DOI: 10.5061/dryad.266h9
title: Data from: Population genomics of a symbiont in the early stages of a pest invasion

description: Invasive species often depend on microbial symbionts, but few studies have
 examined the evolutionary dynamics of symbionts during the early stages of
 an invasion. The insect Megacopta cribraria and its bacterial nutritional
 symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in
 2009. While M. cribraria was initially discovered on wild kudzu plants, it
 was found as a pest on soybeans within 1 year of infestation. Because
 prior research suggests Ishikawaella confers the pest status—that is, the
 ability to thrive on soybeans—in some Megacopta species, we performed a
 genomic study on Ishikawaella from US. Megacopta cribraria populations to
 understand the role of the symbiont in driving host plant preferences. We
 included Ishikawaella samples collected in the first days of the invasion
 in 2009 and from 23 locations across the insect's 2011 US range. The
 0.75 Mb symbiont genome revealed only 47 fixed differences from the
 pest-conferring Ishikawaella in Japan, with only one amino acid change in
 a nutrition-provisioning gene. This similarity, along with a lack of fixed
 substitutions in the US symbiont population, indicates that Ishikawella
 likely arrived in the US capable of being a soybean pest. Analyses of
 allele frequency changes between 2009 and 2011 uncover signatures of both
 positive and negative selection and suggest that symbionts on soybeans and
 kudzu experience differential selection for genes related to nutrient
 provisioning. Our data reveal the evolutionary trajectory of an important
 insect-bacteria symbiosis in the early stages of an invasion, highlighting
 the role microbial symbionts may play in the spread of invasive species.
description: rawvar_rmdup.ind1Raw SNP data from Index 1 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind2Raw SNP data from Index 2 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind3Raw SNP data from Index 3 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind4Raw SNP data from Index 4 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind5Raw SNP data from Index 5 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind6Raw SNP data from Index 6 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind7Raw SNP data from Index 7 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind8Raw SNP data from Index 8 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind9Raw SNP data from Index 9 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind10Raw SNP data from Index 10 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind11Raw SNP data from Index 11 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind12Raw SNP data from Index 12 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind13Raw SNP data from Index 13 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind14Raw SNP data from Index 14 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind15Raw SNP data from Index 15 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind16Raw SNP data from Index 16 for Ishikawaella U.S. 2009 (ground zero) from Illumina HiSeq generated using GATK.rawvar_rmdup.ind17Raw SNP data from Index 17 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind18Raw SNP data from Index 18 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind19Raw SNP data from Index 19 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind20Raw SNP data from Index 20 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind21Raw SNP data from Index 20 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind22Raw SNP data from Index 22 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind23Raw SNP data from Index 23 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.rawvar_rmdup.ind24Raw SNP data from Index 24 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.