1,721,648 research outputs found
Recombination modulates how selection affects linked sites in Drosophila
Get PDFOne of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura physical genome in two separate recombination maps, and 31.3% of the D. miranda physical genome, and we identified both global and local differences in recombination rate between these two closely related species. Using only regions with conserved recombination rates between and within species and accounting for multiple covariates, our data support the conclusion that recombination is positively related to diversity because recombination modulates hitchhiking in the genome. Finally, our data show that diversity around nonsynonymous substitutions is recovered at closer distances in areas of higher recombination than in areas of lower recombination — empirically demonstrating that recombination rate can limit the size and severity of potential selective sweeps
Toxic Y-chromosome in D. miranda
No full textLarge portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity. Repeat-rich Y chromosomes can act as reservoirs for TEs (toxic Y effect), and TEs may exploit vulnerabilities associated with incomplete genomic defenses during early development. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE misexpression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger neo-Y chromosome. In D. miranda, misexpression of TEs is associated with incomplete heterochromatin formation on the neo-Y and results in more de novo insertions of repeats in males compared to females. We find that because the neo-Y of D. miranda still contains many actively transcribed genes embedded in TEs, the formation of silencing heterochromatin is compromised, causing elevated TE expression and mobilization. This lends support to the idea that the 'toxic Y chromosome' can create a mutational burden in males when genome-wide defense mechanisms are compromised, and reveals a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.RNA-seq:
Read counts at TEs are normalized by the median read counts at autosomal genes then averaged across replicate libraries. Read counts at genes are inferred using featureCounts in the Subread package. Libraries are generated by Lott et al 2014.
ChIP-seq:
Sex-specific H3K9me3 enrichment across the genome in 25kb windows. Enrichment is normalized using quantiles of spike-ins. Enrichment is averaged between libraries of the same sex and developmental stages.
de novo TE insertions:
Genomic regions with paired-end reads that span unique sequences and TEs are provided. Insertions with both the 5' and 3' junctions found are deemd true de novo insertions
Dosage compensation of the neo-X, and heterochromatin formation on the neo-Y of <i>D. miranda</i>.
No full text<p>(A) Schematic karyotype of <i>D. miranda</i>. Drosophila chromosomes are labeled as “Muller element” from A to F. In <i>D. miranda</i>, two fusions between element A (ancient X) and D, and the Y chromosome and element C created sex chromosomes of different ages. Element D became chrXR about ∼10–15 MY ago and element C became the neo-X and neo-Y chromosome about ∼1–1.5 MY ago. (B–C) Polytene chromosomes stained for H3K9me2 (green) and HP1a (red) in (B) female <i>D. miranda</i> and (C) male <i>D. miranda</i>. (D) Co-immunolocalization of MSL3-TAP (red) and H3K9me2 (green) in transgenic male <i>D. miranda</i> expressing TAP-tagged MSL3. The neo-Y is becoming heterochromatic, as shown by prominent H3K9me2 and HP1 binding, while all three X-chromosome arms are acquiring dosage compensation in <i>D. miranda</i> males.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Acquisition of CES on the <i>D. miranda</i> neo-X chromosome.
No full text<p>(A) MRE identified in <i>D. miranda </i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001711#pbio.1001711-Alekseyenko3" target="_blank">[32]</a>. (B) Number of occurrences of the different mutational events identified to create a MRE on the neo-X. The “Undecipherable” category refers to CES where no MRE was detected on the neo-X (“No motif hit”; 6 CES), or where <i>D. miranda</i> had an equally scoring (“Presite”; 12 CES) or lower scoring motif than the outgroup species (“Lower scoring motif”; 7 CES). This suggests that some of the CES may be false positives (i.e., they are highly bound by the MSL-complex through spreading rather than through MRE-mediated targeting) or that secondary mutations in adjacent regions occurred to enable efficient recruitment of the MSL complex to suboptimal MREs on the neo-X. (C) Examples of different mutational events identified on the neo-X to create a novel MRE. Multiple species alignments are shown for dmir, <i>D. miranda</i>; dpse, <i>D. pseudoobscura</i>; daff, <i>D. affinis</i>; and the MRE element is highlighted in grey.</p
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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