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32 results for “Convergence Analysis”
Text-fig. 34. Scanning electron microscope (SEM) images of monocolpate pollen of Mayoa portugallica from a fragmentary stamen; Torres Vedras locality, Portugal. a) Stamen fragment that yielded the pollen in this Text-figure; b–d) Pollen grains showing the distinctive perpendicular orientation of two broad bands of striae that converge at the ends of the grains. Specimen, TV44-S136663. Scale bars 150 Μm (a), 6 Μm (b, c), 3 Μm (d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 34. Scanning electron microscope (SEM) images of monocolpate pollen of Mayoa portugallica from a fragmentary stamen; Torres Vedras locality, Portugal. a) Stamen fragment that yielded the pollen in this Text-figure; b–d) Pollen grains showing the distinctive perpendicular orientation of two broad bands of striae that converge at the ends of the grains. Specimen, TV44-S136663. Scale bars 150 Μm (a), 6 Μm (b, c), 3 Μm (d).
Data to reproduce analysis in Convergent evolution of extrachromosomal DNA in mCRPC paper
<p>Targeted cancer therapies can prolong the lives of men with metastatic castration resistant prostate cancer (mCRPC). However, these treatments also selectively favor the growth of tumor cells that harbor therapy resistance, and mCRPC is currently lethal. It has been challenging to study factors influencing how therapy resistance develops in this setting because few autopsy studies of have been performed in the settings of DNA-repair deficient mCRPC. Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 53 mCRPC tumors from six such men using deep whole genome and transcriptome analysis, validating our observations in an independent cohort of 135 mCRPC tumors. We identified intra-patient heterogeneity in clinically actionable DNA repair deficiencies and transcriptionally-defined tumor subtypes. Identical polygenic DNA repair resistance mutations were present in physically distinct tumors within the same individual, suggesting that these mutations pre-exist selection by later targeted therapy. Extra-chromosomal DNA (ecDNA) was present in more than half of mCRPC biopsies and frequently amplified the androgen receptor (<em>AR</em>) and enhancers of <em>AR</em> and <em>MYC</em>. Individual ecDNA amplicons included multiple driver genes on different chromosomes, and arose multiple times within distinct tumors in a single patient. The presence of ecDNA was significantly associated with whole genome doubling, chromothripsis, and with inactivating <em>TP53</em> alterations. We conclude that ecDNA amplification is a major contributor to therapy resistance in mCRPC and that late-stage mCRPC develops intra-patient heterogeneity in response to targeted therapy.</p>
Supplemental Information on the Weighted Gene Co-expression Network Analysis performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide"
<p>Supplemental Information on the Weighted Gene Co-expression Network Analysis (WGNCA) performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide"</p> <p>The results are sorted by the three species analysed: the two algae <em><span>Zygnema circumcarinatum</span></em><span> SAG 698-1b (<em>Zygnema</em>) and <em>Mesotaenium endlicherianum </em></span><span>SAG 12.97 (<em>Mesotaenium</em>); and the bryophyte <em>Physcomitrium patens</em></span><span><em> </em>strain Gransden 2004 (<em>Physcomitrium</em>).</span></p>
Numerical back-analysis of short-term convergence data of sections within zone A (from chainage 1905 to chainage 2723) in the Fréjus road tunnel
<p>Numerical back-analysis of short-term convergence data of sections within zone A (from chainage 1905 to chainage 2723) in the Fréjus road tunnel</p>
Data from: Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes
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Data from: Fish assemblage convergence along stream environmental gradients: an intercontinental analysis
Species that pass through similar environmental filters, regardless of geographic proximity or evolutionary history, are expected to share many traits, resulting in similar assemblage trait distributions. Convergence of assemblage trait distributions among different biotic regions would indicate that consistent ecological processes produce repeated patterns of adaptive evolution. This study analyzes trait-environment relationships across multiple stream fish assemblages representing evolutionarily divergent faunas. We hypothesized that trait-environment patterns converge across regional faunas in response to a common set of environmental filters acting on functional traits. One hundred and ninety-seven species and forty streams were sampled from five regions: Belize, Benin, Brazil, Cambodia, and United States of America. By examining trait-environment plots, multiple congruent trait-environment patterns were found across all regions, indicative of a consistent set of environmental filters acting on local community assembly. The consistency of these patterns strongly suggests that water velocity and habitat structural complexity function as universal environmental filters, producing similar assemblage trait distributions in streams across all regions. Bivariate relationships were not universal, and only one of the associations between a single functional trait and single environmental variable was statistically significant across all five regions. Strong phylogenetic signal was found in traits and habitat use, which implies that niche conservatism also influenced assemblage trait distributions. Overall, results support the idea that habitat templates structure trait distributions of stream fish assemblages and do so in a consistent manner.
Data from: A phylogenetic analysis of the dirt ants, Basiceros Schulz (Formicidae: Myrmicinae): inferring life histories through morphological convergence
Ants of the genus Basiceros (Hymenoptera: Formicidae: Myrmicinae) are elusive species known only from Neotropical rainforests. Little information is available regarding their natural history, and nothing is known about the phylogenetic relationships among species within the genus. The genus has been the subject of some controversy regarding generic delimitation but is currently a member of the "Basiceros-genus group" following recent classification changes. For mouthparts, labral and mandibular morphologies present considerable variation in the Basiceros-genus group, likely a result of adaptive evolution. In Basiceros, those differences can be observed in the labrum shape and the various degrees of development of the labral cleft and the clypeomandibular space. Here, in an attempt to illuminate the evolution of the group, species boundaries are tested for Basiceros. The evolutionary relationships of its species are investigated using molecular and morphological data. Bayesian inference (BI) and maximum likelihood (ML) analyses of a molecular dataset consisting of up to nine genes (three mitochondrial, six nuclear) and including samples from multiple populations of all known Basiceros taxa recovered the monophyly of the genus and of its species, with two well resolved internal clades: the singularis clade and the disciger clade. Focusing on the female castes of Basiceros, an ancestral state reconstruction is presented for mandibles and labrum morphology. The results suggest that the labrum and clypeomandibular morphologies are highly labile, although phylogenetically important characters in the genus. Mouthpart traits indicate a strong correlated evolutionary history potentially associated with specialized feeding habits.
Phylogenomic analysis reveals convergent evolution of shrubby Clematis species
<p><em>Clematis </em>of the buttercup family is one of the most popular garden flowers in the world, being crowned as the “Queen of Climbers.” It is well known for its climbing habit, but it also has shrubby members with poorly known evolutionary origins. The relationships among the major <em>Clematis </em>groups still remain controversial. In this study, we assembled the complete plastome and nrDNA sequences of 56 <em>Clematis </em>species representing most of the sections, and reconstructed the phylogenetic framework using both datasets. Our sampling covered all species of the shrubby <em>C</em>. sect. <em>Fruticella s. str.</em> and the taxonomically controversial species allied to the section to test the monophyly of section <em>Fruticella </em>and trace the evolution of habits in the genus. Using both likelihood and Bayesian methods, the two datasets of DNA sequences generated similar, but not identical, phylogenetic relationships. The complete plastome sequences delivered a better resolved phylogeny, supporting five well-resolved major clades for all sampled species, except for a first-diverged African species. Many of the morphological characters widely used for taxonomy were shown to represent parallel or convergent evolution. Molecular dating inferred that all major <em>Clematis </em>clades radiated during the early Pliocene, with a species radiation during the Quaternary. The erect, shrubby habits of <em>Clematis </em>were inferred to have evolved multiple times in eastern Asia. <em>Clematis</em> sect. <em>Meclatis</em> is likely sister to <em>C</em>. sect.<em> Fruticella</em>, and the latter diversified during the late Quaternary. The cold, dry Quaternary climate was hypothesized to have facilitated species diversification and dispersal of <em>C</em>. sect. <em>Fruticella.</em></p>
Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers
Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for analyzing this dominant marker may not be entirely clear in the context of species delimitation. In this study, we use AFLPs and mtDNA to investigate cryptic speciation in the Trimeresurus macrops complex that belongs to a taxonomically difficult lineage of Asian pitvipers. We analyze AFLPs using population genetic, phylogenetic, multivariate statistical, and Bayes Factor Delimitation methods. A gene tree from three mtDNA markers provided additional evidence. Our results show that the inferences about species boundaries that can be derived from population genetic analysis of AFLPs have certain limitations. In contrast, four multivariate statistical analyses produced clear clusters that are consistent with each other, as well as with Bayes Factor Delimitation results, and with mtDNA and total evidence phylogenies. Furthermore, our results concur with allopatric distributions and patterns of variation in individual morphological characters previously identified in the three proposed species: T. macrops sensu stricto, T. cardamomensis, and T. rubeus. Our study provides evidence for reproductive isolation and genetic distinctiveness that define these taxa as full species. In addition, we re-emphasize the importance of examining congruence of results from multiple methods of AFLP analysis for inferring species diversity.
Analysis workflow and dataset for Maxillary palps of tephritidae are tuned to food rather than oviposition volatiles and converge on ecology
<p>In this repository all data and scripts for generating the figure in the manuscript "Maxillary palps of tephritidae are tuned to food rather than oviposition volatiles and converge on ecology" can be found. <br><br>Data is found under /Data with recording for each fruit and the combined lure can be found under its respective name.</p> <p>In Data/sample GC-EPD .pptx there are also sample traces.</p> <p>In workflow most of the script needed to generate the figure that ends up in Output is available</p>
Fig. 6 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 6. Ancestral trait estimation for labrum (general shape and distal margin) and clypeomandibular space of Basiceros ants. Analyses were conducted with the ace function in the APE R package (Paradis et al. 2004) using the pruned1 topology as input (see Material and Methods section). For all traits, each node is graphically represented for the state with the highest probability for the model favored under a likelihood ratio test (see Supp Figs. S2 and S3 and Table S6 [online only]). Graphic size corresponds with likelihood probabilities for a particular node: small graphics represents 0–50% probability, bigger graphics> 50%. Tips present labrum outline for each of the Basiceros species (see Fig. 2). Outcomes for each node for the ER model are shown in more detail in Supp Figs. S3 and S4 (online only).
Fig. 2 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 2. Dorsal view of the labrum (dorsolabrum) of the worker caste of Basiceros species, dtg: dorsal transverse groove, lo: lateral lobe. (A) B. conjugans; (B) B. convexiceps; (C) B. disciger; (D) B. militaris; (E) B. scambognathus; (F) B. singularis (CASENT063735); (G) B. manni; (H) Basiceros sp. n. A, dashed line: tentative reconstruction of posterolabral limits. Crossed arrows give the orientation: a, anterior; p, posterior. Scale bar: 0.1 mm. Labrum shape in Basiceros can be long triangular and sinuate (A, C, D), long triangular and acute (B, H), triangular short (E) or (F, G) lunate. For the distal margin of labrum lobes can have a wide (C) or narrow clef (A, B, D, H), can be blunt with a short cleft (E) or rounded (F, G).
Fig. 5 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 5. Phylogeny of Basiceros ants, analysis with the pruned1 dataset. See Supp Tables S1 and S2 (online only) for taxon codes and further specimen information.Topology presented was obtained from MrBayes and GARLI analyses. Branch length follows MrBayes output, scale bar indicates estimated number of nucleotide substitutions per site. Bayesian posterior probability (PP, obtained with MrBayes) or maximum likelihood bootstrap support (MLBS, obtained with GARLI) values are indicated in most nodes, except for those recovered with high support (>0.95/95%) for both analyses.
Fig. 7 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 7. Distribution map of Basiceros. (A) singularis clade; (B) disciger clade. Georeferenced specimen records from Probst (2015).
Fig. 3 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 3. Ventral view of the labrum (ventrolabrum) of the female caste of Basiceros species,black arrows:an example of specialized ventral setae. (A) B. conjugans; (B) B. convexiceps; (C) B. disciger; (D) B. militaris; (E) B. scambognathus; white arrows point to the anterior margin of the 'basal plate'; (F) B. singularis (CASENT063735); (G) B. manni, mpfl: posterior frontolabral muscle remnants, mafl: anterior frontolabral muscle remnants, to: torma. Crossed arrows give the orientation: a, anterior; p, posterior. Scale bar: 0.1 mm.
Fig. 4 in A Phylogenetic Analysis of the Dirt Ants, Basiceros (Formicidae: Myrmicinae): Inferring Life Histories Through Morphological Convergence
Fig. 4. Frontal view of Basiceros species, highlighting mandible shape and clypeomandibular space of the female caste. (A) B. conjugans; (B) B. disciger; (C) B. militaris; (D) B. scambognathus; (E) B. manni, clm. space: clypeomandibular space; (F) B. singularis; (G) Basiceros sp. n. A, me: external margin, dashed line: anteroclypeal margin, bold line: basal margin; (H) B. convexiceps. Figures not to scale. In Basiceros, the clypeomandibular space is either absent (B–D), narrow (A), moderate (H), or broad (E–G).
Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"
<p>Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"</p>
Data from: A phylogenetic analysis of the dirt ants, Basiceros Schulz (Formicidae: Myrmicinae): inferring life histories through morphological convergence
Open the record for dataset details and reuse information.
Data from: Fish assemblage convergence along stream environmental gradients: an intercontinental analysis
Open the record for dataset details and reuse information.
Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers
Open the record for dataset details and reuse information.
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