Document Type
Article
Date of Original Version
2018
Department
Biological Sciences
Abstract
Sequencing reduced‐representation libraries of restriction site‐associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RADseq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures.
Citation/Publisher Attribution
O'Leary SJ, Puritz JB, Willis SC, Hollenbeck CM, Portnoy DS. These aren’t the loci you’re looking for: Principles of effective SNP filtering for molecular ecologists. Mol Ecol. 2018;27:1–14. https://doi.org/10.1111/mec.14792 Available at: https://doi.org/10.1111/mec.14792
Suplemental Information
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Table 1 Filtering Summary.docx (18 kB)
Table 1
Table 2 Description filtering schemes.docx (14 kB)
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Table 3 results filtering.docx (16 kB)
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Table data sets.docx (12 kB)
Table: Data Sets
Table minor allele comparison.docx (12 kB)
Table: Minor Allele Comparison
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