Morphology and structure of particles produced by femtosecond laser ablation of fused silica

The aim of the present work was to study the morphology and structure of the nanoparticles produced by femtosecond laser ablation of fused silica. Ultrashort laser pulses of 1030 nm wavelength and 550 fs duration were tightly focused by a high numerical aperture microscope objective at the surface of fused silica samples while scanning the sample in relation to the stationary laser beam. Laser tracks were created with pulse energies in the range 5-100 mu J, resulting in ablation debris of different morphologies. The debris were examined by scanning and transmission electron microscopy for their morphology and crystal structure in relation to the incident laser pulse energy. Ejected particles with sizes ranging from a few nanometers to a few microns were found. Their morphologies can be broadly classified into three categories: very fine round nanoparticles with diameters lower than 20 nm, nanoparticles with intermediate sizes between 50 and 200 nm, and big irregular particles with typical size between 0.5 and 1.5 mu m. The fine nanoparticles of the first category are predominantly observed at higher pulse energies and tend to aggregate to form web-like and arborescent-like structures. The nanoparticles with intermediate sizes are observed for all pulse energies used and may appear isolated or aggregated in clusters. Finally, the larger irregular particles of the third category are observed for all energies and appear normally isolated.

Diagnostic utility of thyroglobulin measurement in the fine needle aspirates from cervical lymph nodes: a case report

Fine needle aspiration cytology (FNAC) is the more accurate diagnostic method for cervical lymph node (CLN) metastasis from differentiated thyroid cancers (DTC). However, FNAC diagnosis of cystic CLN is, in most cases, uninformative due to inadequate cellularity. Recently, thyroglobulin (Tg) detection in FNAC needle washout fluid has been shown to improve the diagnostic accuracy of FNAC, and its routine association with cytology is recommended. We here describe the case of a 20 yr old girl complaining of the recent appearance of palpable non-painful laterocervical nodes in the neck. Ultrasound examination revealed the presence of 3 cystic CLNs and 2 mixed thyroid nodules, with the larger one showing irregular margins. On the latter, and on 2 larger CLNs, FNAC was performed, and both Tg protein and mRNA were determined in the needle washout. The cytological analysis was not diagnostic for the two CLNs, while that of the thyroid nodule reported the presence of colloid and groups of thyrocytes with normal morphology. Both CLNs showed, however, high levels of Tg protein and were positive for Tg mRNA, suggestive of metastatic DTC. Based on these findings, the FNAC analysis was performed on the second smaller thyroid nodule suggesting (Tir4) the presence of PTC. The patient was then subjected to total thyroidectomy with lymph nodes resection of the central and homolateral compartments. The histological diagnosis confirmed the presence of a PTC in the small nodule and metastatic lymph nodes. In conclusion, this case confirms that the cytological diagnosis of cystic lymph nodes is challenging, and that the measurement of Tg protein and/or mRNA in the needle washout may overcome this limitation.

Ecosystem structure of Gomishan Wetland

Gomishan Wetland is situated in the extreme southern part of the eastern coast of Caspian Sea. It is connected to the Caspian Sea, so its hydrological features are directly generated from the sea. The whole wetland area (which also consists of the northern part of the wetland that is situated in Turkmenistan republic) is calculated with the aid of the Satellite Images for the years of 1977, 1987 and 1998 respectively 5070, 16320 and 29520 hectares. To have better ideas about food chains in the aquatic ecosystem, five permanent stations was appointed in different parts of the wetland. During one year field study, at the beginning of each month, physical, chemical and biological characteristics of the water and the sediment was surveyed and different specimens were gathered, fixed and took to the laboratories for the relevant analyses. The factors measured in water samples were mainly consist of turbidity, pH, EC, DO, BOD, PO4, NO3, alkalinity, Cl and hardness . The factors measured from sediment samples were the percentage of Sand, Very Fine Sand, Silt, Clay, K, P, N, and Organic Carbon. Biological examinations of the water has been consist of planktonic sample collections, determination, counting and analysis of both phyto and zoo planktons of the wetland. For example the zooplanktons of the Gomishan Wetland are determined in 15 groups, belonging to 5 phyla. The seasonal changes are recognized considerable. The least density of the zooplanktons is occurred in February. The density of most of the groups is seen from the beginning of the summer until the mid autumn. The annual mean density for any 15-zooplankton groups and also the minimum and maximum density with %95 confidences, for each of them, is calculated for the environment of all of the stations and also for the whole wetland. The spatial distribution of the individuals within the population of each of the groups is introduced, according to regular or contagious or random distribution. Diversity indices are calculated for the zooplanktons living in the environment of the stations. Comparison of the wetland, with the southeastern Caspian Sea, from the point of view of zooplankton density and diversity is also obtained. Benthos invertebrates in each station from sediment samples were also extracted. The specimens were colored by Rose Bengal solvent and then were determinate and counted, in separate groups of macro and meio benthos. Among the macro benthos, the highest density was seen in the species of Fyrgula caspia. After that, more density was seen respectively in Apra ovata, Cerastoderma sp., Balanus sp., Nerds divesicolarr, lifytilaster lineatus and Dreissena sp. Among the meio benthos, the most density was seen in Foraminifera and then respectively in Ostracoda, Nernatoda and Bivalve larvae. The indices of diversity and distribution are also calculated. As the birds in this lagoon are of prime importance, all mid winter waterfowl censuses available from recent 13 years are gathered and analysis. Also a whole year (12 times, each at the beginning of one month) waterfowl census was undertaken, throughout the wetland. According to this study, the Eastern Ecosystem of the wetland, is supporting the most population (%75) of the waterfowls, the Middle Open Water Ecosystem and the Western Reed bed Ecosystem, are supporting respectively %14 and %11 of the population. Four of the species are found in the global threatened red list, and the wintering population of the 20 species of the site, in some years, are observed more than %I of the global populations. The Waterfowl Species Diversity and Similarity Indices are given also.

An experiment on the parameter uncertainty of hydrological models with different levels of complexity in a climate change context

La possibilité d’estimer l’impact du changement climatique en cours sur le comportement hydrologique des hydro-systèmes est une nécessité pour anticiper les adaptations inévitables et nécessaires que doivent envisager nos sociétés. Dans ce contexte, ce projet doctoral présente une étude sur l’évaluation de la sensibilité des projections hydrologiques futures à : (i) La non-robustesse de l’identification des paramètres des modèles hydrologiques, (ii) l’utilisation de plusieurs jeux de paramètres équifinaux et (iii) l’utilisation de différentes structures de modèles hydrologiques. Pour quantifier l’impact de la première source d’incertitude sur les sorties des modèles, quatre sous-périodes climatiquement contrastées sont tout d’abord identifiées au sein des chroniques observées. Les modèles sont calés sur chacune de ces quatre périodes et les sorties engendrées sont analysées en calage et en validation en suivant les quatre configurations du Different Splitsample Tests (Klemeš, 1986;Wilby, 2005; Seiller et al. (2012);Refsgaard et al. (2014)). Afin d’étudier la seconde source d’incertitude liée à la structure du modèle, l’équifinalité des jeux de paramètres est ensuite prise en compte en considérant pour chaque type de calage les sorties associées à des jeux de paramètres équifinaux. Enfin, pour évaluer la troisième source d’incertitude, cinq modèles hydrologiques de différents niveaux de complexité sont appliqués (GR4J, MORDOR, HSAMI, SWAT et HYDROTEL) sur le bassin versant québécois de la rivière Au Saumon. Les trois sources d’incertitude sont évaluées à la fois dans conditions climatiques observées passées et dans les conditions climatiques futures. Les résultats montrent que, en tenant compte de la méthode d’évaluation suivie dans ce doctorat, l’utilisation de différents niveaux de complexité des modèles hydrologiques est la principale source de variabilité dans les projections de débits dans des conditions climatiques futures. Ceci est suivi par le manque de robustesse de l’identification des paramètres. Les projections hydrologiques générées par un ensemble de jeux de paramètres équifinaux sont proches de celles associées au jeu de paramètres optimal. Par conséquent, plus d’efforts devraient être investis dans l’amélioration de la robustesse des modèles pour les études d’impact sur le changement climatique, notamment en développant les structures des modèles plus appropriés et en proposant des procédures de calage qui augmentent leur robustesse. Ces travaux permettent d’apporter une réponse détaillée sur notre capacité à réaliser un diagnostic des impacts des changements climatiques sur les ressources hydriques du bassin Au Saumon et de proposer une démarche méthodologique originale d’analyse pouvant être directement appliquée ou adaptée à d’autres contextes hydro-climatiques.

Structure, transports and transformations of the water masses in the Atlantic Subpolar Gyre

We discuss the distributions and transports of the main water masses in the North Atlantic Subpolar Gyre (NASPG) for the mean of the period 2002–2010 (OVIDE sections 2002–2010 every other year), as well as the inter-annual variability of the water mass structure from 1997 (4x and METEOR sections) to 2010. The water mass structure of the NASPG, quantitatively assessed by means of an Optimum MultiParameter analysis (with 14 water masses), was combined with the velocity fields resulting from previous studies using inverse models to obtain the water mass volume transports. We also evaluate the relative contribution to the Atlantic Meridional Overturning Circulation (AMOC) of the main water masses characterizing the NASPG, identifying the water masses that contribute to the AMOC variability. The reduction of the magnitude of the upper limb of the AMOC between 1997 and the 2000s is associated with the reduction in the northward transport of the Central Waters. This reduction of the northward flow of the AMOC is partially compensated by the reduction of the southward flow of the lower limb of the AMOC, associated with the decrease in the transports of Polar Intermediate Water and Subpolar Mode Water (SPMW) in the Irminger Basin. We also decompose the flow over the Reykjanes Ridge from the East North Atlantic Basin to the Irminger Basin (9.4 ± 4.7 Sv) into the contributions of the Central Waters (2.1 ± 1.8 Sv), Labrador Sea Water (LSW, 2.4 ± 2.0 Sv), Subarctic Intermediate Water (SAIW, 4.0 ± 0.5 Sv) and Iceland–Scotland Overflow Water (ISOW, 0.9 ± 0.9 Sv). Once LSW and ISOW cross over the Reykjanes Ridge, favoured by the strong mixing around it, they leave the Irminger Basin through the deep-to-bottom levels. The results also give insights into the water mass transformations within the NASPG, such as the contribution of the Central Waters and SAIW to the formation of the different varieties of SPMW due to air–sea interaction.

Mixing of 0(+) and 0(-) observed in the hyperfine and Zeeman structure of ultracold Rb-2 molecules

We study the combination of the hyperfine and Zeeman structure in the spin-orbit coupled A(1)Sigma(+)(u) = b(3)Pi(u) complex of Rb-87(2). For this purpose, absorption spectroscopy at a magnetic field around B = 1000 G is carried out. We drive optical dipole transitions from the lowest rotational state of an ultracold Feshbach molecule to various vibrational levels with 0(+) symmetry of the A - b complex. In contrast to previous measurements with rotationally excited alkali-dimers, we do not observe equal spacings of the hyperfine levels. In addition, the spectra vary substantially for different vibrational quantum numbers, and exhibit large splittings of up to 160 MHz, unexpected for 0(+) states. The level structure is explained to be a result of the repulsion between the states 0(+) and 0(-) of b(3)Pi(u), coupled via hyperfine and Zeeman interactions. In general, 0(-) and 0(+) have a spin-orbit induced energy spacing Delta, that is different for the individual vibrational states. From each measured spectrum we are able to extract Delta, which otherwise is not easily accessible in conventional spectroscopy schemes. We obtain values of Delta in the range of +/- 100 GHz which can be described by coupled channel calculations if a spin-orbit coupling is introduced that is different for 0(-) and 0(+) of b(3)Pi(u).

A kinetic energy budget and internal instabilities in the Fine Resolution Antarctic Model

An energy analysis of the Fine Resolution Antarctic Model (FRAM) reveals the instability processes in the model. The main source of time-mean kinetic energy is the wind stress and the main sink is transfer to mean potential energy. The wind forcing thus helps maintain the density structure. Transient motions result from internal instabilities of the Bow rather than seasonal variations of the forcing. Baroclinic instability is found to be an important mechanism in FRAM. The highest values of available potential energy are found in the western boundary regions as well as in the Antarctic Circumpolar Current (ACC) region. All subregions with predominantly zonal flow are found to be baroclinically unstable. The observed deficit of eddy kinetic energy in FRAM occurs as a result of the high lateral friction, which decreases the growth rates of the most unstable waves. This high friction is required for the numerical stability of the model and can only be made smaller by using a finer horizontal resolution. A grid spacing of at least 10-15 km would be required to resolve the most unstable waves in the southern part of the domain. Barotropic instability is also found to be important for the total domain balance. The inverse transfer (that is, transfer from eddy to mean kinetic energy) does not occur anywhere, except in very localized tight jets in the ACC. The open boundary condition at the northern edge of the model domain does not represent a significant source or sink of eddy variability. However, a large exchange between internal and external mode energies is found to occur. It is still unclear how these boundary conditions affect the dynamics of adjacent regions.

Estudo da moagem de alta energia e sinterização de pós compósitos W-Cu

The Tungsten/copper composites are commonly used for electrical and thermal objectives like heat sinks and lectrical conductors, propitiating an excellent thermal and electrical conductivity. These properties are dependents of the composition, crystallite size and production process. The high energy milling of the powder of W-Cu produces an dispersion high and homogenization levels with crystallite size of W very small in the ductile Cu phase. This work discusses the effect of the HEM in preparation of the W-25Cu composite powders. Three techniques of powder preparation were utilized: milling the dry with powder of thick Cu, milling the dry with powder of fine Cu and milling the wet with powder of thick Cu. The form, size and composition of the particles of the powders milled were observed by scanning electron microscopy (SEM). The X-ray diffraction (XRD) was used to analyse the phases, lattice parameters, size and microstrain of the crystallite. The analyse of the crystalline structure of the W-25Cu powders milled made by Rietveld Method suggests the partial solid solubility of the constituent elements of the Cu in lattice of the W. This analyse shows too that the HEM produces the reduction high on the crystallite size and the increase in the lattice strain of both phases, this is more intense in the phase W

Holistic Design In High-Speed Optical Interconnects

Integrated circuit scaling has enabled a huge growth in processing capability, which necessitates a corresponding increase in inter-chip communication bandwidth. As bandwidth requirements for chip-to-chip interconnection scale, deficiencies of electrical channels become more apparent. Optical links present a viable alternative due to their low frequency-dependent loss and higher bandwidth density in the form of wavelength division multiplexing. As integrated photonics and bonding technologies are maturing, commercialization of hybrid-integrated optical links are becoming a reality. Increasing silicon integration leads to better performance in optical links but necessitates a corresponding co-design strategy in both electronics and photonics. In this light, holistic design of high-speed optical links with an in-depth understanding of photonics and state-of-the-art electronics brings their performance to unprecedented levels. This thesis presents developments in high-speed optical links by co-designing and co-integrating the primary elements of an optical link: receiver, transmitter, and clocking.

In the first part of this thesis a 3D-integrated CMOS/Silicon-photonic receiver will be presented. The electronic chip features a novel design that employs a low-bandwidth TIA front-end, double-sampling and equalization through dynamic offset modulation. Measured results show -14.9dBm of sensitivity and energy efficiency of 170fJ/b at 25Gb/s. The same receiver front-end is also used to implement source-synchronous 4-channel WDM-based parallel optical receiver. Quadrature ILO-based clocking is employed for synchronization and a novel frequency-tracking method that exploits the dynamics of IL in a quadrature ring oscillator to increase the effective locking range. An adaptive body-biasing circuit is designed to maintain the per-bit-energy consumption constant across wide data-rates. The prototype measurements indicate a record-low power consumption of 153fJ/b at 32Gb/s. The receiver sensitivity is measured to be -8.8dBm at 32Gb/s.

Next, on the optical transmitter side, three new techniques will be presented. First one is a differential ring modulator that breaks the optical bandwidth/quality factor trade-off known to limit the speed of high-Q ring modulators. This structure maintains a constant energy in the ring to avoid pattern-dependent power droop. As a first proof of concept, a prototype has been fabricated and measured up to 10Gb/s. The second technique is thermal stabilization of micro-ring resonator modulators through direct measurement of temperature using a monolithic PTAT temperature sensor. The measured temperature is used in a feedback loop to adjust the thermal tuner of the ring. A prototype is fabricated and a closed-loop feedback system is demonstrated to operate at 20Gb/s in the presence of temperature fluctuations. The third technique is a switched-capacitor based pre-emphasis technique designed to extend the inherently low bandwidth of carrier injection micro-ring modulators. A measured prototype of the optical transmitter achieves energy efficiency of 342fJ/bit at 10Gb/s and the wavelength stabilization circuit based on the monolithic PTAT sensor consumes 0.29mW.

Lastly, a first-order frequency synthesizer that is suitable for high-speed on-chip clock generation will be discussed. The proposed design features an architecture combining an LC quadrature VCO, two sample-and-holds, a PI, digital coarse-tuning, and rotational frequency detection for fine-tuning. In addition to an electrical reference clock, as an extra feature, the prototype chip is capable of receiving a low jitter optical reference clock generated by a high-repetition-rate mode-locked laser. The output clock at 8GHz has an integrated RMS jitter of 490fs, peak-to-peak periodic jitter of 2.06ps, and total RMS jitter of 680fs. The reference spurs are measured to be –64.3dB below the carrier frequency. At 8GHz the system consumes 2.49mW from a 1V supply.

Raman Spectroscopy and DFT calculations for the Electronic Structure Characterization of Conjugated Polymers

In the last three decades, there has been a broad academic and industrial interest in conjugated polymers as semiconducting materials for organic electronics. Their applications in polymer light-emitting diodes (PLEDs), polymer solar cells (PSCs), and organic field-effect transistors (OFETs) offer opportunities for the resolution of energy issues as well as the development of display and information technologies1. Conjugated polymers provide several advantages including low cost, light weight, good flexibility, as well as solubility which make them readily processed and easily printed, removing the conventional photolithography for patterning2. A large library of polymer semiconductors have been synthesized and investigated with different building blocks, such as acenes or thiophene and derivatives, which have been employed to design new materials according to individual demands for specific applications. To design ideal conjugated polymers for specific applications, some general principles should be taken into account, including (i) side chains (ii) molecular weights, (iii) band gap and HOMO and LUMO energy levels, and (iv) suited morphology.3-6 The aim of this study is to elucidate the impact that substitution exerts on the molecular and electronic structure of π-conjugated polymers with outstanding performances in organic electronic devices. Different configurations of the π-conjugated backbones are analyzed: (i) donor-acceptor configuration, (ii) 1D lineal or 2D branched conjugated backbones, and (iii) encapsulated polymers (see Figure 1). Our combined vibrational spectroscopy and DFT study shows that small changes in the substitution pattern and in the molecular configuration have a strong impact on the electronic characteristics of these polymers. We hope this study can advance useful structure-property relationships of conjugated polymers and guide the design of new materials for organic electronic applications.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Small-scale genetic structure of Cerastoderma glaucum in a lagoonal environment: potential significance of habitat discontinuity and unstable population dynamics

Environmental heterogeneity in coastal lagoons is expected to facilitate local adaptation in response to different ecological conditions, causing significant genetic structuring within lagoon populations at a small scale and also differentiation between lagoons. However, these patterns and processes of genetic structuring are still poorly understood. The aims of our study were (1) to seek genetic structure at a small scale in Cerastoderma glaucum inside the Mar Menor coastal lagoon using a mitochondrial DNA marker (COI) that has previously detected genetic differentiation inside the lagoon in other species and (2) to evaluate the influence of extreme environmental conditions and habitat discontinuity on its genetic composition. The results indicate high levels of haplotype diversity and low values of nucleotide diversity. COI data provide evidence of significant population differentiation among some localities within the lagoon. Limited gene flow and unstable population dynamics (i.e. fluctuations in population size caused by local extinction and recolonization), probably due to the high environmental heterogeneity, could generate the small-scale genetic divergence detected between populations within the lagoon.

Connectivity patterns inferred from the genetic structure of white seabream (Diplodus sargus L.)

Themarine environment seems, at first sight, to be a homogeneousmediumlacking barriers to species dispersal. Nevertheless, populations of marine species show varying levels of gene flow and population differentiation, so barriers to gene flow can often be detected. Weaimto elucidate the role of oceanographical factors ingenerating connectivity among populations shaping the phylogeographical patterns in the marine realm, which is not only a topic of considerable interest for understanding the evolution ofmarine biodiversity but also formanagement and conservation of marine life. For this proposal,we investigate the genetic structure and connectivity between continental and insular populations ofwhite seabreamin North East Atlantic (NEA) and Mediterranean Sea (MS) aswell as the influence of historical and contemporary factors in this scenario using mitochondrial (cytochrome b) and nuclear (a set of 9 microsatellite) molecular markers. Azores population appeared genetically differentiated in a single cluster using Structure analysis. This result was corroborated by Principal Component Analysis (PCA) and Monmonier algorithm which suggested a boundary to gene flow, isolating this locality. Azorean population also shows the highest significant values of FST and genetic distances for both molecular markers (microsatellites and mtDNA). We suggest that the breakdown of effective genetic exchange between Azores and the others' samples could be explained simultaneously by hydrographic (deep water) and hydrodynamic (isolating current regimes) factors acting as barriers to the free dispersal of white seabream(adults and larvae) and by historical factors which could be favoured for the survival of Azorean white seabream population at the last glaciation. Mediterranean islands show similar genetic diversity to the neighbouring continental samples and nonsignificant genetic differences. Proximity to continental coasts and the current system could promote an optimal larval dispersion among Mediterranean islands (Mallorca and Castellamare) and coasts with high gene flow.

GENETIC VARIATION, LOCAL ADAPTATION AND POPULATION STRUCTURE IN NORTH AMERICAN RED OAK SPECIES, QUERCUS RUBRA L. AND Q. ELLIPSOIDALIS E. J. HILL

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same time, populations at the species’ distribution edge, like those in this study, could possess important stores of genetic diversity and adaptive potential, while also being vulnerable to climatic or anthropogenic changes. A survey of the level and distribution of genetic variation and identification of potentially adaptive genes is needed since adaptive genetic variation is essential for their long-term survival. Oaks possess a remarkable characteristic in that they maintain their species identity and specific environmental adaptations despite their propensity to hybridize. Thus, in the face of interspecific gene flow, some areas of the genome remain differentiated due to selection. This characteristic allows the study of local environmental adaptation through genetic variation analyses. Furthermore, using genic markers with known putative functions makes it possible to link those differentiated markers to potential adaptive traits (e.g., flowering time, drought stress tolerance). Demographic processes like gene flow and genetic drift also play an important role in how genes (including adaptive genes) are maintained or spread. These processes are influenced by disturbances, both natural and anthropogenic. An examination of how genetic variation is geographically distributed can display how these genetic processes and geographical disturbances influence genetic variation patterns. For example, the spatial clustering of closely related trees could promote inbreeding with associated negative effects (inbreeding depression), if gene flow is limited. In turn this can have negative consequences for a species’ ability to adapt to changing environmental conditions. In contrast, interspecific hybridization may also allow the transfer of genes between species that increase their adaptive potential in a changing environment. I have studied the ecologically divergent, interfertile red oaks, Quercus rubra and Q. ellipsoidalis, to identify genes with potential roles in adaptation to abiotic stress through traits such as drought tolerance and flowering time, and to assess the level and distribution of genetic variation. I found evidence for moderate gene flow between the two species and low interspecific genetic differences at most genetic markers (Lind and Gailing 2013). However, the screening of genic markers with potential roles in phenology and drought tolerance led to the identification of a CONSTANS-like (COL) gene, a candidate gene for flowering time and growth. This marker, located in the coding region of the gene, was highly differentiated between the two species in multiple geographical areas, despite interspecific gene flow, and may play a role in reproductive isolation and adaptive divergence between the two species (Lind-Riehl et al. 2014). Since climate change could result in a northward migration of trees species like oaks, this gene could be important in maintaining species identity despite increased contact zones between species (e.g., increased gene flow). Finally I examined differences in spatial genetic structure (SGS) and genetic variation between species and populations subjected to different management strategies and natural disturbances. Diverse management activities combined with various natural disturbances as well as species specific life history traits influenced SGS patterns and inbreeding levels (Lind-Riehl and Gailing submitted).

Ecosystem structure in disturbed and restored subtropical seagrass meadows

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.