Discrete Variation Research Articles

Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein

Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggesting possible antigenic-related mechanisms of selection at the sub-genotype level. By comparison of HAstV-1 capsid sequences, lineage-defining residues under positive selection were identified. Structural analysis of HAstV-1 capsid allowed identifying at least six residues exposed on the virion surface. Two residues were located in the VP34 (shell region) whilst four residues were mapped in the VP25/27 (protruding region) of HAstV capsid protein, in proximity of the putative receptor binding S site. These findings suggest that mechanisms similar to those observed and/or hypothesized for other enteric viruses are also shaping the evolution of HAstVs, with intra-typic diversification being a possible mechanism to decrease the antigenic pressure to which these viruses are exposed.

Regularly varying sequences and Emden–Fowler type second-order difference equations

We study asymptotic behavior of positive solutions of nonlinear difference equation where are regularly varying sequences. It is shown that with the help of discrete regular variation, complete information can be acquired about the existence of all possible strongly increasing regularly varying solutions of this equation and their accurate asymptotic behavior at infinity.

Physiological Consequences of Food Limitation for a Color Polymorphic Lizard: Are Coping Responses Morph-Specific?

Color polymorphism in animals often reflects discrete intraspecific variation in suites of traits linked with survival and reproductive success, as well as an ability to exploit diverse habitat types. Given those considerations, it has been hypothesized that color polymorphic species may be better able to withstand broad-scale environmental disturbances compared to monomorphic taxa. An assumption underlying this hypothesis is that morphs differ in their responses to the consequences of a disturbance. We test whether two color morphs of the Ornate Tree Lizard (Urosaurus ornatus) differ in their physiological responses to a likely outcome of a habitat disturbance, food limitation. We subjected blue and yellow morph U. ornatus to one of two feeding treatments (control [fed every other day] and food-limited [fed every five days]) and monitored their changes in body mass and stamina capacity for the next four weeks. We found that in general, food-limited males lost mass and had reduced stamina over time. Altho...

Significance of variation and evaluation of potential characters in three morphologically similar species of Barleria sect. Barleria (Acanthaceae) in southern Africa

The variation exhibited within three species of Barleria (B. bechuanensis, B. irritans and B. jubata) was studied to establish whether it was discrete or continuous. Morphological characters were examined and recorded in matrices. Cluster analysis was employed to impose a hierarchical non-overlapping association among operational taxonomic units (OTUs) while ordination was used to establish whether the variation was discrete or continuous. Discrete characters were determined from quantitative morphological data using box and whisker plots. Locality information for the OTUs was obtained from herbarium labels and used to generate maps to illustrate geographic distribution of taxa. Cluster analysis and ordination demonstrated that there was discrete variation within Barleria bechuanensis, B. irritans and B. jubata, which each split into two distinct clusters, although box and whisker plots illustrated that many quantitative characters overlapped within and between species. Since clear morphological gaps between clusters are assumed to be indicators of breaks in gene flow, the distinct clusters were recognised at species level.

Circadian rhythms vary over the growing season and correlate with fitness components.

Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity. Subtler adjustments via genomic introgression of naturally occurring alleles indicated that clock periods slightly >24hr were adaptive, consistent with prior models describing how well the timing of biological processes is adjusted within a diurnal cycle (referred to as phase). In segregating recombinant inbred lines (RILs), circadian phase varied up to 2hr across months of the growing season, and both period and phase expressed significant genetic variances. Performance metrics including developmental rate, size and fruit set were described by principal components (PC) analyses and circadian parameters correlated with the first PC, such that period lengths slightly >24hr were associated with improved performance in multiple RIL sets. These experiments translate functional analyses of clock behaviour performed in controlled settings to natural ones, demonstrating that quantitative variation in circadian phase is highly responsive to seasonally variable abiotic factors. The results expand upon prior studies in controlled settings, showing that discrete and quantitative variation in clock phenotypes correlates with performance in nature.

Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues.

Plant chemotypes or chemical polymorphisms are defined by discrete variation in secondary metabolites within a species. This variation can have consequences for ecological interactions or the human use of plants. Understanding the molecular basis of chemotypic variation can help to explain how variation of plant secondary metabolites is controlled. We explored the transcriptomes of the 3 cardinal terpene chemotypes of Melaleuca alternifolia in young leaves, mature leaves, and stem and compared transcript abundance to variation in the constitutive profile of terpenes. Leaves from chemotype 1 plants (dominated by terpinen-4-ol) show a similar pattern of gene expression when compared to chemotype 5 plants (dominated by 1,8-cineole). Only terpene synthases in young leaves were differentially expressed between these chemotypes, supporting the idea that terpenes are mainly synthetized in young tissue. Chemotype 2 plants (dominated by terpinolene) show a greater degree of differential gene expression compared to the other chemotypes, which might be related to the isolation of plant populations that exhibit this chemotype and the possibility that the terpinolene synthase gene in M. alternifolia was derived by introgression from a closely related species, Melaleuca trichostachya. By using multivariate analyses, we were able to associate terpenes with candidate terpene synthases.

Second generation prototype of a variable stiffness transverse plane adapter for a lower limb prosthesis

The prescription and fitting of a traditional lower limb prosthesis often focuses on straight walking, neglecting maneuvers such as turning and pivoting that require flexibility in the transverse plane. Current devices that allow transverse plane movement only offer a fixed stiffness and are incapable of adapting to varying daily activities. Pilot testing of a first-generation variable stiffness torsion adapter (VSTA I) showed a benefit for individuals with lower limb amputation by reducing peak transverse plane moments at the residual limb which could lead to increased comfort, but testing was limited due to excessive device height and mass. The VSTA II, a second-generation prototype, is capable of discrete stiffness variation from 0.31 to 1.29 Nm/° in 0.25 Nm/° increments with ±30° of motion in addition to fully locked operation. Stiffness variation is enabled by five independent spring subunits that can be combined in parallel to create different, linear, stiffness settings. The VSTA II features a reduced mass (51% reduction) and height (42% reduction) compared to its predecessor along with a tether-free controller and power system. These improvements will permit greater recruitment for amputee studies, and allow for advanced testing both in and out of the lab.

Partial revision of the Indo-Australian braconine wasp genus Gammabracon Quicke (Hymenoptera: Braconidae) with descriptions of new species from Indonesia (Mollucas), Malaysia, Philippines and Thailand

ABSTRACTTen distinctive new species of the taxonomically difficult braconine wasp genus Gammabracon Quicke, 1984 are described: G. apicoluteus sp. nov. from Malaysia (Negri); G. curticornis sp. nov. from Malaysia (Negri); G. philippinensis sp. nov. from the Philippines; G. siamensis sp. nov. from Thailand; G. striatus sp. nov. from West Malaysia; G. strandorum sp. nov. from Indonesia (Java), G. subvena sp. nov. from Malaysia (Negri and Sabah); G. townesorum sp. nov. from the Philippines; G. variipennis sp. nov. from Thailand; and G. wegeneri sp. nov. from Indonesia. Myosoma forticarinata Cameron, 1902 is transferred to Gammabracon, hence Gammabracon forticarinata comb. nov. A lectotype is designated for Gammabracon erythroura (Cameron). The status of Cratobracon strandiellus (Cameron) is discussed and a new combination proposed, Shelfordia strandiellus Cameron, 1910 comb. nov. (=Bracon strandiellus Cameron). Paucity of discrete morphological variation makes separation of most of the species with orange-red mesosoma, black metasoma and conspicuous back setae currently unrealistic and it may be that there is a single widespread and morphologically variable species.http://zoobank.org/urn:lsid:zoobank.org:pub:56B8884E-99C8-4B53-9747-D011F552312D

Visualizing the structure of RNA-seq expression data using grade of membership models.

Grade of membership models, also known as “admixture models”, “topic models” or “Latent Dirichlet Allocation”, are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple “populations”, and in natural language processing to model documents having words from multiple “topics”. Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells. We also provide methods to help interpret the clusters, by identifying genes that are distinctively expressed in each cluster. By applying these methods to several example RNA-seq applications we demonstrate their utility in identifying and summarizing structure and heterogeneity. Applied to data from the GTEx project on 53 human tissues, the approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to single-cell expression data from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and highlights genes involved in a variety of relevant processes—from germ cell development, through compaction and morula formation, to the formation of inner cell mass and trophoblast at the blastocyst stage. The methods are implemented in the Bioconductor package CountClust.

The Role of DAF-21/Hsp90 in Mouth-Form Plasticity in Pristionchus pacificus.

Phenotypic plasticity is increasingly recognized to facilitate adaptive change in plants and animals, including insects, nematodes, and vertebrates. Plasticity can occur as continuous or discrete (polyphenisms) variation. In social insects, for example, in ants, some species have workers of distinct size classes while in other closely related species variation in size may be continuous. Despite the abundance of examples in nature, how discrete morphs are specified remains currently unknown. In theory, polyphenisms might require robustness, whereby the distribution of morphologies would be limited by the same mechanisms that execute buffering from stochastic perturbations, a function attributed to heat-shock proteins of the Hsp90 family. However, this possibility has never been directly tested because plasticity and robustness are considered to represent opposite evolutionary principles. Here, we used a polyphenism of feeding structures in the nematode Pristionchus pacificus to test the relationship between robustness and plasticity using geometric morphometrics of 20 mouth-form landmarks. We show that reducing heat-shock protein activity, which reduces developmental robustness, increases the range of mouth-form morphologies. Specifically, elevated temperature led to a shift within morphospace, pharmacological inhibition of all Hsp90 genes using radicicol treatment increased shape variability in both mouth-forms, and CRISPR/Cas9-induced Ppa-daf-21/Hsp90 knockout had a combined effect. Thus, Hsp90 canalizes the morphologies of plastic traits resulting in discrete polyphenism of mouth-forms.

Global energy‐tracking identities and global energy‐tracking splitting FDTD schemes for the Drude Models of Maxwell's equations in three‐dimensional metamaterials

In this article, we study the Drude models of Maxwell's equations in three‐dimensional metamaterials. We derive new global energy‐tracking identities for the three dimensional electromagnetic problems in the Drude metamaterials, which describe the invariance of global electromagnetic energy in variation forms. We propose the time second‐order global energy‐tracking splitting FDTD schemes for the Drude model in three dimensions. The significant feature is that the developed schemes are global energy‐preserving, unconditionally stable, second‐order accurate both in time and space, and computationally efficient. We rigorously prove that the new schemes satisfy these energy‐tracking identities in the discrete form and the discrete variation form and are unconditionally stable. We prove that the schemes in metamaterials are second order both in time and space. The superconvergence of the schemes in the discrete H1 norm is further obtained to be second order both in time and space. Their approximations of divergence‐free are also analyzed to have second‐order accuracy both in time and space. Numerical experiments confirm our theoretical analysis results. © 2017 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 33: 763–785, 2017

Modeling of focal-directorial surfaces for application in architecture

The theme of this paper is the modeling of focal-directorial surfaces, starting with their definition, as a locus of points, whose sum of the distances to the focus and/or directrix is constant and predefined. We presented a heuristic algorithm for modeling surfaces and their isocurves, achieved through the use of the Grasshopper visual programming editor in the RhinoCeros environment. Surfaces and their isocurves were generated in a spherical grid, because a Cartesian grid proved unsuitable for the task and the chosen approach. This paper additionally proposes a modeling algorithm of a discrete variation of focal-directorial surfaces. The proposed modeling method is a 3D convex hull implemented on a set of surface points, with the selected points close to that surface. The discrete model is realized both in a Cartesian and spherical grid. There are significant differences between the obtained results.

Variation in growth of Damaraland mole-rats is explained by competition rather than by functional specialization for different tasks.

In some eusocial insect societies, adaptation to the division of labour results in multimodal size variation among workers. It has been suggested that variation in size and growth among non-breeders in naked and Damaraland mole-rats may similarly reflect functional divergence associated with different cooperative tasks. However, it is unclear whether individual growth rates are multimodally distributed (as would be expected if variation in growth is associated with specialization for different tasks) or whether variation in growth is unimodally distributed, and is related to differences in the social and physical environment (as would be predicted if there are individual differences in growth but no discrete differences in developmental pathways). Here, we show that growth trajectories of non-breeding Damaraland mole-rats vary widely, and that their distribution is unimodal, contrary to the suggestion that variation in growth is the result of differentiation into discrete castes. Though there is no evidence of discrete variation in growth, social factors appear to exert important effects on growth rates and age-specific size, which are both reduced in large social groups.

Discrete longitudinal variation in freshwater mussel assemblages within two rivers of central Michigan, USA

A primary focus in the study of lotic ecosystems involves understanding the relationship between changes in the physical environment and changes in biota along a longitudinal gradient. Previous studies examining riverine organisms, primarily fish and aquatic insects, have noted two commonly occurring upstream-to-downstream patterns: either the restriction of species to distinct zones (i.e., discrete variation), or the gradual accumulation of species with increasing distance from the headwaters (i.e., continuous variation). Like other riverine organisms, freshwater mussels exhibit longitudinal patterns in distribution and abundance; however, few studies have quantified these patterns and the environmental variables that influence them. This study examined longitudinal patterns in the assemblage structure of mussels in the Chippewa and Pine rivers, Michigan, United States. A stratified random sampling design was used to sample mussels at 54 sites and timed searches allowed for the characterization of mussel assemblages. Multivariate regression tree models revealed differences in mussel assemblage structure that are consistent with upstream-to-downstream changes in surficial geology and wetland habitat. Certain species were restricted to specific geologies suggesting discrete variation with k-means partitioning and non-metric multidimensional scaling supporting these results. Because the results were consistent between rivers, we expect these patterns to prevail in similarly glaciated regions.

Discrete Total Variation: New Definition and Minimization

We propose a new definition for the gradient field of a discrete image defined on a twice finer grid. The differentiation process from an image to its gradient field is viewed as the inverse operation of linear integration, and the proposed mapping is nonlinear. Then, we define the total variation of an image as the $\ell_1$ norm of its gradient field amplitude. This new definition of the total variation yields sharp edges and has better isotropy than the classical definition.

The relationship between multilevel models and non-parametric multilevel mixture models: Discrete approximation of intraclass correlation, random coefficient distributions, and residual heteroscedasticity.

Multilevel data structures are common in the social sciences. Often, such nested data are analysed with multilevel models (MLMs) in which heterogeneity between clusters is modelled by continuously distributed random intercepts and/or slopes. Alternatively, the non-parametric multilevel regression mixture model (NPMM) can accommodate the same nested data structures through discrete latent class variation. The purpose of this article is to delineate analytic relationships between NPMM and MLM parameters that are useful for understanding the indirect interpretation of the NPMM as a non-parametric approximation of the MLM, with relaxed distributional assumptions. We define how seven standard and non-standard MLM specifications can be indirectly approximated by particular NPMM specifications. We provide formulas showing how the NPMM can serve as an approximation of the MLM in terms of intraclass correlation, random coefficient means and (co)variances, heteroscedasticity of residuals at level 1, and heteroscedasticity of residuals at level 2. Further, we discuss how these relationships can be useful in practice. The specific relationships are illustrated with simulated graphical demonstrations, and direct and indirect interpretations of NPMM classes are contrasted. We provide an R function to aid in implementing and visualizing an indirect interpretation of NPMM classes. An empirical example is presented and future directions are discussed.

Floral biology, reciprocal herkogamy and breeding system in fourPsychotriaspecies (Rubiaceae) in Brazil

Distylous species have two floral morphs with reciprocal positions of sexual whorls, functioning to promote cross-pollination. Additionally, most distylous species have an incompatibility system linked to the discrete variation of anthers and stigmas. Here we provide new data on heterostyly, reproductive biology and pollination in four Psychotria spp. from the Cerrado Region (Brazil). Psychotria deflexa, P. nitidula and P. trichophoroides fitted the distylous morphological syndrome, whereas P. prunifolia was monomorphic and self-compatible. Reciprocity varied across species, with the upper whorl of anthers and stigmas being more reciprocal than the lower whorl. Psychotria nitidula has a heteromorphic incompatibility system, whereas P. deflexa and P. trichophoroides showed partial self-compatibility. Psychotria prunifolia and P. trichophoroides were visited by large bees and exhibited lower reproductive efficacy than P. nitidula and P. deflexa, which are visited by wasps and small bees. Our results provide new evidence that the morphological distylous syndrome does not always co-occur with heteromorphic incompatibility and additional mechanisms (e.g. disassortative pollen transfer) may operate to maintain the polymorphism and isoplethy of species with different incompatibility system.

Environmental predictability of taxonomic and functional community composition in high‐latitude streams

Summary In stream ecology, it has traditionally been proposed that local habitat conditions pose a strong environmental filter resulting in predictable community types. However, recent studies have demonstrated continuous rather than discrete community variation along environmental gradients across streams. Our aim was to examine the continuity of stream communities using functional traits of benthic macroinvertebrates. Using previous studies and the environmental filtering paradigm as a background, we hypothesised that the taxonomic composition of communities should vary continuously over environmental gradients, whereas the functional composition of communities should form discrete community types according to specific habitat conditions. As stream environmental characteristics vary between seasons, we also asked if this had an effect on the characteristics of community variation in time. Our data were collected from 50 streams draining into the River Tenojoki (70°N, 27°E) in Finland and Norway. The first data set was collected during late spring 2013 and the second data set during early autumn of the same year. Using multivariate regression trees and constrained ordination methods, we analysed the relationships of taxonomic and functional composition of macroinvertebrate communities to various in‐stream environmental factors. Our results suggest that the variation in the importance of environmental factors between seasons combined with the high heterogeneity of habitats precludes the formation of clear taxonomic and functional community types in northern streams. Conservation efforts should hence focus on including variability in environmental conditions so as to encompass all components of biological communities. However, as there were some noticeable responses of individual traits to different environmental factors, discrete functional communities may be found if key traits of the organisms can be identified.

Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics.

The molecular mechanisms underlying phenotypic plasticity are not well understood. Identifying mechanisms underlying alternative reproductive tactics (ARTs) in species for which the behavioural and fitness consequences of this variation are well characterized provides an opportunity to integrate evolutionary and mechanistic understanding of the maintenance of variation within populations. In the ocellated wrasse Symphodus ocellatus, the behavioural phenotypes of three distinct male morphs (sneakers, satellites and nesting males), which arise from a single genome, have been thoroughly characterized. To determine the neuroendocrine and genomic mechanisms associated with discrete phenotypic variation and ARTs in S.ocellatus in their natural environment, we constructed a whole-brain de novo transcriptome and compared global patterns of gene expression between sexes and male morphs. Next, we quantified circulating cortisol and 11-ketotestosterone (11-kt), mediators of male reproductive behaviours, as well as stress and gonadal steroid hormone receptor expression in the preoptic area, ventral subpallial division of the telencephalon and dorsolateral telencephalon, critical brain regions for social and reproductive behaviours. We found higher levels of 11-kt in nesting males and higher levels of cortisol in sneaker males relative to other male morphs and females. We also identified distinct patterns of brain region-specific hormone receptor expression between males such that most hormone receptors are more highly expressed in satellites and nesting males relative to sneakers and females. Our results establish the neuroendocrine and molecular mechanisms that underlie ARTs in the wild and provide a foundation for experimentally testing hypotheses about the relationship between neuromolecular processes and reproductive success.

The genetic basis of discrete and quantitative colour variation in the polymorphic lizard, Ctenophorus decresii.

BackgroundColour polymorphic species provide invaluable insight into processes that generate and maintain intra-specific variation. Despite an increasing understanding of the genetic basis of discrete morphs, sources of colour variation within morphs remain poorly understood. Here we use the polymorphic tawny dragon lizard Ctenophorus decresii to test simple Mendelian models for the inheritance of discrete morphs, and to investigate the genetic basis of continuous variation among individuals across morphs. Males of this species express either orange, yellow, orange surrounded by yellow, or grey throats. Although four discrete morphs are recognised, the extent of orange and yellow varies greatly. We artificially elevated testosterone in F0 females and F1 juveniles to induce them to express the male throat colour polymorphism, and quantified colour variation across the pedigree.ResultsInheritance of discrete morphs in C. decresii best fit a model whereby two autosomal loci with complete dominance respectively determine the presence of orange and yellow. However, a single locus model with three co-dominant alleles for orange, yellow and grey could not be definitively rejected. Additionally, quantitative expression of the proportion of orange and yellow on the throat was strongly heritable (orange: h2 = 0.84 ± 0.14; yellow: h2 = 0.67 ± 0.19), with some evidence for covariance between the two.ConclusionsOur study supports the theoretical prediction that polymorphism should be governed by few genes of major effect, but implies broader genetic influence on variation in constituent morph traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0757-2) contains supplementary material, which is available to authorized users.