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

Erin O. Campbell, Corey S. Davis, Julian R. Dupuis, Kevin Muirhead, Felix A.H. Sperling

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

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.

Original languageEnglish
Pages (from-to)e84-e93
JournalMolecular Ecology Resources
Volume17
Issue number6
DOIs
StatePublished - Nov 2017

Bibliographical note

Publisher Copyright:
© 2017 John Wiley & Sons Ltd

Keywords

  • SNP discovery
  • butterfly
  • ddRAD
  • de novo
  • phylogenetics
  • reproducibility

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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