A Phylogenomic Supertree of Birds
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational chall...
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| Format: | Article |
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MDPI AG
2019-07-01
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| Series: | Diversity |
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| Online Access: | https://www.mdpi.com/1424-2818/11/7/109 |
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| author | Rebecca T. Kimball Carl H. Oliveros Ning Wang Noor D. White F. Keith Barker Daniel J. Field Daniel T. Ksepka R. Terry Chesser Robert G. Moyle Michael J. Braun Robb T. Brumfield Brant C. Faircloth Brian Tilston Smith Edward L. Braun |
| author_facet | Rebecca T. Kimball Carl H. Oliveros Ning Wang Noor D. White F. Keith Barker Daniel J. Field Daniel T. Ksepka R. Terry Chesser Robert G. Moyle Michael J. Braun Robb T. Brumfield Brant C. Faircloth Brian Tilston Smith Edward L. Braun |
| author_sort | Rebecca T. Kimball |
| collection | DOAJ |
| description | It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well. |
| first_indexed | 2024-04-11T21:44:55Z |
| format | Article |
| id | doaj.art-6a0b4c28bf3f4244afa0f05ec69d028c |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-04-11T21:44:55Z |
| publishDate | 2019-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-6a0b4c28bf3f4244afa0f05ec69d028c2022-12-22T04:01:26ZengMDPI AGDiversity1424-28182019-07-0111710910.3390/d11070109d11070109A Phylogenomic Supertree of BirdsRebecca T. Kimball0Carl H. Oliveros1Ning Wang2Noor D. White3F. Keith Barker4Daniel J. Field5Daniel T. Ksepka6R. Terry Chesser7Robert G. Moyle8Michael J. Braun9Robb T. Brumfield10Brant C. Faircloth11Brian Tilston Smith12Edward L. Braun13Department of Biology, University of Florida, Gainesville, FL 32607, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USADepartment of Vertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USADepartment of Ecology, Evolution and Behavior; and, Bell Museum of Natural History, St. Paul, MN 55108, USADepartment of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UKBruce Museum, Greenwich, CT 06830, USAU.S. Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Rd., Laurel, MD 20708, USADepartment of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USADepartment of Vertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USADepartment of Biology, University of Florida, Gainesville, FL 32607, USAIt has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.https://www.mdpi.com/1424-2818/11/7/109supertreephylogenyaviangenomemolecular clockfossil calibrationstimetreebootstrap supportphylogenomics |
| spellingShingle | Rebecca T. Kimball Carl H. Oliveros Ning Wang Noor D. White F. Keith Barker Daniel J. Field Daniel T. Ksepka R. Terry Chesser Robert G. Moyle Michael J. Braun Robb T. Brumfield Brant C. Faircloth Brian Tilston Smith Edward L. Braun A Phylogenomic Supertree of Birds Diversity supertree phylogeny avian genome molecular clock fossil calibrations timetree bootstrap support phylogenomics |
| title | A Phylogenomic Supertree of Birds |
| title_full | A Phylogenomic Supertree of Birds |
| title_fullStr | A Phylogenomic Supertree of Birds |
| title_full_unstemmed | A Phylogenomic Supertree of Birds |
| title_short | A Phylogenomic Supertree of Birds |
| title_sort | phylogenomic supertree of birds |
| topic | supertree phylogeny avian genome molecular clock fossil calibrations timetree bootstrap support phylogenomics |
| url | https://www.mdpi.com/1424-2818/11/7/109 |
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