An algorithm for associating the features of two images.

In this paper we describe an algorithm that operates on the distances between features in the two related images and delivers a set of correspondences between them. The algorithm maximizes the inner product of two matrices, one of which is the desired 'pairing matrix' and the other a 'proximity matrix' with elements exp (-rij2/2 sigma 2), where rij is the distance between two features, one in each image, and sigma is an adjustable scale parameter. The output of the algorithm may be compared with the movements that people perceive when viewing two images in quick succession, and it is found that an increase in sigma affects the computed correspondences in much the same way as an increase in interstimulus interval alters the perceived displacements. Provided that sigma is not too small the algorithm will recover the feature mappings that result from image translation, expansion or shear deformation--transformations of common occurrence in image sequences--even when the displacements of individual features depart slightly from the general trend.     

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics,but Suppressors of Selection for Death-Birth Dynamics

We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.     

Multi-gene gateway clone design for expression of multiple heterologous genes in living cells: modular construction of multiple cDNA expression elements using recombinant cloning

Much attention has been focused on manipulating multiple genes in living cells for analyzing protein function. In order to perform high-throughput generation of multi-gene expression clones, gateway cloning technology (which represents a high-throughput DNA transfer from vector to vector) can be anticipated. In the conventional strategy for gateway cloning, the construction of two or more expression elements into tandem elements on a single plasmid requires the recombination of multiple entry clones with a destination vector in a single reaction mixture. Use of increasing numbers of entry clones in a single reaction is inefficient due to the difficulty in successfully recognizing multiple pairs of matched att signals simultaneously. To address this problem, a "Modular Destination" vector has been devised and constructed, whereby cDNA inserts are sequentially introduced, resulting in a tandem structure with multiple inserts. Whereas the standard destination vector contains only Cm(R) and ccdB genes flanked by two attR signals, this destination vector contains, in addition, one or two cDNA expression elements. Here, we show the rapid construction of expression vectors containing three or four tandemly arrayed cDNA expression elements and their expression in mammalian cells.     

The offspring-development-time/offspring-number trade-off

The metabolic theory of ecology (MTE) states that metabolic rate, ruled mainly by individual mass and temperature, determines many other biological rates. This view of ecology as ruled by the laws of physics and thermodynamics contrasts with life-history-optimization (LHO) theories, where traits are shaped by evolutionary processes. Integrating the MTE and LHO can lead, however, to a synthetic theory of ecology. In this work, we link the two theories to show that offspring development time is the result of both maternal investment in offspring and the metabolic constraints on offspring growth. We formulate a model that captures how offspring development time is the consequence of both offspring growth rate, determined by temperature and allometric scaling in accordance with the MTE, and the size reached by offspring at the end of the developmental period, determined mainly by LHO and reproductive strategies. We first extend the trade-off between offspring size and offspring number to ectotherms, showing that increased body temperatures result in increased resources available for reproduction. We then combine this trade-off with the general ontogenetic growth model to show that there is a trade-off between the number of offspring produced and offspring development time. The model predicts a shorter developmental time in organisms producing larger numbers of offspring.     

Optimal rates of dispersal II. Diploid populations

The problem of how an individual should divide its progeny into dispersed and non-dispersed descendants is investigated for a number of haploid models. In each model, a unique optimal ratio of dispersed to non-dispersed has been found, where the type with this optimal strategy has a selective advantage over all other types. Although the survival ability of a dispersed offspring is reduced (compared to that of a non-dispersed offspring), the optimal strategy implies that a substantial part of the progeny will be dispersed.     

Optimal rates of dispersal I. Haploid populations

The problem of how an individual should divide its progeny into dispersed and non-dispersed descendants is investigated for a number of haploid models. In each model, a unique optimal ratio of dispersed to non-dispersed has been found, where the type with this optimal strategy has a selective advantage over all other types. Although the survival ability of a dispersed offspring is reduced (compared to that of a non-dispersed offspring), the optimal strategy implies that a substantial part of the progeny will be dispersed.     

Mathematical identification of critical reactions in the interlocked feedback model

Dynamic simulations are necessary for understanding the mechanism of how biochemical networks generate robust properties to environmental stresses or genetic changes. Sensitivity analysis allows the linking of robustness to network structure. However, it yields only local properties regarding a particular choice of plausible parameter values, because it is hard to know the exact parameter values in vivo. Global and firm results are needed that do not depend on particular parameter values. We propose mathematical analysis for robustness (MAR) that consists of the novel evolutionary search that explores all possible solution vectors of kinetic parameters satisfying the target dynamics and robustness analysis. New criteria, parameter spectrum width and the variability of solution vectors for parameters, are introduced to determine whether the search is exhaustive. In robustness analysis, in addition to single parameter sensitivity analysis, robustness to multiple parameter perturbation is defined. Combining the sensitivity analysis and the robustness analysis to multiple parameter perturbation enables identifying critical reactions. Use of MAR clearly identified the critical reactions responsible for determining the circadian cycle in the Drosophila interlocked circadian clock model. In highly robust models, while the parameter vectors are greatly varied, the critical reactions with a high sensitivity are uniquely determined. Interestingly, not only the per-tim loop but also the dclk-cyc loop strongly affect the period of PER, although the dclk-cyc loop hardly changes its amplitude and it is not potentially influential. In conclusion, MAR is a powerful method to explore wide parameter space without human-biases and to link a robust property to network architectures without knowing the exact parameter values. MAR identifies the reactions critically responsible for determining the period and amplitude in the interlocked feedback model and suggests that the circadian clock intensively evolves or designs the kinetic parameters so that it creates a highly robust cycle.     

Cooperation and Stability through Periodic Impulses

Basic games, where each individual chooses between two strategies, illustrate several issues that immediately emerge from the standard approach that applies strategic reasoning, based on rational decisions, to predict population behavior where no rationality is assumed. These include how mutual cooperation (which corresponds to the best outcome from the population perspective) can evolve when the only individually rational choice is to defect, illustrated by the Prisoner''s Dilemma (PD) game, and how individuals can randomize between two strategies when neither is individually rational, illustrated by the Battle of the Sexes (BS) game that models male-female conflict over parental investment in offspring. We examine these questions from an evolutionary perspective where the evolutionary dynamics includes an impulsive effect that models sudden changes in collective population behavior. For the PD game, we show analytically that cooperation can either coexist with defection or completely take over the population, depending on the strength of the impulse. By extending these results for the PD game, we also show that males and females each evolve to a single strategy in the BS game when the impulsive effect is strong and that weak impulses stabilize the randomized strategies of this game.     

Tests and model selection for the general growth curve model

The model considered here is a generalized multivariate analysis of variance model useful especially for many types of growth curve problems including biological growth and technology substitution. It is defined as Yp x N = Xp x m tau m x r Ar x N + epsilon p x N, where tau is unknown, and X and A are known design matrices of ranks m less than p and r less than N, respectively. Furthermore, the columns of epsilon are independent p-variate normal with mean vector 0 and common covariance matrix sigma. In general, p is the number of time (or spatial) points observed on each of the N cases, (m - 1) is the degree of polynomial in time, and r is the number of groups. The main focus of this paper is the selection of models for the general growth curve model with regard to the covariance matrix sigma. Likelihood ratio tests and selection procedures based on sample reuse and predictions are proposed. Special emphasis is on the serial covariance structure for sigma, which has been shown to be quite important in the prediction of biological data and technology substitution data. One-population and K-population problems are considered. Some of the results are illustrated with two sets of biological data.     

Interspecific Interactions and the Scope for Parent-Offspring Conflict: High Mite Density Temporarily Changes the Trade-Off between Offspring Size and Number in the Burying Beetle,Nicrophorus vespilloides

Parents have a limited amount of resources to invest in reproduction and commonly trade-off how much they invest in offspring size (or quality) versus brood size. A negative relationship between offspring size and number has been shown in numerous taxa and it underpins evolutionary conflicts of interest between parents and their young. For example, previous work on vertebrates shows that selection favours mothers that produce more offspring, at the expense of individual offspring size, yet favours offspring that have relatively few siblings and therefore attain a greater size at independence. Here we analyse how this trade-off is temporarily affected by stochastic variation in the intensity of interspecific interactions. We examined the effect of the mite Poecilochirus carabi on the relationship between offspring size and number in the burying beetle, Nicrophorus vespilloides. We manipulated the initial number of mites in the reproductive event (by introducing either no mites, 4 mites, 10 mites, or 16 mites), and assessed the effect on the brood. We found a similar trade-off between offspring size and number in all treatments, except in the ''16 mite'' treatment where the correlation between offspring number and size flattened considerably. This effect arose because larvae in small broods failed to attain a high mass by dispersal. Our results show that variation in the intensity of interspecific interactions can temporarily change the strength of the trade-off between offspring size and number. In this study, high densities of mites prevented individual offspring from attaining their optimal weight, thus potentially temporarily biasing the outcome of parent-offspring conflict in favour of parents.     

Prospecting and informed dispersal: Understanding and predicting their joint eco‐evolutionary dynamics

The ability of individuals to leave a current breeding area and select a future one is important, because such decisions can have multiple consequences for individual fitness, but also for metapopulation dynamics, structure, and long‐term persistence through non‐random dispersal patterns. In the wild, many colonial and territorial animal species display informed dispersal strategies, where individuals use information, such as conspecific breeding success gathered during prospecting, to decide whether and where to disperse. Understanding informed dispersal strategies is essential for relating individual behavior to subsequent movements and then determining how emigration and settlement decisions affect individual fitness and demography. Although numerous theoretical studies have explored the eco‐evolutionary dynamics of dispersal, very few have integrated prospecting and public information use in both emigration and settlement phases. Here, we develop an individual‐based model that fills this gap and use it to explore the eco‐evolutionary dynamics of informed dispersal. In a first experiment, in which only prospecting evolves, we demonstrate that selection always favors informed dispersal based on a low number of prospected patches relative to random dispersal or fully informed dispersal, except when individuals fail to discriminate better patches from worse ones. In a second experiment, which allows the concomitant evolution of both emigration probability and prospecting, we show the same prospecting strategy evolving. However, a plastic emigration strategy evolves, where individuals that breed successfully are always philopatric, while failed breeders are more likely to emigrate, especially when conspecific breeding success is low. Embedding information use and prospecting behavior in eco‐evolutionary models will provide new fundamental understanding of informed dispersal and its consequences for spatial population dynamics.     

Multiple shRNA expressions in a single plasmid vector improve RNAi against the XPA gene

To improve the efficiency of stable knockdown with short hairpin RNA (shRNA), we inserted multiple shRNA expression sequences into a single plasmid vector. In this study, the DNA repair factor XPA was selected as a target gene since it is not essential for cell viability and it is easy to check the functional knockdown of this gene. The efficiency of knockdown was compared among single and triple expression vectors. The single shRNA-expressing vector caused limited knockdown of the target protein in stable transfectants, however, the multiple expression vectors apparently increased the frequency of knockdown transfectants. There were correlations between the knockdown level and marker expression in multiple-expressing transfectants, whereas poorer correlations were observed in single vector transfectants. Multiple-transfectants exhibited reduced efficiency of repair of UV-induced DNA damage and an increased sensitivity to ultraviolet light-irradiation. We propose that multiple shRNA expression vectors might be a useful strategy for establishing knockdown cells.     

Development and optimization of herpes simplex virus vectors for multiple long-term gene delivery to the peripheral nervous system

Herpes simplex virus (HSV) has often been suggested as a suitable vector for gene delivery to the peripheral nervous system as it naturally infects sensory nerve terminals before retrograde transport to the cell body in the spinal ganglia where latency is established. HSV vectors might therefore be particularly appropriate for the study and treatment of chronic pain following vector administration by relatively noninvasive peripheral routes. However parameters allowing safe and efficient gene delivery to spinal ganglia following peripheral vector inoculation, or the long-term expression of delivered genes, have not been comprehensively studied. We have identified combinations of deletions from the HSV genome which allow highly efficient gene delivery to spinal dorsal root ganglia (DRGs) following either footpad or sciatic nerve injection. These vectors have ICP34.5 deleted and have inactivating mutations in vmw65. We also report that peripheral replication is probably necessary for the efficient establishment of latency in vivo, as fully replication-incompetent HSV vectors allow efficient gene expression in DRGs only after peripheral inoculation at a high virus dose. Very low transduction efficiencies are otherwise achieved. In parallel, promoters have been developed that allow the long-term expression of individual or pairs of genes in DRGs by using elements from the latently active region of the virus to confer a long-term activity onto a number of promoters which otherwise function only in the short term. This work further defines elements and mechanisms within the latently active region that are necessary for long-term gene expression and for the first time allows multiple inserted genes to be expressed from HSV vectors during latency.     

A demographic model for sex ratio evolution and the effects of sex‐biased offspring costs

The evolution of the primary sex ratio, the proportion of male births in an individual's offspring production strategy, is a frequency‐dependent process that selects against the more common sex. Because reproduction is shaped by the entire life cycle, sex ratio theory would benefit from explicitly two‐sex models that include some form of life cycle structure. We present a demographic approach to sex ratio evolution that combines adaptive dynamics with nonlinear matrix population models. We also determine the evolutionary and convergence stability of singular strategies using matrix calculus. These methods allow the incorporation of any population structure, including multiple sexes and stages, into evolutionary projections. Using this framework, we compare how four different interpretations of sex‐biased offspring costs affect sex ratio evolution. We find that demographic differences affect evolutionary outcomes and that, contrary to prior belief, sex‐biased mortality after parental investment can bias the primary sex ratio (but not the corresponding reproductive value ratio). These results differ qualitatively from the widely held conclusions of previous models that neglect demographic structure.     

Parentage assignment reveals multiple paternity in the critically-endangered Guatemalan beaded lizard (Heloderma charlesbogerti)

Within captive management programs for species of conservation concern, understanding the genetic mating system is of fundamental importance, given its role in generating and maintaining genetic diversity and promoting opportunities for sperm competition. If a goal of a conservation program is reintroduction, knowledge of the mating system may also inform prediction models aimed at understanding how genetic diversity may be spatially organized, thus informing decisions regarding where and which individuals should be released to maximize genetic diversity in the wild population. Within captive populations, such information may also influence how animals are maintained in order to promote natural behaviors. Here we investigate the genetic mating system of the Guatemalan beaded lizard, Heloderma charlesbogerti, a member of an entire clade lacking such information. A group of adult male and female H. charlesbogerti co-habited a large outdoor enclosure for five years during the species’ perceived breeding season. Through genomic parentage analysis, 50% of clutches comprising multiple offspring were found to result from multiple paternity, with up to three males siring offspring within single clutches. Both males and females were observed to produce offspring with multiple partners within a given year. As such, within this captive environment, where opportunities existed for mating with multiple partners, the genetic mating system was found to be highly polygamous, with multiple paternity common within clutches. These findings are novel for the family Helodermatidae, and the results have broader implications about how reproductive opportunities should be managed within captive conservation programs.

     

An Infinitely Expandable Cloning Strategy plus Repeat-Proof PCR for Working with Multiple shRNA

Vector construction with restriction enzymes (REs) typically involves the ligation of a digested donor fragment (insert) to a reciprocally digested recipient fragment (vector backbone). Creating a suitable cloning plan becomes increasingly difficult for complex strategies requiring repeated insertions such as constructing multiple short hairpin RNA (shRNA) expression vectors for RNA interference (RNAi) studies. The problem lies in the reduced availability of suitable RE recognition sites with an increasing number of cloning events and or vector size. This report details a technically simple, directional cloning solution using REs with compatible cohesive ends that are repeatedly destroyed and simultaneously re-introduced with each round of cloning. Donor fragments can be made by PCR or sub-cloned from pre-existing vectors and inserted ad infinitum in any combination. The design incorporates several cloning cores in order to be compatible with as many donor sequences as possible. We show that joining sub-combinations made in parallel is more time-efficient than sequential construction (of one cassette at a time) for any combination of 4 or more insertions. Screening for the successful construction of combinations using Taq polymerase based PCR became increasingly difficult with increasing number of repeated sequence elements. A Pfu polymerase based PCR was developed and successfully used to amplify combinations of up to eleven consecutive hairpin expression cassettes. The identified PCR conditions can be beneficial to others working with multiple shRNA or other repeated sequences, and the infinitely expandable cloning strategy serves as a general solution applicable to many cloning scenarios.     

Selection and constraints on offspring size‐number trade‐offs in sand lizards (Lacerta agilis)

The trade‐off between offspring size and number is a central component of life‐history theory, postulating that larger investment into offspring size inevitably decreases offspring number. This trade‐off is generally discussed in terms of genetic, physiological or morphological constraints; however, as among‐individual differences can mask individual trade‐offs, the underlying mechanisms may be difficult to reveal. In this study, we use multivariate analyses to investigate whether there is a trade‐off between offspring size and number in a population of sand lizards by separating among‐ and within‐individual patterns using a 15‐year data set collected in the wild. We also explore the ecological and evolutionary causes and consequences of this trade‐off by investigating how a female's resource (condition)‐ vs. age‐related size (snout‐vent length) influences her investment into offspring size vs. number (OSN), whether these traits are heritable and under selection and whether the OSN trade‐off has a genetic component. We found a negative correlation between offspring size and number within individual females and physical constraints (size of body cavity) appear to limit the number of eggs that a female can produce. This suggests that the OSN trade‐off occurs due to resource constraints as a female continues to grow throughout life and, thus, produces larger clutches. In contrast to the assumptions of classic OSN theory, we did not detect selection on offspring size; however, there was directional selection for larger clutch sizes. The repeatabilities of both offspring size and number were low and we did not detect any additive genetic variance in either trait. This could be due to strong selection (past or current) on these life‐history traits, or to insufficient statistical power to detect significant additive genetic effects. Overall, the findings of this study are an important illustration of how analyses of within‐individual patterns can reveal trade‐offs and their underlying causes, with potential evolutionary and ecological consequences that are otherwise hidden by among‐individual variation.     

The Role of Life Cycle and Migration in Selection for Variance in Offspring Number

For two genotypes that have the same mean number of offspring but differ in the variance in offspring number, naturalselection will favor the genotype with lower variance. In such cases, the average growth rate is not sufficient as a measure of fitness or as a predictor of fixation probability. However, the effect of variance in offspring number on the fixationprobability of mutant strategies has been calculated under several scenarios with the general conclusion that variance in offspring number reduces fitness in proportion to the inverse of the population size [Gillespie, J., Genetics 76:601–606, 1974; Proulx, S.R., Theor. Popul. Biol. 58:33–47, 2000]. This relationship becomes more complicated under a metapopulation scenario where the “effective” population size depends on migration rate, population structure, and lifecycle. It is shown that in a life cycle where reproduction and migration (the birth-migration-regulation life cycle, or BMR)occur prior to density regulation within every deme, the fitness of a strategy depends on migration rate. When migration rates are near zero, the fitness of the strategy is determined by the size of individual demes, so that the strategy favoredin small populations tends to be fixed. As migration rate increases and approaches panmixis between demes, the fitness ofa reproductive strategy approaches what its value would be in a single, panmictic deme with a population size correspondingtothe census size of the metapopulation. Interestingly, when the life cycle is characterized by having density regulation in each deme prior to migration (the BRM life cycle) the fixation probability of a strategy is independent of migration rate. These results are found to be qualitatively consistent with the individual-based simulation results in Shpak [Theor. Biosci.124:65–85, 2005]. An erratum to this article can be found at