Phylogenetic inheritance of genetic variability produced by neutral models of evolution.

The amount of genetic variability in species and populations has been mainly related to microevolutionary forces operating in natural populations and the influence of phylogenetic processes for the distribution of genetic variability has been neglected. To investigate how the current genetic variability distribution depends on the genetic variability of ancestral species, we simulated the evolution of heterozygosity on a pre-determined phylogeny under three neutral models of evolution: genetic drift, drift vs mutation and drift vs migration. The distribution of genetic variability resulting from the simulations was used to estimate the phylogenetic signal by the phylogenetic comparative method of autocorrelation. Phylogenetic signal in genetic variability was observed for each of the three models, and its intensity was generally higher and persisted longer when forces of drift, mutation and migration were reduced. The prediction of a phylogenetic signal in genetic variability has consequences for: population genetics, which must consider biological processes acting at the species level influencing the amount and distribution of genetic variability; the macroevolutionary theory, by giving a theoretical basis for species selection by suggesting a heritability of genetic variability between species, and the meta-analyses of genetic variability, which must deal with the non-independence of species. The patterns observed in phylogenetic signal produced by different models of evolution can be used further to compare with data obtained from molecular markers. This is the first study that analyzes the theoretical expectations for the existence of a phylogenetic signal in a population genetic trait.

Sex ratio and dynamic behavior in populations of the exotic blowfly Chrysomya albiceps (Diptera, Calliphoridae).

Sex ratio is an essential component of life history to be considered in population growth. Chrysomya albiceps is a blowfly species with a naturally biased sex ratio. In this study, we evaluated the impact of changes in sex ratio on the dynamic behavior of C. albiceps using a density-dependent mathematical model that incorporated demographic parameters such as survival and fecundity. These parameters were obtained by exponential regression, with survival and fecundity being estimated experimentally as a function of larval density. Bifurcation diagram of the results indicated the evolution of stable equilibrium points as a function of sex ratio. A continually increasing sex ratio yielded a hierarchy of bifurcating stable equilibrium points that evolved into a chaotic regime. The demographic parameters obtained by exponential regression were also changed to maximum and minimum values in order to analyze their influence on dynamic behavior with sex ratio being considered as an independent variable. Bifurcations with periodicity windows between chaos regimes were also found.

Sex ratio and dynamic behavior in populations of the exotic blowfly Chrysomya albiceps (Diptera, Calliphoridae)

Sex ratio is an essential component of life history to be considered in population growth. Chrysomya albiceps is a blowfly species with a naturally biased sex ratio. In this study, we evaluated the impact of changes in sex ratio on the dynamic behavior of C. albiceps using a density-dependent mathematical model that incorporated demographic parameters such as survival and fecundity. These parameters were obtained by exponential regression, with survival and fecundity being estimated experimentally as a function of larval density. Bifurcation diagram of the results indicated the evolution of stable equilibrium points as a function of sex ratio. A continually increasing sex ratio yielded a hierarchy of bifurcating stable equilibrium points that evolved into a chaotic regime. The demographic parameters obtained by exponential regression were also changed to maximum and minimum values in order to analyze their influence on dynamic behavior with sex ratio being considered as an independent variable. Bifurcations with periodicity windows between chaos regimes were also found.

A razão sexual é um componente essencial da biologia de organismos a ser considerado em crescimento populacional. Chrysomya albiceps é uma espécie de mosca varejeira que exibe um desvio na razão sexual em relação à proporção 1:1. Neste estudo avaliamos o impacto de alterações na razão sexual sobre o comportamento dinâmico de C. albiceps utilizando um modelo matemático dependente da densidade que incorpora parâmetros demográficos como sobrevivência e fecundidade. Os parâmetros foram obtidos por regressão exponencial, com sobrevivência e fecundidade sendo estimadas experimentalmente em função da densidade larval. O diagrama de bifurcação gerado pelos resultados indicou a evolução de pontos de equilíbrio estável em função da razão sexual. A sucessão contínua dos valores da razão sexual resultou em uma hierarquia de pontos de equilíbrio estável produzida por bifurcações, resultando em regime caótico. Os parâmetros demográficos obtidos por regressão exponencial foram também mudados para valores máximos e mínimos, a fim de analisar a influência deles sobre o comportamento dinâmico da espécie, tendo a razão sexual como variável independente. Bifurcações com janelas de periodicidade intercaladas com o regime caótico também foram encontradas.

A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization

The computationally challenging problem of reconstructing the phylogeny of a set of contemporary data, such as DNA sequences or morphological attributes, was treated by an extended version of the neighbor-joining (NJ) algorithm. The original NJ algorithm provides a single-tree topology, after a cascade of greedy pairing decisions that tries to simultaneously optimize the minimum evolution and the least squares criteria. Given that some sub-trees are more stable than others, and that the minimum evolution tree may not be achieved by the original NJ algorithm, we propose a multi-neighbor-joining (MNJ) algorithm capable of performing multiple pairing decisions at each level of the tree reconstruction, keeping various partial solutions along the recursive execution of the NJ algorithm. The main advantages of the new reconstruction procedure are: 1) as is the case for the original NJ algorithm, the MNJ algorithm is still a low-cost reconstruction method; 2) a further investigation of the alternative topologies may reveal stable and unstable sub-trees; 3) the chance of achieving the minimum evolution tree is greater; 4) tree topologies with very similar performances will be simultaneously presented at the output. When there are multiple unrooted tree topologies to be compared, a visualization tool is also proposed, using a radial layout to uniformly distribute the branches with the help of well-known metaheuristics used in computer science.

Recent advances in gene expression data clustering: a case study with comparative results

Several advanced techniques have been proposed for data clustering and many of them have been applied to gene expression data, with partial success. The high dimensionality and the multitude of admissible perspectives for data analysis of gene expression require additional computational resources, such as hierarchical structures and dynamic allocation of resources. We present an immune-inspired hierarchical clustering device, called hierarchical artificial immune network (HaiNet), especially devoted to the analysis of gene expression data. This technique was applied to a newly generated data set, involving maize plants exposed to different aluminum concentrations. The performance of the algorithm was compared with that of a self-organizing map, which is commonly adopted to deal with gene expression data sets. More consistent and informative results were obtained with HaiNet.

Spatio-temporal dynamics and transition from asymptotic equilibrium to bounded oscillations in Chrysomya albiceps (Diptera, Calliphoridae).

The sensitivity of parameters that govern the stability of population size in Chrysomya albiceps and describe its spatial dynamics was evaluated in this study. The dynamics was modeled using a density-dependent model of population growth. Our simulations show that variation in fecundity and mainly in survival has marked effect on the dynamics and indicates the possibility of transitions from one-point equilibrium to bounded oscillations. C. albiceps exhibits a two-point limit cycle, but the introduction of diffusive dispersal induces an evident qualitative shift from two-point limit cycle to a one fixed-point dynamics. Population dynamics of C. albiceps is here compared to dynamics of Cochliomyia macellaria, C. megacephala and C. putoria.

Automatic determination of radial basis functions: an immunity-based approach.

The appropriate operation of a radial basis function (RBF) neural network depends mainly upon an adequate choice of the parameters of its basis functions. The simplest approach to train an RBF network is to assume fixed radial basis functions defining the activation of the hidden units. Once the RBF parameters are fixed, the optimal set of output weights can be determined straightforwardly by using a linear least squares algorithm, which generally means reduction in the learning time as compared to the determination of all RBF network parameters using supervised learning. The main drawback of this strategy is the requirement of an efficient algorithm to determine the number, position, and dispersion of the RBFs. The approach proposed here is inspired by models derived from the vertebrate immune system, that will be shown to perform unsupervised cluster analysis. The algorithm is introduced and its performance is compared to that of the random, k-means center selection procedures and other results from the literature. By automatically defining the number of RBF centers, their positions and dispersions, the proposed method leads to parsimonious solutions. Simulation results are reported concerning regression and classification problems.

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): geometric analysis of a complex morphological structure.

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinical trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.

In vivo formation of electron paramagnetic resonance-detectable nitric oxide and of nitrotyrosine is not impaired during murine leishmaniasis.

Recent studies have provided evidence for a dual role of nitric oxide (NO) during murine leishmaniasis. To explore this problem, we monitored the formation of NO and its derived oxidants during the course of Leishmania amazonensis infection in tissues of susceptible (BALB/c) and relatively resistant (C57BL/6) mice. NO production was detected directly by low-temperature electron paramagnetic resonance spectra of animal tissues. Both mouse strains presented detectable levels of hemoglobin nitrosyl (HbNO) complexes and of heme nitrosyl and iron-dithiol-dinitrosyl complexes in the blood and footpad lesions, respectively. Estimation of the nitrosyl complex levels demonstrated that most of the NO is synthesized in the footpad lesions. In agreement, immunohistochemical analysis of the lesions demonstrated the presence of nitrotyrosine in proteins of macrophage vacuoles and parasites. Since macrophages lack myeloperoxidase, peroxynitrite is likely to be the nitrating NO metabolite produced during the infection. The levels of HbNO complexes in the blood reflected changes occurring during the infection such as those in parasite burden and lesion size. The maximum levels of HbNO complexes detected in the blood of susceptible mice were higher than those of C57BL/6 mice but occurred at late stages of infection and were accompanied by the presence of bacteria in the cutaneous lesions. The results indicate that the local production of NO is an important mechanism for the elimination of parasites if it occurs before the parasite burden becomes too high. From then on, elevated production of NO and derived oxidants aggravates the inflammatory process with the occurrence of a hypoxic environment that may favor secondary infections.

Diffusion model applied to postfeeding larval dispersal blowflies (Diptera: Calliphoridae)

This paper presents a diffusion model of larval dispersal especifically designed to account for particular aspects of postfeeding larval dispersal from the food source in organisms such as blowflies. In these organisms the dispersal of immatures includes two groups of individuals, those that are actively migrating and those that initiated the pupation process. The classical diffusion equation in one dimension was modified to incorporate a function which describes the burying of larvae to become pupae. The analytical solution of this equation predicts oscillatory and monotonic dispersal behaviors, which are observed in experimental populations of blowfly species.

Diffusion model applied to postfeeding larval dispersal in blowflies (Diptera:Calliphoridae).

This paper presents a diffusion model of larval dispersal specifically designed to account for particular aspects of postfeeding larval dispersal from the food source in organisms such as blowflies. In these organisms the dispersal of immatures includes two groups of individuals, those that are actively migrating and those that have initiated the pupation process. The classical diffusion equation in one dimension was modified to incorporate a function which describes the burying of larvae to become pupae. The analytical solution of this equation predicts oscillatory and monotonic dispersal behaviors, which are observed in experimental populations of blowfly species.

Theoretical dynamics of experimental populations of introduced and native blowflies (Diptera:Calliphoridae).

Equilibrium dynamics in experimental populations of Chrysomya megacephala (F.) and C. putoria (Wiedemann), which have recently invaded the Americas, and the native species Cochliomyia macellaria (F.), were investigated using nonlinear difference equations. A theoretical analysis of the mathematical model using bifurcation theory established the combination of demographic parameters responsible for producing shifts in blowfly population dynamics from stable equilibria to bounded cycles and aperiodic behavior. Mathematical modeling shows that the populations of the 2 introduced Chrysomya species will form stable oscillations with numbers fluctuating 3-4 times in successive generations. However, in the native species C. macellaria, the dynamics is characterized by damping oscillations in population size, leading to a stable population level.

Theoretical estimates of consumable food and probability of acquiring food in larvae of Chrysomya putoria (Diptera: Calliphoridae)

An indirect estimate of consumable food and probability of acquiring food in a blowfly species, Chrysomya putoria, is presented. This alternative procedure combines three distinct models to estimate consumable food in the context of the exploitative competition experienced by immature individuals in blowfly populations. The relevant parameters are derived from data for pupal weight and survival and estimates of density-independent larval mortality in twenty different larval densities. As part of this procedure, the probability of acquiring food per unit of time and the time taken to exhaust the food supply are also calculated. The procedure employed here may be valuable for estimations in insects whose immature stages develop inside the food substrate, where it is difficult to partial out confounding effects such as separation of faeces. This procedure also has the advantage of taking into account the population dynamics of immatures living under crowded conditions, which are particularly characteristic of blowflies and other insects as well.

Theoretical estimates of consumable food and probability of acquiring food in larvae of Chrysomya putoria (Diptera: Calliphoridae).

An indirect estimate of consumable food and probability of acquiring food in a blowfly species, Chrysomya putoria, is presented. This alternative procedure combines three distinct models to estimate consumable food in the context of the exploitative competition experienced by immature individuals in blowfly populations. The relevant parameters are derived from data for pupal weight and survival and estimates of density-independent larval mortality in twenty different larval densities. As part of this procedure, the probability of acquiring food per unit of time and the time taken to exhaust the food supply are also calculated. The procedure employed here may be valuable for estimations in insects whose immature stages develop inside the food substrate, where it is difficult to partial out confounding effects such as separation of faeces. This procedure also has the advantage of taking into account the population dynamics of immatures living under crowded conditions, which are particularly characteristic of blowflies and other insects as well.