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PubMed1980

A two-reservoir recycling model for mantle-crust evolution.

The exact solutions for the isotopic compositions and the concentrations of the two-reservoir model for mantle-crust evolution are given for arbitrary rates of crustal growth and of back flow to the mantle. The critical parameters are the chemical fractionation factors for crustal growth and refluxing and the integrated fractional mass-removal rates from the crust and the mantle. For the case where refluxing is proportional to crustal growth, all the solutions reduce to simple analytic expressions. The expression for the mean age of the mass of the crust with refluxing is given. If refluxing is significant, the model shows that highly incompatible elements have short residence times in the mantle. With plausible concentration values, material balance implies that the continents were derived from only a small fraction of the mantle.

Journal Article↗
PubMed1998

Effects of branch length errors on the performance of phylogenetically independent contrasts.

We examined Type I error rates of Felsenstein's (1985; Am. Nat. 125:1-15) comparative method of phylogenetically independent contrasts when branch lengths are in error and the model of evolution is not Brownian motion. We used seven evolutionary models, six of which depart strongly from Brownian motion, to simulate the evolution of two continuously valued characters along two different phylogenies (15 and 49 species). First, we examined the performance of independent contrasts when branch lengths are distorted systematically, for example, by taking the square root of each branch segment. These distortions often caused inflated Type I error rates, but performance was almost always restored when branch length transformations were used. Next, we investigated effects of random errors in branch lengths. After the data were simulated, we added errors to the branch lengths and then used the altered phylogenies to estimate character correlations. Errors in the branches could be of two types: fixed, where branch lengths are either shortened or lengthened by a fixed fraction; or variable, where the error is a normal variate with mean zero and the variance is scaled to the length of the branch (so that expected error relative to branch length is constant for the whole tree). Thus, the error added is unrelated to the microevolutionary model. Without branch length checks and transformations, independent contrasts tended to yield extremely inflated and highly variable Type I error rates. Type I error rates were reduced, however, when branch lengths were checked and transformed as proposed by Garland et al. (1992; Syst. Biol. 41:18-32), and almost never exceeded twice the nominal P-value at alpha = 0.05. Our results also indicate that, if branch length transformations are applied, then the appropriate degrees of freedom for testing the significance of a correlation coefficient should, in general, be reduced to account for estimation of the best branch length transformation. These results extend those reported in Díaz-Uriarte and Garland (1996; Syst. Biol. 45:27-47), and show that, even with errors in branch lengths and evolutionary models different from Brownian motion, independent contrasts are a robust method for testing hypotheses of correlated evolution.

Computer Simulation↗
PubMedDate not supplied

Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution.

We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we examined four classes of tandemly repeated elements in six species of equids (Equus). Distribution of these sequences among species, as determined from slot blot analysis, and restriction site variation, shown by Southern blot hybridization, document that these sequences are in an evolutionarily dynamic state, and in situ hybridization documents extensive intragenomic movement among nonhomologous chromosomes and chromosomal fields. These data are interpreted as being compatible with the predictions of this model. Although this is clearly not the sole molecular factor driving chromosomal evolution, the model appears to be viable as an explanation of certain patterns of chromosomal evolution such as karyotypic megaevolution and some types of karyotypic orthoselection.

Animals↗
PubMed2005

Toward a neutral evolutionary model of gene expression.

We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level according to a given probability distribution. The model produces simple estimators for model parameters and allows discrimination between symmetric and asymmetric distributions of evolutionary expression changes along an evolutionary lineage. Furthermore, we introduce two measures, the skewness of expression difference distributions and relative difference of evolutionary branch lengths, which are used to quantify deviation from clock-like behavior of gene expression distances. Model-based analyses of gene expression profiles in primate liver and brain samples yield the following results: (1) The majority of gene expression changes are consistent with a neutral model of evolution; (2) along evolutionary lineages, upward changes in expression are less frequent but of greater average magnitude than downward changes; and (3) the skewness measure and the relative branch length difference confirm that an acceleration of gene expression evolution occurred on the human lineage in brain but not in liver. We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data.

Animals↗
PubMed1994

Aligning genomes with inversions and swaps.

The decision about what operators to allow and how to charge for these operations when aligning strings that arise in a biological context is the decision about what model of evolution to assume. Frequently the operators used to construct an alignment between biological sequences are limited to deletion, insertion, or replacement of a character or block of characters, but there is biological evidence for the evolutionary operations of exchanging the positions of two segments in a sequence and the replacement of a segment by its reversed complement. In this paper we describe a family of heuristics designed to compute alignments of biological sequences assuming a model of evolution with swaps and inversions. The heuristics will necessarily be approximate since the appropriate way to charge for the evolutionary events (delete, insert, substitute, swap, and invert) is not known. The paper concludes with a pairwise comparison of 20 Picornavirus genomes, and a detailed comparison of the hepatitis delta virus with the citrus exocortis viroid.

Amino Acid Sequence↗
PubMed1986

On the evolution of mammalian kininogens.

A model for the evolution of mammalian kininogens has been constructed which is based on sequence homology. This model suggests that several gene elements coding for the major constituents of the kininogens, i.e. the heavy chain, the light chain and the kinin segment, arose independently from their progenitors. The heavy chain of the kininogens known to execute their inhibitory function against cysteine proteinases has evolved by gene triplication from an ancestor which is closely related to the present-day form of the low molecular weight cysteine proteinase inhibitor cystatin. Part of the light chain of the mammalian kininogens which contains a unique region extremely rich in histidine and glycine has descended by gene multiplication from smaller units, possibly even from the dipeptide Gly-His. At present, the mode and timepoint of fusion of the various gene elements coding for the various structural constituents of the mammalian kininogens is not known.

Amino Acid Sequence↗
PubMed2004

Effects of insect population size on evolution of resistance to transgenic crops.

Models of the evolution of insect resistance to transgenic crops have often assumed that population size is infinite or that carrying capacity is fixed. To evaluate potential effects of population size on resistance evolution, we conducted sensitivity analyses by using a stochastic, spatially explicit model based partly on the interaction between pink bollworm and Bacillus thuringiensis (Bt) cotton. We examined interactions of carrying capacity, region size, dispersal, and percentage of fields planted with Bt cotton. The median and variance in the time to resistance decreased as region size increased, regardless of carrying capacity. This occurred because larger regions were more likely to have at least one field in which resistance evolved rapidly and served as a source from which resistance spread throughout the region. Carrying capacity significantly affected the median time to resistance with 75% of fields planted with Bt cotton, but not with 50% Bt cotton. In contrast, carrying capacity significantly influenced the variance in the time to resistance with 50% Bt cotton, but not with 75% Bt cotton. We also found resistance evolution was affected by interactions between carrying capacity, dispersal, and the percentage of fields planted with Bt cotton. The high variability observed in our simulations indicates that factors affecting stochastic events can play an important role in the evolution of resistance. Because population size determines the extent to which stochastic events are important, reasonable estimates of population size are essential for devising robust models of resistance evolution.

Animals↗
PubMed2000

Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.

We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022 (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and members of the lambdoid or lambda-like group of phages. We provide a comparative analysis of these sequences with each other and with two previously determined lambdoid family genome sequences, those of E. coli phage lambda and Salmonella typhimurium phage P22. The comparisons confirm that these phages are genetic mosaics, with mosaic segments separated by sharp transitions in the sequence. The mosaicism provides clear evidence that horizontal exchange of genetic material is a major component of evolution for these viruses. The data suggest a model for evolution in which diversity is generated by a combination of illegitimate and homologous recombination and mutational drift, and selection for function produces a population in which most of the surviving mosaic boundaries are located at gene boundaries or, in some cases, at protein domain boundaries within genes. Comparisons of these genomes highlight a number of differences that allow plausible inferences of specific evolutionary scenarios for some parts of the genome. The comparative analysis also allows some inferences about function of genes or other genetic elements. We give examples for the generalized recombination genes of HK97, HK022 and P22, and for a putative headtail adaptor protein of HK97 and HK022. We also use the comparative approach to identify a new class of genetic elements, the morons, which consist of a protein-coding region flanked by a putative delta 70 promoter and a putative factor-independent transcription terminator, all located between two genes that may be adjacent in a different phage. We argue that morons are autonomous genetic modules that are expressed from the repressed prophage. Sequence composition of the morons implies that they have entered the phages' genomes by horizontal transfer in relatively recent evolutionary time.

Amino Acid Sequence↗
PubMed1999

Mathematical model of gas bubble evolution in a straight tube.

Deep sea divers suffer from decompression sickness (DCS) when their rate of ascent to the surface is too rapid. When the ambient pressure drops, inert gas bubbles may form in blood vessels and tissues. The evolution of a gas bubble in a rigid tube filled with slowly moving fluid, intended to simulate a bubble in a blood vessel, is studied by solving a coupled system of fluid-flow and gas transport equations. The governing equations for the fluid motion are solved using two techniques: an analytical method appropriate for small nondeformable spherical bubbles, and the boundary element method for deformable bubbles of arbitrary size, given an applied steady flow rate. A steady convection-diffusion equation is then solved numerically to determine the concentration of gas. The bubble volume, or equivalently the gas mass inside the bubble for a constant bubble pressure, is adjusted over time according to the mass flux at the bubble surface. Using a quasi-steady approximation, the evolution of a gas bubble in a tube is obtained. Results show that convection increases the gas pressure gradient at the bubble surface, hence increasing the rate of bubble evolution. Comparing with the result for a single gas bubble in an infinite tissue, the rate of evolution in a tube is approximately twice as fast. Surface tension is also shown to have a significant effect. These findings may have important implications for our understanding of the mechanisms of inert gas bubbles in the circulation underlying decompression sickness.

Atmospheric Pressure↗
PubMed2003

A model for the emergence of adaptive subsystems.

We investigate the interaction of learning and evolution in a changing environment. A stable learning capability is regarded as an emergent adaptive system evolved by natural selection of genetic variants. We consider the evolution of an asexual population. Each genotype can have 'fixed' and 'flexible' alleles. The former express themselves as synaptic connections that remain unchanged during ontogeny and the latter as synapses that can be adjusted through a learning algorithm. Evolution is modelled using genetic algorithms and the changing environment is represented by two optimal synaptic patterns that alternate a fixed number of times during the 'life' of the individuals. The amplitude of the change is related to the Hamming distance between the two optimal patterns and the rate of change to the frequency with which both exchange roles. This model is an extension of that of Hinton and Nowlan in which the fitness is given by a probabilistic measure of the Hamming distance to the optimum. We find that two types of evolutionary pathways are possible depending upon how difficult (costly) it is to cope with the changes of the environment. In one case the population loses the learning ability, and the individuals inherit fixed synapses that are optimal in only one of the environmental states. In the other case a flexible subsystem emerges that allows the individuals to adapt to the changes of the environment. The model helps us to understand how an adaptive subsystem can emerge as the result of the tradeoff between the exploitation of a congenital structure and the exploration of the adaptive capabilities practised by learning.

Adaptation, Biological↗
PubMed1993

Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model.

A computer simulation of the process of nucleotide substitutions in a finite haploid population subject to selection in a randomly fluctuating environment provides a number of unexpected results. For rapidly fluctuating environments, substitutions are more regular than random. A small mutation-rate approximation is used to explain the regularity. The explanation does not depend heavily on the particulars of the haploid model, leading to the conjecture that many symmetrical models of molecular evolution with rapidly changing parameters may exhibit substitutions that are more regular than random. When fitnesses change very slowly, the simulation shows that substitutions are more clumped than random. Here a small-mutation approximation shows that the clustering is due to the increase in fitness that accompanies each successive substitution with a consequent lowering of the effective mutation rate. The two observations taken together suggest that the common observation that amino acid substitutions are clustered in time is due to the presence of parameters that change very slowly.

Biological Evolution↗
PubMed2004

Influences of breathing patterns on respiratory sinus arrhythmia in humans during exercise.

Persistence of respiratory sinus arrhythmia (RSA) has been described in humans during intense exercise and attributed to an increase in ventilation. However, the direct influence of ventilation on RSA has never been assessed. The dynamic evolution of RSA and its links to ventilation were investigated during exercise in 14 healthy men using an original modeling approach. An evolutive model was estimated from the detrended and high-pass-filtered heart period series. The instantaneous RSA frequency (FRSA, in Hz) and amplitude (ARSA, in ms) were then extracted from all recordings. A(RSA) was calculated with short-time Fourier transform. First, measurements of FRSA and ARSA were performed from data obtained during a graded and maximal exercise test. Influences of different ventilation regimens [changes in tidal volume (VT) and respiratory frequency (FR)] on ARSA were then tested during submaximal [70% peak O2 consumption (VO2peak)] rectangular exercise bouts. Under graded and maximal exercise conditions, ARSA decreased from the beginning of exercise to 61.9 +/- 3.8% VO2peak and then increased up to peak exercise. During the paced breathing protocol, normoventilation (69.4 +/- 8.8 l/min), hyperventilation (81.8 +/- 8.3 l/min), and hypoventilation (56.4 +/- 6.2 l/min) led to significantly (P < 0.01) different ARSA values (3.8 +/- 0.5, 4.6 +/- 0.8, and 2.9 +/- 0.5 ms, respectively). In addition, no statistical difference was found in ARSA when ventilation was kept constant, whatever the FR-VT combinations. Those results indicate that RSA persists for all exercise intensities and increases during the highest intensities. Its persistence and increase are strongly linked to both the frequency and degree of lung inflation, suggesting a mechanical influence of breathing on RSA.

Adult↗
PubMed1981

Constitutive gene expression and restoration of the normal phenotype in malignant cells: a model for the origin and evolution of leukemia.

The change from normal to malignant cells involves a sequence of changes including specific chromosome changes. After this sequence, some leukemias can still be induced to revert with a high frequency from a malignant to a non-malignant phenotype. Results obtained from the analysis of regulation of growth and differentiation in normal and leukemic myeloid cells, restoration of the normal phenotype by induction of normal differentiation in myeloid leukemia, and the blocks in differentiation defective leukemic cell mutants have been used to propose a general model for the origin and evolution of leukemia. The model states that leukemia originates by changing specific pathways of gene expression required for growth from inducible to constitutive, in cells that can still be induced to differentiate normally by the physiological inducer of differentiation. The malignant, unlike the normal cells, then no longer require the physiological inducer for growth. This changes the requirements for growth and uncouples growth from differentiation. Constitutive expression of other specific pathways of gene expression can uncouple other controls, which then causes blocks in differentiation and the further evolution of leukemia. The existence of specific constitutive pathways of gene expression that uncouple controls in malignant cells, can also explain the origin and evolution of other types of malignancies.

Animals↗
PubMed1976

Simulation studies on the evolution of amino acid sequences.

A model of molecular evolution in which the parameter (intrinsic rate of amino acid substitution) fluctuates from time to time was investigated by simulating the process. It was found that the usual method of estimation such as Poisson fitting underestimates this variation of the parameter when remote comparisons are made. At the same time, four distance measures (minimun base difference, Poisson fitting, random nucleotide substitutions and negative binomial fitting) were tested for their accuracy. When the substitution rate is not uniform among the amino acid sites, the negative bionomial fitting gives most satisfactory results, however, one needs to know the parameter beforehand in order to use this method. It was pointed out that the fluctuation of the evolutionary rate is expected if the nearly neutral but very slightly deleterious mutations play an important role on molecular evolution.

Amino Acid Sequence↗
PubMed1994

Evolution of dioecy: can nuclear-cytoplasmic interactions select for maleness?

A model of evolution of reproductive systems, when sex is determined by both nuclear and cytoplasmic genes, is presented. Such a control of sex is known to facilitate the occurrence of female individuals in hermaphroditic populations, thus leading to gynodioecy. A two-cytotypes two-nuclear loci (two alleles at each nuclear locus) model for gynodioecy has been developed previously. Such gynodioecious systems are usually considered as stable, i.e. not leading to dioecy. In order to find out if the presence of females can select for male individuals when sex determination is nuclear-cytoplasmic, we followed the evolution of alleles responsible for female sterility. These alleles can be at the preceding loci or at a third locus. We show that male individuals can be selected. Dioecy evolves in less restrictive conditions than under nuclear sex determination. The same also holds for trioecy (coexistence of females, hermaphrodites and males). Nuclear-cytoplasmic polymorphism can be maintained in these reproductive systems.

Biological Evolution↗
PubMed1981

Tempo and mode in hominid evolution.

The nature of human evolution has been viewed recently as a specific example of a more general model of evolution termed "punctuated equilibrium". The characteristics of this model are long periods of little or not evolutionary change (stasis) interspersed with periods of rapid (punctuated) morphological change. Careful analysis of the hominid fossil record over the past 4.0 million years, however, suggests no well documented examples of either stasis or punctuation. The evidence for the evolution of the hominid lineage is most reasonably interpreted by a model of more gradual change with periods of varying rates of evolution.

Anthropometry↗