Mutation rates and intraspecific divergence of the mitochondrial genome of pristionchus pacificus

Molecular Biology and Evolution

Volumn 28, Issue 8, 2011, Pages 2317-2326

  Molnar, Ruxandra I ^a   Bartelmes, Gabi ^a   Dinkelacker, Iris ^a   Witte, Hanh ^a   Sommer, Ralf J ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

Caenorhabditis elegans; divergence times; mitochondrial DNA; mutation accumulation lines; Pristionchus pacificus

Indexed keywords

TRANSFER RNA;

ARTICLE; BEETLE; CAENORHABDITIS ELEGANS; CODON; DROSOPHILA; ECOLOGY; GENETIC VARIABILITY; MITOCHONDRIAL GENOME; MOLECULAR CLOCK; MUTATION RATE; NEMATODE; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRISTIONCHUS PACIFICUS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES;

ANIMALS; CODON; EVOLUTION, MOLECULAR; GENE ORDER; GENES, HELMINTH; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; MUTATION; NEMATODA; OPEN READING FRAMES; PHYLOGENY;

CAENORHABDITIS ELEGANS; NEMATODA; PRISTIONCHUS PACIFICUS; SCARABAEIDAE;

EID: 79961041294     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr057     Document Type: Article

References (63)

1. Armstrong MR, Blok VC, Phillips MS. 2000. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181-192. (Pubitemid 30045911)
2. Avise JC. 1998. The history and purview of phylogeography: a personal reflection. Mol Ecol. 7:371-379. (Pubitemid 28226686)
3. Baer CF, Shaw F, Steding C, et al. (11 authors). 2005. Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes. Proc Natl Acad Sci U S A. 102:5785-5790. (Pubitemid 40559637)
4. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247.
5. Blaxter ML, De Ley P, Garey JR, et al. (12 co-authors) 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75. (Pubitemid 28150590)
6. Borchert N, Dieterich C, Krug K, Schütz W, Jung S, Nordheim A, Sommer RJ, Macek B. 2010. Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res. 20:837-846.
7. Chang DD, Hauswirth WW, Clayton DA. 1985. Replication priming and transcription initiate from precisely the same site in mouse mitochondrial DNA. EMBO J. 4:1559-1567.
8. Charlesworth B. 2009. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 10:195-205.
9. Cutter AD. 2008. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol. 25:778-786. (Pubitemid 351398333)
10. Denver DR, Morris K, Lynch M, Thomas WK. 2004. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430:679-682. (Pubitemid 39061683)
11. 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.
12. Dieterich C, Clifton SW, Schuster L, et al. (17 co-authors). 2008. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 40:1193-1198.
13. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
14. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113.
15. Gernhard T. 2008. The conditioned reconstructed process. J Theor Biol. 253:769-778.
16. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704. (Pubitemid 37365050)
17. 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. 6:1706-1714.
18. Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Houle D, Charlesworth B, Keightley PD. 2007. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445:82-85. (Pubitemid 46067305)
19. He Y, Jones J, Armstrong M, Lamberti F, Moens M. 2005. The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes. J Mol Evol. 61:819-833. (Pubitemid 41706029)
20. Herrmann M, Kienle S, Rochat J, Mayer WE, Sommer RJ. 2010. Haplotype diversity of the nematode Pristionchus pacificus on Réunion in the Indian Ocean suggests multiple independent invasions. Biol J Linn Soc. 100:170-179.
21. Herrmann M, Mayer WE, Hong R, Kienle S, Minasaki R, Sommer RJ. 2007. The nematode Pristionchus pacificus (Nematoda: Diplogastridae) is associated with the oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan. Zool Sci. 24:883-889. (Pubitemid 350095724)
22. Herrmann M, Mayer WE, Sommer RJ. 2006a. Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe. Zoology. 109:96-108.
23. Herrmann M, Mayer WE, Sommer RJ. 2006b. Sex, bugs and Haldane's rule: the nematode genus Pristionchus in the United States. Front Zool. 3:14.
24. Hong RL, Sommer RJ. 2006. Pristionchus pacificus: a well-rounded nematode. BioEssays 28:651-659. (Pubitemid 43886190)
25. Hong RL, Witte H, Sommer RJ. 2008. Natural variation in P. pacificus insect pheromone attraction involves the protein kinase EGL-4. Proc Natl Acad Sci U S A. 105:7779-7784. (Pubitemid 351872715)
26. Howe DK, Baer CF, Denver DR. 2010. High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes. Genome Biol Evol. 2010:29-38.
27. Howe DK, Denver DR. 2008. Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution. BMC Evol Biol. 8:62.
28. Hu M, Chilton NB, Gasser RB. 2002. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Int J Parasitol. 32:145-158. (Pubitemid 34112620)
29. Hu M, Chilton NB, Gasser RB. 2003. The mitochondrial genome of Strongyloides stercoralis (Nematoda) - Idiosyncratic gene order and evolutionary implications. Int J Parasitol. 33:1393-1408. (Pubitemid 37176984)
30. Hyman BC, Azevedo JLB. 1996. Similar evolutionary patterning nematode mitochondrial genes among repeated and single copy. Mol Biol Evol. 13:221-232. (Pubitemid 26012468)
31. Jacob JE, Vanholme B, Van Leeuwen T, Gheysen G. 2009. A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes. 2:192.
32. Kass R, Raftery A. 1995. Bayes factors. J Am Stat Assoc. 90:773-795.
33. Keddie EM, Higazi T, Unnasch TR. 1998. The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis. Mol Biochem Parasitol. 95:111-127. (Pubitemid 28404742)
34. Lavrov DV, Brown WM. 2001. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 157:621-637. (Pubitemid 32165021)
35. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
36. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964. (Pubitemid 27298263)
37. Lynch M. 2007. The origin of genome architecture. Sunderland (MA): Sinauer.
38. Lynch M. 2010. Evolution of the mutation rate. Trends Genet. 26:345-352.
39. Lynch M, Sung W, Morris K, et al. (11 co-authors). 2008. A genomewide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105:9272-9277.
40. Mayer MG, Sommer RJ. 2011. Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones. Proc R Soc B Biol Sci. Advance access published February 9, 2011, doi:10.1098/rspb.2010.2760.
41. Mayer WE, Herrmann M, Sommer RJ. 2007. Phylogeny of the nematode genus Pristionchus and implications for biodiversity, biogeography and the evolution of hermaphroditism. BMC Evol Biol. 7:104.
42. Mayer WE, Herrmann M, Sommer RJ. 2009. Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution. BMC Evol Biol. 9:212.
43. Megen H van, Elsen S van den, Holterman M, Karssen G, Mooyman P, Bongers T, Holovachov O, Bakker J, Helder J. 2009. A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences. Nematology 11:927-950.
44. Montiel R, Lucena MA, Medeiros J, Simões N. 2006. The complete mitochondrial genome of the entomopathogenic nematode Steinernema carpocapsae: insights into nematode mitochondrial DNA evolution and phylogeny. J Mol Evol. 62:211-25.
45. Mukai T. 1964. The genetic structure of natural populations of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability. Genetics 50:1-19.
46. Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470-474. (Pubitemid 11159076)
47. Okimoto R, Chamberlin HM, Macfarlane JL, Wolstenholme DR. 1991. Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): nucleotide sequences, genome location and potential for host-race identification. Nucleic Acids Res. 19:1619-1626. (Pubitemid 21913260)
48. Okimoto R, Macfarlane JL, Clary D, Wolstenholme DR. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471-498.
49. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M. 2010. The rate and molecular spectrum of spontaneous mutations in. Arabidopsis thaliana. Science 327:92-94.
50. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253-1256. (Pubitemid 351882013)
51. Schlager B, Wang X, Braach G, Sommer RJ. 2009. Molecular cloning of a dominant roller mutant and establishment of DNA-mediated transformation in the nematode model Pristionchus pacificus. Genesis 47:300-304.
52. Seyfert AL, Cristescu ME, Frisse L, Schaack S, Thomas WK, Lynch M. 2008. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178:2113-2121.
53. Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of proteincoding sequences. Mol Biol Evol. 23:7-9. (Pubitemid 41785947)
54. Sommer RJ. 2009. The future of evo-devo: model systems and evolutionary theory. Nat Rev Genet. 10:416-422.
55. Sommer RJ, Carta LK, Kim S-Y, Sternberg PW. 1996. Morphological, genetic and molecular description of Pristionchus pacificus sp. n. (Nematoda, Diplogastridae). Fundam Appl Nematol. 19:511-521. (Pubitemid 127769004)
56. Suchard MA, Weiss RE, Sinsheimer JS. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol. 18:1001-1013. (Pubitemid 32520473)
57. Tian H, Schlager B, Xiao H, Sommer RJ. 2008. Wnt signaling by differentially expressed Wnt ligands induces vulva development in Pristionchus pacificus. Curr Biol. 18:142-146.
58. Vassilieva LL, Lynch M. 1999. The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans. Genetics 151:119-129. (Pubitemid 29031881)
59. Weller AM, Mayer WE, Rae R, Sommer RJ. 2010. Quantitative assessment of the nematode fauna present on Geotrupes dung beetles reveals species-rich communities with a heterogeneous distribution. J Parasitol. 96:525-531.
60. Wolstenholme DR. 1992. Animal mitochondrial DNA: structure and evolution. Int Rev Cytol. 141:173-216. (Pubitemid 23072888)
61. Zauner H, Sommer RJ. 2007. Evolution of robustness in the signaling network of Pristionchus vulva development. Proc Natl Acad Sci U S A. 104:10086-10091. (Pubitemid 47175267)
62. Zheng M, Messerschmidt D, Jungblut B, Sommer RJ. 2005. Conservation and diversification of Wnt signaling function during the evolution of nematode vulva development. Nat Genet. 37:300-304. (Pubitemid 41716258)
63. Zouros E, Freeman KR, Ball AO, Pogson GH. 1992. Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus. Nature 359:412-414.