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Identifying genetic markers for a range of phylogenetic utility-From species to family level

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dc.contributor.author Choi, Bokyung en
dc.contributor.author Crisp, Michael D. en
dc.contributor.author Cook, Lyn G. en
dc.contributor.author Meusemann, Karen en
dc.contributor.author Edwards, Robert D. en
dc.contributor.author Toon, Alicia en
dc.contributor.author Külheim, Carsten en
dc.date.accessioned 2019-08-09T02:01:46Z
dc.date.available 2019-08-09T02:01:46Z
dc.date.issued 2019
dc.identifier.citation Choi, Bokyung, Crisp, Michael D., Cook, Lyn G., Meusemann, Karen, Edwards, Robert D., Toon, Alicia, and Külheim, Carsten. 2019. "<a href="https://repository.si.edu/handle/10088/98488">Identifying genetic markers for a range of phylogenetic utility-From species to family level</a>." <em>PloS One</em>. 14 (8):Article e0218995. <a href="https://doi.org/10.1371/journal.pone.0218995">https://doi.org/10.1371/journal.pone.0218995</a> en
dc.identifier.issn 1932-6203
dc.identifier.uri https://hdl.handle.net/10088/98488
dc.description.abstract Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies. en
dc.relation.ispartof PloS One en
dc.title Identifying genetic markers for a range of phylogenetic utility-From species to family level en
dc.type Journal Article en
dc.identifier.srbnumber 151949
dc.identifier.doi 10.1371/journal.pone.0218995
rft.jtitle PloS One
rft.volume 14
rft.issue 8
rft.spage Article e0218995
dc.description.SIUnit NH-Botany en
dc.description.SIUnit NMNH en
dc.description.SIUnit Peer-reviewed en
dc.citation.spage Article e0218995


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