A Simple Attack on Some Clock-Controlled Generators

We present a new approach to edit distance attacks on certain clock-controlled generators, which applies basic concepts of Graph Theory to simplify the search trees of the original attacks in such a way that only the most promising branches are analyzed. In particular, the proposed improvement is based on cut sets defined on some graphs so that certain shortest paths provide the edit distances. The strongest aspects of the proposal are that the obtained results from the attack are absolutely deterministic, and that many inconsistent initial states of the target registers are recognized beforehand and avoided during search

Alternatives to Robinson and Redford's method of assessing overharvest from incomplete demographic data

Conservation biologists often must make decisions about the sustainability of harvest rates based on minimal demographic information. To assist them Robinson anti Redford (1991) formulated a method to estimate maximum rates of production which could be used to detect overharvesting based on only age at first reproduction, fecundity, and maximum longevity. By assuming constant adult survival we reduced the Euler equation to a simple form that allows calculation of population growth from the same minimal demographic data, brit that can incorporate empirical prereproductive and adult survival rates if available. With this formula, we computed growth rates rising various explicit survival schedules, and we compared these rates and those from Robinson and Redford's (1991) method to rates calculated from 19 relatively complete mammalian life tables gleaned from the literature. When we applied our method (assuming 1% survival to maximum longevity) and that of Robinson and Redford (1991) to the same minimal demographic data, we found that our growth rates were closer to those from complete life tables. We therefore reexamined the data of Fa et al (1995) and Fitzgibbon et al. (1995), who analyzed overharvesting of several populations of commercially exploited African mammals based on Robinson and Redford's (1991) methods Our reanalysis indicates that several additional populations may be overharvested. Our analysis also suggests that data on survival to age at first reproduction improves estimates of population growth rates more than data on age-specific adult survival. Regardless of the method, approximate growth rates based on incomplete life tables can be used to detect when populations are overharvested, brit one should not conclude that harvest rates are sustainable when they are less than approximate production rates because simplifying assumptions often lend to overestimates

Complex population dynamics as a competition between multiple time-scale phenomena

The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The mean-field level of description allows to highlight the delicate interplay between the different time-scale processes in the resulting complex dynamics of the system. We clarify the influence of the amplitude and period of the environmental changes on the critical value of the selection pressure corresponding to a phase-transition "extinct-alive" of the population. However, the intrinsic stochasticity and the dynamically-built in correlations among the individuals, as well as the role of the mutation-induced variety in population's evolution are not appropriately accounted for. A more refined level of description, which is an individual-based one, has to be considered. The inherent fluctuations do not destroy the phase transition "extinct-alive", and the mutation amplitude is strongly influencing the value of the critical selection pressure. The phase diagram in the plane of the population's parameters -- selection and mutation is discussed as a function of the environmental variation characteristics. The differences between a smooth variation of the environment and an abrupt, catastrophic change are also addressesd.Comment: 15 pages, 12 figures. Accepted for publication in Phys. Rev.

Natural history of Arabidopsis thaliana and oomycete symbioses

Molecular ecology of plant–microbe interactions has immediate significance for filling a gap in knowledge between the laboratory discipline of molecular biology and the largely theoretical discipline of evolutionary ecology. Somewhere in between lies conservation biology, aimed at protection of habitats and the diversity of species housed within them. A seemingly insignificant wildflower called Arabidopsis thaliana has an important contribution to make in this endeavour. It has already transformed botanical research with deepening understanding of molecular processes within the species and across the Plant Kingdom; and has begun to revolutionize plant breeding by providing an invaluable catalogue of gene sequences that can be used to design the most precise molecular markers attainable for marker-assisted selection of valued traits. This review describes how A. thaliana and two of its natural biotrophic parasites could be seminal as a model for exploring the biogeography and molecular ecology of plant–microbe interactions, and specifically, for testing hypotheses proposed from the geographic mosaic theory of co-evolution

Towards an Integrated Framework for Assessing the Vulnerability of Species to Climate Change

Climate change is a major threat to global biodiversity. A novel integrated framework to assess vulnerability and prioritize research and management action aims to improve our ability to respond to this emerging crisis

Spatial Geographic Mosaic in an Aquatic Predator-Prey Network

The geographic mosaic theory of coevolution predicts 1) spatial variation in predatory structures as well as prey defensive traits, and 2) trait matching in some areas and trait mismatching in others mediated by gene flow. We examined gene flow and documented spatial variation in crushing resistance in the freshwater snails Mexipyrgus churinceanus, Mexithauma quadripaludium, Nymphophilus minckleyi, and its relationship to the relative frequency of the crushing morphotype in the trophically polymorphic fish Herichthys minckleyi. Crushing resistance and the frequency of the crushing morphotype did show spatial variation among 11 naturally replicated communities in the Cuatro Ciénegas valley in Mexico where these species are all endemic. The variation in crushing resistance among populations was not explained by geographic proximity or by genetic similarity in any species. We detected clear phylogeographic patterns and limited gene flow for the snails but not for the fish. Gene flow among snail populations in Cuatro Ciénegas could explain the mosaic of local divergence in shell strength and be preventing the fixation of the crushing morphotype in Herichthys minckleyi. Finally, consistent with trait matching across the mosaic, the frequency of the fish morphotype was negatively correlated with shell crushing resistance likely reflecting the relative disadvantage of the crushing morphotype in communities where the snails exhibit relatively high crushing resistance

Adaptive Evolution in Ecological Communities

Multi-species interactions can influence evolution in ways that are unpredictable from studies that focus on simpler communities because direct and indirect species interactions alter the strength and direction of selection

Smaller Gene Networks Permit Longer Persistence in Fast-Changing Environments

The environments in which organisms live and reproduce are rarely static, and as the environment changes, populations must evolve so that phenotypes match the challenges presented. The quantitative traits that map to environmental variables are underlain by hundreds or thousands of interacting genes whose allele frequencies and epistatic relationships must change appropriately for adaptation to occur. Extending an earlier model in which individuals possess an ecologically-critical trait encoded by gene networks of 16 to 256 genes and random or scale-free topology, I test the hypothesis that smaller, scale-free networks permit longer persistence times in a constantly-changing environment. Genetic architecture interacting with the rate of environmental change accounts for 78% of the variance in trait heritability and 66% of the variance in population persistence times. When the rate of environmental change is high, the relationship between network size and heritability is apparent, with smaller and scale-free networks conferring a distinct advantage for persistence time. However, when the rate of environmental change is very slow, the relationship between network size and heritability disappears and populations persist the duration of the simulations, without regard to genetic architecture. These results provide a link between genes and population dynamics that may be tested as the -omics and bioinformatics fields mature, and as we are able to determine the genetic basis of ecologically-relevant quantitative traits

Evolution of Competitive Ability: An Adaptation Speed vs. Accuracy Tradeoff Rooted in Gene Network Size

Ecologists have increasingly come to understand that evolutionary change on short time-scales can alter ecological dynamics (and vice-versa), and this idea is being incorporated into community ecology research programs. Previous research has suggested that the size and topology of the gene network underlying a quantitative trait should constrain or facilitate adaptation and thereby alter population dynamics. Here, I consider a scenario in which two species with different genetic architectures compete and evolve in fluctuating environments. An important trade-off emerges between adaptive accuracy and adaptive speed, driven by the size of the gene network underlying the ecologically-critical trait and the rate of environmental change. Smaller, scale-free networks confer a competitive advantage in rapidly-changing environments, but larger networks permit increased adaptive accuracy when environmental change is sufficiently slow to allow a species time to adapt. As the differences in network characteristics increase, the time-to-resolution of competition decreases. These results augment and refine previous conclusions about the ecological implications of the genetic architecture of quantitative traits, emphasizing a role of adaptive accuracy. Along with previous work, in particular that considering the role of gene network connectivity, these results provide a set of expectations for what we may observe as the field of ecological genomics develops

An Indirect Cue of Predation Risk Counteracts Female Preference for Conspecifics in a Naturally Hybridizing Fish Xiphophorus birchmanni

Mate choice is context dependent, but the importance of current context to interspecific mating and hybridization is largely unexplored. An important influence on mate choice is predation risk. We investigated how variation in an indirect cue of predation risk, distance to shelter, influences mate choice in the swordtail Xiphophorus birchmanni, a species which sometimes hybridizes with X. malinche in the wild. We conducted mate choice experiments to determine whether females attend to the distance to shelter and whether this cue of predation risk can counteract female preference for conspecifics. Females were sensitive to shelter distance independent of male presence. When conspecific and heterospecific X. malinche males were in equally risky habitats (i.e., equally distant from shelter), females associated primarily with conspecifics, suggesting an innate preference for conspecifics. However, when heterospecific males were in less risky habitat (i.e., closer to shelter) than conspecific males, females no longer exhibited a preference, suggesting that females calibrate their mate choices in response to predation risk. Our findings illustrate the potential for hybridization to arise, not necessarily through reproductive “mistakes”, but as one of many potential outcomes of a context-dependent mate choice strategy