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1,423 results for “separation”
Data from: Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA genes (rDNA) organisation
In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (~30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants.
Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes
Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (1) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (2) in dioecious populations, male clones are larger and flower more often than female clones because of sex-differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet- and genet-based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in eastern N. America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations there was no difference in clone size between females and males; ramet- and genet-based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.
Data from: Spatial separation without territoriality in shark communities
Spatial separation within predator communities can arise via territoriality but also from competitive interactions between and within species. However, linking competitive interactions to predator distribution patterns is difficult and theoretical models predict different habitat selection patterns dependent on habitat quality and how competition manifests itself. While models generally consider competitors to be either equal in ability, or for one phenotype to have a fixed advantage over the other, few studies consider that an animal may only have a competitive advantage in specific habitats. We used > 10 years of telemetry data, habitat surveys and behavioral experiments, to show spatial partitioning between and within two species of reef shark (grey reef, Carcharhinus amblyrhinchos, and blacktip reef sharks, C. melanopterus) at an unfished Pacific atoll. Within a species, sharks remained within small 'sub-habitats' with very few movements of individuals between sub-habitats, which previous models have suggested could be caused by intra-specific competition. Blacktip reef sharks were more broadly distributed across habitat types but a greater proportion used lagoon and backreef habitats, while grey reef sharks preferred forereef habitats. Grey reef sharks at a nearby atoll where blacktip reef sharks are absent, were distributed more broadly between habitat types than when both species were present. A series of individual-based models predict that habitat separation would only arise if there are competitive interactions between species that are habitat-specific, with grey reefs having a competitive advantage on the forereefs and blacktips in the lagoons and backreef. We provide compelling evidence that competition drives distribution patterns and spatial separation of a marine predator community, and highlight that competitive advantages may not be constant but rather dependent on habitats.
Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data
Proportional and separate models able to apply different combination of substitution rate matrix and among-site rate variation model to each locus are frequently used in phylogenetic studies of multilocus data. However, the selection from among nonpartitioned (i.e., a common combination of models is applied to all-loci concatenated sequences), proportional, and separate models is usually based on the researcher's preference rather than on any information criteria. The present study describes two programs, "Kakusan4" (for DNA sequences) and "Aminosan" (for amino-acid sequences), that allow the selection of evolutionary models based on several types of information criteria. The programs can handle both multilocus and single-locus data, in addition to providing an easy-to-use wizard interface and a non-interactive command line interface. In the case of multilocus data, substitution rate matrices and among-site rate variation models are compared at each locus and at all-loci concatenated sequences, after which nonpartitioned, proportional, and separate models are compared based on information criteria. The programs also provide model configuration files for MrBayes, PAUP*, PHYML, RAxML, and Treefinder to support further phylogenetic analysis using a selected model. The best-fit models were found to differ depending on the data set. Furthermore, differences in the information criteria among nonpartitioned, proportional, and separate models were much larger than those among the nonpartitioned models. These findings suggest that selecting from nonpartitioned, proportional, and separate models results in a better phylogenetic tree. Kakusan4 and Aminosan are available at http://www.fifthdimension.jp/. They are licensed under GNU GPL Ver.2, and are able to run on Windows, MacOS X, and Linux.
Data from: Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change
To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.
Data from: Separate block based parameter estimation method for Hammerstein systems
Different from the output-input representation based identification methods of two-block Hammerstein systems, this paper concerns a separate block based parameter estimation method for each block of a two-block Hammerstein CARMA system, without combining the parameters of two parts together. The idea is to consider each block as a subsystem and to estimate the parameters of the nonlinear block and the linear block separately (interactively), by using two least squares algorithms in one recursive step. The internal variable between the two blocks (the output of the nonlinear block, and also the input of the linear block) is replaced by different estimates: when estimating the parameters of the nonlinear part, the internal variable between the two blocks is computed by the linear function; when estimating the parameters of the linear part, the internal variable is computed by the nonlinear function. The proposed parameter estimation method possesses property of the higher computational efficiency compared with the previous over-parameterization method in which many redundant parameters need to be computed. The simulation results show the effectiveness of the proposed algorithm.
Data from: Niche separation, ontogeny, and heterospecific alarm responses in centrarchid sunfish
Behavioral responses to alarm cues in aquatic species are typically examined with emphasis on the potential survival benefits accrued by conspecific receivers. By contrast, heterospecific responses to alarm cues and changes in responses with ontogeny in fishes are relatively unexplored. Taking an ecological niche perspective, we hypothesized that the response patterns of fish to risky chemical cues should be closely related to their degree of niche differentiation, which increases with ontogeny. We tested this hypothesis using the responses of adults from sympatric bluegill (Lepomis macrochirus) and pumpkinseed (L. gibbosus) populations to the alarm cues of conspecific and heterospecific adults and juveniles, including water as a control treatment. Responses measured consisted of changes in body posture (time spent with the dorsal fin <30º, between 30º and 60º, or >60º) and behavior (times spent still, frozen, at the surface, or on the bottom of the tank). Both adult bluegill and pumpkinseed spent significantly more time with their fins held >60º in response to adult versus juvenile alarm cues, with these responses mediated by donor species such that adult conspecific cues resulted in greater responses than heterospecific cues. The same general pattern was observed in the behavioral measures. These results demonstrate that behavioral response patterns to chemical alarm cues in sunfishes are highly plastic, and are likely related to niche separation in adults. Our findings open new lines of research into the role of ecological niches in shaping behavioral responses of fish to risky information.
Data from: Heteroploid Knautia drymeia (Caprifoliaceae) includes K. gussonei and cannot be separated into diagnosable subspecies
Premise of the study: Knautia drymeia is a morphologically variable, diploid and tetraploid temperate forest understory species distributed in southeastern Europe and adjacent areas. The species is an excellent system to explore the influence of polypoidy on taxonomic delineations, the role of hybridization among genetically distant populations in polyploid evolution, as well as the impact of glacial refugia on the evolution of polyploids. Methods: Amplified fragment length polymorphism fingerprinting and multivariate analyses of morphological characters were performed on 57 populations spanning the distribution area of K. drymeia. K-means clustering, comparison of in-silico tetraploids and observed tetraploids, and a phylogeographic analysis using relaxed random walks were used to explore the genetic structure within the diploids, to infer the origin of the tetraploids and to reconstruct range expansion through time. Further, we contrasted morphology and genetic groups with current taxonomy and evaluated the status of the tetraploid Apennine endemic K. gussonei and the intraspecific taxa of K. drymeia. Key Results: The genetic structure was strongly geographically correlated and yielded four genetic groups; K. gussonei was inseparable from K. drymeia. Distributions of diploid lineages are suggestive of glacial refugia in the northwestern-most and southeastern Balkan Peninsula. Polyploids originated at least two times, as autopolyploids and probably additionally also as allopolyploids. Morphological divergence corresponded with neither genetic groups nor current taxonomy. Conclusions: Genetic and morphometric data neither confirmed divergence of K. gussonei nor recognition of subspecies within K. drymeia. We therefore propose treating K. drymeia as morphologically and genetically variable species without infraspecific taxa.
Data from: Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness
Antagonistic pleiotropy (AP) – where alleles of a gene increase some components of fitness at a cost to others – can generate balancing selection, and contribute to the maintenance of genetic variation in fitness traits, such as survival, fecundity, fertility, and mate competition. Previous theory suggests that AP is unlikely to maintain variation unless antagonistic selection is strong, or AP alleles exhibit pronounced differences in genetic dominance between the affected traits. We show that conditions for balancing selection under AP expand under the likely scenario that the strength of selection on each fitness component differs between the sexes. Our model also predicts that the vast majority of balanced polymorphisms have sexually antagonistic effects on total fitness, despite the absence of sexual antagonism for individual fitness components. We conclude that AP polymorphisms are less difficult to maintain than predicted by prior theory, even under our conservative assumption that selection on components of fitness is universally sexually concordant. We discuss implications for the maintenance of genetic variation, and for inferences of sexual antagonism that are based on sex-specific phenotypic selection estimates – many of which are based on single fitness components.
Data from: Various competitive interactions explain niche separation in crop-dwelling web spiders
Competition for resources is a major organizing principle in communities of organisms that share similar ecological niches. Niche separation by means of exploitation or interference competition was investigated in two taxa of crop-inhabiting spiders that overlap in microhabitat use and have similar web design. Competition for prey and web sites was tested in microcosm experiments with the most common species that build sheet-webs: Enoplognatha gemina (Theridiidae) and Alioranus pastoralis (Linyphiidae). A field survey over the crop season provided data on spatial and temporal dispersion of Enoplognatha spp. (Theridiidae) and linyphiid spiders (Linyphiidae) and on availability of prey over the season. In the microcosm experiments, both taxa took springtails as prey, but only Enoplognatha fed on aphids. Differences in diet, however, could not be attributed to either exploitative or interference competition. Spatial separation of websites was attained by vertical displacement of webs in the vegetation (Enoplognatha) and by avoidance of patches occupied by conspecific or heterospecific individuals (linyphiids). In the field, densities of linyphiids and Enoplognatha were correlated negatively and webs were over-dispersed relative to a random distribution. Both taxa colonized the field at the start of the season; linyphiids colonized as adults, quickly reproduced, and had a second adult peak; Enoplognatha matured in the middle of the season and their numbers remained fairly constant over the season. The combined experimental manipulations and field data suggest that niche separation occurs at different scales. The hypothesis of competition for websites was partially supported, while prey preference (or tolerance) and temporal differences in life history stages also may explain the negative correlations between densities of the two taxa.
Data from: The genetic covariance between life-cycle stages separated by metamorphosis.
Metamorphosis is common in animals, yet the genetic associations between life cycle stages are poorly understood. Given the radical changes that occur at metamorphosis, selection may differ before and after metamorphosis, and the extent that genetic associations between pre- and post-metamorphic traits constrain evolutionary change is a subject of considerable interest. In some instances, metamorphosis may allow the genetic decoupling of life cycle stages, whereas in others, metamorphosis could allow complementary responses to selection across the life cycle. Using a diallel breeding design, we measured viability at four ontogenetic stages (embryo, larval, juvenile and adult viability), in the ascidian Ciona intestinalis and examined the orientation of additive genetic variation with respect to the metamorphic boundary. We found support for one eigenvector of G (gobsmax), which contrasted larval viability against embryo viability and juvenile viability. Target matrix rotation confirmed that while gobsmax shows genetic associations can extend beyond metamorphosis, there is still considerable scope for decoupled phenotypic evolution. Therefore, although genetic associations across metamorphosis could limit that range of phenotypes that are attainable, traits on either side of the metamorphic boundary are capable of some independent evolutionary change in response to the divergent conditions encountered during each life cycle stage.
FIGURE 1 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 1. Assignment of specimens examined in the course of this study to species.
FIGURE 5. Neighbour Joining tree obtained from the 505 in On the identity of Isoperla curtata (Plecoptera: Perlodidae): behavioural and molecular approaches show the existence of two separate species
FIGURE 5. Neighbour Joining tree obtained from the 505 bp COI fragment for studied populations.
FIGURE 2 in On the identity of Isoperla curtata (Plecoptera: Perlodidae): behavioural and molecular approaches show the existence of two separate species
FIGURE 2. Drumming signal of a male from a southern population (Arroyo de la Nava del Rey).
FIGURE 1 in On the identity of Isoperla curtata (Plecoptera: Perlodidae): behavioural and molecular approaches show the existence of two separate species
FIGURE 1. Drumming signal of a male from a north-central population (Garganta de Iruelas).
FIGURE 4 in On the identity of Isoperla curtata (Plecoptera: Perlodidae): behavioural and molecular approaches show the existence of two separate species
FIGURE 4. Drumming signal of a female from a southern population (Arroyo de la Nava del Rey).
FIGURE 4. Blattisocius everti n in Blattisocius (Acari, Blattisociidae) species from Brazil, with description of a new species, redescription of Blattisocius keegani and a key for the separation of the world species of the genus
FIGURE 4. Blattisocius everti n. sp., larva. A. Dorsal view; B. Ventral view; C. Chelicera.
MUSDB18-HQ Test Set Inference Outputs for Models from "A Generalized Bandsplit Neural Network for Cinematic Audio Source Separation"
Open the record for dataset details and reuse information.
FIG. 3 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 3.—Populationstructure inference based on STRUCTURE analysis of 199,921 sites for individual bats from four Hawaiian Islands. (A) Ad hoc statistic delta Kanalysis indicates a peak at the Κ = 5; (B) STRUCTURE population inference with Κ = 3, 4, 5. Sample information included in supplementary table S4, Supplementary Material online.
Online repository for: "Dielectrophoretic particle chromatography: From batch processing to semi-continuous high throughput separation"
<p>Please check the readme.odt file for details.</p>
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