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PubMed1995

Molecular phylogeny and divergence times of drosophilid species.

The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.

Animals↗
PubMed1992

Character analysis and the integration of molecular and morphological data in an understanding of sand dollar phylogeny.

Reconciling discordant morphological and molecular phylogenies remains a problem in modern systematics. By examining conflicting DNA-hybridization and morphological phylogenies of sand dollars, I show that morphological criteria may be used to help evaluate the reliability of molecular phylogenies where they differ from morphological trees. All available criteria for assessing the reliability of DNA-hybridization phylogenies suggest that the sand dollar DNA-hybridization phylogeny is robust. Standard homology-recognition criteria are used to assess the a priori reliabilities of the morphological attributes associated with the node drawn into question by the DNA data, and it is shown that these attributes are among the least phylogenetically informative of all the morphological characters. Moreover, the questioned node has the smallest number of supporting characters, and most of these characters are associated with the food grooves, which suggests that they may be functionally correlated. Thus, on the basis of the analysis of the morphological data and given the robustness of the DNA tree, the DNA phylogeny is preferred. Further, paleobiogeographic data support the DNA tree rather than the morphological tree, and a plausible heterochronic mechanism has been proposed that may account for the homoplasious morphological evolution that must have occurred if the DNA tree is correct.

Animals↗
PubMed2006

Extreme convergence in the body plans of an early suchian (Archosauria) and ornithomimid dinosaurs (Theropoda).

Living archosaurs comprise birds (dinosaurs) and crocodylians (suchians). The morphological diversity of birds and stem group dinosaurs is tremendous and well-documented. Suchia, the archosaurian group including crocodylians, is generally considered more conservative. Here, we report a new Late Triassic suchian archosaur with unusual, highly specialized features that are convergent with ornithomimid dinosaurs. Several derived features of the skull and postcranial skeleton are identical to conditions in ornithomimids. Such cases of extreme convergence in multiple regions of the skeleton in two distantly related vertebrate taxa are rare. This suggests that these archosaurs show iterative patterns of morphological evolution. It also suggests that this group of suchians occupied the adaptive zone that was occupied by ornithomimosaurs later in the Mesozoic.

Adaptation, Physiological↗
PubMed2001

Nonequilibrium dynamics of the complex Ginzburg-Landau equation: analytical results.

We present a detailed analytical and numerical study of nonequilibrium dynamics for the complex Ginzburg-Landau equation. In particular, we characterize evolution morphologies using spiral defects. This paper is the first in a two-stage exposition. Here, we present analytical results for the correlation function arising from a single-spiral morphology. We also critically examine the utility of the Gaussian auxiliary field ansatz in characterizing a multispiral morphology. In the next paper of this exposition we will present detailed numerical results.

Journal Article↗
PubMed2001

Nonequilibrium dynamics in the complex Ginzburg-Landau equation.

Results from a comprehensive analytical and numerical study of nonequilibrium dynamics in the two-dimensional complex Ginzburg-Landau equation have been presented. In particular, spiral defects have been used to characterize the domain growth law and the evolution morphology. An asymptotic analysis of the single-spiral correlation function shows a sequence of singularities-analogous to those seen for time-dependent Ginzburg-Landau models with O(n) symmetry, where n is even.

Journal Article↗
PubMed2004

Anomalous self-assembly of gelatin in ethanol-water marginal solvent.

Light scattering, rheology, and atomic force microscope (AFM) studies have been performed on solutions of a polyampholyte (gelatin) prepared in water-ethanol marginal solvent. At ethanol concentration approximately 45+/-2% v/v anomalous aggregation led to formation of fractal (on hydrophilic substrates; glass, quartz and silicon) aggregate of polypeptide molecules having fractal dimension d(f) in 2D=1.60+/-0.08. The time evolution morphology of these self-assembled and self-organized structures formed on hydrophilic substrates was driven by selective ethanol evaporation and was observed by an AFM. These fractal aggregates eventually transformed into near-spherical clusters with fractal corona having same fractal dimension (d(f)=1.58+/-0.05) and finally, the corona separated and regular aggregates were formed. The kinetics of aggregation on substrates could be modeled through random sequential adsorption of particles with continuum power-law size distribution. The temporal growth of aggregate hydrodynamic radius R(h)(t) and scattered intensity I(s)(t) measured in the bulk were observed to exhibit; R(h)-t(z) and I(s)-t(z)-with z=1/d(f), giving a fractal dimension d(f) in 3D approximately equal to 2.6+/-0.2, which is discussed within the framework of Smoluchowski aggregation kinetics. This growth in R(h) is accompanied by narrowing down of the particle size distribution. Solution rheology at this ethanol concentration revealed minimum thixotropy and maximum infinite shear viscosity features.

Journal Article↗
PubMed2005

Phase separation driven by surface diffusion: a Monte Carlo study.

We propose a kinetic Ising model to study phase separation driven by surface diffusion. This model is referred to as Model S, and consists of the usual Kawasaki spin-exchange kinetics (Model B) in conjunction with a kinetic constraint. We use multispin coding techniques to develop fast algorithms for Monte Carlo simulations of Models B and S. We use these algorithms to study the late stages of pattern dynamics in these systems, and compare properties of the evolution morphologies, e.g., growth laws, domain distribution functions, and spatial and temporal correlation functions.

Journal Article↗
PubMed2000

Enhanced instability in thin liquid films by improved compatibility

We investigated experimentally the morphological evolution of thin polydimethylsiloxane films sandwiched between a silicon wafer and different bounding liquids with interfacial tensions varying by 2 orders of magnitude. It is shown that increasing the compatibility between film and bounding liquid by adding a few surfactant molecules results in a faster instability of shorter characteristic wavelength. Inversely, based on the characteristic parameters describing the instability we determined extremely small interfacial tensions with a remarkable accuracy.

Journal Article↗
PubMed2002

Origin of the stability of Ge(105) on si: a new structure model and surface strain relaxation.

The structure of Ge(105)-(1 x 2) grown on Si(105) is examined by scanning tunneling microscopy (STM) and first-principles calculations. The morphology evolution with an increasing amount of Ge deposited documents the existence of a tensile surface strain in Si(105) and its relaxation with increasing coverage of Ge. A detailed analysis of high-resolution STM images and first-principles calculations produce a new stable model for the Ge(105)-(1 x 2) structure formed on the Si(105) surface that includes the existence of surface strain. It corrects the model developed from early observations of the facets of "hut" clusters grown on Si(001).

Journal Article↗
PubMed2002

Competing roughening mechanisms in strained heteroepitaxy: a fast kinetic Monte Carlo study.

We study the morphological evolution of strained heteroepitaxial films using kinetic Monte Carlo simulations in two dimensions. A novel Green's function approach, analogous to boundary integral methods, is used to calculate elastic energies efficiently. We observe island formation at low lattice misfit and high temperature that is consistent with the Asaro-Tiller-Grinfeld instability theory. At high misfit and low temperature, islands or pits form according to the nucleation theory of Tersoff and LeGoues.

Journal Article↗
PubMed2004

Liquid-liquid transition in the molecular liquid triphenyl phosphite.

We found both nucleation-growth-type and spinodal-decomposition-type transformation from one liquid state to another in a "molecular liquid," triphenyl phosphite (TPP). Binodal and spinodal temperatures of this transition at ambient pressure were determined by the characteristics of morphological evolution, domain-growth kinetics, and rheological evolution. Furthermore, a distinct thermal signature of the glass transition of a second liquid was also detected in addition to that of an ordinary liquid. These findings strongly suggest the existence of a liquid-liquid transition; more precisely, a transformation of one supercooled liquid to a glassy state of another liquid, in TPP.

Journal Article↗
PubMed2004

Kinetic roughening of ion-sputtered Pd(001) surface: beyond the Kuramoto-Sivashinsky model.

We investigate the kinetic roughening of Ar+ ion-sputtered Pd(001) surface both experimentally and theoretically. In situ real-time x-ray reflectivity and in situ scanning tunneling microscopy show that nanoscale adatom islands form and grow with increasing sputter time t. Surface roughness W(t) and lateral correlation length xi(t) follow the scaling laws W(t) approximately t(beta) and xi(t) approximately t(1/z) with the exponents beta approximately 0.20 and 1/z approximately 0.20, for an ion beam energy epsilon=0.5 keV, which is inconsistent with the prediction of the Kuramoto-Sivashinsky (KS) model. We thereby extend the KS model by applying the coarse-grained continuum approach of the Sigmund theory to the order of O(inverted Delta(4),h(2)), where h is the surface height, and derive a new term of the form inverted Delta(2)(inverted Delta h)(2) which plays a decisive role in describing the observed morphological evolution of the sputtered surface.

Journal Article↗
PubMed2005

Transient topographies of ion patterned Si(111).

The surface of high fluence ion-sputtered Si(111) was found to exhibit a rich variety of transient one- and two-dimensional topographies that may be exploited as tunable self-organized arrays of nanostructures. Such transient effects are only partially described by analytical models of sputter patterning. However, a discrete atom kinetic Monte Carlo simulation model incorporating curvature-dependent sputtering and surface diffusion reproduces many aspects of the transient morphological evolution, and clarifies the minimal model of sputter patterning.

Journal Article↗
PubMed2005

Island, pit, and groove formation in strained heteroepitaxy.

We study the morphological evolution of strained heteroepitaxial films using a kinetic Monte Carlo method in three dimensions. The elastic part of the problem uses a Green's function method. Isolated islands are observed under deposition conditions for deposition rates slow compared with intrinsic surface roughening rates. They are hemispherical and truncated conical for high and low temperature cases, respectively. Annealing of films at high temperature leads to the formation of closely packed islands as in instability theory. At low temperature, pits form via a multistep layer-by-layer nucleation mechanism in contrast to the conventional single-step nucleation process. They subsequently develop into grooves, which are energetically more favorable.

Journal Article↗
PubMed2006

Effects of warming conditions in eastern North American forests on red-backed salamander morphology.

Several studies have reported climate-associated changes in phenotypically plastic traits of amphibians, yet it remains unknown whether amphibians can manifest an evolutionary response to global climate change at the rate and magnitude that it is occurring. To assess this issue, we examined temporal change in the morphology of the red-backed salamander (Plethodon cinereus), a small, abundant woodland salamander distributed widely in eastern North America with two distinct morphotypes: striped individuals associated with cooler microclimates and unstriped individuals associated with warmer microclimates. We compiled morph frequencies for 50,960 individual salamanders from 558 sites as recorded in the published literature and in unpublished field notes of herpetologists between 1908 and 2004. We observed that striping probability increased with increasing latitude, longitude, and elevation and decreased (from 80% to 74% range wide) with time. The combined forces of regional climate warming and, particularly, forest disturbance have evidently been sufficient to cause morphological evolution in this amphibian over the last century.

Animals↗
PubMed2001

A new look at microbial leaching patterns on sulfide minerals.

Leaching patterns on sulfide minerals were investigated by high-resolution scanning electron microscopy (SEM). Our goal was to evaluate the relative contributions of inorganic surface reactions and reactions localized by attached cells to surface morphology evolution. Experiments utilized pyrite (FeS(2)), marcasite (FeS(2)) and arsenopyrite (FeAsS), and two iron-oxidizing prokaryotes in order to determine the importance of cell type, crystal structure, and mineral dissolution rate in microbially induced pit formation. Pyrite surfaces were reacted with the iron-oxidizing bacterium Acidithiobacillus ferrooxidans (at 25 degrees C), the iron-oxidizing archaeon 'Ferroplasma acidarmanus' (at 37 degrees C), and abiotically in the presence of Fe(3+) ions. In all three experiments, discrete bacillus-sized (1-2 µm) and -shaped (elliptical) pits developed on pyrite surfaces within 1 week of reaction. Results show that attaching cells are not necessary for pit formation on pyrite. Marcasite and arsenopyrite surfaces were reacted with A. ferrooxidans (at 25 degrees C) and 'F. acidarmanus' (at 37 degrees C). Cell-sized and cell-shaped dissolution pits were not observed on marcasite or arsenopyrite at any point during reaction with A. ferrooxidans, or on marcasite surfaces reacted with 'F. acidarmanus'. However, individual 'F. acidarmanus' cells were found within individual shallow (<0.5 µm deep) pits. The size and shape (round rather than elliptical) of the pits conformed closely to the shape of F. acidarmanus (cells) pits on arsenopyrite. We infer these pits to be cell-induced. We attribute the formation of pits readily detectable (by SEM) to the higher reactivity of arsenopyrite compared to pyrite and marcasite under the conditions the experiment was conducted. These pits contributed little to the overall surface topographical evolution, and most likely did not significantly increase surface area during reaction. Our results suggest that overall sulfide mineral dissolution may be dominated by surface reactions with Fe(3+) rather than by reactions at the cell-mineral interface.

Journal Article↗
PubMed1986

Histopathologic and immunopathologic study of pyoderma gangrenosum.

Sixty-three patients with pyoderma gangrenosum were seen and studied at the Mayo Clinic from 1971 to 1980. Biopsies from the erythematous border or necrotic edge of the pyoderma gangrenosum lesions usually demonstrated a characteristic pathogenic morphologic evolution. The early lesions revealed mild to moderate perivascular lymphocytic infiltrate associated with endothelial swelling. The fully developed lesions demonstrated necrosis in addition to a dense lymphocytic infiltration surrounding as well as involving the blood vessels. Extravasation of erythrocytes and thrombosis sometimes were seen. Ulceration, infarction, and abscess formation were found in the later stages of evolution. Direct immunofluorescence results were positive in the blood vessels of 36 of 65 (55%) specimens. IgM, C3, and fibrin were found in the papillary and reticular dermal vessels. IgG and IgA were only occasionally present. Pyoderma gangrenosum appears to be a reactive process that is manifested as a vasculitis. Biopsy material from the advancing active erythematous border has early characteristic dermatopathologic findings of lymphocytic vasculitis. Cutaneous vascular immune deposits suggest an immune pathogenesis of either an immune complex disease or lymphocytotoxic reaction.

Biopsy↗