دورية أكاديمية
Environmental genomics of Late Pleistocene black bears and giant short-faced bears.
| العنوان: | Environmental genomics of Late Pleistocene black bears and giant short-faced bears. |
|---|---|
| المؤلفون: | Pedersen MW; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark., De Sanctis B; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK., Saremi NF; Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA., Sikora M; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark., Puckett EE; Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA., Gu Z; State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China., Moon KL; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA., Kapp JD; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA., Vinner L; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark., Vardanyan Z; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark., Ardelean CF; Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada., Arroyo-Cabrales J; Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico., Cahill JA; Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA., Heintzman PD; The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway., Zazula G; Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada., MacPhee RDE; Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA., Shapiro B; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Durbin R; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Willerslev E; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany. Electronic address: ew482@cam.ac.uk. |
| المصدر: | Current biology : CB [Curr Biol] 2021 Jun 21; Vol. 31 (12), pp. 2728-2736.e8. Date of Electronic Publication: 2021 Apr 19. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: England NLM ID: 9107782 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0445 (Electronic) Linking ISSN: 09609822 NLM ISO Abbreviation: Curr Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Cambridge, MA : Cell Press Original Publication: London, UK : Current Biology Ltd., c1991- |
| مواضيع طبية MeSH: | Ursidae*/genetics, Animals ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Metagenomics ; Phylogeny |
| مستخلص: | Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time, 1-3 by allowing for parallel sequencing of DNA from all trophic levels. 4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, 9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies. 5 , 6 , 10 , 11 This is in contrast to data from fossils 12 , 13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable. 14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics. Competing Interests: Declaration of interests All authors declare no competing interests. (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.) |
| معلومات مُعتمدة: | 207492/Z/17/Z United Kingdom WT_ Wellcome Trust; WT207492 United Kingdom WT_ Wellcome Trust; WT220023 United Kingdom WT_ Wellcome Trust |
| فهرسة مساهمة: | Keywords: American black bear; ancient environmental genomics; environmental DNA; genomics; giant short-faced bear; paleoontology; phylogeny; population genetics |
| المشرفين على المادة: | 0 (DNA, Ancient) 0 (DNA, Mitochondrial) |
| تواريخ الأحداث: | Date Created: 20210420 Date Completed: 20220118 Latest Revision: 20240313 |
| رمز التحديث: | 20240313 |
| DOI: | 10.1016/j.cub.2021.04.027 |
| PMID: | 33878301 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1879-0445 |
|---|---|
| DOI: | 10.1016/j.cub.2021.04.027 |