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PubMed2000

The evolution of recombination in a heterogeneous environment.

Most models describing the evolution of recombination have focused on the case of a single population, implicitly assuming that all individuals are equally likely to mate and that spatial heterogeneity in selection is absent. In these models, the evolution of recombination is driven by linkage disequilibria generated either by epistatic selection or drift. Models based on epistatic selection show that recombination can be favored if epistasis is negative and weak compared to directional selection and if the recombination modifier locus is tightly linked to the selected loci. In this article, we examine the joint effects of spatial heterogeneity in selection and epistasis on the evolution of recombination. In a model with two patches, each subject to different selection regimes, we consider the cases of mutation-selection and migration-selection balance as well as the spread of beneficial alleles. We find that including spatial heterogeneity extends the range of epistasis over which recombination can be favored. Indeed, recombination can be favored without epistasis, with negative and even with positive epistasis depending on environmental circumstances. The selection pressure acting on recombination-modifier loci is often much stronger with spatial heterogeneity, and even loosely linked modifiers and free linkage may evolve. In each case, predicting whether recombination is favored requires knowledge of both the type of environmental heterogeneity and epistasis, as none of these factors alone is sufficient to predict the outcome.

Alleles↗
PubMed2001

A model for the interaction of learning and evolution.

We present a simple model in order to discuss the interaction of the genetic and behavioral systems throughout evolution. This considers a set of adaptive perceptrons in which some of their synapses can be updated through a learning process. This framework provides an extension of the well-known Hinton and Nowlan model by blending together some learning capability and other (rigid) genetic effects that contribute to the fitness. We find a halting effect in the evolutionary dynamics, in which the transcription of environmental data into genetic information is hindered by learning, instead of stimulated as is usually understood by the so-called Baldwin effect. The present results are discussed and compared with those reported in the literature. An interpretation is provided of the halting effect.

Algorithms↗
PubMed1999

Raman microspectrometry studies of brushite cement: in vivo evolution in a sheep model.

Calcium phosphate hydraulic cements are promising synthetic bone grafting materials. Brushite-based cements were implanted for 6 and 12 months in the distal condyle of sheep femur, and their in vivo evolution was investigated by Raman microspectrometry. This new technique can probe small volumes in the cubic micrometer range. Its resolution allows a very fine analysis of crystalline changes in calcium phosphate mixtures at the microscopic level. First, Raman spectra of pure brushite, monetite, and beta-tricalcium phosphate (beta-TCP) were recorded, in order to set a data base for the basic components of brushite cements. These spectra show significant differences in the vibration mode v1 for the phosphate ion (988 and 878 cm(-1) for brushite, 988 and 900 cm(-1) for monetite, 968 and 948 cm(-1) for beta-TCP). These differences are strong enough as to allow the qualitative and quantitative analysis of these crystalline phases in the cement. Implanted sheep femur samples were harvested after 24 and 52 weeks post-op, and prepared for Raman analysis in the form of 1-mm-thick sections. Implants at 24 weeks show a core of residual cement isolated from the surrounding bone by fibroconnective tissue. No trace of brushite was detected by micro-Raman analysis in this area, but instead, a mixture of beta-TCP and Type-B carbonated apatite, the latter being very close in composition and structure to the mineral fraction of normal bone in the vicinity of the implant. Implants recovered after 52 weeks show a decrease of the bone/residual cement perimeter, whereas new trabeculations are formed in the implanted zone; the small amounts of residual cement still present are substantially transformed into Type-B carbonated apatite containing small amounts of proteins. In the same area, some beta-TCP particles are also detected showing that, contrary to brushite, the excess beta-TCP originally present in the cement is not completely metabolized. In the implanted zone already converted into trabecular bone, Raman microspectrometry shows the characteristic spectrum of normal bone.

Animals↗
PubMed2002

Multiscale modeling of precipitate microstructure evolution.

We demonstrate how three "state-of-the-art" techniques may be combined to build a bridge between atomistics and microstructure: (1) first-principles calculations, (2) a mixed-space cluster expansion approach, and (3) the diffuse-interface phase-field model. The first two methods are used to construct the driving forces for a phase-field microstructural model of theta'- Al2Cu precipitates in Al: bulk, interfacial, and elastic energies. This multiscale approach allows one to isolate the physical effects responsible for precipitate microstructure evolution.

Journal Article↗
PubMed2000

A generalization of Pontryagin's maximum principle for dynamic evolutionary games among relatives.

We present two theorems that generalize Pontryagin's maximum principle to the setting of dynamic evolutionary games between genetically related individuals. The two theorems correspond to two types of interactions among individuals: patch-structured populations in which individuals locally "play the field" and pairwise interactions. These generalizations can be used in the same way that Pontryagin's maximum principle is used and they are valid for diploid organisms under a single locus, diallelic genetic model. These generalizations involve an interesting, dynamic version of Hamilton's Rule from inclusive fitness theory. We illustrate how these theoretical results can be applied by modeling the evolution of lifetime resource allocation to growth and reproduction in an annual plant when there is competition for resources among related individuals.

Biological Evolution↗
PubMed1999

Multiple origins of cyclodiene insecticide resistance in Tribolium castaneum (Coleoptera: Tenebrionidae).

The number of origins of pesticide resistance-associated mutations is important not only to our understanding of the evolution of resistance but also in modeling its spread. Previous studies of amplified esterase genes in a highly dispersive Culex mosquito have suggested that insecticide resistance-associated mutations (specifically a single-gene duplication event) can occur a single time and then spread throughout global populations. In order to provide data for resistance-associated point mutations, which are more typical of pesticide mechanisms as a whole, we studied the number of independent origins of cyclodiene insecticide resistance in the red flour beetle Tribolium castaneum. Target-site insensitivity to cyclodienes is conferred by single point mutations in the gene Resistance to dieldrin (Rdl), which codes for a subunit of a gamma-aminobutyric acid (GABA) receptor. These point mutations are associated with replacements of alanine 302 which render the receptor insensitive to block by the insecticide. We collected 141 strains of Tribolium worldwide and screened them for resistance. Twenty-four strains contained resistant individuals. After homozygosing 23 of these resistance alleles we derived a nucleotide sequence phylogeny of the resistant strains from a 694-bp section of Rdl, encompassing exon 7 (which contains the resistance-associated mutation) and part of a flanking intron. The phylogeny also included six susceptible alleles chosen at random from a range of geographical locations. Resistance alleles fell into six clades and three clades contained both resistant and susceptible alleles. Although statistical analysis provided support at only the 5-6% level, the pattern of variation in resistance alleles is more readily explained by multiple independent origins of resistance than by spread of a single resistance-associated mutation. For example, two resistance alleles differed from two susceptible alleles only by the resistance-associated mutation itself, suggesting that they form the susceptible ancestors and that resistance arose independently in several susceptible backgrounds. This suggests that in Tribolium Rdl, de novo mutations for resistance have arisen independently in several populations. Identical alleles were found in geographically distant regions as well, also implying that some Rdl alleles have been exported in stored grain. These differences from the Culex study may stem both from differences in the population genetics of Tribolium versus that of mosquitoes and differences in mutation rates associated with point mutations versus gene duplication events. The Tribolium data therefore suggest that multiple origins of insecticide resistance (associated with specific point mutations) may be more common than the spread of single events. These findings have implications for the way in which we model the evolution and spread of insecticide resistance genes and also suggest that parallel adaptive substitutions may not be uncommon in phyletic evolution.

Animals↗
PubMed2005

Cloning and molecular modeling of duodenase with respect to evolution of substrate specificity within mammalian serine proteases that have lost a conserved active-site disulfide bond.

Mammalian serine proteases such as the chromosome 14 (Homo sapiens, Mus musculus) located granzymes, chymases, cathepsin G, and related enzymes including duodenase collectively represent a special group within the chymotrypsin family which we refer to here as "granases". Enzymes of this group have lost the ancient active-site disulfide bond Cys191-Cys220 (bovine chymotrypsinogen A numbering) which is strongly conserved in classic serine proteases such as pancreatic, blood coagulation, and fibrinolysis proteases and others (granzymes A, M, K and leukocyte elastases). We sequenced the cDNA encoding bovine (Bos taurus) duodenase, a granase with unusual dual trypsin-like and chymotrypsin-like specificity. The sequence revealed a 17-residue signal peptide and two-residue (GlyLys) activation peptide typical for granases. Production of the mature enzyme is apparently accompanied by further proteolytic processing of the C-terminal pentapeptide extension of duodenase. Similar C-terminal processing is known for another dual-specific granase, human cathepsin G. Using phylogenetic analysis based on 39 granases we retraced the evolution of residues 189 and 226 crucial for serine protease primary specificity. The analysis revealed that while there is no obvious link between mutability of residue 189 and the appearance of novel catalytic properties in granases, the mutability of residue 226 evidently gives rise to different specificity subgroups within this enzyme group. The architecture of the extended substrate-binding site of granases and structural basis of duodenase dual specificity based on molecular dynamic method are discussed. We conclude that the marked selectivity of granases that is crucial to their role as regulatory proteases has evolved through the fine-tuning of specificity at three levels--primary, secondary, and conformational.

Amino Acid Sequence↗
PubMed2003

Metapopulation-level adaptation of insect host plant preference and extinction-colonization dynamics in heterogeneous landscapes.

Species living in highly fragmented landscapes typically occur as metapopulations with frequent turnover of local populations. The turnover rate depends on population sizes and connectivities, but it may also depend on the phenotypic and genotypic composition of populations. The Glanville fritillary butterfly (Melitaea cinxia) in Finland uses two host plant species, which show variation in their relative abundances at two spatial scales: locally among individual habitat patches and regionally among networks of patches. Female butterflies in turn exhibit spatial variation in genetically determined host plant preference within and among patch networks. Emigration, immigration and establishment of new populations have all been shown to be strongly influenced by the match between the host plant composition of otherwise suitable habitat patches and the host plant preference of migrating butterflies. The evolutionary consequences of such biased migration and colonization with respect to butterfly phenotypes might differ depending on spatial configuration and plant species composition of the patches in heterogeneous patch networks. Using a spatially realistic individual-based model we show that the model-predicted evolution of host plant preference due to biased migration explains a significant amount of the observed variation in host plant use among metapopulations living in dissimilar networks. This example illustrates how the ecological extinction-colonization dynamics may be linked with the evolutionary dynamics of life history traits in metapopulations.

Adaptation, Physiological↗
PubMed1997

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.

Algorithms↗
PubMed2003

Blind prediction of broadband coherence time at basin scales.

A blind comparison with data is made with a model for the coherence time of broadband sound (133 Hz, 17-Hz bandwidth) at 3709 km. Coherence time is limited by changes in the ocean because the acoustic instruments are fixed to the Earth on the bottom of the sea with time bases maintained by atomic clocks. Although the modeled coherence time depends a bit on the difficult problem of correctly modeling relative signal-to-noise ratios, normalized correlation coefficients of the broadband signals for the data (model) are 0.90 (0.83), 0.72 (0.59), and 0.51 (0.36) at lags of 2, 4.1, and 6.2 min, respectively. In all these cases, observed coherence times are a bit longer than modeled. The temporal evolution of the model is based on the linear dispersion relation for internal waves. Acoustic propagation is modeled with the parabolic approximation and the sound-speed insensitive operator.

Journal Article↗
PubMed2005

Influence of gravity waves on the internal rotation and Li abundance of solar-type stars.

The Sun's rotation profile and lithium content have been difficult to understand in the context of conventional models of stellar evolution. Classical hydrodynamic models predict that the solar interior must rotate highly differentially, in disagreement with observations. It has recently been shown that internal waves produced by convection in solar-type stars produce an asymmetric, shear layer oscillation, similar to Earth's quasi-biennial oscillation, that leads to efficient angular momentum redistribution from the core to the envelope. We present results of a model that successfully reproduces both the rotation profile and the surface abundance of lithium in solar-type stars of various ages.

Journal Article↗
PubMed2002

Stress and infertility.

This review highlights new directions for research on stress and infertility. The question of whether stress causes infertility is examined, using theoretical models derived from natural history and evolution, current models of the effects of chronic stress on the hypothalamic pituitary adrenal axis, and data relating the effects of stress on the reproductive cycle. Research on the stress of infertility treatment is reviewed, with the conclusion that there is a lack of solid evidence that infertility patients demonstrate more psychopathology than controls, and that there is modest evidence for an association between distress during treatment and the outcome of the treatment itself. The effects of infertility and infertility treatment on quality of life is discussed thematically, using previous literature and previously unpublished qualitative data from infertility patients. The effects of infertility on social, interpersonal, and identity aspects of quality of life are emphasized.

Adaptation, Psychological↗
PubMed2002

Evolution of the Koch model of the biomechanics of the hip: clinical perspective.

Over the past several decades numerous researchers have revisited the model of the biomechanics of the hip first predicated by John Koch in 1917. The contributions of Blount (1956), Frankel (1960), Pauwels (1976), Toridis (1969), Rybicki (1972), Fetto (1994, 1995), Ling (1996), and Lu (1997, 1998) among others created a more complete picture. The present article briefly reviews the previous biomechanical concept and its clinical inconsistencies and offers a model that includes the dynamic and static input of the soft tissues. The action of the iliotibial band (ITB) and the vastus lateralis-gluteus medius complex (as static and dynamic tension bands lateral to the femur) counterbalance the varus bending torque of the loads acting on the hip, transforming the tensile stresses in the lateral femur (as hypothesized by Koch) into compressive stresses. The inclusion of the soft tissues, extending the previous model, widens our understanding of the forces acting on the hip. Thus, a variety of clinical observations can be better explained in a comprehensive theoretical framework.

Biological Evolution↗
PubMed1983

On the evolution of dominance modifiers I. A nonlinear analysis.

A well known mathematical model of evolution of dominance is subjected to a nonlinear analysis. For the case where the primary locus and the modifying locus are completely linked (r = 0) a global Ljapunov function is given. This proves that selection of dominance modifiers entirely due to their modifying effect is possible. This result is also extended to small recombination fractions r by using the method of Ljapunov functions in a more sophisticated way. For r = 0 and mu = 0 a lower bound for the success of selection of the modifier is given. Furthermore, the influence of the dominance relations between the alleles (measured by the parameters h and k) is investigated. Finally it is shown that differential and difference equations lead to the same results (which need not be the case in general). As a by-product we obtain a new equilibrium point in the classical one locus selection-mutation model.

Alleles↗
PubMed2003

Partial begging: an empirical model for the early evolution of offspring signalling.

Species where, from birth, the offspring feed themselves in addition to begging for food from the parents can be described as 'partially begging'. Such species provide a unique opportunity to examine the evolution of offspring begging from non-signalling offspring foraging strategies. We used the partially begging burying beetle Nicrophorus vespilloides to test specific hypotheses concerning the coexistence of begging and self-feeding. We first tested whether the cessation of larval begging coincided with an increase in the efficiency of self-feeding. As predicted, begging ceased when the efficiency of self-feeding reached the point where the larvae grew just as well without as with access to food provided by the parent. We next tested whether the transition to nutritional independence was under parental or offspring control. The parent did not change its behaviour towards the larvae over time, while the larvae changed their behaviour by reducing the time spent begging in the presence of the parent. Food allocation during the transition to nutritional independence was therefore under offspring control. Our results on partial begging provide a starting point for new theoretical models for the origin of begging. We suggest that these should be constructed as scramble-competition models because the offspring control food allocation.

Animal Communication↗
PubMed2005

Evolution of searching and life history characteristics in individual-based models of host-parasitoid-microbe associations.

In this paper we develop a novel discrete, individual-based mathematical model of the evolution of life history, dispersal and other behavioural characteristics in insect host-parasitoid-microbe associations, and use it to investigate their evolutionary dynamics. For any individual characteristic the model begins with an even, rectangular distribution of characteristic values. Selection is then allowed to act, and the change in the distribution of the characteristic values is observed. Evolutionary change in the population variance of the characteristic value is also observed, since we would expect this to decline under selection in most cases. The paper, therefore, introduces a general framework for modeling problems of evolution in stochastic, spatially structured environments, where movement and dispersal are under selection. The model then extends this approach to include the sex-distorting bacterium Wolbachia in order to investigate aspects of its horizontal and vertical transmission under different levels of superparasitism by parasitoids. The model also includes a neutral genetic marker, in order to be able to detect changes in phenotype frequency caused by genetic drift, as well as a simplified simulation of sexual reproduction so as to allow the possibility of recombination between genotypes. Key results from the model simulations show that: (i) the refractory time after oviposition affects the value of superparasitism, with short refractory times favouring high rates of superparasitism; (ii) variable levels of superparasitism do not affect the stable proportion of the population of parasitoids infected with Wolbachia, but this is achieved by different evolutionary pathways under low and high superparasitism, respectively. In the case of low superparasitism Wolbachia spreads mainly by vertical transmission, leading to population replacement, whereas when superparasitism rates are high there is significant horizontal transfer.

Animals↗