Complex patterns of global spread in invasive insects: eco-evolutionary and management consequences

The advent of simple and affordable tools for molecular identification of novel insect invaders and assessment of population diversity has changed the face of invasion biology in recent years. The widespread application of these tools has brought with it an emerging understanding that patterns in biogeography, introduction history and subsequent movement and spread of many invasive alien insects are far more complex than previously thought. We reviewed the literature and found that for a number of invasive insects, there is strong and growing evidence that multiple introductions, complex global movement, and population admixture in the invaded range are commonplace. Additionally, historical paradigms related to species and strain identities and origins of common invaders are in many cases being challenged. This has major consequences for our understanding of basic biology and ecology of invasive insects and impacts quarantine, management and biocontrol programs. In addition, we found that founder effects rarely limit fitness in invasive insects and may benefit populations (by purging harmful alleles or increasing additive genetic variance). Also, while phenotypic plasticity appears important post-establishment, genetic diversity in invasive insects is often higher than expected and increases over time via multiple introductions. Further, connectivity among disjunct regions of global invasive ranges is generally far higher than expected and is often asymmetric, with some populations contributing disproportionately to global spread. We argue that the role of connectivity in driving the ecology and evolution of introduced species with multiple invasive ranges has been historically underestimated and that such species are often best understood in a global context.

Phase diagram and complex patterns in the modeling of the bromate-oxalic acid-Ce-acetone oscillating reaction

Simulations have been carried out on the bromate - oxalic acid - Ce(IV) - acetone oscillating reaction, under flow conditions, using Field and Boyd's model (J. Phys. Chem. 1985, 89, 3707). Many different complex dynamic behaviors were found, including simple periodic oscillations, complex periodic oscillations, quasiperiodicity and chaos. Some of these complex oscillations can be understood as belonging to a Farey sequence. The many different behaviors were systematized in a phase diagram which shows that some regions of complex patterns were nested with one inside the other. The existence of almost all known dynamic behavior for this system allows the suggestion that it can be used as a model for some very complex phenomena that occur in biological systems.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

Abstract Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.

Geometric diagnostics of complex patterns: Spiral defect chaos

Motivated by the observation of spiral patterns in a wide range of physical, chemical, and biological systems, we present an automated approach that aims at characterizing quantitatively spiral-like elements in complex stripelike patterns. The approach provides the location of the spiral tip and the size of the spiral arms in terms of their arc length and their winding number. In addition, it yields the number of pattern components (Betti number of order 1), as well as their size and certain aspects of their shape. We apply the method to spiral defect chaos in thermally driven Rayleigh- Bénard convection and find that the arc length of spirals decreases monotonically with decreasing Prandtl number of the fluid and increasing heating. By contrast, the winding number of the spirals is nonmonotonic in the heating. The distribution function for the number of spirals is significantly narrower than a Poisson distribution. The distribution function for the winding number shows approximately an exponential decay. It depends only weakly on the heating, but strongly on the Prandtl number. Large spirals arise only for larger Prandtl numbers. In this regime the joint distribution for the spiral length and the winding number exhibits a three-peak structure, indicating the dominance of Archimedean spirals of opposite sign and relatively straight sections. For small Prandtl numbers the distribution function reveals a large number of small compact pattern components.

Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: Many losses of photosynthesis and complex patterns of rate variation

The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism.

Complex Patterns of Alternative Splicing Mediate the Spatial and Temporal Distribution of Perlecan/UNC-52 in Caenorhabditis elegans

The unc-52 gene encodes the nematode homologue of mammalian perlecan, the major heparan sulfate proteoglycan of the extracellular matrix. This is a large complex protein with regions similar to low-density lipoprotein receptors, laminin, and neural cell adhesion molecules (NCAMs). In this study, we extend our earlier work and demonstrate that a number of complex isoforms of this protein are expressed through alternative splicing. We identified three major classes of perlecan isoforms: a short form lacking the NCAM region and the C-terminal agrin-like region; a medium form containing the NCAM region, but still lacking the agrin-like region; and a newly identified long form that contains all five domains present in mammalian perlecan.  Using region-specific antibodies and unc-52 mutants, we reveal a complex spatial and temporal expression pattern for these UNC-52 isoforms. As well, using a series of mutations affecting different regions and thus different isoforms of UNC-52, we demonstrate that the medium NCAM-containing isoforms are sufficient for myofilament lattice assembly in developing nematode body-wall muscle. Neither short isoforms nor isoforms containing the C-terminal agrin-like region are essential for sarcomere assembly or muscle cell attachment, and their role in development remains unclear.

Hierarchical Logical Description and Neural Recognition of Complex Patterns

Authors suggested earlier hierarchical method for definition of class description at pattern recognition problems solution. In this paper development and use of such hierarchical descriptions for parallel representation of complex patterns on the base of multi-core computers or neural networks is proposed.

Sibling competition and parental control: Patterns of begging in parrots

Begging and food allocation patterns are the outcome of complex and repeated interactions between parents and young. In most systems studied, food allocation is regulated by begging and scramble competition. In contrast, little is understood about how nestling solicitation behaviours will evolve in systems where parents engage in complex patterns of food allocation. Parrots appear to be an excellent group in which to examine the shifting balance between sibling competition and parental control. Studies to date have shown that levels of sibling competition within parrot broods are low, possibly in response to parental control over food distribution. I assess what is known about the function of nestling begging in parrots and evaluate why begging signals appear to function differently in this group.

Dance movement patterns recognition

"Es tracta d'un projecte dividit en dues parts independents però complementàries, realitzades per autors diferents. Aquest document conté originàriament altre material i/o programari només consultable a la Biblioteca de Ciència i Tecnologia"

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

Patterns in and kinetics of phase separation in binary mixtures

This work focused mainly on two aspects of kinetics of phase separation in binary mixtures. In the first part, we studied the interplay of hydrodynamics and the phase separation of binary mixtures. A considerably flat container (a laterally extended geometry), at an aspect ratio of 14:1 (diameter: height) was chosen, so that any hydrodynamic instabilities, if they arise, could be tracked. Two binary mixtures were studied. One was a mixture of methanol and hexane, doped with 5% ethanol, which phase separated under cooling. The second was a mixture of butoxyethanol and water, doped with 2% decane, which phase separated under heating. The dopants were added to bring down the phase transition temperature around room temperature.rnrnAlthough much work has been done already on classical hydrodynamic instabilities, not much has been done in the understanding of the coupling between phase separation and hydrodynamic instabilities. This work aimed at understanding the influence of phase separation in initiating any hydrodynamic instability, and also vice versa. Another aim was to understand the influence of the applied temperature protocol on the emergence of patterns characteristic to hydrodynamic instabilities. rnrnOn slowly cooling the system continuously, at specific cooling rates, patterns were observed in the first mixture, at the start of phase separation. They resembled the patterns observed in classical Rayleigh-Bénard instability, which arises when a liquid continuously is heated from below. To suppress this classical convection, the cooling setup was tuned such that the lower side of the sample always remained cooler by a few millikelvins, relative to the top. We found that the nature of patterns changed with different cooling rates, with stable patterns appearing for a specific cooling rate (1K/h). On the basis of the cooling protocol, we estimated a modified Rayleigh number for our system. We found that the estimated modified Rayleigh number is near the critical value for instability, for cooling rates between 0.5K/h and 1K/h. This is consistent with our experimental findings. rnrnThe origin of the patterns, in spite of the lower side being relatively colder with respect to the top, points to two possible reasons. 1) During phase separation droplets of either phases are formed, which releases a latent heat. Our microcalorimetry measurements show that the rise in temperature during the first phase separation is in the order of 10-20millikelvins, which in some cases is enough to reverse the applied temperature bias. Thus phase separation in itself initiates a hydrodynamic instability. 2) The second reason comes from the cooling protocol itself. The sample was cooled from above and below. At sufficiently high cooling rates, there are situations where the interior of the sample is relatively hotter than both top and bottom of the sample. This is sufficient to create an instability within the cell. Our experiments at higher cooling rates (5K/h and above) show complex patterns, which hints that there is enough convection even before phase separation occurs. Infact, theoretical work done by Dr.Hayase show that patterns could arise in a system without latent heat, with symmetrical cooling from top and bottom. The simulations also show that the patterns do not span the entire height of the sample cell. This is again consistent with the cell sizes measured in our experiment.rnrnThe second mixture also showed patterns at specific heating rates, when it was continuously heated inducing phase separation. In this case though, the sample was turbid for a long time until patterns appeared. A meniscus was most probably formed before the patterns emerged. We attribute the reason of patterns in this case to Marangoni convection, which is present in systems with an interface, where local differences in surface tension give rise to an instability. Our estimates for the Rayleigh number also show a significantly lower number than that's required for RB-type instability.rnrnIn the first part of the work, therefore, we identify two different kinds of hydrodynamic instabilities in two different mixtures. Both are observed during, or after the first phase separation. Our patterns compare with the classical convection patterns, but here the origins are from phase separation and the cooling protocol.rnrnIn the second part of the work, we focused on the kinetics of phase separation in a polymer solution (polystyrene and methylcyclohexane), which is cooled continuously far down into the two phase region. Oscillations in turbidity, denoting material exchange between the phases are seen. Three processes contribute to the phase separation: Nucleation of droplets, their growth and coalescence, and their subsequent sedimentation. Experiments in low molecular binary mixtures had led to models of oscillation [43] which considered sedimentation time scales much faster than the time scales of nucleation and growth. The size and shape of the sample therefore did not matter in such situations. The oscillations in turbidity were volume-dominated. The present work aimed at understanding the influence of sedimentation time scales for polymer mixtures. Three heights of the sample with same composition were studied side by side. We found that periods increased with the sample height, thus showing that sedimentation time determines the period of oscillations in the polymer solutions. We experimented with different cooling rates and different compositions of the mixture, and we found that periods are still determined by the sample height, and therefore by sedimentation time. rnrnWe also see that turbidity emerges in two ways; either from the interface, or throughout the sample. We suggest that oscillations starting from the interface are due to satellite droplets that are formed on droplet coalescence at the interface. These satellite droplets are then advected to the top of the sample, and they grow, coalesce and sediment. This type of an oscillation wouldn't require the system to pass the energy barrier required for homogenous nucleation throughout the sample. This mechanism would work best in sample where the droplets could be effectively advected throughout the sample. In our experiments, we see more interface dominated oscillations in the smaller cells and lower cooling rates, where droplet advection is favourable. In larger samples and higher cooling rates, we mostly see that the whole sample becomes turbid homogenously, which requires the system to pass the energy barrier for homogenous nucleation.rnrnOscillations, in principle, occur since the system needs to pass an energy barrier for nucleation. The height of the barrier decreases with increasing supersaturation, which in turn is from the temperature ramp applied. This gives rise to a period where the system is clear, in between the turbid periods. At certain specific cooling rates, the system can follow a path such that the start of a turbid period coincides with the vanishing of the last turbid period, thus eliminating the clear periods. This means suppressions of oscillations altogether. In fact we experimentally present a case where, at a certain cooling rate, oscillations indeed vanish. rnrnThus we find through this work that the kinetics of phase separation in polymer solution is different from that of a low molecular system; sedimentation time scales become relevant, and therefore so does the shape and size of the sample. The role of interface in initiating turbid periods also become much more prominent in this system compared to that in low molecular mixtures.rnrnIn summary, some fundamental properties in the kinetics of phase separation in binary mixtures were studied. While the first part of the work described the close interplay of the first phase separation with hydrodynamic instabilities, the second part investigated the nature and determining factors of oscillations, when the system was cooled deep into the two phase region. Both cases show how the geometry of the cell can affect the kinetics of phase separation. This study leads to further fundamental understandings of the factors contributing to the kinetics of phase separation, and to the understandings of what can be controlled and tuned in practical cases. rn

HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns

The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv.techfak.uni-bielefeld.de/HyPa/.

From detection of complex motion to descriptions of moving surfaces in human vision

A preliminary study by Freeman et al (1996b) has suggested that when complex patterns of motion elicit impressions of 2-dimensionality, odd-item-out detection improves given targets can be differentiated on the basis of surface properties. Their results can be accounted for, it if is supposed that observers are permitted efficient access to 3-D surface descriptions but access to 2-D motion descriptions is restricted. To test the hypothesis, a standard search technique was employed, in which targets could be discussed on the basis of slant sign. In one experiment, slant impressions were induced through the summing of deformation and translation components. In a second theory were induced through the summing of shear and translation components. Neither showed any evidence of efficient access. A third experiment explored the possibility that access to these representations may have been hindered by a lack of grouping between the stimuli. Attempts to improve grouping failed to produce convincing evidence in support of life. An alternative explanation is that complex patterns of motion are simply not processed simultaneously. Psychophysical and physiological studies have, however, suggested that multiple mechanisms selective for complex motion do exist. Using a subthreshold summation technique I found evidence supporting the notion that complex motions are processed in parallel. Furthermore, in a spatial summation experiment, coherence thresholds were measured for displays containing different numbers of complex motion patches. Consistent with the idea that complex motion processing proceeds in parallel, increases in the number of motion patches were seen to decrease thresholds, both for expansion and rotation. Moreover, the rates of decrease were higher than those typically expected from probability summation, thus implying mechanisms are available, which can pool signals from spatially distinct complex motion flows.

The Roles of Phenotypic Plasticity and Plant-Microbe Interactions in the Evolution of Complex Traits in Boechera stricta

All organisms live in complex habitats that shape the course of their evolution by altering the phenotype expressed by a given genotype (a phenomenon known as phenotypic plasticity) and simultaneously by determining the evolutionary fitness of that phenotype. In some cases, phenotypic evolution may alter the environment experienced by future generations. This dissertation describes how genetic and environmental variation act synergistically to affect the evolution of glucosinolate defensive chemistry and flowering time in Boechera stricta, a wild perennial herb. I focus particularly on plant-associated microbes as a part of the plant’s environment that may alter trait evolution and in turn be affected by the evolution of those traits. In the first chapter I measure glucosinolate production and reproductive fitness of over 1,500 plants grown in common gardens in four diverse natural habitats, to describe how patterns of plasticity and natural selection intersect and may influence glucosinolate evolution. I detected extensive genetic variation for glucosinolate plasticity and determined that plasticity may aid colonization of new habitats by moving phenotypes in the same direction as natural selection. In the second chapter I conduct a greenhouse experiment to test whether naturally-occurring soil microbial communities contributed to the differences in phenotype and selection that I observed in the field experiment. I found that soil microbes cause plasticity of flowering time but not glucosinolate production, and that they may contribute to natural selection on both traits; thus, non-pathogenic plant-associated microbes are an environmental feature that could shape plant evolution. In the third chapter, I combine a multi-year, multi-habitat field experiment with high-throughput amplicon sequencing to determine whether B. stricta-associated microbial communities are shaped by plant genetic variation. I found that plant genotype predicts the diversity and composition of leaf-dwelling bacterial communities, but not root-associated bacterial communities. Furthermore, patterns of host genetic control over associated bacteria were largely site-dependent, indicating an important role for genotype-by-environment interactions in microbiome assembly. Together, my results suggest that soil microbes influence the evolution of plant functional traits and, because they are sensitive to plant genetic variation, this trait evolution may alter the microbial neighborhood of future B. stricta generations. Complex patterns of plasticity, selection, and symbiosis in natural habitats may impact the evolution of glucosinolate profiles in Boechera stricta.