Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs.

Evolution and coevolution in mutualistic networks

A major current challenge in evolutionary biology is to understand how networks of interacting species shape the coevolutionary process. We combined a model for trait evolution with data for twenty plant-animal assemblages to explore coevolution in mutualistic networks. The results revealed three fundamental aspects of coevolution in species-rich mutualisms. First, coevolution shapes species traits throughout mutualistic networks by speeding up the overall rate of evolution. Second, coevolution results in higher trait complementarity in interacting partners and trait convergence in species in the same trophic level. Third, convergence is higher in the presence of super-generalists, which are species that interact with multiple groups of species. We predict that worldwide shifts in the occurrence of super-generalists will alter how coevolution shapes webs of interacting species. Introduced species such as honeybees will favour trait convergence in invaded communities, whereas the loss of large frugivores will lead to increased trait dissimilarity in tropical ecosystems.

Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution

Evolutionary novelties in the skeleton are usually expressed as changes in the timing of growth of features intrinsically integrated at different hierarchical levels of development(1). As a consequence, most of the shape- traits observed across species do vary quantitatively rather than qualitatively(2), in a multivariate space(3) and in a modularized way(4,5). Because most phylogenetic analyses normally use discrete, hypothetically independent characters(6), previous attempts have disregarded the phylogenetic signals potentially enclosed in the shape of morphological structures. When analysing low taxonomic levels, where most variation is quantitative in nature, solving basic requirements like the choice of characters and the capacity of using continuous, integrated traits is of crucial importance in recovering wider phylogenetic information. This is particularly relevant when analysing extinct lineages, where available data are limited to fossilized structures. Here we show that when continuous, multivariant and modularized characters are treated as such, cladistic analysis successfully solves relationships among main Homo taxa. Our attempt is based on a combination of cladistics, evolutionary- development- derived selection of characters, and geometric morphometrics methods. In contrast with previous cladistic analyses of hominid phylogeny, our method accounts for the quantitative nature of the traits, and respects their morphological integration patterns. Because complex phenotypes are observable across different taxonomic groups and are potentially informative about phylogenetic relationships, future analyses should point strongly to the incorporation of these types of trait.

Shape classification using complex network and Multi-scale Fractal Dimension

Shape provides one of the most relevant information about an object. This makes shape one of the most important visual attributes used to characterize objects. This paper introduces a novel approach for shape characterization, which combines modeling shape into a complex network and the analysis of its complexity in a dynamic evolution context. Descriptors computed through this approach show to be efficient in shape characterization, incorporating many characteristics, such as scale and rotation invariant. Experiments using two different shape databases (an artificial shapes database and a leaf shape database) are presented in order to evaluate the method. and its results are compared to traditional shape analysis methods found in literature. (C) 2009 Published by Elsevier B.V.

A complex network-based approach for boundary shape analysis

This paper introduces a novel methodology to shape boundary characterization, where a shape is modeled into a small-world complex network. It uses degree and joint degree measurements in a dynamic evolution network to compose a set of shape descriptors. The proposed shape characterization method has all efficient power of shape characterization, it is robust, noise tolerant, scale invariant and rotation invariant. A leaf plant classification experiment is presented on three image databases in order to evaluate the method and compare it with other descriptors in the literature (Fourier descriptors, Curvature, Zernike moments and multiscale fractal dimension). (C) 2008 Elsevier Ltd. All rights reserved.

Realized evolvability: quantifying phenotypic evolution in a Drosophila clade

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Evolution of a collapsing and exploding Bose-Einstein condensate in different trap symmetries

Based on the time-dependent Gross-Pitaevskii equation we study the evolution of a collapsing and exploding Bose-Einstein condensate in different trap symmetries to see the effect of confinement on collapse and subsequent explosion, which can be verified in future experiments. We make a prediction for the evolution of the shape of the condensate and the number of atoms in it for different trap symmetries (cigar to pancake) as well as in the presence of an optical lattice potential. We also make a prediction for the jet formation in different cases when the collapse is suddenly terminated by changing the scattering length to zero via a Feshbach resonance. In addition to the usual global collapse to the center of the condensate, in the presence of an optical-lattice potential one could also have in certain cases independent collapse of parts of the condensate to local centers, which could be verified in experiments.

Cranial differentiation and evolution in Thrichomys apereoides (Rodentia: Echimyidae)

Thrichomys apereoides is an echimyid rodent which ranges in distribution from north-eastern and central Brazil into Paraguay, and currently five subspecies are recognized. Recent morphometric analyses of population samples formally assignable to T. a. laurentius and T. a. inermis, which occur in north-eastern Brazil, have shown that a major group of populations including both subspecies differ in cranial shape from a single population allocated to T. a. laurentius. In this study we employed mathematical models of evolutionary quantitative genetics to assess the role that random drift and selection may have played in the evolution of cranial shape differences in T. apereoides. The hypothesis of evolution due to drift was rejected and the selective forces necessary to account for shape differences were estimated. Minimum selective mortalities of the order of 10(-3) per generation were sufficient to explain the observed morphologic differentiation.

Evolution of caste in neotropical swarm-founding wasps (Hymenoptera : Vespidae; Epiponini)

Reproductive castes are compared in species of swarming wasps representing all currently recognized genera of Epiponini (Polistinae). New morphometric data for nine measures of body parts and ovarian data are presented for 13 species. These are integrated with all similarly conducted available studies, giving a total of 30 species. Analysis reveals several syndromes relating reproductive and nonreproductive individuals: no meaningful distinction, physiological differences only, reproductives larger than nonreproductives with intermediate individuals present, reproductives different in shape from nonreproductives with no intermediates, and reproductives smaller in some aspects than nonreproductives. Distribution of these syndromes among species is consistent with phylogenetic relationships derived from other data. Optimizing these syndromes on the cladogram indicates that the basal condition of Epiponini is a casteless society that is not comparable to the primitively social genus Polistes where dominant queens control reproduction. Castes originate several times in Epiponini, with different results in different lineages. The best documented evolutionary sequence passes from casteless societies, to those with reproductives larger, to those with reproductives differing in shape from nonreproductives, to those with reproductives smaller in some measures. This sequence is consistent with Wheeler's theory of the origin of caste through developmental switches, and represents the most thorough test of that theory to date.

Barrier penetration for supersymmetric shape-invariant potentials

Exact reflection and transmission coefficients for supersymmetric shape-invariant potentials barriers are calculated by an analytical continuation of the asymptotic wavefunctions obtained via the introduction of new generalized ladder operators. The general form of the wavefunction is obtained by the use of the F(-infinity, +infinity)-matrix formalism of Froman and Froman which is related to the evolution of asymptotic wavefunction coefficients.

Thermal decomposition and rehydration of strontium oxalate: morphological evolution

Undoped and Eu3+ doped monohydrate strontium oxalate samples were precipitated under ultrasound and conventional stirring and were heated at different temperatures. All samples were characterized by X-ray powder diffraction (XDR), infrared spectra (IR) and scanning electron microscopy (SEM). Monohydrate, dehydrate oxalates and carbonate particles are ellipsoids indicating a topotatic process. Particle size decrease is observed when ultrasound stirring and europium. doping are used and rehydration of strontium oxalate results in uniform hexagonal particle shape. An oxide and carbonate mixture is obtained from oxalates treated at 1050 degreesC and its suspension in water undergoes incomplete hydrolysis. The products from this incomplete hydrolysis present dendrite shape particles only when the former is precipitated under ultrasound stirring. In this process, surface energy is important for particle dispersion and ultrasound supplies activation energy to oxalate precursor. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

Allometric analysis of the ontogenetic variation and evolution of the skull in Caiman spix, 1825 (Crocodylia: Alligatoridae)

We studied ontogenetic variation in the shape of the skull among species of Caiman using principal component analysis. Comparison of multivariate allometric coefficients and ontogenetic trends between size and shape reveals that C. sclerops and C. yacare have similar ontogenetic processes, and they are more related to each other than either is to C. latirostris. Allometric relationships of the characters measured are similar in all species studied. The greater differences were in the width measurements, with higher coefficients in shape (second principal component) for C. latirostris, and length measurements with higher coefficients in shape for C. yacare and C. sclerops. The ontogenetic process leading to change in skull shape in the group seems to be plesiomorphic for elongation and derived for broadening. Statistical comparison of the ontogenetic trends with models of allometric heterochrony suggests that C. latirostris has diverged from the other species by a neotenic process, and that C. sclerops is separated from C. yacare by ontogenetic scaling (progenesis).

Supersymmetric and shape-invariant generalization for nonresonant and intensity-dependent Jaynes-Cummings systems

A class of shape-invariant bound-state problems which represent transitions in a two-level system introduced earlier are generalized to include arbitrary energy splittings between the two levels as well as intensity-dependent interactions. We show that the coupled-channel Hamiltonians obtained correspond to the generalizations of the nonresonant and intensity-dependent Jaynes-Cummings Hamiltonians, widely used in quantized theories of lasers. In this general context, we determine the eigenstates, eigenvalues, the time evolution matrix and the population inversion matrix factor.

Comparative ontogenetic shape changes in the skull of Caiman species (Crocodylia, Alligatoridae)

Ontogenetic shape changes in the skull of three species of the genus Caiman (C. latirostris, C. sclerops, and C. yacare) are compared by geometric morphometrics for three-dimensional configurations (the least-squares analysis). The technique for obtaining the landmark coordinates is a simplification of the algorithm for multidimensional scaling. The ontogenetic nonlinear shape changes are similar in the three species but occur in a lesser extent in C. latirostris. These seem to be correlated with functional changes in the skull. The uniform shape change corresponds to an elongation of the skull, dorsoventral flattening, and lateral compression in C. sclerops and C. yacare. There is some lateral broadening in C. latirostris. Differences in the ontogenetic processes probably cause the differences in diet observed between C. latirostris and the other two species. Neotenic evolution seems to have acted in the skull of C. latirostris, and a posterior amplification of the early divergence led to a repatterning of the shape ontogenetic trajectory in this species. (C) 1997 Wiley-Liss, Inc.

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): Geometric analysis of a complex morphological structure

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinal trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.