Timing of disturbance alters competitive outcomes and mechanisms of coexistence in an annual plant model

Ecological disturbance is inherently a multi-faceted phenomenon; disturbance events can differ in distinct quantifiable aspects, such as intensity, duration, spatial extent, and time since last disturbance. Though effects of disturbance timing (specifically, time within a season) have been investigated empirically, theoretical work is lacking, in part because effects of disturbance may depend on the timing relative to the life cycle of the species in question. To demonstrate a theoretical basis for the effects of timing, we develop a model of annual plants subject to soil disturbance. We show that timing of disturbance can have significant effects on community composition. In addition, we quantify the mechanisms of coexistence acting under different timing regimes and show that differences in timing lead to different coexistence mechanisms. Specifically, we find that early disturbance (which enhances germination from the seed bank) generates the storage effect, whereas coexistence under late disturbance (which reduces adult fecundity and contributions to the soil seed bank) depends more on relative nonlinearity of competition. We discuss these two distinct mechanisms within the context of the underlying ecological processes, and we also briefly consider the broader implications of our analyses for disturbance timing in real communities. Our findings extend ecological disturbance theory by linking timing to specific competitive outcomes and can be applied to a wide range of disturbance-prone communities. Because we identify the underlying mechanisms resulting from different disturbance timings, our results can potentially inform theory for conservation and invasive species management practice.     

Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids

Plasmids play an important role in shaping bacterial evolution and adaptation to heterogeneous environments. As modular genetic elements that are often conjugative, the selective pressures that act on plasmid-borne genes are distinct from those that act on the chromosome. Many bacteria are co-infected by multiple plasmids that impart niche-specific phenotypes. Thus, in addition to host–plasmid dynamics, interactions between co-infecting plasmids are likely to be important drivers of plasmid population dynamics, evolution and ecology. Agrobacterium tumefaciens is a facultative plant pathogen that commonly harbours two distinct megaplasmids. Virulence depends on the presence of the tumour-inducing (Ti) plasmid, with benefits that are primarily restricted to the disease environment. Here, we demonstrate that a second megaplasmid, the At plasmid, confers a competitive advantage in the rhizosphere. To assess the individual and interactive costs of these plasmids, we generated four isogenic derivatives: plasmidless, pAt only, pTi only and pAtpTi, and performed pairwise competitions under carbon-limiting conditions. These studies reveal a low cost to the virulence plasmid when outside of the disease environment, and a strikingly high cost to the At plasmid. In addition, the costs of pAt and pTi in the same host were significantly lower than predicted based on single plasmid costs, signifying the first demonstration of non-additivity between naturally occurring co-resident plasmids. Based on these empirically demonstrated costs and benefits, we developed a resource–consumer model to generate predictions about the frequencies of these genotypes in relevant environments, showing that non-additivity between co-residing plasmids allows for their stable coexistence across environments.     

Canalization breakdown and evolution in a source-sink system

Understanding the process of adaptation to novel environments may help to elucidate several ecological phenomena, from the stability of species range margins to host-pathogen specificity and persistence in degraded habitats. We study evolution in one type of novel environment: a sink habitat where populations cannot persist without recurrent immigration from a source population. Previous studies on source-sink evolution have focused on how extrinsic environmental factors influence adaptation to a sink, but few studies have examined how intrinsic genetic factors influence adaptation. We use an individual-based model to explore how genetic canalization that evolves in gene regulation networks influences the adaptation of a population to a sink. We find that as canalization in the regulation network increases, the probability of adaptation to the novel habitat decreases. When adaptation to the habitat does occur, it is usually preceded by a breakdown of canalization. As evolution continues in the novel habitat, canalization reemerges, but a legacy of the breakdown may remain, even after several generations. We also find that environmental noise tends to increase the probability of adaptation to the novel habitat. Our results suggest that the details of genetic architecture can significantly influence the likelihood of niche evolution in novel environments.     

Complex dynamics in a model microbial system

The forced double-Monod model (for a chemostat with a predator, a prey and periodically forced inflowing substrate) displays quasiperiodicity, phase locking, period doubling and chaotic dynamics. Stroboscopic sections reveal circle maps for the quasiperiodic regimes and noninvertible maps of the interval for the chaotic regimes. Criticality in the circle maps sets the stage for chaos in the model. This criticality may arise with an increase in the period or amplitude of forcing.     

Testing a simple stochastic model for the dynamics of waterfowl aggregations

We consider a simple stochastic model for the dynamics of mixed-species waterfowl aggregations and describe two methods for assessing the fit of this model to field data. The model does not incorporate species-specific behavior. It assumes that all birds act independently and incorrectly predicts an exponential distribution for inter-event times. We reject this model, show that 29% of the birds move in groups of two or more birds, and demonstrate that the distribution of inter-event times between the movements of groups of birds is exponential. We find no difference in movement rates or group sizes between seasons, and no difference between groups arriving into or departing from the observed aggregations. An analysis of group composition suggests that species at low abundance behave differently than species at high abundance: birds with few conspecifics are more likely to move in mixed-species groups than birds with many conspecifics. We suggest that simple stochastic models provide a useful way to explore the dynamics of animal behavior.     

Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system

The use of transposable elements (TEs) as genetic drive mechanisms was explored using Drosophila melanogaster as a model system. Alternative strategies, employing autonomous and nonautonomous P element constructs were compared for their efficiency in driving the ry⁺ allele into populations homozygous for a ry^- allele at the genomic rosy locus. Transformed flies were introduced at 1%, 5%, and 10% starting frequencies to establish a series of populations that were monitored over the course of 40 generations, using both phenotypic and molecular assays. The transposon-borne ry⁺ marker allele spread rapidly in almost all populations when introduced at 5% and 10% seed frequencies, but 1% introductions frequently failed to become established. A similar initial rapid increase in frequency of the ry⁺ transposon occurred in several control populations lacking a source of transposase. Constructs carrying ry⁺ markers also increased to moderate frequencies in the absence of selection on the marker. The results of Southern and in situ hybridization studies indicated a strong inverse relationship between the degree of conservation of construct integrity and transposition frequency. These finding have relevance to possible future applications of transposons as genetic drive mechanisms. This revised version was published online in July 2006 with corrections to the Cover Date.     

核桃-小麦复合系统中细根生长动态及竞争策略

以核桃(Juglans regia)-小麦(Triticum aestivum)间作复合系统为研究对象,用微根窗和根钻相结合的方法采样,研究复合系统中核桃和小麦细根年内年际的生长动态和竞争适应策略,为农林复合系统的经营管理和竞争模型的建立提供理论依据和技术支持。结果表明,间作核桃和小麦根系均在上半年有一个大的生长高峰(5月和4月),在下半年有一个小的生长高峰(9月和11月),二者的竞争主要发生在上半年的大生长高峰期。在各年份各土层,间作核桃的根长密度均低于单作核桃,且在从第7年开始存在显著差异。在0—20 cm土层间作小麦根长密度在第3—7年间获得迅速提高,从第7年开始显著高于单作小麦,但在20 cm以下土层则相反。间作使核桃和小麦细根生态位实现了分离,11年的观察期内间作核桃比单作核桃细根的垂直分布中心下移了6.59 cm,间作小麦比单作小麦的上移了8.59 cm。在根系竞争策略方面,小麦根系是通过短期内的快速生长,迅速占据土壤空间获得竞争优势;而核桃根系是通过根系的逐年积累,逐步占据土壤空间从而获得竞争优势。可以干扰核桃根系积累过程的"竞争-干扰-再平衡"农林复合经营管理策略可以让复合系统中核桃和小麦保持各自竞争优势的情况下实现共存。在根系形态方面,自身细根直径较小者小麦在剧烈竞争区域以增加细根直径减小比根长来适应竞争,而自身细根直径较大者核桃则相反。     

Testing a model for the dynamics of actin structures with biological parameter values

A simple mathematical model for the dynamics of network-bundle transitions in actin filaments has been previously proposed and some of its mathematical properties have been described. Other models in this class have since been considered and investigated mathematically. In this paper, we have made the first steps in connecting parameters in the model with biologically measurable quantities such as published values of rate constants for filament-crosslinker association. We describe how this connection was made, and give some preliminary numerical simulation results for the behavior of the model under biologically realistic parameter regimes. A key result is that filament length influences the bundle-network transition.     

Coexistence in a competitive parasitoid-host system

The main objective of this work is to determine the conditions for coexistence and competitive exclusion in a discrete model for a community of three species: a stage-structured host and two competing parasitoids sharing the same host developmental stage. Coexistence of the community of the species is found to depend on the host life history parameters in the first place, and on competitive ability and parasitoid efficiency in the second place. In particular, parasitoids equilibrium densities are defined by the size of the refuge. Extinction is expected with low growth rate and with low adult survival. Host life histories are also associated with oscillations in population density, and depending on the combination of host adult survival from one generation to the next and host growth rate, the minimum of fluctuations approaches zero, implying a higher potential risk of extinction because of stochastic factors. Our results suggest that equally reduced survival of parasitoids in hosts parasitized by both species determines extinction of the parasitoid with lower population density, in contrast to the case when both parasitoids benefit with 50% of all doubly parasitized hosts, leading to the hypothesis that a community where competitors in multiparasitized hosts die, easily becomes extinct. Competitive exclusion is expected for highly asymmetric competitive interactions, independent of population densities, allowing us to hypothesize that coexistence of competitors in systems with limited resources and refuges is associated with a clearly defined competitive hierarchy.     

Mutations which alter the kinetics of calcium transport alter the regulation of competence in Streptococcus pneumoniae.

In Streptococcus pneumoniae, Ca2+ induces a stress response which is regulated by a proteic activator known as competence factor (CF). This stress response is expressed as the induction of competence for DNA uptake and genetic transformation in exponentially growing cultures and by autolysis in late exponential phase. DNA transport during competence can be described as a homeostatic response that prevents autolysis of the cultures. Electrogenic and cooperative calcium transport with a Hill number (nH) of 2 appears to mediate this Ca2+ response. Mutant strains altered in their kinetics for Ca2+ transport, with nHs of 1 and 4, were isolated and characterized in order to address the role of the kinetics of Ca2+ transport in the Ca2+ response. The reduced cooperativity of Ca2+ uptake in mutant strain Cp2200 was associated with an absolute requirement for added CF to develop competence and with resistance to autolysis. The enhanced cooperativity of Ca2+ uptake in mutant strain Cp3300 was associated with facilitated competence and hypersensitivity to autolysis. Moreover, the mutation carried by strain Cp3300 increases the CF response of previously described competence-defective mutants. The pleiotropic mutants Cp2200 and Cp3300 allowed us to demonstrate that cooperativity of transport determines the Ca2+ response in S. pneumoniae.     

The dynamics of sperm cooperation in a competitive environment

Sperm cooperation has evolved in a variety of taxa and is often considered a response to sperm competition, yet the benefit of this form of collective movement remains unclear. Here, we use fine-scale imaging and a minimal mathematical model to study sperm aggregation in the rodent genus Peromyscus. We demonstrate that as the number of sperm cells in an aggregate increase, the group moves with more persistent linearity but without increasing speed. This benefit, however, is offset in larger aggregates as the geometry of the group forces sperm to swim against one another. The result is a non-monotonic relationship between aggregate size and average velocity with both a theoretically predicted and empirically observed optimum of six to seven sperm per aggregate. To understand the role of sexual selection in driving these sperm group dynamics, we compared two sister-species with divergent mating systems. We find that sperm of Peromyscus maniculatus (highly promiscuous), which have evolved under intense competition, form optimal-sized aggregates more often than sperm of Peromyscus polionotus (strictly monogamous), which lack competition. Our combined mathematical and experimental study of coordinated sperm movement reveals the importance of geometry, motion and group size on sperm velocity and suggests how these physical variables interact with evolutionary selective pressures to regulate cooperation in competitive environments.     

Mutations which alter splicing in the human hypoxanthine-guanine phosphoribosyltransferase gene.

A large proportion of mutations at the human hprt locus result in aberrant splicing of the hprt mRNA. We have been able to relate the mutation to the splicing abnormality in 30 of these mutants. Mutations at the splice acceptor sites of introns 4, 6 and 7 result in splicing out of the whole of the downstream exons, whereas in introns 1, 7 or 8 a cryptic site in the downstream exon can be used. Mutations in the donor site of introns 1 and 5 result in the utilisation of cryptic sites further downstream, whereas in the other introns, the upstream exons are spliced out. Our most unexpected findings were mutations in the middle of exons 3 and 8 which resulted in splicing out of these exons in part of the mRNA populations. Our results have enabled us to assess current models of mRNA splicing. They emphasize the importance of the polypyrimidine tract in splice acceptor sites, they support the role of the exon as the unit of assembly for splicing, and they are consistent with a model proposing a stem-loop structure for exon 8 in the hprt mRNA.     

Testing the Wiegand–Milton model: A long‐term experiment to understand mechanisms driving vegetation dynamics in arid shrublands

The Wiegand and Milton (1996) simulation model predicts that vegetation dynamics in arid shrublands are characterized by event‐driven stochasticity (weather events), and demographic inertia (persistence of a species in a community) that lead to a lagged response in vegetation compositional change. Slow plant growth is one of the mechanisms driving slow vegetation change. We test this model at the same location (Tierberg Long‐term Ecological Research site) on which the model was based. Three dwarf shrub species, differing in palatability, were tracked over 25 years (1988–2014) at two levels of the past herbivory (pre‐1960) and three levels of the present herbivory (post‐1988). In the period between 1960 and 1988, all sites were grazed at the recommended agricultural stocking rate. For each species, plant density and a number of size attributes (basal diameter, height, canopy area) were surveyed. Analyses using a two‐way Analysis of Covariance (ANCOVA) took initial starting size into consideration. As the model predicted, event‐driven stochasticity (rainfall) resulted in an increase in density of the smaller size classes following a single large recruitment event across all grazing regimes for the palatable and unpalatable species. Size‐class distribution curve types remained unchanged illustrating that population demography remains unaffected for long periods and responses are slow (lagged response). Slow plant growth was evident in that there were no changes in height, canopy area, or density under present grazing regimes over the 25‐year period. Palatable species had a reduced canopy area and density compared to unpalatable species. Our findings provide empirical evidence supporting the predictions of the Wiegand and Milton (1996) model, notably event‐driven stochasticity, demographic inertia, and a lagged response in vegetation change in arid shrublands. In addition, our results support the model assumption of the significance of slow growth in long‐lived plant species and the influence of grazing regime.     

DNA sequence motifs which direct adeno-associated virus site-specific integration in a model system

The DNA sequence motifs which direct adeno-associated virus type 2 site-specific integration are being investigated using a shuttle vector, propagated as a stable episome in cultured cell lines, as the target for integration. Previously, we reported that the minimum episomal targeting elements comprise a 16-bp binding motif (Rep binding site [RBS]) for a viral regulatory protein (Rep) separated by a short DNA spacer from a sequence (terminal resolution site [TRS]) that can serve as a substrate for Rep-mediated nicking activity (R. M. Linden, P. Ward, C. Giraud, E. Winocour, and K. I. Berns, Proc. Natl. Acad. Sci. USA 93:11288-11294, 1996; R. M. Linden, E. Winocour, and K. I. Berns, Proc. Natl. Acad. Sci. USA 93:7966-7972, 1996). We now report that episomal integration depends upon both the sequence and the position of the spacer DNA separating the RBS and TRS motifs. The spacer thus constitutes a third element required for site-specific episomal integration.     

Splice junction mutations in a yeast tRNA gene which alter the rate and precision of processing

We have introduced mutations into a tRNALeu3 gene which alter the intron boundaries and examined their effects on RNA splicing. Our results show that the 5'-proximal splice junction is not specified by the position of an adjacent base-paired stem present in all naturally occurring tRNA precursors. Also, efficient cleavage of 5'-splice junctions unique to these mutants, -CpU-, -UpA- and -UpG-, indicates the purine found at the 5'-side of this site in all natural precursors is dispensable. Some alterations of the sequence and structure at the 5'-proximal splice site reduce the rate of cleavage therein and result in accumulation of molecules composed of the 5'-half of the tRNA plus the intron. The precise position of the 5'-proximal cleavage site can vary +/- 1 base in these mutants. The 3'-proximal splice junction is rendered inactive by changing the prospective splice junction sequence from -ApC- to -CpC- and reducing the size of an unpaired loop at this site from six to two bases. Very small amounts of RNA composed of the 3'-half of the tRNA plus the intron accumulate from this precursor. We conclude that splice junction sequence and structure affect both the rate and precision of intervening sequence removal.     

Eye movement instabilities and nystagmus can be predicted by a nonlinear dynamics model of the saccadic system

The study of eye movements and oculomotor disorders has, for four decades, greatly benefitted from the application of control theoretic concepts. This paper is an example of a complementary approach based on the theory of nonlinear dynamical systems. Recently, a nonlinear dynamics model of the saccadic system was developed, comprising a symmetric piecewise-smooth system of six first-order autonomous ordinary differential equations. A preliminary numerical investigation of the model revealed that in addition to generating normal saccades, it could also simulate inaccurate saccades, and the oscillatory instability known as congenital nystagmus (CN). By varying the parameters of the model, several types of CN oscillations were produced, including jerk, bidirectional jerk and pendular nystagmus. The aim of this study was to investigate the bifurcations and attractors of the model, in order to obtain a classification of the simulated oculomotor behaviours. The application of standard stability analysis techniques, together with numerical work, revealed that the equations have a rich bifurcation structure. In addition to Hopf, homoclinic and saddlenode bifurcations organised by a Takens-Bogdanov point, the equations can undergo nonsmooth pitchfork bifurcations and nonsmooth gluing bifurcations. Evidence was also found for the existence of Hopf-initiated canards. The simulated jerk CN waveforms were found to correspond to a pair of post-canard symmetry-related limit cycles, which exist in regions of parameter space where the equations are a slow-fast system. The slow and fast phases of the simulated oscillations were attributed to the geometry of the corresponding slow manifold. The simulated bidirectional jerk and pendular waveforms were attributed to a symmetry invariant limit cycle produced by the gluing of the asymmetric cycles. In contrast to control models of the oculomotor system, the bifurcation analysis places clear restrictions on which kinds of behaviour are likely to be associated with each other in parameter space, enabling predictions to be made regarding the possible changes in the oscillation type that may be observed upon changing the model parameters. The analysis suggests that CN is one of a range of oculomotor disorders associated with a pathological saccadic braking signal, and that jerk and pendular nystagmus are the most probable oscillatory instabilities. Additionally, the transition from jerk CN to bidirectional jerk and pendular nystagmus observed experimentally when the gaze angle or attention level is changed is attributed to a gluing bifurcation. This suggests the possibility of manipulating the waveforms of subjects with jerk CN experimentally to produce waveforms with an extended foveation period, thereby improving visual resolution.