DOI: 10.5061/dryad.f4g56
title: Data from: Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: resistance to biological control catalyzes resurgence of an old pest

description: Biological control agents have several advantages over chemical control
 for pest management, including the capability to restore ecosystem balance
 with minimal non-target effects and a lower propensity for targets to
 develop resistance. These factors are particularly important in the
 invasive species control. The coconut rhinoceros beetle (Oryctes
 rhinoceros Linnaeus) is a major palm pest that invaded many Pacific
 islands in the early 20th century through human-mediated dispersal.
 Application of the Oryctes nudivirus in the 1960’s successfully halted the
 beetle’s first invasion wave and made it a textbook example of successful
 biological control. However, a recently discovered O. rhinoceros biotype
 that is resistant to the nudivirus appears to be correlated with a new
 invasion wave. We performed a population genomics analysis of 172 O.
 rhinoceros from seven regions, including native and invasive populations,
 to reconstruct invasion pathways and explore correlation between recent
 invasions and biotypes. From ddRAD sequencing, we generated datasets
 ranging from 4,000 to 209,000 loci using STACKS and IPYRAD software
 pipelines and compared genetic signal in downstream clustering and
 phylogenetic analyses. Analysis suggests that the O. rhinoceros resurgence
 is mediated by the nudivirus-resistant biotype. Genomic data has proven
 essential to understanding the new O. rhinoceros biotype’s, invasion
 patterns and interactions with the original biotype. Such information is
 crucial to optimization of strategies for quarantine and control of
 resurgent pests. Our results demonstrate that while invasions are
 relatively rare events, new introductions can have significant ecological
 consequences, and quarantine vigilance is required even in previously
 invaded areas.
description: Tree
 FilesPhylogenetic tree files
 obtained from RAxML and SVDquartets in .tre format. Newick tree for
 IPYsh4snp used for supplemental locus sharing plots.CRB ggplots2 R Script -
 Coverage PlotsR script documenting
 packages and code used to generate coverage plots used to summarize data
 used in this report.CRB_ggplots2_StatsPlots.RCRB pophelper R Script - Structure bar plotsR script documenting packages and code used to generate bar plots for visualizing Structure and fastStructure analyses performed in this report.CRB_Pophelper_StructurePlots.RCRB RADami R Script - Locus Sharing PlotsR script documenting packages and code used to generate locus sharing plots from IPYRAD loci data generated for this report.CRB_RADami_LocusSharingPlots.RCRB SNPrelate R Script - PCAR script documenting packages and code used to conduct a principle component analysis on Stacks SNP data in VCF format.CRB_SNPrelate_PCA.RCRB Undefined Removal R ScriptR script documenting the packages and steps taken to remove potentially potentially undefined sites from data matrices used in RAxML. Ascertainment Bias corrections require that potentially undefined sites due to missing data or uncertainty are removed.CRB_UndefinedRemoval.RStacks ScriptScript (command line) used for running STACKS for data filtering and assembly. Flag settings and parameters vary based on filtering requirements and desired outputs.Stacks_Script.txtIPYRAD parameters file - Shared by Min. 4 TaxaIPYRAD parameters file used for processing data files; Loci must be shared by a minimum of 4 taxa to be retained.ipyrad_share4_params.txtIPYRAD parameters file - Shared by Min. 35 TaxaIPYRAD parameters file used for processing data files; Loci must be shared by a minimum of 35 taxa to be retained.ipyrad_share35_params.txtDatasets and Alignments (Updated 9-11-18)A selection of key data sets and sequence alignments used for the associated project. VCF files generated using IPYRAD and STACKS pipelines. Conversions between VCF and other formats using PGDSpider. '.data' and '.xlsx' files used for MOMMENTS and GenAlEx respectively. COI sequence data set used for biotype assessment derived from Sanger sequencing. Please see associated manuscript for further details.Momments_Script_Palau1xPalau2Python script used to perform the MOMMENTS analysis described in this report.