DOI: 10.5061/dryad.6qh25
title: Data from: Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages

description: Background: Sex presents evolutionary costs and benefits, leading to the
 expectation that the amount of genetic exchange should vary in conditions
 with contrasting cost-benefit equations. Like eukaryotes, viruses also
 engage in sex, but the rate of genetic exchange is often assumed to be a
 relatively invariant property of a particular virus. However, the rates of
 genetic exchange can vary within one type of virus according to geography,
 as highlighted by phylogeographic studies of cystoviruses. Here we merge
 environmental microbiology with experimental evolution to examine sex in a
 diverse set of cystoviruses, consisting of the bacteriophage φ6 and its
 relatives. To quantify reassortment we manipulated – by experimental
 evolution – electrophoretic mobility of intact virus particles for use as
 a phenotypic marker to estimate genetic exchange. Results: We generated
 descendants of φ6 that exhibited fast and slow mobility during gel
 electrophoresis. We identified mutations associated with slow and fast
 phenotypes using whole genome sequencing and used crosses to establish the
 production of hybrids of intermediate mobility. We document natural
 variation in electrophoretic mobility among environmental isolates of
 cystoviruses and use crosses against a common fast mobility φ6 strain to
 monitor the production of hybrids with intermediate mobility, thus
 estimating the amount of genetic exchange. Cystoviruses from different
 geographic locations have very different reassortment rates when measured
 against φ6, with viruses isolated from California showing higher
 reassortment rates than those from the Northeastern US. Conclusions: The
 results confirm that cystoviruses from different geographic locations have
 remarkably different reassortment rates –despite similar genome structure
 and replication mechanisms– and that these differences are in large part
 due to sexual reproduction. This suggests that particular viruses may
 indeed exhibit diverse sexual behavior, but wide geographic sampling,
 across varying environmental conditions may be necessary to characterize
 the full repertoire. Variation in reassortment rates can assist in the
 delineation of viral populations and are likely to provide insight into
 important viral evolutionary dynamics including the rate of coinfection,
 virulence and host range shifts. Electrophoretic mobility could be an
 indicator of important determinants of fitness and the techniques herein
 could be applied to the study of other viruses.
description: READMEREADME File for all Data
 from: Electrophoretic mobility confirms reassortment bias among geographic
 isolates of segmented RNA phagesphenotypic_mixing_experiment.csv (Phenotypic Mixing Experiment Data)See Table2_phenotypic_mixing.txt for information.phenotypic_mixing_experiment.csvTable2_phenotypic_mixing.txt (Table2 Phenotypic Mixing)Has code used for generating data for Table 2 of manuscript. Describes data in phenotypic_mixing_experiment.csv.Table2_phenotypic_mixing.txtFigure2 Genbank Accession Numbers from Genome SequencingGenbank Accession Numbers from Genome Sequencing used to generate Figure 2Figure2_genbank_numbers_genome_sequencing.txtFigure4_single_plaques.txt (Figure 4 Single Plaques)Description of data in single_plaques_from_single_burst.csv and code to generate Figure 4.Figure4_single_plaques.txtmobility_of_crosses.txt (Hybridization Rate Estimation Determination of Mobility)Describes data in mobility_of_crosses.csv and the analyses for that data set. This perhaps should be viewed first. The data here was used to generate Table 1, Figure 1C, Figure 5, and Figure 7.mobility_of_crosses.txtCalculation of Rf valuesIllustrates the process used to calculate Rf values (x axis on most graphs).calculation_of_Rf_values.pdfSchematic of Selection for Electrophoretic Mobilityllustrates the selection process used to generate the phi6-Fast and phi6-Slow strains as described in the methods. This figure is helpful while reading the Methods section "Selection for fast and slow electrophoretic mobility" in the paper.schematic_of_selection_for_electrophoretic_mobility.pdfsingle_plaques_from_single_burst.csvFigure 4 was generated using data from single_plaques_from_single_burst.csv as explained in Figure4_single_plaques.txtmobility_of_crosses.csv (Hybridization Rate Estimation Determination of Mobility)This file has the bulk of the data in the paper and the analyses are in mobility_of_crosses.txt. The data here was used to generate Table 1, Figure 1C, Figure 5, and Figure 7.mobility_of_crosses.csv