دورية أكاديمية
أعرض في EDS

Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs.

التفاصيل البيبلوغرافية
العنوان: Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs.
المؤلفون: Portik DM; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.; Department of Herpetology, California Academy of Sciences, USA., Streicher JW; Department of Life Sciences, The Natural History Museum, London, United Kingdom., Blackburn DC; Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL., Moen DS; Department of Integrative Biology, 501 Life Sciences West, Oklahoma State University, Stillwater, OK., Hutter CR; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA., Wiens JJ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.
المصدر: Molecular biology and evolution [Mol Biol Evol] 2023 May 02; Vol. 40 (5).
نوع المنشور: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE
أسماء مطبوعة: Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
مواضيع طبية MeSH: Anura*/genetics, Animals ; Phylogeny ; Sequence Analysis, DNA ; Probability
مستخلص: The 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.)
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فهرسة مساهمة: Keywords: amphibians; missing data; phylogenomics; phylogeny; supermatrix
سلسلة جزيئية: Dryad 10.5061/dryad.f7m0cfz0n
تواريخ الأحداث: Date Created: 20230504 Date Completed: 20230524 Latest Revision: 20230524
رمز التحديث: 20230524
مُعرف محوري في PubMed: PMC10202597
DOI: 10.1093/molbev/msad109
PMID: 37140129
قاعدة البيانات: MEDLINE
الوصف
تدمد:1537-1719
DOI:10.1093/molbev/msad109