Experimental studies on the nature of species

"Literature cited": v.1, p. 437-442; v.2, p. 154-163; v.3, p. 124-125; v.5, p. 198-204; v.6, p. 113-115.

Certain observations concerning the effects of epistasis on complex traits and the evolution of genomes.

Thesis (Ph.D.)--University of Washington, 2016-05

The evolution of microRNA in primates

Thesis (Ph.D.)--University of Washington, 2016-06

Experimental tests of quantum nonlinear dynamics in atom optics

Cold atoms in optical potentials provide an ideal test bed to explore quantum nonlinear dynamics. Atoms are prepared in a magneto-optic trap or as a dilute Bose-Einstein condensate and subjected to a far detuned optical standing wave that is modulated. They exhibit a wide range of dynamics, some of which can be explained by classical theory while other aspects show the underlying quantum nature of the system. The atoms have a mixed phase space containing regions of regular motion which appear as distinct peaks in the atomic momentum distribution embedded in a sea of chaos. The action of the atoms is of the order of Planck's constant, making quantum effects significant. This tutorial presents a detailed description of experiments measuring the evolution of atoms in time-dependent optical potentials. Experimental methods are developed providing means for the observation and selective loading of regions of regular motion. The dependence of the atomic dynamics on the system parameters is explored and distinct changes in the atomic momentum distribution are observed which are explained by the applicable quantum and classical theory. The observation of a bifurcation sequence is reported and explained using classical perturbation theory. Experimental methods for the accurate control of the momentum of an ensemble of atoms are developed. They use phase space resonances and chaotic transients providing novel ensemble atomic beamsplitters. The divergence between quantum and classical nonlinear dynamics is manifest in the experimental observation of dynamical tunnelling. It involves no potential barrier. However a constant of motion other than energy still forbids classically this quantum allowed motion. Atoms coherently tunnel back and forth between their initial state of oscillatory motion and the state 180 out of phase with the initial state.

A refined solution to Earth's hidden niobium: implications for evolution of continental crust and mode of core formation

New high-precision niobium (Nb) and tantalum (Ta) concentration data are presented for early Archaean metabasalts, metabasaltic komatiites and their erosion products (mafic metapelites) from SW Greenland and the Acasta gneiss complex, Canada. Individual datasets consistently show sub-chondritic Nb/Ta ratios averaging 15.1+/-11.6. This finding is discussed with regard to two competing models for the solution of the Nb-deficit that characterises the accessible Earth. Firstly, we test whether Nb could have sequestered into the core due to its slightly siderophile (or chalcophile) character under very reducing conditions, as recently proposed from experimental evidence. We demonstrate that troilite inclusions of the Canyon Diablo iron meteorite have Nb and V concentrations in excess of typical chondrites but that the metal phase of the Grant, Toluca and Canyon Diablo iron meteorites do not have significant concentrations of these lithophile elements. We find that if the entire accessible Earth Nb-deficit were explained by Nb in the core, only ca. 17% of the mantle could be depleted and that by 3.7 Ga, continental crust would have already achieved ca. 50% of its present mass. Nb/Ta systematics of late Archaean metabasalts compiled from the literature would further require that by 2.5 Ga, 90% of the present mass of continental crust was already in existence. As an alternative to this explanation, we propose that the average Nb/Ta ratio (15.1+/-11.6) of Earth's oldest mafic rocks is a valid approximation for bulk silicate Earth. This would require that ca. 13% of the terrestrial Nb resided in the Ta-free core. Since the partitioning of Nb between silicate and metal melts depends largely on oxygen fugacity and pressure, this finding could mean that metal/silicate segregation did not occur at the base of a deep magma ocean or that the early mantle was slightly less reducing than generally assumed. A bulk silicate Earth Nb/Ta ratio of 15.1 allows for depletion of up to 40% of the total mantle. This could indicate that in addition to the upper mantle, a portion of the lower mantle is depleted also, or if only the upper mantle were depleted, an additional hidden high Nb/Ta reservoir must exist. Comparison of Nb/Ta systematics between early and late Archaean metabasalts supports the latter idea and indicates deeply subducted high Nb/Ta eclogite slabs could reside in the mantle transition zone or the lower mantle. Accumulation of such slabs appears to have commenced between 2.5 and 2.0 Ga. Regardless of these complexities of terrestrial Nb/Ta systematics, it is shown that the depleted mantle Nb/Th ratio is a very robust proxy for the amount of extracted continental crust, because the temporal evolution of this ratio is dominated by Th-loss to the continents and not Nb-retention in the mantle. We present a new parameterisation of the continental crust volume versus age curve that specifically explores the possibility of lithophile element loss to the core and storage of eclogite slabs in the transition zone. (C) 2003 Elsevier Science B.V. All rights reserved.

Mechanical alloying of MoSi2 with ternary alloying elements. Part 1: Experimental

Phase evolution during the mechanical alloying of Mo and Si elemental powders with a ternary addition of Al, Mg, Ti or Zr was monitored using X-ray diffraction. Rietveld analysis was used to quantify the phase proportions. When Mo and Si are mechanically alloyed in the absence of a ternary element, the tetragonal C11b polymorph of MoSi2 (t-MoSi2) forms by a self-propagating combustion reaction. With additional milling, the tetragonal phase transforms to the hexagonal C40 structure (h-MoSi2). The mechanical alloying of Al, Mg and Ti additions with Mo and Si tend to promote a more rapid transformation of t-MoSi2 to h-MoSi2. In high concentrations, the addition of these ternary elements inhibits the initial combustion reaction, instead promoting the direct formation of h-MoSi2. The addition of Zr tends to stabilise the tetragonal phase.

Experimental evidence for multivariate stabilizing sexual selection

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This prediction has seldom been tested, particularly for suites of correlated traits. The lack of tests for an evolutionary match between population means and adaptive peaks may be due, at least in part, to problems associated with empirically detecting multivariate stabilizing selection and with testing whether population means are at the peak of multivariate fitness surfaces. Here we show how canonical analysis of the fitness surface, combined with the estimation of confidence regions for stationary points on quadratic response surfaces, may be used to define multivariate stabilizing selection on a suite of traits and to establish whether natural populations reside on the multivariate peak. We manufactured artificial advertisement calls of the male cricket Teleogryllus commodus and played them back to females in laboratory phonotaxis trials to estimate the linear and nonlinear sexual selection that female phonotactic choice imposes on male call structure. Significant nonlinear selection on the major axes of the fitness surface was convex in nature and displayed an intermediate optimum, indicating multivariate stabilizing selection. The mean phenotypes of four independent samples of males, from the same population as the females used in phonotaxis trials, were within the 95% confidence region for the fitness peak. These experiments indicate that stabilizing sexual selection may play an important role in the evolution of male call properties in natural populations of T. commodus.

Divergent selection and the evolution of signal traits and mating preferences

Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among- population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by- product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.

Response of heart rate and cloacal ventilation in the bimodally respiring freshwater turtle, Rheodytes leukops to experimental changes in aquatic PO2

Changes in heart rate (f(H)) and cloacal ventilation frequency (f(C)) were investigated in the Fitzroy turtle, Rheodytes leukops, under normoxic (17.85 kPa) and hypoxic (3.79 kPa) conditions at 25 degrees C. Given R. leukops' high reliance on aquatic respiration via the cloacal bursae, the objective Of this Study was to examine the effect of varying aquatic PO2 levels upon the expression of a bradycardia in a freely diving, bimodally respiring turtle. In normoxia, mean diving f(H) and f(C) for R. leukops remained constant with increasing submergence length, indicating that a bradycardia failed to develop during extended dives of up to 3 days. Alternatively, exposure to aquatic hypoxia resulted in the expression of a bradycardia as recorded by a decreasing mean diving f(H) with increasing dive duration. The observed bradycardia is attributed to a hypoxic-induced metabolic depression, possibly facilitated by a concurrent decrease in f(C). Results suggest that R. leukops alters its strategy from aquatic O-2 extraction via cloacal respiration in normoxia to O-2 conservation when exposed to aquatic hypoxia for the purpose of extending dive duration. Upon surfacing, a significant tachycardia was observed for R. leukops regardless of aquatic PO2, presumably functioning to rapidly equilibrate blood and tissue gas tensions with alveolar gas to reduce surfacing duration.

New oil modified acrylic polymer for pH sensitive drug release:experimental results and statistical analysis

We report results of an experimental study, complemented by detailed statistical analysis of the experimental data, on the development of a more effective control method of drug delivery using a pH sensitive acrylic polymer. New copolymers based on acrylic acid and fatty acid are constructed from dodecyl castor oil and a tercopolymer based on methyl methacrylate, acrylic acid and acryl amide were prepared using this new approach. Water swelling characteristics of fatty acid, acrylic acid copolymer and tercopolymer respectively in acid and alkali solutions have been studied by a step-change method. The antibiotic drug cephalosporin and paracetamol have also been incorporated into the polymer blend through dissolution with the release of the antibiotic drug being evaluated in bacterial stain media and buffer solution. Our results show that the rate of release of paracetamol getss affected by the pH factor and also by the nature of polymer blend. Our experimental data have later been statistically analyzed to quantify the precise nature of polymer decay rates on the pH density of the relevant polymer solvents. The time evolution of the polymer decay rates indicate a marked transition from a linear to a strictly non-linear regime depending on the whether the chosen sample is a general copolymer (linear) or a tercopolymer (non-linear). Non-linear data extrapolation techniques have been used to make probabilistic predictions about the variation in weight percentages of retained polymers at all future times, thereby quantifying the degree of efficacy of the new method of drug delivery.

Unravelling the photodegradation mechanisms of a low bandgap polymer by combining experimental and modeling approaches

Large-scale introduction of Organic Solar Cells (OSCs) onto the market is currently limited by their poor stability in light and air, factors present in normal working conditions for these devices. Thus, great efforts have to be undertaken to understand the photodegradation mechanisms of their organic materials in order to find solutions that mitigate these effects. This study reports on the elucidation of the photodegradation mechanisms occurring in a low bandgap polymer, namely, Si-PCPDTBT (poly[(4,4′-bis(2-ethylhexyl)dithieno[3,2-b:2′,3′-d]silole)-2,6-diyl-alt-(4,7-bis(2-thienyl)-2,1,3-benzothiadiazole)-5,5′-diyl]). Complementary analytical techniques (AFM, HS-SPME-GC-MS, UV-vis and IR spectroscopy) have been employed to monitor the modification of the chemical structure of the polymer upon photooxidative aging and the subsequent consequences on its architecture and nanomechanical properties. Furthermore, these different characterization techniques have been combined with a theoretical approach based on quantum chemistry to elucidate the evolution of the polymer alkyl side chains and backbone throughout exposure. Si-PCPDTBT is shown to be more stable against photooxidation than the commonly studied p-type polymers P3HT and PCDTBT, while modeling demonstrated the benefits of using silicon as a bridging atom in terms of photostability. (Figure Presented).

Experimental full duplex simultaneous transmission of LTE over a DWDM directly modulated RoF system

In this paper, we experimentally demonstrate the seamless integration of full duplex system frequency division duplex (FDD) long-term evolution (LTE) technology with radio over fiber (RoF) for eNodeB (eNB) coverage extension. LTE is composed of quadrature phase-shift keying (QPSK), 16-quadrature amplitude modulation (16-QAM) and 64-QAM, modulated onto orthogonal frequency division multiplexing (OFDM) and single-carrier-frequency division multiplexing for downlink (DL) and uplink (UL) transmissions, respectively. The RoF system is composed of dedicated directly modulated lasers for DL and UL with dense wavelength division multiplexing (DWDM) for instantaneous connections and for Rayleigh backscattering and nonlinear interference mitigation. DL and UL signals have varying carrier frequencies and are categorized as broad frequency spacing (BFS), intermediate frequency spacing (IFS), and narrow frequency spacing (NFS). The adjacent channel leakage ratio (ACLR) for DL and UL with 64-QAM are similar for all frequency spacings while cross talk is observed for NFS. For the best case scenario for DL and UL transmissions we achieve error vector magnitude (EVM) values of ~2.30%, ~2.33%, and ~2.39% for QPSK, 16-QAM, and 64-QAM, respectively, while for the worst case scenario with a NFS EVM is increased by 0.40% for all schemes. © 2009-2012 OSA.

Bound dissipative-pulse evolution in the all-normal dispersion fiber laser using a 45° tilted fiber grating

The formation and evolution of bound dissipative pulses in the all-normal dispersion Yb-fiber laser based on a novel 45° tilted fiber grating (TFG) are first investigated both numerically and experimentally. Based on the nonlinear polarization rotation technique, the TFG and two polarization controllers (PCs) are exploited for stable self-started passive mode locking. Numerical results show that the formation of bound-state pulses in the all-normal dispersion region is the progress of soliton shaping through the dispersive waves and follows the soliton energy quantization effect. Theoretical and experimental results demonstrate that the formation mechanism of bound-state pulses can be attributed to the high pump strength and effective filter bandwidth. The obtained bound-state dissipative pulses with quasi-rectangular spectral profile have fixed pulse separation as a function of pump power. © 2013 Astro Ltd.

Spectral characteristics and thermal evolution of long-period gratings in photonic crystal fibers fabricated with a near-IR radiation femtosecond laser using point-by-point inscription

The spectral properties of long-period gratings (LPGs) fabricated in photonic crystal fibers using femtosecond laser pulses by the point-by-point technique, without oil-immersion of the fiber, are investigated in detail. Postfabrication spectral monitoring at room temperature showed significant long-term instability of the gratings and stable spectra only after 600 h. The stabilized spectral properties of the gratings improved with increasing annealing temperature. The observed changes in resonant wavelength, optical strength, and grating birefringence were correlated to the laser inscription energy and were further used to study the mechanism of femtosecond inscription. Furthermore, the femtosecond-laser inscribed LPGs were compared to electric-arc fabricated LPGs. Comparison of experimental results with theoretical models of LPGs and laser propagation during inscription indicate that the major processes responsible for the index change are permanent compaction and thermally induced strain, the latter can be significantly changed through annealing. © 2011 Optical Society of America.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.