A genomic timescale for placental mammal evolution
Author:
Foley Nicole M.1ORCID, Mason Victor C.2, Harris Andrew J.13ORCID, Bredemeyer Kevin R.13ORCID, Damas Joana4ORCID, Lewin Harris A.45ORCID, Eizirik Eduardo6ORCID, Gatesy John7ORCID, Karlsson Elinor K.8910ORCID, Lindblad-Toh Kerstin911ORCID, Springer Mark S.12ORCID, Murphy William J.13ORCID, Andrews Gregory, Armstrong Joel C., Bianchi Matteo, Birren Bruce W., Bredemeyer Kevin R., Breit Ana M., Christmas Matthew J., Clawson Hiram, Damas Joana, Di Palma Federica, Diekhans Mark, Dong Michael X., Eizirik Eduardo, Fan Kaili, Fanter Cornelia, Foley Nicole M., Forsberg-Nilsson Karin, Garcia Carlos J., Gatesy John, Gazal Steven, Genereux Diane P., Goodman Linda, Grimshaw Jenna, Halsey Michaela K., Harris Andrew J., Hickey Glenn, Hiller Michael, Hindle Allyson G., Hubley Robert M., Hughes Graham M., Johnson Jeremy, Juan David, Kaplow Irene M., Karlsson Elinor K., Keough Kathleen C., Kirilenko Bogdan, Koepfli Klaus-Peter, Korstian Jennifer M., Kowalczyk Amanda, Kozyrev Sergey V., Lawler Alyssa J., Lawless Colleen, Lehmann Thomas, Levesque Danielle L., Lewin Harris A., Li Xue, Lind Abigail, Lindblad-Toh Kerstin, Mackay-Smith Ava, Marinescu Voichita D., Marques-Bonet Tomas, Mason Victor C., Meadows Jennifer R. S., Meyer Wynn K., Moore Jill E., Moreira Lucas R., Moreno-Santillan Diana D., Morrill Kathleen M., Muntané Gerard, Murphy William J., Navarro Arcadi, Nweeia Martin, Ortmann Sylvia, Osmanski Austin, Paten Benedict, Paulat Nicole S., Pfenning Andreas R., Phan BaDoi N., Pollard Katherine S., Pratt Henry E., Ray David A., Reilly Steven K., Rosen Jeb R., Ruf Irina, Ryan Louise, Ryder Oliver A., Sabeti Pardis C., Schäffer Daniel E., Serres Aitor, Shapiro Beth, Smit Arian F. A., Springer Mark, Srinivasan Chaitanya, Steiner Cynthia, Storer Jessica M., Sullivan Kevin A. M., Sullivan Patrick F., Sundström Elisabeth, Supple Megan A., Swofford Ross, Talbot Joy-El, Teeling Emma, Turner-Maier Jason, Valenzuela Alejandro, Wagner Franziska, Wallerman Ola, Wang Chao, Wang Juehan, Weng Zhiping, Wilder Aryn P., Wirthlin Morgan E., Xue James R., Zhang Xiaomeng,
Affiliation:
1. Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA. 2. Institute of Cell Biology, University of Bern, Bern, Switzerland. 3. Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA. 4. The Genome Center, University of California, Davis, CA, USA. 5. Department of Evolution and Ecology, University of California, Davis, CA, USA. 6. School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil. 7. Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA. 8. Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA. 9. Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA. 10. Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA. 11. Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden. 12. Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
Publisher
American Association for the Advancement of Science (AAAS)
Subject
Multidisciplinary
Cited by
48 articles.
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