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dc.contributor.authorDodsworth, Stevenen
dc.contributor.authorChase, Mark W.en
dc.contributor.authorKelly, Laura J.en
dc.contributor.authorLeitch, Ilia J.en
dc.contributor.authorMacas, Jiříen
dc.contributor.authorNovak, Petren
dc.contributor.authorPiednoel, Mathieuen
dc.contributor.authorWeiss-Schneeweiss, Hannaen
dc.contributor.authorLeitch, Andrew R.en
dc.date.accessioned2019-02-11T13:22:27Z
dc.date.available2019-02-11T13:22:27Z
dc.date.issued2014-09-25
dc.identifier.citationDodsworth S., Chase M., Kelly L., Leitch I., Macas J., Novak P., Piednoel M., Weiss-Schneeweiss H., Leitch A. (2015) 'Genomic repeat abundances contain phylogenetic signal', Systematic Biology, 64 (1), pp.112-126.en
dc.identifier.issn1063-5157
dc.identifier.doi10.1093/sysbio/syu080
dc.identifier.urihttp://hdl.handle.net/10547/623135
dc.description.abstractA large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urlhttps://academic.oup.com/sysbio/article/64/1/112/2848261en
dc.rightsYellow - can archive pre-print (ie pre-refereeing)
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectgenomicsen
dc.subjectnext-generation sequencingen
dc.subjectmolecular systematicsen
dc.subjectrepetitive DNAen
dc.subjectphylogeneticsen
dc.subjectcontinuous charactersen
dc.subjectC400 Geneticsen
dc.titleGenomic repeat abundances contain phylogenetic signalen
dc.typeArticleen
dc.identifier.journalSystematic Biologyen
dc.date.updated2019-02-11T12:04:37Z
dc.description.noteoa article Creative Commons Attribution License
html.description.abstractA large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.


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