Data from: Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations

Phylogeographic analyses of the gall fly Urophora cardui have in earlier
studies based on allozymes and mtDNA identified small-scale,
parapatrically diverged populations within an expanding Western Palearctic
population. However, the low polymorphism of these markers prohibited an
accurate delimitation of the evolutionary origin of the parapatric
divergence. Urophora cardui from the Western Palearctic have been
introduced into Canada as biological control agents of the host plant
Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-,
penta- and tetra-nucleotide repeat motifs and report a
genotyping-by-sequencing SNP protocol. We test the markers for genetic
variation among three parapatric U. cardui populations. Microsatellite
variability (N=59 individuals) was high: expected
heterozygosity/locus/population (0.60-0.90), allele
number/locus/population (5-21). One locus was alternatively sex-linked in
males or females. Cross-species amplification in the sister species U.
stylata was successful or partially successful for seven loci. For
genotyping-by-sequencing (N=18 individuals), different DNA extraction
methods did not affect data quality. Depending on sequence sorting
criteria, 1177-2347 unlinked SNPs and 1750-4469 parsimony informative
sites were found in 3514-5767 loci recovered after paralog filtering. Both
marker systems quantified the same population partitions with high
probabilities. Many and highly differentiated loci in both marker systems
indicate genome-wide diversification and genetically distinct populations.