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Inferring Patterns and Processes of Emergence in Clonal Phytophthora Epidemics using Population Genomic Approaches
No full textOomycete and fungal pathogens threaten food, fiber, and forests around the world. With climate change, these pathogens are expected to emerge more frequently. Evolution can facilitate their emergence through mechanisms such as mutations that change or expand host range. Characterizing evolutionary mechanisms in plant pathogens will contribute to our ability to predict how or when a pathogen might emerge. This dissertation used population and comparative genomic approaches to characterize patterns of emergence in two species of plant pathogenic oomycetes.
The focus of this dissertation is on Phytophthora ramorum, the causal agent of sudden oak death and a threat to forests in the Western US and in Europe. Many oomycetes and fungi including P. ramorum have mixed mating systems, allowing them to reproduce sexually and asexually. Divergent lineages of P. ramorum have survived millions of years primarily clonally, and lineages have repeatedly re- emerged, making this a useful study system to understand how the costs of asexuality can be overcome.
Describing pathways in which pathogens move into and within ecosystems is important to reduce disease outbreaks. The nursery industry is an important component of the pathway in which pathogens are introduced to ecosystems. In chapter two we analyzed a collection of P. plurivora from Oregon nurseries to characterize genetic diversity. I show that the meta-population among four nurseries is dominated by one single clone, but there is additional cryptic diversity. In chapters three and four, I show that the clonal lineage EU1 was introduced only once in a four- year period after the outbreak was found. I also show that currently, there is more diversity in the population of the clonal lineage NA1 than in the population of the EU1 clonal lineage. This is consistent with population genetic theory, since the NA1 population has accumulated mutations over a longer period of time.
This work also compares the two P. ramorum lineages during the initial period of establishment in Oregon. While the EU1 population had lower diversity, we found cryptic diversity in the NA1 population. This is contrary to population genetic theory, as both populations were expected to show a similar pattern of variation. I show that this variation can mostly be attributed to losses of heterozygosity (LOH), a chromosomal aberration resulting in the spontaneous loss of one allele or chromosomal region in the diploid genome.
Plasticity can be an important factor in pathogen emergence. In chapter two, I show phenotypic plasticity in fungicide tolerance within a dominant clone of P. plurivora. In chapter four, I show genomic plasticity at a population-level is generated through LOH in an NA1 population of P. ramorum. In chapter five, I show plasticity of effector content among divergent lineages of P. ramorum. I do not attribute causality of pathogen emergence to the plasticity I characterize in this dissertation. However, this work proposes important contributions to a greater understanding of various roles plasticity could influence pathogen emergence.
Despite international efforts to prevent the movement of pathogens, the inadvertent transportation of infected plants and plant materials continues to challenge and threaten natural ecosystems. Understanding of population genetic and evolutionary biology of emerging and reemerging pathogens will be indispensable in our ability to understand and, eventually, predict epidemics
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
Intraspecific Variation and Recent Loss of Ancient, Conserved Effector Genes in the Sudden Oak Death Pathogen Phytophthora ramorum
No full textMembers of the Phytophthora genus are responsible for many important diseases in agricultural and natural ecosystems. Phytophthora ramorum causes devastating diseases of oak and tanoak stands in U.S. forests and larch in the United Kingdom. The four evolutionary lineages involved express different virulence phenotypes on plant hosts, and characterization of gene content is foundational to understanding the basis for these differences. Recent discovery of P. ramorum at its candidate center of origin in Asia provides a new opportunity for investigating the evolutionary history of the species. We assembled high-quality genome sequences of six P. ramorum isolates representing three lineages from Asia and three causing epidemics in Western U.S. forests. The six genomes were assembled into 13 putative chromosomes. Analysis of structural variation revealed multiple chromosome fusion and fission events. Analysis of putative virulence genes revealed variations in effector gene composition among the sequenced lineages. We further characterized their evolutionary history and inferred a contraction of crinkler-encoding genes in the subclade of Phytophthora containing P. ramorum. There were losses of multiple families and a near complete loss of paralogs in the largest core crinkler family in the ancestor of P. ramorum and sister species P. lateralis. Secreted glycoside hydrolase enzymes showed a similar degree of variation in abundance among genomes of P. ramorum lineages as that observed among several Phytophthora species. We found plasticity among genomes from multiple lineages in a Phytophthora species and provide insights into the evolutionary history of a class of anciently conserved effector genes.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license
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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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