These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists

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dc.contributor.authorO'Leary, Shannon
dc.contributor.authorPuritz, Jonathan
dc.contributor.authorWillis, Stuart
dc.contributor.authorHollenbeck, Christopher
dc.contributor.authorPortnoy, David S.
dc.creator.orcidhttp://orcid.org/0000-0001-9775-9846en_US
dc.creator.orcidhttp://orcid.org/0000-0003-1404-4680en_US
dc.creator.orcidhttp://orcid.org/0000-0002-2274-1112en_US
dc.creator.orcidhttp://orcid.org/0000-0003-0227-7225en_US
dc.creator.orcidhttps://orcid.org/0000-0001-9775-9846
dc.creator.orcidhttps://orcid.org/0000-0003-1404-4680
dc.creator.orcidhttps://orcid.org/0000-0002-2274-1112
dc.creator.orcidhttps://orcid.org/0000-0003-0227-7225
dc.creator.orcidhttps://orcid.org/0000-0001-9775-9846
dc.creator.orcidhttps://orcid.org/0000-0003-1404-4680
dc.creator.orcidhttps://orcid.org/0000-0002-2274-1112
dc.creator.orcidhttps://orcid.org/0000-0003-0227-7225http://orcid.org/0000-0001-9775-9846
dc.creator.orcidhttp://orcid.org/0000-0003-1404-4680
dc.creator.orcidhttp://orcid.org/0000-0002-2274-1112
dc.creator.orcidhttp://orcid.org/0000-0003-0227-7225
dc.date.accessioned2022-03-15T13:58:21Z
dc.date.available2022-03-15T13:58:21Z
dc.date.issued2019-08-04
dc.description.abstractSequencing 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.en_US
dc.identifier.citationO'Leary, S.J., Puritz, J.B., Willis, S.C., Hollenbeck, C.M. and Portnoy, D.S., 2018. These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists.en_US
dc.identifier.doihttps://doi.org/10.1111/mec.14792
dc.identifier.urihttps://hdl.handle.net/1969.6/90264
dc.language.isoen_USen_US
dc.publisherWileyen_US
dc.subjectconservation geneticsen_US
dc.subjectecological geneticsen_US
dc.subjectlandscape geneticsen_US
dc.subjectmolecular evolutionen_US
dc.subjectpopulation ecologyen_US
dc.subjectpopulation genetics—empiricalen_US
dc.titleThese aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologistsen_US
dc.typeArticleen_US

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