphogenesis is described.

Animals↗
PubMedDate not supplied

The mutational meltdown in asexual populations.

Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown, and provides a powerful explanation for the rarity of obligate asexuality. We give an overview of the theory of the mutational meltdown, showing how the process depends on the demographic properties of a population, the properties of mutations, and the relationship between fitness and number of mutations incurred.

Biological Evolution↗
PubMedDate not supplied

The effects of different levels of genetic exchange on organelle evolution.

Each mitochondrion and chloroplast organelle has tens to hundreds of genomes, and there are tens to hundreds of such organelles within each cell. This results in a genetic organization generating a population structure akin to a geographically structured population. Since genomes and organelles replicate and gene conversion can occur between copies, this offers the possibility for directional evolutionary forces acting within the cell. The consequences of genetic exchange within the cell (between genomes within an organelle and between individual organelles) and between individuals (biparental inheritance) when within-cell directional forces are present is examined. The net effect of genetic exchange is to increase the importance of any directional forces present within the cell. The consequences of within-cell forces when the variants they act on also have fitness consequences for individuals are also examined.

Biological Evolution↗
PubMed2003

Factors affecting the errors in the estimation of evolutionary distances between sequences.

Phylogenetic methods that use matrices of pairwise distances between sequences (e.g., neighbor joining) will only give accurate results when the initial estimates of the pairwise distances are accurate. For many different models of sequence evolution, analytical formulae are known that give estimates of the distance between two sequences as a function of the observed numbers of substitutions of various classes. These are often of a form that we call "log transform formulae". Errors in these distance estimates become larger as the time t since divergence of the two sequences increases. For long times, the log transform formulae can sometimes give divergent distance estimates when applied to finite sequences. We show that these errors become significant when t approximately 1/2 |lambda(max)|(-1) logN, where lambda(max) is the eigenvalue of the substitution rate matrix with the largest absolute value and N is the sequence length. Various likelihood-based methods have been proposed to estimate the values of parameters in rate matrices. If rate matrix parameters are known with reasonable accuracy, it is possible to use the maximum likelihood method to estimate evolutionary distances while keeping the rate parameters fixed. We show that errors in distances estimated in this way only become significant when t approximately 1/2 |lambda(1)|(-1) logN, where lambda(1) is the eigenvalue of the substitution rate matrix with the smallest nonzero absolute value. The accuracy of likelihood-based distance estimates is therefore much higher than those based on log transform formulae, particularly in cases where there is a large range of timescales involved in the rate matrix (e.g., when the ratio of transition to transversion rates is large). We discuss several practical ways of estimating the rate matrix parameters before distance calculation and hence of increasing the accuracy of distance estimates.

Evolution, Molecular↗
PubMed1998

Evolution of immunoglobulin kappa chain variable region genes in vertebrates.

The major source of immunoglobulin diversity is variation in DNA sequence among multiple copies of variable region (V) genes of the heavy- and light-chain multigene families. In order to clarify the evolutionary pattern of the multigene family of immunoglobulin light kappa chain V region (V kappa) genes, phylogenetic analyses of V kappa genes from humans and other vertebrate species were conducted. The results obtained indicate that the V kappa genes so far sequenced can be grouped into three major monophyletic clusters, the cartilaginous fish, bony fish and amphibian, and mammalian clusters, and that the cartilaginous fish cluster first separated from the rest of the V kappa genes and then the remaining two clusters diverged. The mammalian V kappa genes can further be divided into 10 V kappa groups, 7 of which are present in the human genome. Human and mouse V kappa genes from different V kappa groups are intermingled rather than clustered on the chromosome, and there are a large number of pseudogenes scattered on the chromosome. This indicates that the chromosomal locations of V kappa genes have been shuffled many times by gene duplication, deletion, and transposition in the evolutionary process and that many genes have become nonfunctional during this process. This mode of evolution is consistent with the model of birth-and-death evolution rather than with the model of concerted evolution. An analysis of duplicate V kappa functional genes and pseudogenes in the human genome has indicated that pseudogenes evolve faster than functional genes but that the rate of nonsynonymous nucleotide substitution in the complementarity-determining regions of V kappa genes has been enhanced by positive Darwinian selection.

Animals↗
PubMed2000

Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.

We introduce a distance-based phylogeny reconstruction method called "weighted neighbor joining," or "Weighbor" for short. As in neighbor joining, two taxa are joined in each iteration; however, the Weighbor criterion for choosing a pair of taxa to join takes into account that errors in distance estimates are exponentially larger for longer distances. The criterion embodies a likelihood function on the distances, which are modeled as correlated Gaussian random variables with different means and variances, computed under a probabilistic model for sequence evolution. The Weighbor criterion consists of two terms, an additivity term and a positivity term, that quantify the implications of joining the pair. The first term evaluates deviations from additivity of the implied external branches, while the second term evaluates confidence that the implied internal branch has a positive branch length. Compared with maximum-likelihood phylogeny reconstruction, Weighbor is much faster, while building trees that are qualitatively and quantitatively similar. Weighbor appears to be relatively immune to the "long branches attract" and "long branch distracts" drawbacks observed with neighbor joining, BIONJ, and parsimony.

Animals↗
PubMed2001

External doses in the environment from the Tokai-mura criticality accident.

On 30 September 1999, a criticality accident occurred at a uranium processing plant operated by JCO in Tokai-mura, Japan and the criticality remained for about 20 h. Almost all doses to the neighbouring residents were brought by neutrons and gamma rays emitted from the facility rather than fission products released to the environment. External doses in the environment were evaluated using radiation monitoring data and radiation transport calculation. A pattern of the dose rate evolution was modelled based on the records of gamma ray monitors in the JCO facilities. Relations between the ambient dose equivalent rates of neutrons/gamma rays and the distance from the facility were determined from the monitoring data obtained around the accident site. Conversion from the ambient dose equivalent to the effective dose equivalent was made assuming the energy spectra calculated by the radiation transport code, ANISN. It was estimated that the people who stayed outside the 350 m zone would receive doses of less than 1 mSv.

Gamma Rays↗
PubMed1990

Local protein sequence similarity does not imply a structural relationship.

A database search often will find a seemingly strong sequence similarity between two fragments of proteins that are not expected to have an evolutionary or functional relationship. It is tempting to suggest that the two fragments will adopt a similar conformation due to a common pattern of residues that dictate a particular substructure. To investigate the likelihood of such a structural similarity, local sequence similarities between proteins of known conformation were identified by a standard database search algorithm. Significant sequence similarity was identified as when the chance probability of obtaining the relatedness score from a scan of the entire database was less than 1%. In this region both true homologies and false homologies are detected. A total of 69 false homologies was located of length between 20 and 262 aligned positions. Many of these alignments had approximately 25% sequence identity and a further 25% of conservative changes. However, the results show in general these aligned fragments did not have a significant similarity in secondary or tertiary structure. Thus local sequence does not indicate a structural similarity when there is neither an evolutionary nor functional explanation to support this. Accordingly structure predictions based on finding a local sequence similarity with an evolutionary unrelated protein of known conformation are unlikely to be valid.

Algorithms↗
PubMed2004

Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase.

The conformational switch from open to closed of the flexible loop 6 of triosephosphate isomerase (TIM) is essential for the catalytic properties of TIM. Using a directed evolution approach, active variants of chicken TIM with a mutated C-terminal hinge tripeptide of loop 6 have been generated (Sun,J. and Sampson,N.S., Biochemistry, 1999, 38, 11474-11481). In chicken TIM, the wild-type C-terminal hinge tripeptide is KTA. Detailed enzymological characterization of six variants showed that some of these (LWA, NPN, YSL, KTK) have decreased catalytic efficiency, whereas others (KVA, NSS) are essentially identical with wild-type. The structural characterization of these six variants is reported. No significant structural differences compared with the wild-type are found for KVA, NSS and LWA, but substantial structural adaptations are seen for NPN, YSL and KTK. These structural differences can be understood from the buried position of the alanine side chain in the C-hinge position 3 in the open conformation of wild-type loop 6. Replacement of this alanine with a bulky side chain causes the closed conformation to be favored, which correlates with the decreased catalytic efficiency of these variants. The structural context of loop 6 and loop 7 and their sequence conservation in 133 wild-type sequences is also discussed.

Animals↗
PubMed1996

A genetic algorithm approach to optimization for the radiological worker allocation problem.

This paper describes a new approach to the radiological worker allocation problem using a multiple objective genetic algorithm. The worker allocation problem in radiological facilities involves various types of constraints and even mutually conflicting ones, such as individual dose limits, working time limits, etc. A major difficulty of this highly working time limits, etc. A major difficulty of this highly constrained problem is the way of finding an optimal solution in the huge search space where a large proportion of solutions are not feasible because some of the constraints cannot be satisfied. The paper proposes a model of evolution to establish an optimal assignment efficiently, based on the biological insights into the evolutionary process and heuristic ideas. The experimental results show a very rapid evolution to produce feasible solutions, and the application of multiple evaluation functions converges the feasible solutions to good ones. The genetic algorithm approach was found to be superior to the goal programming and simplex methods.

Algorithms↗
PubMed2003

Time-updated CD4+ T lymphocyte count and HIV RNA as major markers of disease progression in naive HIV-1-infected patients treated with a highly active antiretroviral therapy: the Aquitaine cohort, 1996-2001.

In naive HIV-1 infected patients who start a highly active antiretroviral therapy (HAART), the relationship between time-updated CD4+ cell count, HIV RNA, and clinical progression (new AIDS-defining event or death) is incompletely understood. A 2-step statistical approach was adopted: first, modeling the evolution of the 2 markers taking into account left-censoring of HIV RNA and, second, studying their respective effect on clinical progression. The study sample consisted in 551 previously untreated patients of the Aquitaine Cohort who started their first HAART regimen between 1996 and 2000. During a median follow-up of 33 months, 46 patients experienced a new AIDS-defining diagnosis and 23 died. In multivariate survival analysis, time-updated CD4+ cell count (hazard ratio [HR] = 1.92 for 100 cells/mm3 lower, P < 10(-4) and HIV RNA (HR = 1.30 for 1 log(10) copies/mL higher, P = 0.04) on continuous scale were associated with clinical progression. When analyzing the effect of updated biomarkers using usual thresholds, the association with clinical progression was weaker for CD4+ but still significant (P = 0.007) whereas it remained only significant for updated HIV RNA above 4 log(10) copies/mL (P = 0.01). The prognostic information of updated HIV RNA adjusted on updated CD4+ is significant but depends on how the markers are taken into account. Clinical decisions and interpretation of clinical trial results must weigh the signification of each of these 2 biomarkers.

Adult↗
PubMed2005

Dynamics of the circadian blood pressure profiles after renal transplantation.

BACKGROUND: Abnormalities of diurnal blood pressure (BP) rhythm ("nondipping") are well-described in dialysis patients, and have prognostic importance. It is controversial whether successful renal transplantation (RTx) improves diurnal BP rhythm. To date, no study has attempted to define and model the evolution of diurnal BP rhythm profiles from dialysis to engraftment, focusing on the immediate (4-6 weeks) and medium-term (>1 year) postengraftment periods. METHODS: To test if kidney transplantation normalizes the BP profile, ambulatory blood pressure monitoring (ABPM) was performed in 20 living related transplants (age, 30.3+/-5.1 years; 11 males, on dialysis for 25.6 months) 1 month preRTx and repeated 1 month and >1 year (ABPM3) after successful RTx. Dipping was defined as a sleep-to-awake ratio>0.92 (for systolic BP) and >0.90 (for diastolic BP). RESULTS: PreRTx only 15% patients were dippers. At 1 month postRTx (creatinine clearance, 65.8 ml/min), all patients were complete nondippers. However, after >1 year postRTx (creatinine clearance, 70.4 ml/min), 40% were now dippers. Most importantly, overall, 30% of the patients improved significantly their circadian rhythm (35.3% of the initial preRTx nondippers). Despite successful renal transplantation, 55% patients maintained unchanged their nondipping profile throughout all three ABPM recordings. The only determinants of "long-term" postRTx circadian rhythm are the contemporary level of the renal function and the baseline, dialysis dipping profile: SBP3 sleep-to-awake ratio is related with serum creatinine3 (r=0.58, P=0.001), creatinine clearance (r=-0.41, P=0.036) and SBP1 sleep-to-awake ratio (r=0.48, P=0.034); similarly DBP3 sleep-to-awake ratio is related with serum creatinine3 (r=0.63, P=0.001), creatinine clearance (r=-0.471, P=0.036) and SBP1 sleep-to-awake ratio (r=0.53, P=0.016). In all, 57% of the variance in dipping status can be attributed and explained by the contribution of renal function and initial circadian variability. CONCLUSIONS: Half of the nondipper dialysis patients maintain a permanently abnormal circadian rhythm, despite successful RTx. In the short term, RTx is associated with a highly abnormal diurnal profile, exclusively related to ciclosporin dose and levels. However, in the longer term, renal transplantation leads to a significant improvement of the circadian blood pressure profile, influenced by the renal function level and by the pretransplantation dipping profile.

Adult↗
PubMed1998

Rapid parapatric speciation on holey adaptive landscapes.

A classical view of speciation is that reproductive isolation arises as a by-product of genetic divergence. Here, individual-based simulations are used to evaluate whether the mechanisms implied by this view may result in rapid speciation if the only source of genetic divergence are mutation and random genetic drift. Distinctive features of the simulations are the consideration of the complete process of speciation (from initiation until completion), and of a large number of loci, which was only one order of magnitude smaller than that of bacteria. It is demonstrated that rapid speciation on the time-scale of hundreds of generations is plausible without the need for extreme founder events, complete geographic isolation, the existence of distinct adaptive peaks or selection for local adaptation. The plausibility of speciation is enhanced by population subdivision. Simultaneous emergence of more than two new species from a subdivided population is highly probable. Numerical examples relevant to the theory of centrifugal speciation and to the conjectures about the fate of 'ring species' and 'sexual continuums' are presented.

Biological Evolution↗
PubMed1998

Gene-pool variation in caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple-sequence repeats.

We have used polymorphic chloroplast simple-sequence repeats to analyse levels of genetic variation within and between seven native Scottish and eight mainland European populations of Scots pine (Pinus sylvestris L.). Diversity levels for the Scottish populations based on haplotype frequency were far in excess of those previously obtained using monoterpenes and isozymes and confirmed lower levels of genetic variation within the derelict population at Glen Falloch. The diversity levels were higher than those reported in similar studies in other Pinus species. An analysis of molecular variance (AMOVA) showed that small (3.24-8.81%) but significant (p < or = 0.001) portions of the variation existed between the populations and that there was no significant difference between the Scottish and the mainland European populations. Evidence of population substructure was found in the Rannoch population, which exhibited two subgroups. Finally, one of the loci studied exhibited an allele distribution uncharacteristic of the stepwise mutation model of evolution of simple-sequence repeats, and sequencing of the PCR products revealed that this was due to a duplication rather than slippage in the repeat region. An examination of the distribution of this mutation suggests that it may have occurred fairly recently in the Wester Ross region or that it may be evidence of a refugial population.

Alleles↗
PubMed1999

The approach to mutation-selection balance in an infinite asexual population, and the evolution of mutation rates.

A method is described for calculating the dynamics of the distribution of fitness in an infinite asexual population which is subject to unconditionally deleterious mutations with independent effects. This method is applied to the problem of calculating the frequency of a mutator subpopulation, at equilibrium between mutation and indirect selection due to association with deleterious mutations. Many mutator alleles are produced by loss-of-function mutations in polymerase or mismatch repair genes. Previous calculations have ignored the fact that this creates a flux of higher fitness individuals into the mutator subpopulation. This flux raises the mean fitness of the mutator subpopulation, and when this factor is taken into account, the frequency of the mutator may be more than an order of magnitude greater than recent theoretical work has suggested.

Alleles↗
PubMed2003

Hamilton goes empirical: estimation of inclusive fitness from life-history data.

Hamilton's theory of kin selection is one of the most important advances in evolutionary biology since Darwin. Central to the kin-selection theory is the concept of inclusive fitness. However, despite the importance of inclusive fitness in evolutionary theory, empirical estimation of inclusive fitness has remained an elusive task. Using the concept of individual fitness, I present a method for estimating inclusive fitness and its components for diploid organisms with age-structured life histories. The method presented here: (i) allows empirical estimation of inclusive fitness from life-history data; (ii) simultaneously considers all components of fitness, including timing and magnitude of reproduction; (iii) is consistent with Hamilton's definition of inclusive fitness; and (iv) adequately addresses shortcomings of existing methods of estimating inclusive fitness. I also demonstrate the application of this new method for testing Hamilton's rule.

Altruism↗
PubMed2005

Do unprofitable prey evolve traits that profitable prey find difficult to exploit?

Prey that are unprofitable to attack (for example, those containing noxious chemicals) are often conspicuously patterned and move in a slower and more predictable manner than species lacking these defences. Contemporary theories suggest these traits have evolved as warning signals because they can facilitate both associative and discriminative avoidance learning in predators. However, it is unclear why these particular traits and not others have tended to evolve in unprofitable prey. Here we show using a signal detection model that unprofitable prey will evolve conspicuous colours and patterns partly because these characteristics cannot readily evolve in profitable prey without close mimicry. The stability of this signal is maintained through the costs of dishonesty in profitable prey. Indeed, unprofitable prey will sometimes evolve a conspicuous form to reduce mimetic parasitism, even in the unlikely event that this form can be more closely mimicked. This is one of the first mathematical models of the evolution of warning signals to allow for the possibility of mimicry, yet our analyses suggest it may offer a general explanation as to why warning signals take the form that they do. Warning signals and mimicry may therefore be more closely related than is currently supposed.

Animals↗