Evolutionary constraint and innovation across hundreds of placental mammals-Reference-Cited by-同舟云学术

Evolutionary constraint and innovation across hundreds of placental mammals

Published:2023-04-28 Issue:6643 Volume:380 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Christmas Matthew J.¹^ORCID,Kaplow Irene M.²³^ORCID,Genereux Diane P.⁴^ORCID,Dong Michael X.¹^ORCID,Hughes Graham M.⁵^ORCID,Li Xue⁴⁶⁷^ORCID,Sullivan Patrick F.⁸⁹^ORCID,Hindle Allyson G.¹⁰^ORCID,Andrews Gregory⁷^ORCID,Armstrong Joel C.¹¹,Bianchi Matteo¹^ORCID,Breit Ana M.¹²^ORCID,Diekhans Mark¹¹^ORCID,Fanter Cornelia¹⁰^ORCID,Foley Nicole M.¹³^ORCID,Goodman Daniel B.¹⁴^ORCID,Goodman Linda¹⁵^ORCID,Keough Kathleen C.¹⁵¹⁶¹⁷^ORCID,Kirilenko Bogdan¹⁸¹⁹²⁰^ORCID,Kowalczyk Amanda²³^ORCID,Lawless Colleen⁵^ORCID,Lind Abigail L.¹⁶¹⁷^ORCID,Meadows Jennifer R. S.¹^ORCID,Moreira Lucas R.⁴⁷^ORCID,Redlich Ruby W.²¹,Ryan Louise⁵^ORCID,Swofford Ross⁴^ORCID,Valenzuela Alejandro²²^ORCID,Wagner Franziska²³,Wallerman Ola¹^ORCID,Brown Ashley R.²³^ORCID,Damas Joana²⁴^ORCID,Fan Kaili⁷^ORCID,Gatesy John²⁵^ORCID,Grimshaw Jenna²⁶^ORCID,Johnson Jeremy⁴^ORCID,Kozyrev Sergey V.¹^ORCID,Lawler Alyssa J.³⁴²¹^ORCID,Marinescu Voichita D.¹^ORCID,Morrill Kathleen M.⁴⁶⁷^ORCID,Osmanski Austin²⁷^ORCID,Paulat Nicole S.²⁶^ORCID,Phan BaDoi N.²³²⁷^ORCID,Reilly Steven K.²⁸^ORCID,Schäffer Daniel E.²^ORCID,Steiner Cynthia²⁹^ORCID,Supple Megan A.³⁰^ORCID,Wilder Aryn P.²⁹^ORCID,Wirthlin Morgan E.²³³¹^ORCID,Xue James R.⁴³²^ORCID,Birren Bruce W.⁴,Gazal Steven³³^ORCID,Hubley Robert M.³⁴^ORCID,Koepfli Klaus-Peter³⁵³⁶³⁷,Marques-Bonet Tomas³⁸³⁹⁴⁰⁴¹^ORCID,Meyer Wynn K.⁴²^ORCID,Nweeia Martin⁴³⁴⁴⁴⁵⁴⁶^ORCID,Sabeti Pardis C.⁴³²⁴⁷^ORCID,Shapiro Beth³⁰⁴⁸^ORCID,Smit Arian F. A.³⁴^ORCID,Springer Mark S.⁴⁹^ORCID,Teeling Emma C.⁵^ORCID,Weng Zhiping⁷^ORCID,Hiller Michael¹⁸¹⁹²⁰^ORCID,Levesque Danielle L.¹²^ORCID,Lewin Harris A.²⁴⁵⁰⁵¹^ORCID,Murphy William J.¹³^ORCID,Navarro Arcadi³⁸⁴⁰⁵²⁵³^ORCID,Paten Benedict¹¹^ORCID,Pollard Katherine S.¹⁶¹⁷⁵⁴^ORCID,Ray David A.²⁶^ORCID,Ruf Irina⁵⁵^ORCID,Ryder Oliver A.²⁹⁵⁶^ORCID,Pfenning Andreas R.²³^ORCID,Lindblad-Toh Kerstin¹⁴^ORCID,Karlsson Elinor K.⁴⁷⁵⁷^ORCID,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. Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden.

2. Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

3. Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

4. Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.

5. School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.

6. Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA.

7. Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA.

8. Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA.

9. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

10. School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.

11. Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

12. School of Biology and Ecology, University of Maine, Orono, ME 04469, USA.

13. Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.

14. Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA.

15. Fauna Bio, Inc., Emeryville, CA 94608, USA.

16. Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.

17. Gladstone Institutes, San Francisco, CA 94158, USA.

18. Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany.

19. LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.

20. Senckenberg Research Institute, 60325 Frankfurt, Germany.

21. Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

22. Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain.

23. Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.

24. The Genome Center, University of California Davis, Davis, CA 95616, USA.

25. Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.

26. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

27. Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

28. Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA.

29. Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.

30. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

31. Allen Institute for Brain Science, Seattle, WA 98109, USA.

32. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

33. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

34. Institute for Systems Biology, Seattle, WA 98109, USA.

35. Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC 20008, USA.

36. Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia.

37. Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA.

38. Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.

39. CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain.

40. Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain.

41. Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.

42. Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.

43. Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.

44. Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada.

45. Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA.

46. Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA.

47. Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.

48. Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

49. Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA.

50. Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA.

51. John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA.

52. BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain.

53. CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.

54. Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

55. Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany.

56. Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA.

57. Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA.

Abstract

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth’s vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Link

https://www.science.org/doi/pdf/10.1126/science.abn3943

Reference335 articles.

1. How many species of mammals are there?

2. Ecology and evolution of mammalian biodiversity

3. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals

4. A comparative genomics multitool for scientific discovery and conservation

5. University of California Santa Cruz Genomics Institute Conservation track settings; http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cons100way.

Cited by 37 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy;iScience;2024-02

2. Selection on synonymous sites: the unwanted transcript hypothesis;Nature Reviews Genetics;2024-01-31

3. Evolutionary innovation in conserved regulatory elements across the mammalian tree of life;2024-01-31

4. Comparative genomics of monotremes provides insights into the early evolution of mammalian epidermal differentiation genes;Scientific Reports;2024-01-16

5. Evolutionary feedback from the environment shapes mechanisms that generate genome variation;The Journal of Physiology;2024-01-09