Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatricUrophora cardui(Tephritidae) populations

Abstract

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, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 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.

A refined panel of 42 microsatellite loci to universally genotype catarrhine primates

“…With microsatellite genotyping‐by‐sequencing (GBS) using high‐throughput sequencing technologies most of the difficulties can be mitigated (Barbian et al., 2018; Johannesen et al., 2017; Pimentel et al., 2018; Vartia et al., 2016). For instance, with GBS the exact length of the microsatellite alleles can be determined, which is a typical problem of FLA genotyping, particularly when alleles differ by only one basepair (bp) (Barbian et al., 2018; Vartia et al., 2016).…”

A refined panel of 42 microsatellite loci to universally genotype catarrhine primates

“…With microsatellite genotyping-by-sequencing (GBS) using high-throughput sequencing technologies most of the difficulties can be mitigated (Barbian et al, 2018;Johannesen, Fabritzek, Ebner, & Bikar, 2017;Pimentel et al, 2018;Vartia et al, 2016). For instance, with GBS the exact length of the microsatellite alleles can be determined, which is a typical problem of FLA genotyping, particularly when alleles differ by only one basepair (bp) (Barbian et al, 2018;Vartia et al, 2016).…”

Identity and relationships of Sempervivum tectorum (Crassulaceae) in the Rhine Gorge area

“…2015;Derkarabetian & al. 2016;Johannesen & al. 2017) used and tested different levels (5 -55 %) of maximum number of heterozygous sites and reported a strong effect on number of loci recovered but a small effect on derived tree topologies or on structure analyses.…”