Different combinations of gap repressors for common stripes in Anopheles and Drosophila embryos

Drosophila segmentation is governed by a well-defined gene regulation network. The evolution of this network was investigated by examining the expression profiles of a complete set of segmentation genes in the early embryos of the mosquito, Anopheles gambiae. There are numerous differences in the expression profiles as compared with Drosophila. The germline determinant Oskar is expressed in both the anterior and posterior poles of Anopheles embryos but is strictly localized within the posterior plasm of Drosophila. The gap genes hunchback and giant display inverted patterns of expression in posterior regions of Anopheles embryos, while tailless exhibits an expanded pattern as compared with Drosophila. These observations suggest that the segmentation network has undergone considerable evolutionary change in the dipterans and that similar patterns of pair-rule gene expression can be obtained with different combinations of gap repressors. We discuss the evolution of separate stripe enhancers in the eve loci of different dipterans.     

Structural distance and evolutionary relationship of networks

Exploring common features and universal qualities shared by a particular class of networks in biological and other domains is one of the important aspects of evolutionary study. In an evolving system, evolutionary mechanism can cause functional changes that forces the system to adapt to new configurations of interaction pattern between the components of that system (e.g. gene duplication and mutation play a vital role for changing the connectivity structure in many biological networks. The evolutionary relation between two systems can be retraced by their structural differences). The eigenvalues of the normalized graph Laplacian not only capture the global properties of a network, but also local structures that are produced by graph evolutions (like motif duplication or joining). The spectrum of this operator carries many qualitative aspects of a graph. Given two networks of different sizes, we propose a method to quantify the topological distance between them based on the contrasting spectrum of normalized graph Laplacian. We find that network architectures are more similar within the same class compared to between classes. We also show that the evolutionary relationships can be retraced by the structural differences using our method. We analyze 43 metabolic networks from different species and mark the prominent separation of three groups: Bacteria, Archaea and Eukarya. This phenomenon is well captured in our findings that support the other cladistic results based on gene content and ribosomal RNA sequences. Our measure to quantify the structural distance between two networks is useful to elucidate evolutionary relationships.     

Chemotaxonomy of the Oleaceae: iridoids as taxonomic markers

The distribution and biosynthesis of iridoid glucosides in the Oleaceae is reviewed and five distinct biosynthetic pathways to iridoids have been identified in the family, deoxyloganic acid apparently being a common intermediate. Likewise, the distributions of caffeoyl phenylethanoid glycosides (CPGs), i.e. verbascoside and its analogues, as well as cornoside are listed. Iridoid glucoside data exist for 17 genera of Oleaceae and the occurrence of iridoids from the different biosynthetic pathways correlate extremely well with the phylogenetic classification inferred from recent chloroplast DNA sequence data. Thus the tribe Fontanesieae (Fontanesia) contains "normal" secoiridoids, Forsythieae (Abeliophyllum, Forsythia) contains cornoside and/or iridoids from the forsythide pathway, Myxopyreae (Myxopyrum, Nyctanthes) have iridoids from the myxopyroside pathway, and finally, the two tribes Jasmineae and Oleeae (the remaining genera) both contain iridoids from the oleoside pathway. Within Jasmineae, one group of Jasminum sp. is characterized by the presence of jasminin or similar compounds, while another group of Jasminum species and Menodora display derivatives of 10-hydroxyoleoside, compounds not present in the other group. CPGs are reported from about half of the species investigated. With regard to taxonomy at the order level, the chemical data might support a position within or close to Lamiales due to the common presence of CPGs, the iridoids being of less significance since they are of a type that are barely found elsewhere.     

Things fall apart: biological species form unconnected parsimony networks

The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.     

Evolutionary history as a driver of ecological networks: a case study of plant–hummingbird interactions

Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio–temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis of its importance in structuring ecological networks. We hypothesized different possible phylogenetic scenarios to predict frequencies of interactions between species by combining concepts from the fields of ecological networks and ecophylogenetics. The usage of these scenarios is illustrated in a plant–hummingbird interaction network database from the Atlantic Forest, southeastern Brazil. We first evaluated which phylogenetic hypotheses better predict the observed network; subsequently, we evaluated the relative importance of species evolutionary histories, abundances, and matching on species morphologies and phenologies as drivers of their frequencies of interactions. The results suggest that the evolutionary histories of hummingbirds are more important than the species abundances in structuring the studied plant–hummingbird network but less important than the morphological and phenological matching among species. The approach developed here offers the potential to advance our understanding of the multiple factors structuring ecological networks.     

Phylogenetic and evolutionary analysis of the septin protein family in metazoan

Septins, a conserved family of cytoskeletal GTP-binding proteins, were presented in diverse eukaryotes. Here, a comprehensive phylogenetic and evolutionary analysis for septin proteins in metazoan was carried out. First, we demonstrated that all septin proteins in metazoan could be clustered into four subgroups, and the representative homologue of every subgroup was presented in the non-vertebrate chordate Ciona intestinalis, indicating that the emergence of the four septin subgroups should have occurred prior to divergence of vertebrates and invertebrates, and the expansion of the septin gene number in vertebrates was mainly by the duplication of pre-existing genes rather than by the appearance of new septin subgroup. Second, the direct orthologues of most human septins existed in zebrafish, which suggested that human septin gene repertoire was mainly formed by as far as before the split between fishes and land vertebrates. Third, we found that the evolutionary rate within septin family in mammalian lineage varies significantly, human SEPT1, SEPT 10, SEPT 12, and SEPT 14 displayed a relative elevated evolutionary rate compared with other septin members. Our data will provide new insights for the further function study of this protein family.     

Early Miocene catarrhine dietary behaviour: the influence of the Red Queen Effect on incisor shape and curvature

The early Miocene catarrhine fossil record of East Africa represents a diverse and extensive adaptive radiation. It is well accepted that these taxa encompass a dietary range similar to extant hominoids, in addition to some potentially novel dietary behaviour. There have been numerous attempts to infer diet for these taxa from patterns of dental allometry and incisor and molar microwear, however, morphometric analyses until now have been restricted to the post-canine dentition. It has already been demonstrated that given the key functional role of the incisors in pre-processing food items prior to mastication, there is a positive correlation between diet and incisal curvature (Deane, A.S., Kremer, E.P., Begun, D.R., 2005. A new approach to quantifying anatomical curvatures using High Resolution Polynomial Curve Fitting (HR-PCF). Am. J. Phys. Anthropol. 128(3), 630-638.; Deane, A.S., 2007. Inferring dietary behaviour for Miocene hominoids: A high-resolution morphometric approach to incisal crown curvature. Ph.D. Dissertation. The University of Toronto.). This study seeks to re-examine existing dietary hypotheses for large-bodied early Miocene fossil catarrhines by contrasting the incisal curvature for these taxa with comparative models derived from prior studies of the correlation between extant hominoid incisor curvature and feeding behaviour. Incisor curvature was quantified for 78 fossil incisors representing seven genera, and the results confirm that early Miocene fossil catarrhines represent a dietary continuum ranging from more folivorous (i.e., Rangwapithecus) to more frugivorous (i.e., Proconsul) diets, as well as novel dietary behaviours that are potentially similar to extant ceboids (i.e., Afropithecus). Additionally, early Miocene fossil catarrhine incisors are less curved than extant hominoid incisors, indicating a general pattern of increasing mesio-distal and labial curvature through time. This pattern of morphological shifting is consistent with the Red Queen Effect (Van Valen, L., 1973. A new evolutionary law. Evol. Theory 1, 1-30), which predicts that taxa that are removed from one another by geological time, although potentially having similar diets, may exhibit differing degrees of a similar dietary adaptation (i.e., differing degrees of incisal curvature).     

Automated identification of social interaction criteria in Drosophila melanogaster

The study of social behaviour within groups has relied on fixed definitions of an ‘interaction’. Criteria used in these definitions often involve a subjectively defined cut-off value for proximity, orientation and time (e.g. courtship, aggression and social interaction networks) and the same numerical values for these criteria are applied to all of the treatment groups within an experiment. One universal definition of an interaction could misidentify interactions within groups that differ in life histories, study treatments and/or genetic mutations. Here, we present an automated method for determining the values of interaction criteria using a pre-defined rule set rather than pre-defined values. We use this approach and show changing social behaviours in different manipulations of Drosophila melanogaster. We also show that chemosensory cues are an important modality of social spacing and interaction. This method will allow a more robust analysis of the properties of interacting groups, while helping us understand how specific groups regulate their social interaction space.     

Bistable responses in bacterial genetic networks: designs and dynamical consequences

A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles networks with bistable responses.     

Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoni

The genus Schistosoma is composed of blood flukes that infect vertebrates, from which three species are major causative agents of human schistosomiasis, a tropical disease that affects more than 200 million people. Current models of the recent evolution of Schistosoma indicate multiple events of migration and speciation from an Asian ancestral species. Transposable elements are important drivers of genome evolution and have been hypothesised to have an important role in speciation. In this work, we describe a comprehensive inventory of Schistosoma mansoni and Schistosoma japonicum retrotransposons, based on their recently published genomic data. We find a considerable difference in retrotransposon representation between the two species (22% and 13%, respectively). A large part of this difference can be attributed to higher representation of two previously described families of S. mansoni retrotransposons (SR2 and Perere-3/SR3), compared with the representation of their closest relative families in S. japonicum. A more detailed analysis suggests that these two S. mansoni families were the subject of recent bursts of transposition that were not paralleled by their S. japonicum counterparts. We hypothesise that these bursts could be a consequence of the evolutionary pressure resulting from migration of Schistosoma from Asia to Africa and their establishment in this new environment, helping both speciation and adaptation.     

Distinct population structure for co-occurring Anopheles goeldii and Anopheles triannulatus in Amazonian Brazil

To evaluate whether environmental heterogeneity contributes to the genetic heterogeneity in Anopheles triannulatus, larval habitat characteristics across the Brazilian states of Roraima and Pará and genetic sequences were examined. A comparison with Anopheles goeldii was utilised to determine whether high genetic diversity was unique to An. triannulatus. Student t test and analysis of variance found no differences in habitat characteristics between the species. Analysis of population structure of An. triannulatus and An. goeldii revealed distinct demographic histories in a largely overlapping geographic range. Cytochrome oxidase I sequence parsimony networks found geographic clustering for both species; however nuclear marker networks depicted An. triannulatus with a more complex history of fragmentation, secondary contact and recent divergence. Evidence of Pleistocene expansions suggests both species are more likely to be genetically structured by geographic and ecological barriers than demography. We hypothesise that niche partitioning is a driving force for diversity, particularly in An. triannulatus.     

It takes two to tango: reproductive skew and social correlates of male mating success in a lek-breeding bird

Variance in reproductive success among individuals is a defining characteristic of many social vertebrates. Yet, our understanding of which male attributes contribute to reproductive success is still fragmentary in most cases. Male–male reproductive coalitions, where males jointly display to attract females, are of particular interest to evolutionary biologists because one male appears to forego reproduction to assist the social partner. By examining the relationship between social behaviour and reproductive success, we can elucidate the proximate function of coalitions in the context of mate choice. Here, we use data from a 4-year study of wire-tailed manakins (Pipra filicauda) to provide molecular estimates of reproductive skew and to test the hypothesis that male–male social interactions, in the context of coordinated displays, positively influence a male''s reproductive success. More specifically, we quantify male–male social interactions using network metrics and predict that greater connectivity will result in higher relative reproductive success. Our data show that four out of six leks studied had significant reproductive skew, with success apportioned to very few individuals in each lek. Metrics of male social affiliations derived from our network analysis, especially male connectivity, measured as the number of males with whom the focal male has extended interactions, were strong predictors of the number of offspring sired. Thus, network connectivity is associated with male fitness in wire-tailed manakins. This pattern may be the result of shared cues used by both sexes to assess male quality, or the result of strict female choice for coordinated display behaviour.     

Hormonal correlates of social status and courtship display in the cooperatively lekking lance-tailed manakin

Though cooperative behavior has long been a focus of evolutionary biology, the proximate hormonal mechanisms underlying cooperative interactions remain poorly understood. Lance-tailed manakins (Chiroxiphia lanceolata) are tropical passerines that form long-term male-male partnerships and cooperate in paired male courtship displays. To elucidate patterns of natural hormonal variation in relation to cooperation and reproductive behavior, we examined circulating androgen levels of male lance-tailed manakins in relation to social status, display behavior, and time of year. We found significantly higher circulating androgen levels in alpha-ranked (breeding) males compared to non-alpha adult males in the population. Beta males, which participated in courtship displays but did not copulate, had androgen levels indistinguishable from those of unpaired adult males that never displayed for females, suggesting that an elevated concentration of plasma testosterone in tropical lekking birds may be associated primarily with copulatory behavior or other status-specific traits, and not the performance of courtship display. Androgens decreased throughout the breeding season for males of all status categories. Interestingly, alphas that displayed for females in the observation session prior to sampling had lower androgen levels than alphas that did not display for females. This pattern may result from female discrimination against alpha males at display areas with high levels of social conflict among males, as social disruption is linked to elevated testosterone in many species. However, recent change of a display partner was not related to alpha androgen levels. We discuss alternative explanations and the possible implications of these results, and generate several testable predictions for future investigations.     

Pollen morphology of Chinese Curcuma L. and Boesenbergia Kuntz (Zingiberaceae): Taxonomic implications

In order to find new non-molecular evidence to support the phylogenetic and taxonomic position, pollen grains of 20 populations of 16 species of Chinese Curcuma L. and Boesenbergia Kuntz (Zingiberaceae) were investigated under SEM and TEM. The pollen grains are spherical and ovoid, nonaperturate. The pollen wall is composed of a very thin exine and a thick intine. The exine is psilate or echinate. The intine consists of two layers, i.e., a thick, channeled layer (exintine) and an inner homogenous layer (endintine). The results reveal morphological congruence between the pollen grains of species of Curcuma, which according to DNA sequence data appears to be a polyphyletic genus. However the uniform pollen morphology in Curcuma provides no evidence to divide this genus into separate taxonomic entities. Our results on pollen morphology also do not provide any additional evidence to either unite or segregate Boesenbergia albomaculata and Curcumorpha longiflora in the same genus and demonstrate that more taxonomic data on the genus Boesenbergia and its relatives are needed before a final decision can be made.