Erratum: Mitochondrialmutation rate, spectrum and heteroplasmy in caenorhabditis elegans spontaneousmutation accumulation lines of differing population size (Molecular Biology and Evolution (2017) DOI: 10.1093/molbev/msx051);Mitochondrial mutation rate, spectrum and heteroplasmy in Caenorhabditis elegans spontaneous mutation accumulation lines of differing population size

Molecular Biology and Evolution

Volumn 34, Issue 6, 2017, Pages 1319-1334

  Konrad, Anke ^a   Thompson, Owen ^b   Waterston, Robert H ^b   Moerman, Donald G ^c   Keightley, Peter D ^d   Bergthorsson, Ulfar ^a   Katju, Vaishali ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Caenorhabditis elegans; Genetic drift; Heteroplasmy; Mitochondria; Mitochondrial effective population size; Mutation rate; Selection; Spontaneous mutation

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; CAENORHABDITIS ELEGANS; DNA BASE COMPOSITION; EFFECTIVE POPULATION SIZE; HERMAPHRODITE; HETEROPLASMY; MICROBIAL GENOME; MITOCHONDRIAL GENOME; MUTATION ACCUMULATION; MUTATION RATE; NONHUMAN; PARASITE ISOLATION; POPULATION SIZE; SPONTANEOUS MUTATION; ANIMAL; DNA SEQUENCE; EVOLUTION; GENETIC SELECTION; GENETICS; MITOCHONDRION; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DENSITY; PROCEDURES;

ANIMALS; BIOLOGICAL EVOLUTION; CAENORHABDITIS ELEGANS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME, MITOCHONDRIAL; MITOCHONDRIA; MUTATION; MUTATION ACCUMULATION; MUTATION RATE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DENSITY; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 85027421116     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msx063     Document Type: Erratum

References (69)

1. Aanen DK, Spelbrink JN, Beekman M. 2014. What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations. Philos Trans R Soc Lond B Biol Sci. 369:20130438.
2. Avise JC. 1994. Molecular markers, natural history, and evolution. New York: Chapman & Hall.
3. Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge: Harvard University Press.
4. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst. 18:489–522.
5. Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol Ecol. 13:729–744.
6. Barr CM, Neiman M, Taylor DR. 2005. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol. l68:39–50.
7. Bergstrom CT, Pritchard J. 1998. Germline bottlenecks and the evolutionary maintenance of mitochondrial genome. Genetics 149:2135–2146.
8. Birky CW.Jr 2001. The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms and models. Annu Rev Genet. 35:125–148.
9. Bowe LM, Coat G, dePamphilis CW. 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers. Proc Natl Acad Sci U S A. 97:4092–4097.
10. Brown WM, George M Jr, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A. 76:1967–1971.
11. Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature 325:31–36.
12. Chaw S-M, Chang C-C, Chen H-L, Li W-H. 2004. Dating the monocotdicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol. 58:424–441.
13. Cho Y, Mower JP, Qiu YL, Palmer JD. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci U S A. 101:17741–17746.
14. Clark KA, Howe DK, Gafner K, Kusuma D, Ping S, Estes S, Denver DR. 2012. Selfish little circles: transmission bias and evolution of large deletion-bearing mitochondrial DNA in Caenorhabditis briggsae nematodes. PLoS One 7:e41433.
15. Cooper BS, Burrus CR, Ji C, Hahn MW, Montooth KL. 2015. Similar efficacies of selection shape mitochondrial and nuclear genes in both Drosophila melanogaster and Homo sapiens. G3 Genes|Genomes|Genetics 5:2165–2176.
16. Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK. 2000. High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289:2342–2344.
17. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
18. Eyre-Walker A, Smith NH, Smith JM. 1999. How clonal are human mitochondria? Proc Biol Sci. 266:477–483.
19. Flibotte S, Edgley ML, Chaudhry I, Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfield Y, Jones SJ, et al. 2010. Whole-genome profiling of mutagenesis in Caenorhabditis elegans. Genetics 185:431–441.
20. Gaut BS. 1998. Molecular clocks and nucleotide substitution rates in higher plants. Evol Biol. 30:93–120.
21. Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. 2016. Homeostatic responses regulate selfish mitochondrial genome dynamics in C. elegans. Cell Metab. 24:91–103.
22. Gyllensten U, Wharton D, Josefsson A, Wilson AC. 1991. Paternal inheritance of mitochondrial DNA in mice. Nature 352:255–257.
23. Haag-Liautard C, Coffey N, Houle D, Lynch M, Charlesworth B, Keightley PD. 2008. Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol. 6:e204.
24. Hall HG, Muralidharan K. 1989. Evidence from mitochondrial DNA that African honey bees spread as continuous maternal lineages. Nature 339:211–213.
25. Halligan DL, Keightley PD. 2009. Spontaneous mutation accumulation studies in evolutionary genetics. Annu Rev Ecol Evol Syst. 40:151–172.
26. Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, et al. 2010. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 38:D463–D467.
27. Havird JC, Sloan DB. 2016. The roles of mutation, selection, and expression in determining relative rates of evolution in mitochondrial versus nuclear genomes. Mol Biol Evol. 33:3042–3053.
28. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, et al. 2011. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 83:8604–8610.
29. Howe DK, Baer CF, Denver DR. 2010. High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes. Genome Biol Evol. 2:29–38.
30. Katju V, Packard LB, Bu L, Keightley PD, Bergthorsson U. 2015. Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes. Evolution 69:104–116.
31. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
32. Kondo R, Satta Y, Matsuura ET, Ishiwas H, Takahata N, Chigusa SI. 1990. Incomplete maternal transmission of mitochondrial DNA in Drosophila. Genetics 126:657–663.
33. Kvist L, Martens J, Nazarenko AA, Orell M. 2003. Paternal leakage of mitochondrial DNA in the great tit (Parus major). Mol Biol Evol. 20:243–247.
34. Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. 2011. The sequence read archive. Nucleic Acids Res. 39:D19–D21.
35. Lemire B. 2005. Mitochondrial genetics. Wormbook 14:1–10.
36. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
37. Lynch M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller’s ratchet in mitochondrial genomes. Mol Biol Evol. 13:209–220.
38. Lynch M, Koskella B, Schaack S. 2006. Mutation pressure and the evolution of organelle genomic architecture. Science 311:1727–1730.
39. Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, et al. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105:9272–9277.
40. Ma H, O’Farrell PH. 2016. Selfish drive can trump function when animal mitochondrial genomes compete. Nat Genet. 48:798–802.
41. McCauley DE, Bailey MF, Sherman NA, Darnell MZ. 2005. Evidence for paternal transmission and heteroplasmy in the mitochondrial genome of Silene vulgaris, a gynodioecious plant. Heredity 95:50–58.
42. Molnar RI, Bartelmes G, Dinkelacker I, Witte H, Sommer RJ. 2011. Mutation rates and intraspecific divergence of the mitochondrial genome of Pristionchus pacificus. Mol Biol Evol. 28:2317–2326.
43. Montooth KL, Rand DM. 2008. The spectrum of mitochondrial mutations differs across species. PLoS Biol. 6:e213.
44. Moritz C, Dowling TE, Brown WM. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst. 18:269–292.
45. Neale DB, Marshall KA, Sederoff RR. 1989. Choloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don. Endl. Proc Natl Acad Sci U S A. 86:9347–9349.
46. Neiman M, Taylor DR. 2009. The causes of mutation accumulation in mitochondrial genomes. Proc Biol Sci. 276:1201–1209.
47. Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471–498.
48. Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol. 28:87–97.
49. Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290.
50. R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
51. Rand DM. 2001. The units of selection on mitochondrial DNA. Annu Rev Ecol Syst. 32:415–448.
52. Rand DM. 2008. Mitigating mutational meltdown in mammalian mitochondria. PLoS Biol. 6:e35.
53. Rand DM. 2011. Population genetics of the cytoplasm and the units of selection on mitochondrial DNA in Drosophila melanogaster. Genetica 139:685–697.
54. Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, et al. 2014. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A. 111:15474–15479.
55. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol. 29:24–26.
56. Sajantilla A, Salem AH, Savolainen P, Bauer K, Gierig C, Pääbo S. 1996. Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population. Proc Natl Acad Sci U S A. 93:12035–12039.
57. Saxer G, Havlak P, Fox SA, Quance MA, Gupta S, Fofanov Y, Strassmann JE, Queller DC. 2012. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum. PLoS One 7:e46759.
58. Seabury CM, Seabury PM, Decker JE, Schnabel RD, Taylor JF, Womack JE. 2010. Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. Proc Natl Acad Sci U S A. 107:151–156.
59. Smith SM, Maughan PJ. 2015. SNP genotyping using KASPar assays. Methods Mol Biol. 1245:243–256.
60. Stewart JB, Chinnery PF. 2015. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat Rev Genet. 16:530–542.
61. Sueoka N. 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci U S A. 48:582–592.
62. Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc Natl Acad Sci U S A. 109:19339–19344.
63. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30:2725–2729.
64. Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudhury I, Fernando L, Hutter H, et al. 2013. The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Res. 23:1749–1762.
65. Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14:178–192.
66. Wallace DC, Chalkia D. 2013. Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. Cold Spring Harb Perspect Biol. 5:a021220.
67. White DJ, Wolff JN, Pierson M, Gemmell NJ. 2008. Revealing the hidden complexities of mtDNA inheritance. Mol Ecol. 17:4925–4942.
68. Wolfe KH, Li W-H, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc Natl Acad Sci U S A. 84:9054–9058.
69. Xu S, Schaack S, Seyfert A, Choi E, Lynch M, Cristescu ME. 2012. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol Biol Evol. 29:763–769.