MODULARITY, NOISE, AND NATURAL SELECTION

Most biological systems are formed by component parts that are to some degree interrelated. Groups of parts that are more associated among themselves and are relatively autonomous from others are called modules. One of the consequences of modularity is that biological systems usually present an unequal distribution of the genetic variation among traits. Estimating the covariance matrix that describes these systems is a difficult problem due to a number of factors such as poor sample sizes and measurement errors. We show that this problem will be exacerbated whenever matrix inversion is required, as in directional selection reconstruction analysis. We explore the consequences of varying degrees of modularity and signal-to-noise ratio on selection reconstruction. We then present and test the efficiency of available methods for controlling noise in matrix estimates. In our simulations, controlling matrices for noise vastly improves the reconstruction of selection gradients. We also perform an analysis of selection gradients reconstruction over a New World Monkeys skull database to illustrate the impact of noise on such analyses. Noise-controlled estimates render far more plausible interpretations that are in full agreement with previous results.

Molecular evolution of a malaria resistance gene (DARC) in primates

Genes involved in host-pathogen interactions are often strongly affected by positive natural selection. The Duffy antigen, coded by the Duffy antigen receptor for chemokines (DARC) gene, serves as a receptor for Plasmodium vivax in humans and for Plasmodium knowlesi in some nonhuman primates. In the majority of sub-Saharan Africans, a nucleic acid variant in GATA-1 of the gene promoter is responsible for the nonexpression of the Duffy antigen on red blood cells and consequently resistance to invasion by P. vivax. The Duffy antigen also acts as a receptor for chemokines and is expressed in red blood cells and many other tissues of the body. Because of this dual role, we sequenced a 3,000-bp region encompassing the entire DARC gene as well as part of its 5' and 3' flanking regions in a phylogenetic sample of primates and used statistical methods to evaluate the nature of selection pressures acting on the gene during its evolution. We analyzed both coding and regulatory regions of the DARC gene. The regulatory analysis showed accelerated rates of substitution at several sites near known motifs. Our tests of positive selection in the coding region using maximum likelihood by branch sites and maximum likelihood by codon sites did not yield statistically significant evidence for the action of positive selection. However, the maximum likelihood test in which the gene was subdivided into different structural regions showed that the known binding region for P. vivax/P. knowlesi is under very different selective pressures than the remainder of the gene. In fact, most of the gene appears to be under strong purifying selection, but this is not evident in the binding region. We suggest that the binding region is under the influence of two opposing selective pressures, positive selection possibly exerted by the parasite and purifying selection exerted by chemokines.

Do extrafloral nectaries present a defensive role against herbivores in two species of the family Bignoniaceae in a Neotropical savannas?

Despite the general belief that the interaction between extrafloral nectaries (EFNs) and ants is mutualistic, the defensive function of EFNs has been poorly documented in South American savannas. In this article, we evaluate the potential impact of EFNs (benefits and costs) on two species of plants from the dry areas of Central Brazil, Anemopaegma album and Anemopaegma scabriusculum (Bignoniaceae). In particular, we characterize the composition of substances secreted by the EFNs, test whether EFNs attract ants, and whether ants actually present a defensive role, leading to reduced herbivory and increased plant fitness. Histochemical analyses indicated that EFNs from both species of Anemopaegma secrete an exudate that is composed of sugars, and potentially lipids and proteins. Furthermore, EFNs from both species were shown to present a significant role in ant attraction. However, contrary to common expectations, ants were not found to protect plants against herbivore attack. No effect was found between ant visitation and flower or fruit production in A. album, while the presence of ants led to a significant decrease in flower production in A. scabriusculum. These results suggest that EFNs might present a similar cost and benefit in A. album, and a higher cost than benefit in A. scabriusculum. Since the ancestor of Anemopaegma occupied humid forests and already presented EFNs that were maintained in subsequent lineages that occupied savannas, we suggest that phylogenetic inertia might explain the presence of EFNs in the species of Anemopaegma in which EFNs lack a defensive function.

Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC x GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.

Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes

Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schltterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

Biological evolution of replicator systems: towards a quantitative approach

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312–316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth’s geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

Utility Harmonic Impedance Measurement Based on Data Selection

Determination of the utility harmonic impedance based on measurements is a significant task for utility power-quality improvement and management. Compared to those well-established, accurate invasive methods, the noninvasive methods are more desirable since they work with natural variations of the loads connected to the point of common coupling (PCC), so that no intentional disturbance is needed. However, the accuracy of these methods has to be improved. In this context, this paper first points out that the critical problem of the noninvasive methods is how to select the measurements that can be used with confidence for utility harmonic impedance calculation. Then, this paper presents a new measurement technique which is based on the complex data-based least-square regression, combined with two techniques of data selection. Simulation and field test results show that the proposed noninvasive method is practical and robust so that it can be used with confidence to determine the utility harmonic impedances.

Clinical strategies for esthetic excellence in anterior tooth restorations: understanding color and composite resin selection

Direct composite resin restorations have become a viable alternative for patients that require anterior restorative procedures to be integrated to the other teeth that compose the smile, especially for presenting satisfactory esthetic results and minimum wear of the dental structure. Technological evolution along with a better understanding of the behavior of dental tissues to light incidence has allowed the development of new composite resins with better mechanical and optical properties, making possible a more artistic approach for anterior restorations. The combination of the increasing demand of patients for esthetics and the capacity to preserve the dental structure resulted in the development of different incremental techniques for restoring fractured anterior teeth in a natural way. In order to achieve esthetic excellence, dentists should understand and apply artistic and scientific principles when choosing color of restorative materials, as well as during the insertion of the composite resin. The discussion of these strategies will be divided into two papers. In this paper, the criteria for color and material selection to obtain a natural reproduction of the lost dental structures and an imperceptible restoration will be addressed.