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 language | English |
|---|---|
| Pages (from-to) | e84-e93 |
| Journal | Molecular Ecology Resources |
| Volume | 17 |
| Issue number | 6 |
| DOIs | |
| State | Published - Nov 2017 |
Bibliographical note
Publisher Copyright:© 2017 John Wiley & Sons Ltd
Funding
We thank Ed Gage, Thomas Simonsen, Tom Sperling, Simon Fergu-son and Margot Hervieux for specimen collections. As well, we thank Brian Boyle from the Institut de biologie integrative et des systèmes (IBIS) at Université Laval in Quebec City and Sophie Dang from the University of Alberta Molecular Biology Services Unit (MBSU) for specimen sequencing and the anonymous reviewers for their thoughtful comments during revision. Funding for this research was provided by an NSERC Discovery Grant to FAH Sperling (RES0016259) and an Alberta Conservation Association Grant in Biodiversity to EO Campbell. We thank Ed Gage, Thomas Simonsen, Tom Sperling, Simon Ferguson and Margot Hervieux for specimen collections. As well, we thank Brian Boyle from the Institut de biologie integrative et des syst?mes (IBIS) at Universit? Laval in Quebec City and Sophie Dang from the University of Alberta Molecular Biology Services Unit (MBSU) for specimen sequencing and the anonymous reviewers for their thoughtful comments during revision. Funding for this research was provided by an NSERC Discovery Grant to FAH Sperling (RES0016259) and an Alberta Conservation Association Grant in Biodiversity to EO Campbell.
| Funders | Funder number |
|---|---|
| Institut de biologie integrative et des syst?mes | |
| University of Alberta Molecular Biology Services Unit | |
| City, University of London | |
| Alberta Conservation Association | |
| Natural Sciences and Engineering Research Council of Canada | RES0016259 |
Keywords
- SNP discovery
- butterfly
- ddRAD
- de novo
- phylogenetics
- reproducibility
ASJC Scopus subject areas
- Biotechnology
- Ecology, Evolution, Behavior and Systematics
- Genetics