17 research outputs found

    PhyBin: binning trees by topology

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    A major goal of many evolutionary analyses is to determine the true evolutionary history of an organism. Molecular methods that rely on the phylogenetic signal generated by a few to a handful of loci can be used to approximate the evolution of the entire organism but fall short of providing a global, genome-wide, perspective on evolutionary processes. Indeed, individual genes in a genome may have different evolutionary histories. Therefore, it is informative to analyze the number and kind of phylogenetic topologies found within an orthologous set of genes across a genome. Here we present PhyBin: a flexible program for clustering gene trees based on topological structure. PhyBin can generate bins of topologies corresponding to exactly identical trees or can utilize Robinson-Fould’s distance matrices to generate clusters of similar trees, using a user-defined threshold. Additionally, PhyBin allows the user to adjust for potential noise in the dataset (as may be produced when comparing very closely related organisms) by pre-processing trees to collapse very short branches or those nodes not meeting a defined bootstrap threshold. As a test case, we generated individual trees based on an orthologous gene set from 10 Wolbachia species across four different supergroups (A–D) and utilized PhyBin to categorize the complete set of topologies produced from this dataset. Using this approach, we were able to show that although a single topology generally dominated the analysis, confirming the separation of the supergroups, many genes supported alternative evolutionary histories. Because PhyBin’s output provides the user with lists of gene trees in each topological cluster, it can be used to explore potential reasons for discrepancies between phylogenies including homoplasies, long-branch attraction, or horizontal gene transfer events

    Complete genome sequence of Campylobacter fetus isolated from a sheep

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    Campylobacter fetusis an important reproductive pathogen of ruminantsthat occasionally infects humans. Here, we describe the complete circularized genomeof a strain ofCampylobacter fetussubsp.fetusisolated from a sheep. Thefinal assem-bly consisted of a unique contig with a length of 1,849,237 bp

    fig3_data_trip

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    mitochondria and wolbachia titers in TRiP knockdown experiment

    suppfig8_data_triprelexp

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    data for relative expression of mitochondria and wolbachi

    fig4c_data_intensitymid

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    wolbachia abundance from microscopy measured through fluorescence intensity in mid oogenesis from TRiP knockdow

    fig5_data_mitokd

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    wolbachia and mitochondria titers in mito knockdown experiment

    fig2_data_mitowols

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    data comparing mitochondria and wolbachia titers in wMel genotypes where wolbachia genotype determines wolbachia tite

    fig4a_data_intensitygerm

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    wolbachia abundance from microscopy measured through fluorescence intensity in germaria from TRiP knockdow

    fig1a_data_mitos

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    mitochondria titers in multiple lab genotype

    fig4b_data_intensityearly

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    wolbachia abundance from microscopy measured through fluorescence intensity in early oogenesis from TRiP knockdow
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