Fast-evolving mitochondrial DNA in Ceriantharia: A reflection of hexacorallia paraphyly?

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Stampar, Sérgio N ^a,b   Maronna, Maximiliano M ^b   Kitahara, Marcelo V ^b   Reimer, James D ^c   Morandini, André C ^b  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c UNIVERSITY OF THE RYUKYUS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MITOCHONDRIAL DNA;

ANTHOZOA; ARTICLE; CELL NUCLEUS; CERIANTHARIA; CLADISTICS; CNIDARIA; CONTROLLED STUDY; DNA SEQUENCE; GENETIC VARIABILITY; HEXACORALLIA; MEDUSOZOA; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEA ANEMONES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84897906578     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086612     Document Type: Article

References (73)

1. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270 Suppl 1: 96-99.
2. Ortman BD, Bucklin A, Pagès F, Youngbluth M (2010) DNA barcoding the Medusozoa using mtCOI. Deep Sea Res Part 2 Top Stud Oceanogr 57: 2148-2156.
3. Shearer TL, van Oppen MJH, Romano SL, Wörheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11, 2475-2487. (Pubitemid 35436670)
4. Shearer TL, Coffroth Ma (2008) DNA BARCODING: Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Resour 8: 247-255.
5. Pont-Kingdon GA, Okada NA, Macfarlane JL, Beagley CT, Wolstenholme DR, et al. (1995) A coral mitochondrial MutS gene. Nature 375: 109-111.
6. Pont-Kingdon G, Okada NA, Macfarlane JL, Beagley CT, Watkins-Sims CD, et al. (1998) Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion. J Mol Evol 46, 419-431. (Pubitemid 28164946)
7. Culligan KM, Meyer-Gauen G, Lyons-Weiler J, Hays JB (2000) Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins. Nucl Acids Res 28: 463-471. (Pubitemid 30057985)
8. France SC, Hoover LC (2001) Analysis of variation in mitochondrial DNA sequences (ND3, ND4L, MSH) among Octocorallia (= Alcyonaria) (Cnidaria: Anthozoa). Bull Biol Soc Wash 10: 110-118.
9. McFadden CS, France SC, Sánchez JA, Alderslade P (2006) A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial proteincoding sequences. Mol Phylogenet Evol 41: 513-527. (Pubitemid 44739331)
10. Bridge D, Cunningham CW, DeSalle R, Buss LW (1995) Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. Mol Biol Evol 12: 679-89.
11. Collins AG, Schuchert P, Marques AC, Jankowski T, Medina M, et al. (2006) Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Syst Biol 55: 97-115.
12. Ogata H, Ray J, Toyoda K, Sandaa RA, Nagasaki K, et al. (2011) Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME Journal 5: 1143-1151.
13. Stampar SN, Maronna MM, Vermeij MJa, Silveira FLd, Morandini AC (2012) Evolutionary diversification of banded tube-dwelling anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean. PLoS ONE 7: e41091.
14. Chen CA, Odorico DM, Lohuis M, Veron JEN, Miller DJ (1995) Systematic relationships within the Anthozoa (Cnidaria: Anthozoa) using the 5′-end of the 28S rDNA. Mol Phylogenet Evol 4: 175-183.
15. Won JH, Rho BJ, Song JI (2001) A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters. Coral Reefs 20: 39-50. (Pubitemid 32770400)
16. Vandamme AM (2009) Basic concepts of molecular evolution, in: Lemey, P, Salemi, M, Vandamme, A-M, (Eds). The Phylogenetic Handbook. 2 ed Cambridge University Press, New York, 3-32.
17. Cruickshank RH (2002) Molecular markers for the phylogenetics of mites and ticks. Syst Appl Acarol 7: 3-14.
18. Higgins D, Lemey P (2009) Multiple sequence alignment, in: Lemey, P, Salemi, M, Vandamme, A-M (eds). The Phylogenetic Handbook. 2 ed Cambridge University Press, New York, 68-108.
19. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial Cytochrome C Oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3: 294-299.
20. Prendini L, Weygoldt P, Wheeler WC (2005) Systematics of the Damon variegatus group of African whip spiders (Chelicerata: Amblypygi): evidence from behaviour, morphology and DNA. Org Div Evol 5: 203-236. (Pubitemid 41128005)
21. Dawson MN (2005) Renaissance taxonomy: integrative evolutionary analyses in the classification of Scyphozoa. J Mar Biol Assoc UK 85: 733-739.
22. Cunningham CW, Buss LW (1993) Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae. Biochem Syst Ecol 21: 57-69.
23. Schroth W, Jarms G, Streit B, Schierwater B (2002) Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp. BMC Evol Biol 2: 1-10.
24. Apakupakul K, Siddall ME, Burreson EM (1999) Higher level relationships of leeches (Annelida, Clitellata, Euhirudinea) based on morphology and gene sequences. Mol Phylogenet Evol 2: 350-359. (Pubitemid 129499313)
25. Medina M, Collins AG, Silberman JD, Sogin ML (2001) Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. P Natl Acad Sci-Biol 98: 9707-9712.
26. Leclère L, Schuchert P, Cruaud C, Couloux A, Manuel M (2009) Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes. Syst Biol 58: 509-526.
27. Voigt O, Collins AG, Pearse VB, Pearse JS, Ender A, et al. (2004) Placozoa no longer a phylum of one. Curr Biol 14: R944-R945.
28. Molodtsova TN (2004) On the taxonomy and presumable evolutionary pathways of planktonic larvae of Ceriantharia (Anthozoa, Cnidaria). Hydrobiologia 530/531: 261-266.
29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739.
30. Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537: 39-64.
31. Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF (2009) Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res 37: 6184-6193.
32. Suchard MA, Redelings BD (2006) BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22 (16): 2047-2048. (Pubitemid 44283019)
33. Wheeler TJ, Kececioglu JD (2007) Multiple alignment by aligning alignments. Bioinformatics 23 (13): i559-i568. (Pubitemid 47244443)
34. Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, et al. (2012) SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees. Syst Biol 61 (1): 90-106.
35. Varón A, Vinh LS, Wheeler WC (2010) POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26 (1): 72-85.
36. Borchsenius F (2009) FastGap 1.2. Available: http://www.aubot.dk/FastGap- home.htm.
37. Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, et al. (2010) Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Front Zool 7: 10.
38. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
39. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3): 539-542.
40. Goloboff PA, Farris JS, Nixon KC (2008) TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.
41. Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches, A fast, accurate, and powerful alternative. Syst Biol 55: 539-552. (Pubitemid 43922340)
42. Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60: 685-699.
43. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
44. López-Giráldez F, Townsend JP (2011) PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol Biol 11: 152.
45. Schmidt HA (2009) Testing Tree Topologies. In P. Lemey, M. Salemi, A.M. Vandamme (eds.) The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, Cambridge University Press, Cambridge, 381-404.
46. Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. P Natl Acad Sci-Biol 76: 1967-1971.
47. Ferris SD, Sage RD, Prager EM, Ritte U, Wilson AC (1983) Mitochondrial DNA evolution in mice. Genetics 105: 681-721. (Pubitemid 14246278)
48. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the quagga, and extinct member of the horse family. Nature 312: 282-284. (Pubitemid 15202007)
49. Wilson AC, Cann RL, Carr SM, Georgej M, Gyllenstenk UB (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26: 375-400.
50. Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66: 167-174.
51. France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher TD (1996) DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-subclass organization of the Anthozoa (Cnidaria). Mol Mar Biol Biotech 5: 15-28.
52. Daly M, Fautin DG, Cappola VA (2003) Systematics of the Hexacorallia (Cnidaria: Anthozoa). Zool J Linn Soc-Lond 139: 419-437. (Pubitemid 37457858)
53. Kayal E, Roure B, Phillipe H, Collins AG, Lavrov DV (2013) Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol 13: 5.
54. Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B (2013) Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 69(2): 339-351.
55. Bernt M, Bleidorn C, Braband A, Dambach J, Donath A et al. (2013) A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol 69(2): 352-364.
56. Schierwater B, Stadler P, Desalle R, Podsiadlowski L (2013) Mitogenomics and metazoan evolution. Mol Phylogenet Evol 69(2): 311-312.
57. Bernt M, Braband A, Schierwater B, Stadler PF (2013) Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol 69(2): 328-338.
58. Ghiselli F, Milani L, Guerra D, Chang PL, Breton S, et al. (2013) Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system. Genome Biol Evol 5(8): 1535-1554.
59. Bilewitch JP, Degnan SM (2011) A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function. BMC Evol Biol 11: 228.
60. Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S (2011) Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biol Evol 4: 1-12.
61. Brockman Sa, McFadden CS (2012) The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 4: 882-894.
62. Venton D (2013) Highlight: the mystery of mitochondrial genomes. Genome Biol Evol 5 (6): 1115-1116.
63. Kohn AB, Citarella MR, Kocot KM, Bobkova YV, Halanych KM, et al. (2012) Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Mol Phylogenet Evol 63(1): 203-207.
64. Pett WJ, Ryan F, Pang K, Mullikin JC, Martindale MQ, et al. (2011) Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. Mitochondrial DNA 22(4): 130-142.
65. Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA, et al. (2006) Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci USA 103(23): 8751-8756. (Pubitemid 43878091)
66. Smith DR, Keeling PJ (2013) Gene conversion shapes linear mitochondrial genome architecture. Genome Biol Evol 5(5): 905-912.
67. Park E, Hwang D-S, Lee J-S, Song J-I, Seo T-K, et al. (2012) Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Mol Phylogenet Evol 62: 329-345.
68. Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, et al. (2013) State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol Biol 13: 161.
69. Lee MS, Hugall AF (2003) Partitioned likelihood support and the evaluation of data set conflict. Syst Biol 52: 15-22. (Pubitemid 36300055)
70. Appeltans W, Ahyong ST, Anderson G, Angel MV, Artois T, et al. (2012) The magnitude of global marine species diversity. Curr Biol 22(23): 2189-2202.
71. Glor RE (2010) Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 41: 251-270.
72. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.
73. Lanfear R, Calcott B, Ho SY, Guindon S (2012) Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29(6): 1695-1701.