دورية أكاديمية
أعرض في EDS

De Novo Mutation Rate Estimation in Wolves of Known Pedigree.

التفاصيل البيبلوغرافية
العنوان: De Novo Mutation Rate Estimation in Wolves of Known Pedigree.
المؤلفون: Koch EM; Department of Ecology and Evolution, University of Chicago, Chicago, IL., Schweizer RM; Division of Biological Sciences, University of Montana, Missoula, MT., Schweizer TM; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA.; Department of Biology, Colorado State University, Fort Collins, CO., Stahler DR; Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY., Smith DW; Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY., Wayne RK; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA., Novembre J; Department of Ecology and Evolution, University of Chicago, Chicago, IL.; Department of Human Genetics, University of Chicago, Chicago, IL.
المصدر: Molecular biology and evolution [Mol Biol Evol] 2019 Nov 01; Vol. 36 (11), pp. 2536-2547.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: PubMed not MEDLINE; MEDLINE
أسماء مطبوعة: Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
مستخلص: Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 × 10-9 per base pair per generation and provide conservative bounds between 2.6 × 10-9 and 7.1 × 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 × 10-9 and 3.0-4.5 × 10-9), it suggests a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000-64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates and is likely to be vital to future investigations of mutation rate evolution.
(© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
References: Nat Genet. 2011 Jun 12;43(7):712-4. (PMID: 21666693)
PLoS Genet. 2016 Mar 04;12(3):e1005851. (PMID: 26943675)
Nat Genet. 2011 May;43(5):491-8. (PMID: 21478889)
Curr Biol. 2015 Jun 1;25(11):1515-9. (PMID: 26004765)
Annu Rev Genomics Hum Genet. 2014;15:47-70. (PMID: 25000986)
Genome Res. 2005 Dec;15(12):1787-97. (PMID: 16339377)
Science. 2016 Jun 3;352(6290):1228-31. (PMID: 27257259)
PLoS One. 2016 Jun 03;11(6):e0156682. (PMID: 27258193)
Nat Rev Genet. 2017 Dec;18(12):705-720. (PMID: 28944780)
Nat Rev Genet. 2012 Oct;13(10):745-53. (PMID: 22965354)
Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):1588-93. (PMID: 26811451)
Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
Nat Ecol Evol. 2019 Feb;3(2):286-292. (PMID: 30664699)
Nat Genet. 2016 Apr;48(4):349-55. (PMID: 26878723)
PLoS One. 2012;7(8):e42543. (PMID: 22900027)
Nat Rev Genet. 2003 Mar;4(3):216-24. (PMID: 12610526)
Nat Commun. 2013;4:1860. (PMID: 23673645)
Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):803-8. (PMID: 11792858)
Cell. 2017 Oct 19;171(3):710-722.e12. (PMID: 28965761)
Mol Ecol. 2008 Jan;17(1):252-74. (PMID: 17877715)
Nat Genet. 2011 Sep 18;43(10):1031-4. (PMID: 21926973)
Nat Methods. 2013 Oct;10(10):985-7. (PMID: 23975140)
Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10607-12. (PMID: 27601674)
Bioinformatics. 2012 Oct 1;28(19):2520-2. (PMID: 22908215)
Nature. 2005 Dec 8;438(7069):803-19. (PMID: 16341006)
Mol Biol Evol. 2018 May 1;35(5):1190-1209. (PMID: 29688543)
Nature. 1968 Feb 17;217(5129):624-6. (PMID: 5637732)
Sci Adv. 2016 Jul 27;2(7):e1501714. (PMID: 29713682)
Nature. 2015 Jul 23;523(7561):463-7. (PMID: 26176923)
Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2560-2569. (PMID: 31964835)
Nat Genet. 2016 Feb;48(2):126-133. (PMID: 26656846)
Genome Res. 2015 Aug;25(8):1125-34. (PMID: 26129709)
Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18488-92. (PMID: 23077252)
Genome Res. 2016 Feb;26(2):163-73. (PMID: 26680994)
Nat Genet. 2014 Aug;46(8):919-25. (PMID: 24952747)
Heredity (Edinb). 2017 Feb;118(2):111-124. (PMID: 27759079)
Nature. 2012 Aug 23;488(7412):471-5. (PMID: 22914163)
Evolution. 2011 Oct;65(10):2800-15. (PMID: 21967423)
Nat Genet. 2012 Oct;44(10):1161-5. (PMID: 22922873)
Science. 2010 May 7;328(5979):710-722. (PMID: 20448178)
Nat Biotechnol. 2011 Jan;29(1):24-6. (PMID: 21221095)
Evolution. 2017 Dec;71(12):2858-2870. (PMID: 29068052)
Mol Biol Evol. 2015 Jan;32(1):239-43. (PMID: 25371432)
Proc Natl Acad Sci U S A. 1985 Mar;82(6):1741-5. (PMID: 3856856)
Genome Res. 2016 Sep;26(9):1211-8. (PMID: 27412854)
J Anim Ecol. 2013 Jan;82(1):222-34. (PMID: 23043440)
Genetics. 2014 Jan;196(1):313-20. (PMID: 24214343)
PLoS Genet. 2014 Jan;10(1):e1004016. (PMID: 24453982)
G3 (Bethesda). 2016 Nov 8;6(11):3517-3524. (PMID: 27591755)
BMC Genomics. 2017 Jun 29;18(1):495. (PMID: 28662691)
Nature. 2011 Jul 13;475(7357):493-6. (PMID: 21753753)
Science. 2014 Jun 13;344(6189):1272-5. (PMID: 24926018)
Nat Rev Genet. 2016 Oct 14;17(11):704-714. (PMID: 27739533)
Brief Bioinform. 2013 Mar;14(2):178-92. (PMID: 22517427)
Annu Rev Genet. 2015;49:243-67. (PMID: 26631512)
Curr Biol. 2018 Oct 8;28(19):3193-3197.e5. (PMID: 30270182)
معلومات مُعتمدة: R01 GM108805 United States GM NIGMS NIH HHS; S10 RR027303 United States RR NCRR NIH HHS; S10 RR029668 United States RR NCRR NIH HHS; T32 GM007197 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: demographic history; dog domestication; mutation rate
تواريخ الأحداث: Date Created: 20190713 Latest Revision: 20231014
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC6805234
DOI: 10.1093/molbev/msz159
PMID: 31297530
قاعدة البيانات: MEDLINE
الوصف
تدمد:1537-1719
DOI:10.1093/molbev/msz159