Cross‐platform compatibility of de novo‐aligned SNPs in a nonmodel butterfly genus

Abstract

High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of nonmodel organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in nonmodel systems. Using double-digest restriction site-associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation. We then used a de novo approach to bioinformatic locus assembly and SNP discovery for subsequent phylogenetic analyses. We found a high rate of locus recovery despite differences in library preparation and sequencing platforms, as well as overall high levels of data compatibility after data processing and filtering. These results provide the first application of NGS methods for phylogenetic reconstruction in Speyeria and support the use and long-term viability of SNP genotyping applications in nonmodel systems.

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

“…On average, Run 2 had 47% more unique read locations per sample than Run 1, but average read depths in Run 2 were 39% lower. The consistency and reproducibility of GBS across both genotyping platforms is supported by Campbell et al ().…”

“…DNA extraction and library preparation methods followed Campbell, Davis, Dupuis, Muirhead, and Sperling (). Extractions from the 2005–2014 samples (Run 1) were sent to l'Institut de Biologie Intégrative et des Systems (IBIS) at Laval University for library preparation and sequencing on an Illumina HiSeq 2000 platform to produce 100 bp single‐end sequences.…”

“…DNA extraction and library preparation methods followed Campbell, Davis, Dupuis, Muirhead, and Sperling (2017). The 2015 and laboratory-bred samples (Run 2) were extracted and sequenced at the University of Alberta Molecular Biology Services Unit (MBSU) in Edmonton, Alberta, on an Illumina NextSeq500 platform to produce 75 bp single-end sequences.…”

Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance

“…The ddRAD and two‐enzyme GBS sequence data were different lengths, as they were sequenced on different Illumina platforms, and sequence read trimming and initial data processing followed Campbell et al . (). The final length of each sequence read input into stacks for de novo locus construction was 62 bp.…”

“…For NGS, we followed Campbell et al . (), with library preparation and single‐end sequencing performed using either the double digest restriction site‐associated DNA sequencing (ddRAD) protocol of Peterson et al . () on a Nextseq 500 (Illumina, San Diego, CA, USA) or the two‐enzyme genotyping by sequencing (GBS) protocol of Poland et al .…”