Show simple item record

dc.contributor.authorPortik, D.M.
dc.contributor.authorStreicher, J.W.
dc.contributor.authorBlackburn, D.C.
dc.contributor.authorMoen, D.S.
dc.contributor.authorHutter, C.R.
dc.contributor.authorWiens, J.J.
dc.date.accessioned2024-08-12T01:35:52Z
dc.date.available2024-08-12T01:35:52Z
dc.date.issued2023-05-04
dc.identifier.citationDaniel M Portik, Jeffrey W Streicher, David C Blackburn, Daniel S Moen, Carl R Hutter, John J Wiens, Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs, Molecular Biology and Evolution, Volume 40, Issue 5, May 2023, msad109, https://doi.org/10.1093/molbev/msad109
dc.identifier.issn0737-4038
dc.identifier.pmid37140129
dc.identifier.doi10.1093/molbev/msad109
dc.identifier.urihttp://hdl.handle.net/10150/674114
dc.description.abstractThe data available for reconstructing molecular phylogenies have become wildly disparate. Phylogenomic studies can generate data for thousands of genetic markers for dozens of species, but for hundreds of other taxa, data may be available from only a few genes. Can these two types of data be integrated to combine the advantages of both, addressing the relationships of hundreds of species with thousands of genes? Here, we show that this is possible, using data from frogs. We generated a phylogenomic data set for 138 ingroup species and 3,784 nuclear markers (ultraconserved elements [UCEs]), including new UCE data from 70 species. We also assembled a supermatrix data set, including data from 97% of frog genera (441 total), with 1–307 genes per taxon. We then produced a combined phylogenomic–supermatrix data set (a “gigamatrix”) containing 441 ingroup taxa and 4,091 markers but with 86% missing data overall. Likelihood analysis of the gigamatrix yielded a generally well-supported tree among families, largely consistent with trees from the phylogenomic data alone. All terminal taxa were placed in the expected families, even though 42.5% of these taxa each had >99.5% missing data and 70.2% had >90% missing data. Our results show that missing data need not be an impediment to successfully combining very large phylogenomic and supermatrix data sets, and they open the door to new studies that simultaneously maximize sampling of genes and taxa. © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
dc.language.isoen
dc.publisherOxford University Press
dc.rights© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
dc.rights.urihttps://creativecommons.org/ licenses/by/4.0/
dc.subjectamphibians
dc.subjectmissing data
dc.subjectphylogenomics
dc.subjectphylogeny
dc.subjectsupermatrix
dc.titleRedefining Possible: Combining Phylogenomic and Supersparse Data in Frogs
dc.typeArticle
dc.typetext
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, University of Arizona
dc.identifier.journalMolecular Biology and Evolution
dc.description.noteOpen access article
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.
dc.eprint.versionFinal Published Version
dc.source.journaltitleMolecular Biology and Evolution
refterms.dateFOA2024-08-12T01:35:53Z


Files in this item

Thumbnail
Name:
msad109.pdf
Size:
889.5Kb
Format:
PDF
Description:
Final Published Version

This item appears in the following Collection(s)

Show simple item record

© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Except where otherwise noted, this item's license is described as © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).