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A genomic timescale for placental mammal evolution
- Foley, Nicole M;
- Mason, Victor C;
- Harris, Andrew J;
- Bredemeyer, Kevin R;
- Damas, Joana;
- Lewin, Harris A;
- Eizirik, Eduardo;
- Gatesy, John;
- Karlsson, Elinor K;
- Lindblad-Toh, Kerstin;
- Springer, Mark S;
- Murphy, William J;
- 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 RS;
- 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 FA;
- Springer, Mark;
- Srinivasan, Chaitanya;
- Steiner, Cynthia;
- Storer, Jessica M;
- Sullivan, Kevin AM;
- 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
Published Web Location
https://doi.org/10.1126/science.abl8189Abstract
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.
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