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dc.contributor.authorCarter, Katherine A
dc.contributor.authorListon, Aaron
dc.contributor.authorBassil, Nahla V
dc.contributor.authorAlice, Lawrence A
dc.contributor.authorBushakra, Jill M
dc.contributor.authorSutherland, Brittany L
dc.contributor.authorMockler, Todd C
dc.contributor.authorBryant, Douglas W
dc.contributor.authorHummer, Kim E
dc.date.accessioned2020-02-01T03:00:24Z
dc.date.available2020-02-01T03:00:24Z
dc.date.issued2019-12-20
dc.identifier.citationCarter KA, Liston A, Bassil NV, Alice LA, Bushakra JM, Sutherland BL, Mockler TC, Bryant DW and Hummer KE (2019) Target Capture Sequencing Unravels Rubus Evolution. Front. Plant Sci. 10:1615. doi: 10.3389/fpls.2019.01615en_US
dc.identifier.issn1664-462X
dc.identifier.pmid31921259
dc.identifier.doi10.3389/fpls.2019.01615
dc.identifier.urihttp://hdl.handle.net/10150/636871
dc.description.abstractRubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.en_US
dc.description.sponsorshipUSDA ARS CRIS United States Department of Agriculture (USDA) [2072-21000-044-00D, 2072-21000-049-00D]; NSF DEB award; NSF KY EPSCoR National Laboratory Initiative [019-14]en_US
dc.language.isoenen_US
dc.publisherFRONTIERS MEDIA SAen_US
dc.rightsCopyright © 2019 Carter, Liston, Bassil, Alice, Bushakra, Sutherland, Mockler, Bryant and Hummer. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en_US
dc.subjectbiogeographyen_US
dc.subjectcaneberriesen_US
dc.subjectgenetic resourcesen_US
dc.subjectphylogenomicsen_US
dc.subjectplant migrationen_US
dc.subjectsystematicsen_US
dc.subjecttaxonomyen_US
dc.titleTarget Capture Sequencing Unravels Rubus Evolutionen_US
dc.typeArticleen_US
dc.contributor.departmentUniv Arizona, Dept Ecol & Evolutionary Biolen_US
dc.identifier.journalFRONTIERS IN PLANT SCIENCEen_US
dc.description.noteOpen access journalen_US
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en_US
dc.eprint.versionFinal published versionen_US
dc.source.journaltitleFrontiers in plant science
dc.source.volume10
dc.source.beginpage1615
dc.source.endpage
refterms.dateFOA2020-02-01T03:00:25Z
dc.source.countrySwitzerland


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