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Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus
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Campbell, Erin O.; Davis, Corey S.; Dupuis, Julian R.; Muirhead, Kevin; Sperling, Felix A.H.; Sperling, Felix A. H. — 2017-06-20 High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model 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 non-model 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 non-model systems.
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Data from: Would an RRS by any other name sound as RAD?
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Campbell, Erin O.; Brunet, Bryan M.T.; Dupuis, Julian R.; Sperling, Felix A.H.; Brunet, Bryan M. T.; Sperling, Felix A. H. — 2019-06-11 1. Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as restriction site-associated DNA sequencing (RADseq). But naming conventions have often been more creative than consistent and criteria for recognizing unique methods have been unclear, resulting in a proliferation of names characterized by ambiguity. 2. We give an overview of methodological and etymological relationships among 36 restriction enzyme-based methods, and survey the consistency of references to five prominent methods in the literature. 3. We identified several instances of methodological convergence, and note that many published derivatives have modified only minor elements of parent protocols. Misattribution through ambiguous or inconsistent literature references was observed in 8.4% of journal articles citing the original one and two-enzyme RADseq and GBS, as well as SBG publications. 4. The rapid expansion of names associated with derivative protocols is confusing and, in many cases, unwarranted. We urge greater restraint in naming derivative methods and suggest general guidelines for naming that promote a balance between clarity, descriptiveness, and recognition of scientific innovation.

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(Author: Dupuis, Julian R.)

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