1,721,004 research outputs found
FIG. 4 in Genetic diversity of Malagasy baobabs: implications for conservation
No full textFIG. 4. — Observed nucleotide diversity PI (π) for the six Adansonia L. species endemic to Madagascar. Northern and southern populations of A. za Baill. are combined here. When distinguishing between geographic populations of A. za, nucleotide diversity was the same as combined for southern populations (π = 0.0029), but less for northern populations (π = 0.0026).Published as part of Karimi, Nisa, Grover, Corrinne E., Gallagher, Joseph P., Conover, Justin L., Miller, Emma R., Wendel, Jonathan F. & Baum, David A., 2022, Genetic diversity of Malagasy baobabs: implications for conservation, pp. 37-47 in Adansonia (3) 44 (6) on page 43, DOI: 10.5252/adansonia2022v44a6, http://zenodo.org/record/622517
FIG. 1 in Genetic diversity of Malagasy baobabs: implications for conservation
No full textFIG. 1. — Flowers of the six species of baobabs endemic to Madagascar: A, Adansonia grandidieri Baill.; B, A. madagascariensis Baill.; C, A. perrieri Capuron; D, A. rubrostipa Jum. & H. Perrier; E, A. suarezensis H. Perrier; F, A. za Baill. Photographs by David A. Baum and Nisa Karimi.Published as part of Karimi, Nisa, Grover, Corrinne E., Gallagher, Joseph P., Conover, Justin L., Miller, Emma R., Wendel, Jonathan F. & Baum, David A., 2022, Genetic diversity of Malagasy baobabs: implications for conservation, pp. 37-47 in Adansonia (3) 44 (6) on page 39, DOI: 10.5252/adansonia2022v44a6, http://zenodo.org/record/622517
Evolutionary dynamics of mechanisms that affect genome size in the cotton genus (Gossypium)
Full text linkEukaryotic genomes vary remarkably in size even between closely related species. This variation reflects a balance between mechanisms that expand and contract genomes, and which vary in their magnitude during evolution. While much is known about mechanisms that affect genome size expansion, particularly the effects of transposable elements (TEs), less is known concerning deletional mechanisms and the rates and scales at which they operate. The goal of this thesis was to extend our understanding of genome size evolution by studying diploid Gossypium species that vary twofold in genome size as well as their polyploid derivative, and using a phylogenetic approach employing as an outgroup Gossypioides kirkii. We assessed the rates and mechanisms operating in four Gossypium genomes: the two co-resident genomes of the allopolyploid G. hirsutum and its model diploid progenitors, G. arboreum and G. raimondii. Two BAC-sized regions of the cotton genome were sequenced and analyzed with respect to the mechanisms that alter genome size, and rates of sequence change (insertions, deletions, and net) were calculated for each region and genome. These regions were similar in that they both represent gene islands with extraordinary conservation of intergenic space; however, the regions did differ in terms of amount of genome size change. Whereas the first region showed no signs of the twofold genome size difference characterizing the species, the second region mirrored this difference, as the smaller genomes were represented by half the amount of sequence as the larger genomes. Notably, while still gene dense, this region had nearly half the gene density of the previous region. Analysis of the mechanisms responsible for shaping these regions led to several conclusions. First, genome size change is attributable to many mechanisms, some of which are unknown. Second, while TEs had the greatest impact on genome size differences, other mechanisms, such as intra-strand homologous recombination, played key roles as well. Finally, genomes of diploid Gossypium species have experienced growth, whereas the polyploid has experienced contraction; however, the rates and direction of change vary between regions and over time.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing
Full text linkWe employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33X genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following trans-oceanic dispersal from Africa about 6.6 mya, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 mya), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNA vs. nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per my, with non-synonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a two-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared to the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.This is a manuscript of an article published as Grover, Corrinne E., I. I. Arick, A. Mark, Adam Thrash, Justin L. Conover, William S. Sanders, Daniel G. Peterson et al. "Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing." Genome Biology and Evolution (2018). doi: 10.1093/gbe/evy256.</p
Variations on the Author
Full text link“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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe 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
Full text linkWe 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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