Phylogenetic signal in mitochondrial and nuclear markers in sea anemones (cnidaria, Actiniaria)

Integrative and Comparative Biology

Volumn 50, Issue 3, 2010, Pages 371-388

  Daly, Marymegan ^a   Gusmão, Luciana C ^a   Reft, Abigail J ^a   Rodríguez, Estefanía ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; DNA; MITOCHONDRIAL DNA; RIBOSOME DNA;

ANIMAL; CELL NUCLEUS; COMPARATIVE STUDY; CONFERENCE PAPER; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; PHYLOGENY; SEA ANEMONE; SIGNAL TRANSDUCTION;

ANIMALS; BIOLOGICAL MARKERS; CELL NUCLEUS; DNA; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; GENETIC VARIATION; PHYLOGENY; SEA ANEMONES; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION;

ACTINIARIA; ANIMALIA; BILATERIA; CNIDARIA; COELENTERATA; ZOANTHARIA;

EID: 77956278441     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/icq081     Document Type: Conference Paper

References (76)

1. Acuña FH, Excoffon AC, McKinstry SR, Martínez DE. 2007. Characterization of Aulactinia (Actiniaria: Actiniidae) species from Mar del Plata (Argentina) using morphological and molecular data. Hydrobiologia 592:249-56.
2. Berntson EA, Bayer FM, MacArthur AG, France SC. 2001. Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18S rRNA sequences. Mar Biol 138:235-46.
3. Brugler M, France SC. 2007. The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria: Anthozoa: Antipatharia) supports classification of antipatharians within the subclass Hexacorallia. Mol Phyl Evol 42:776-8.
4. Berntson EA, France SC, Mullineaux LS. 1999. Phylogenetic relationships within the class Anthozoa (Phylum Cnidaria) based on nuclear 18S rDNA sequences. Mol Phyl Evol 13:417-33.
5. Chen CA, Odorico DM, ten Lohuis M, Veron JEN, Miller DJ. 1995. Systematic relationships within the Anthozoa using the 50-end of the 28S rDNA. Mol Phyl Evol 4:175-83.
6. Chen CA, Wallace CC, Wolstenholme JA. 2002. Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Mol Phyl Evol 23:137-49.
7. Cuif J-P, Lecointre G, Perrin C, Tillier A, Tillier S. 2003. Patterns of septal biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a dual approach for a new taxonomic framework. Zool Scripta 32:459-73.
8. Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, Winka K. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol 52:477-87.
9. Daly M, et al. 2007. The phylum Cnidaria: a review of phylogenetic patterns and diversity three hundred years after Linnaeus. Zootaxa 1668:127-86.
10. Daly M, Chaudhuri A, Gusmão LC, Rodriguez E. 2008. Phylogenetic relationships among sea anemones (Cnidaria: Anthozoa: Actiniaria). Mol Phyl Evol 48:292-301.
11. Daly M, Fautin DG, Cappola VA. 2003. Systematics of the Hexacorallia (Cnidaria: Anthozoa). Zool J Linn Soc 139:419-37.
12. Daly M, Lipscomb DL, Allard MW. 2002. A simple test:evaluating explanations for the relative simplicity of the Edwardsiidae. Evolution 56:502-10.
13. Duran S, Pascual M, Turon X. 2004. Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge Crambe crambe (Poecilosclerida). Mar Biol 144:31-5.
14. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-97.
15. Farris JS, Källersjö M, Bult C, Kluge AG. 1994. Testing significance of incongruence. Cladistics 10:315-9.
16. Erixon P, Svennblad B, Britton T, Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol 52:665-73.
17. Eytan RI, Hayes M, Patricia Arbour-Reily P, Miller M, Hellberg ME. 2009. Nuclear sequences reveal mid-range isolation of an imperiled deep-water coral population. Mol Ecol 18:2375-89.
18. Fautin DG, Goodwill RH. 2009. Neoaiptasia morbilla new species (Cnidaria: Actiniaria), a sea anemone symbiont of sand-dwelling gastropods on Saipan, Mariana Islands, with comments on some other such associations. Micronesica 41:101-15.
19. France SC, Hoover LL. 2002. DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). Hydrobiologia 471:149-55.
20. France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher TD. 1996. DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-sublass organization of the Anthozoa (Cnidaria). Mol Mar Biol Biotech 5:15-28.
21. France SC. 2007. Genetic analysis of bamboo corals (Cnidaria: Octocorallia: Isididae): does lack of colony branching distinguish Lepidisis from Keratoisis? Bull Mar Sci 81:323-33.
22. Fredslund J. 2006. PHY FI: fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics 7:315.
23. Fukami H, Budd AF, Levitan DR, Jara J, Kersanach R, Knowlton N. 2004a. Geographic differences in species boundaries among members of the Montastraea annularis complex based on molecular and morphological markers. Evolution 58:324-7.
24. Fukami H, Budd AF, Paulay G, Sole-Cava AM, Chen CA, Iwao K, Knowlton N. 2004b. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427:832-5.
25. Fukami H, et al. 2008. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (order Scleractinia, class Anthozoa, phylum Cnidaria). PLoS ONE 3:e3222.
26. Geller JB, Walton ED. 2001. Breaking up and getting back together: evolution of symbiosis and cloning in sea anemones (genus Anthopleura) inferred from a molecular phylogeny. Evolution 55:1781-94.
27. Goloboff PA. 1991. Homoplasy and the choice among cladograms. Cladistics 7: 215-32.
28. Goloboff P, Farris JS, Nixon K. 2000. TNT (Tree analysis using New Technology). Tucumán, Argentina: Published by the authors.
29. Gusmão LC, Daly M. 2010. Evolution of sea anemones (Cnidaria: Actiniaria: Hormathiidae) symbiotic with hermit crabs. Mol Phyl Evol (In press).
30. Hellberg ME. 2006. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol 6:24.
31. Hellberg ME. 2007. Footprints on water: the genetic wake of dispersal among reefs. Coral Reefs 26:463-73.
32. Holder MT, Sukumaran J, Lewis PO. 2008. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Syst Biol 57:814-21.
33. 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 6:167-74.
34. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-5.
35. Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-20.
36. Lavrov DV. 2007. Key transitions in animal evolution: a mitochondrial DNA perspective. Int Comp Biol 47:734-43.
37. Lavrov D, Forget L, Kelly M, Lang BF. 2005. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol Biol Evol 22:1231-9.
38. Le Goff-Vitry MC, Rogers AD, Baglowa D. 2003. A deep-sea slant on the molecular phylogeny of the Scleractinia. Mol Phyl Evol 30:167-77.
39. Mackenzie JB, Munday PL, Willis BL, Miller DJ, Van Oppen MJH. 2004. Unexpected patterns of genetic structuring among locations but not colour morphs in Acropora nasuta (Cnidaria: Scleractinia). Mol Ecol 13:9-20.
40. Maddison WP, Maddison DR. 2009. Mesquite: a modular system for evolutionary analysis. Version 2.72. Available from: http://mesquiteproject.org (January 2010, date last accessed).
41. McFadden CS, France SC, Sánchez JA, Alderslade P. 2006. A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial proteincoding sequences. Mol Phyl Evol 41:513-27.
42. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. 2006. Naked corals: skeleton loss in Scleractinia. Proc Nat Acad Sci 103:9096-100.
43. Miller MA, Holder MT, Vos R, Midford PE, Liebowitz T, Chan L, Hoover P, Warnow T. 2009. The CIPRES Portals. CIPRES. Available from: http://www.phylo. org/sub-sections/portal (30 March 2010, date last accessed).
44. Nixon K, Carpenter J. 1996. On simultaneous analysis. Cladistics 12: 221-41.
45. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
46. Park M-H, Sim C-J, Baek J, Min G-S. 2007. Identification of genes suitable for DNA barcoding of morphologically indistinguishable Korean Halichondriidae sponges. Mol Cells 23:220-7.
47. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808.
48. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-18.
49. Reimer JD, Ono S, Takishita K, Fujiwara Y, Tsukahara J. 2004. Reconsidering Zoanthus spp. diversity: molecular evidence of conspecifity within four previously presumed species. Zool Sci 21:517-25.
50. Reimer JD, Ono S, Iwama A, Takishita K, Tsukahara J, Maruyama T. 2006. Morphological and molecular revision of Zoanthus (Anthozoa: Hexacorallia) from southwestern Japan with description of two new species. Zool Sci 23:261-75.
51. Reimer JD, Nonaka M, Sinniger F, Iwase F. 2008a. Morphological and molecular characterization of a new genus and new species of parazoanthid (Anthozoa: Hexacorallia: Zoantharia) associated with Japanese Red Coral. Coral Reefs 27:935-49.
52. Reimer JD, Sinniger F, Hickman CP Jr. 2008b. Zoanthid diversity (Anthozoa: Hexacorallia) in the Galapagos Islands: a molecular examination. Coral Reefs 27:641-54.
53. Rodríguez E, Daly M. 2010. Phylogenetic relationships among deep-sea and chemosynthetic sea anemones: Actinoscyphiidae and Actinostolidae (Actiniaria: Mesomyaria). PLoS ONE 5(6):e10958.
54. Romano SL, Cairns SD. 2000. Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bull Mar Sci 67:1043-68.
55. Sánchez JA, Lasker HR, Taylor DJ. 2003. Phylogenetic analyses among octocorals (Cnidaria): mitochondrial and nuclear DNA sequences (lsu-rRNA, 16S and ssu-rRNA, 18S) support two convergent clades of branching gorgonians. Mol Phyl Evol 29:31-42.
56. Shearer TL, Coffroth MA. 2008. Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Res 8:247-55.
57. Shearer TL, van Oppen MJH, Romano SL, Wörheide G. 2002. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11:2475-87.
58. Simmons M, Pickett K, Miya M. 2004. How meaningful are Bayesian support values? Mol Biol Evol 21:188-99.
59. Sinniger F, Montoya-Burgos JI, Chevaldonne P, Pawlowski J. 2005. Phylogeny of the order Zoantharia (Anthozoa, Hexacorallia) based on the mitochondrial ribosomal genes. Mar Biol 147:1121-8.
60. Sinniger F, Pawlowski J. 2009. The partial mitochondrial genome of Leiopathes glaberrima (Hexacorallia: Antipatharia) and the first report of the presence of an intron in COI in black corals. Galaxea 11:21-6.
61. Sinniger F, Reimer JD, Pawlowski J. 2008. Potential of DNA sequences to identify zoanthids (Cnidaria: Zoantharia). Zool Sci 25:1253-60.
62. Sinniger F, Reimer JD, Pawlowski J. 2010. The Parazoanthidae (Hexacorallia: Zoantharia) DNA taxonomy: description of two new genera. Mar Biodiv 40:57-70.
63. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-90.
64. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57(5):758-71.
65. Stoletzki N, Schierwater B. 2005. Genetic and color morph differentiation in the Caribbean sea anemone Condylactis gigantea. Mar Biol 147:747-54.
66. Swain TD. 2009. Phylogeny-based species delimitations and the evolution of host associations in symbiotic zoanthids (Anthozoa, Zoanthidea) of the wider Caribbean region. Zool J Linn Soc 156:223-38.
67. Swain TD, Wulff JL. 2007. Diversity and specificity of Caribbean sponge-zoanthid symbioses: a foundation for understanding the adaptive significance of symbioses and generating hypotheses about higher-order systematics. Biol J Linn Soc 92:695-711.
68. Swofford DL. 2003. PAUP*: Phylogenetic Analyses using Parsimony (* and other methods), Version 4.0b10. Sinauer, Sunderland.
69. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-9.
70. Tseng CC, Wallace CC, Chen CA. 2005. Mitogenomic analysis of Montipora cactus and Anacropora matthai (Cnidaria; Scleractinia; Acroporidae) indicates an unequal rate of mitochondrial evolution among Acroporidae corals. Coral Reefs 24:502-8.
71. van Oppen MJH, Willis BL, Miller DJ. 1999. Atypically low rate of Cytochrome b evolution in the scleractinian coral genus Acropora. Proc Roy Soc London Ser B Biol Sci 266:179-83.
72. Wolstenholme JK, Wallace CC, Chen CA. 2003. Species boundaries within the Acropora humilis species group (Cnidaria; Scleractinia): a morphological and molecular interpretation of evolution. Coral Reefs 22:155-66.
73. Won J, Rho B, Song J. 2001. A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters. Coral Reefs 20:39-50.
74. Wörheide G. 2006. Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific. Mar Biol 148:907-12.
75. Worthington-Wilmer J, Mitchell ML. 2008. A preliminary investigation of the utility of ribosomal genes for species identification of sea anemones (Cnidaria: Actiniaria). Mem Queensl Mus Nature 54:65-74.
76. Xia X. 2001. DAMBE: Data Analysis in Molecular Biology and Evolution. J Heredity 92:371-3.