BMC Evolutionary Biology | |
Cnidarian phylogenetic relationships as revealed by mitogenomics | |
Dennis V Lavrov3  Allen G Collins4  Hervé Philippe2  Béatrice Roure2  Ehsan Kayal1  | |
[1] Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 20013-7012, Washington, DC, USA;Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada;Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA;National Systematics Laboratory of NOAA’s Fisheries Service, National Museum of Natural History, MRC-153, Smithsonian Institution, PO Box 37012, 20013-7012, Washington, DC, USA | |
关键词: mito-phylogenomics; Anthozoa; Acraspeda; Medusozoa; Cnidaria; | |
Others : 1130392 DOI : 10.1186/1471-2148-13-5 |
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received in 2012-05-16, accepted in 2012-12-21, 发布年份 2013 | |
【 摘 要 】
Background
Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution.
Results
We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans.
Conclusions
Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.
【 授权许可】
2013 Kayal et al; licensee BioMed Central Ltd.
【 预 览 】
Files | Size | Format | View |
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20150226220316334.pdf | 647KB | download | |
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Figure 2. | 129KB | Image | download |
Figure 1. | 21KB | Image | download |
【 图 表 】
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【 参考文献 】
- [1]Daly M, Brugler MR, Cartwright P, Collins AG, Dawson MN, Fautin DG, France SC, Mcfadden CS, Opresko DM, Rodriguez E, Romano SL, Stake JL: The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus*. Zootaxa 2007, 182:127-128.
- [2]Collins AG: Recent insights into cnidarian phylogeny. Smithsonian Contributions to Marine Sciences 2009, 38:139-149.
- [3]Cavalier-Smith T, Allsopp MTEP, Chao EE, Boury-Esnault N, Vacelet J: Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S rRNA evidence. Can J Zool 1996, 74:2031-2045.
- [4]France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher T: DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-subclass organization of the Anthozoa (Cnidaria). Mol. Mar. Biol. Biotechnolog 1996, 5:15-28.
- [5]Odorico DM, Miller DJ: Internal and external relationships of the Cnidaria: implications of primary and predicted secondary structure of the 5’-end of the 23S-like rDNA. Proc Biol Sci/R. Soc 1997, 264:77-82.
- [6]Berntson EA, France SC, Mullineaux LS: Phylogenetic relationships within the class Anthozoa (phylum Cnidaria) based on nuclear 18S rDNA sequences. Mol Phylogenet Evol 1999, 13:417-433.
- [7]Collins AG: Phylogeny of Medusozoa and the evolution of cnidarian life cycles. J Evolution Biol 2002, 15:418-432.
- [8]Kayal E, Lavrov DV: The mitochondrial genome of Hydra oligactis (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny. Gene 2008, 410:177-186.
- [9]Lavrov DV, Wang X, Kelly M: Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Mol Phylogenet Evol 2008, 49:111-124.
- [10]Park E, Hwang D-S, Lee J-S, Song J-I, Seo T-K, Won Y-J: Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Mol Phylogenet Evol 2012, 62:329-345.
- [11]Shao Z, Graf S, Chaga OY, Lavrov DV: Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene 2006, 381:92-101.
- [12]Kim J, Kim W, Cunningham CW: A new perspective on lower metazoan relationships from 18S rDNA Sequences. Mol Biol Evol 1999, 16:423-427.
- [13]Dawson MN: Some implications of molecular phylogenetics for understanding biodiversity in jellyfishes, with emphasis on Scyphozoa. Hydrobiologia 2004, 530–531:249-260.
- [14]Collins AG, Schuchert P, Marques AC, Jankowski T, Medina M, Schierwater B: 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 Bio 2006, 55:97-115.
- [15]Mayer AG: Medusae of the world. Washington, D.C: Carnegie institution of Washington; 1910:386.
- [16]Thiel H: The evolution of Scyphozoa: A review. In Cnidaria and their Evolution. London: Academic Press; 1966.
- [17]Bayha KM, Dawson MN, Collins AG, Barbeitos MS, Haddock SHD: Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA. Integr Comp Biol 2010, 50:436-455.
- [18]Cartwright P, Nawrocki AM: Character evolution in hydrozoa (phylum Cnidaria). Integr Comp Biol 2010, 50(3):456-472.
- [19]Cartwright P, Evans NM, Dunn CW, Marques AC, Miglietta MP, Schuchert P, Collins AG: Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria). J. Mar. Biol. Assoc. U.K 2008, 88:1663-1672.
- [20]Kitahara MV, Cairns SD, Stolarski J, Blair D, Miller DJ: A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS One 2010, 5:e11490.
- [21]Fukami H, Chen CA, Budd AF, Collins A, Wallace C, Chuang Y-Y, Chen C, Dai C-F, Iwao K, Sheppard C, Knowlton N: 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 2008, 3:e3222.
- [22]Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL: Naked corals: skeleton loss in Scleractinia. Proc Nat Acad Sci USA 2006, 103:9096-9100.
- [23]Bentlage B, Cartwright P, Yanagihara AA, Lewis C, Richards GS, Collins AG: Evolution of box jellyfish (Cnidaria: Cubozoa), a group of highly toxic invertebrates. Proc Biol Sci/R Soc 2010, 277:493-501.
- [24]McFadden CS, Sanchez JA, France SC: Molecular phylogenetic insights into the evolution of octocorallia: a review. Integr Comp Biol 2010, 50:389-410.
- [25]Barbeitos MS, Romano SL, Lasker HR: Repeated loss of coloniality and symbiosis in scleractinian corals. Proc Nat Acad Sci USA 2010, 107:11877-11882.
- [26]Costello JH, Colin SP, Dabiri JO: Medusan morphospace: phylogenetic constraints, biomechanical solutions, and ecological consequences. Invertebr Biol 2008, 127:265-290.
- [27]Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S, Lavrov DV: Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biol Evol 2012, 4:1-12.
- [28]Marques AC, Collins AG: Cladistic analysis of Medusozoa and cnidarian evolution. Invertebr Biol 2004, 123:23-42.
- [29]Collins AG, Bentlage B, Lindner A, Lindsay D, Haddock SHD, Jarms G, Norenburg JL, Jankowski T, Cartwright P: Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa. J Mar Biol Assoc U.K 2008, 88:1673-1685.
- [30]Leclère L, Schuchert P, Cruaud C, Couloux A, Manuel M: Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes. Syst Biol 2009, 58:509-526.
- [31]Leclère L, Schuchert P, Manuel M: Phylogeny of the Plumularioidea (Hydrozoa, Leptothecata): evolution of colonial organisation and life cycle. Zoologica Scripta 2007, 36:371-394.
- [32]Kan X-Z, Yang J-K, Li X-F, Chen L, Lei Z-P, Wang M, Qian C-J, Gao H, Yang Z-Y: Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. Genet Mol Res: GMR 2010, 9(3):1625-1633.
- [33]Podsiadlowski L, Braband A, Struck TH, Von Döhren J, Bartolomaeus T: Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea. BMC Genomics 2009, 10:364. BioMed Central Full Text
- [34]Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, Blaxter M, Lavrov DV: Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the panarthropoda. Genome Biol Evol 2010, 2:425-440.
- [35]Hoelzer GA: Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees revisited. Evolution 1997, 51:622-626.
- [36]Boore JL, Fuerstenberg SI: Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philosophical transactions of the Royal Society of London. Series B, Biol Sci 2008, 363:1445-1451.
- [37]Lavrov DV, Forget L, Kelly M, Lang BF: Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol Biol Evol 2005, 22:1231-1239.
- [38]Gazave E, Lapébie P, Renard E, Vacelet J, Rocher C, Ereskovsky AV, Lavrov DV, Borchiellini C: Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One 2010, 5:e14290.
- [39]Brugler MR, France SC: The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria: Anthozoa: Antipatharia) supports classification of antipatharians within the subclass Hexacorallia. Mol Phylogenet Evol 2007, 42:776-788.
- [40]Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, Wrede P, Wiens M, Alié A, Morgenstern B, Manuel M, Wörheide G: Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 2010, 27:1983-1987.
- [41]Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D: Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 2011, 9:e1000602.
- [42]Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F: Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol 2005, 5:50. BioMed Central Full Text
- [43]Roure BB, Philippe HH: Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference. BMC Evol Biol 2011, 11:17. BioMed Central Full Text
- [44]Stabelli OR, Lartillot N, Philippe H, Pisani D: Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol 2012.
- [45]Zrzavy J, Mihulka S, Kepka P, Bezdek A, Tietz D: Phylogeny of the Metazoa Based on Morphological and 18S Ribosomal DNA Evidence. Cladistics 1998, 14:249-285.
- [46]Siddall ME, Martin DS, Bridge D, Desser SS, David K, Martint DS, Bridget D, Conell DK: The demise of a phylum of protists: phylogeny of myxozoa and other parasitic cnidaria. J Parasitol 1995, 81:961-967.
- [47]Schuchert P: Phylogenetic analysis of the Cnidaria. J. Zoolog. Syst. Evol. Res 1993, 31:161-173.
- [48]Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P: The phylogenetic position of myxozoa: exploring conflicting signals in phylogenomic and ribosomal datasets. Mol Biol 2010, 8:139.
- [49]Evans NM, Lindner A, Raikova EV, Collins AG, Cartwright P: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria. BMC Evol Biol 2008, 8:139. BioMed Central Full Text
- [50]Lartillot N, Brinkmann H, Philippe H: Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 2007, 7(Suppl 1):S4. BioMed Central Full Text
- [51]Collins AG, Winkelmann S, Hadrys H, Schierwater B: Phylogeny of Capitata and Corynidae (Cnidaria, Hydrozoa) in light of mitochondrial 16S rDNA data. Zoologica Scripta 2005, 34:91-99.
- [52]Budd AF, Romano SL, Smith ND, Barbeitos MS: Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integr Comp Biol 2010, 50:411-427.
- [53]McFadden CS, Benayahu Y, Pante E, Thoma JN, Nevarez AP, France SC: Limitations of mitochondrial gene barcoding in Octocorallia. Mol Ecol Res 2011, 11:19-31.
- [54]Bilewitch JP, Degnan SM: 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 2011, 11:228. BioMed Central Full Text
- [55]McFadden CS, France SC, Sánchez JA, Alderslade P: A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences. Mol Phylogenet Evol 2006, 41:513-27.
- [56]Finnerty JR, Pang K, Burton P, Paulson D, Martindale MQ: Origins of bilateral symmetry: Hox and dpp expression in a sea anemone. Science 2004, 304:1335-1337.
- [57]Matus DQ, Pang K, Marlow H, Dunn CW, Thomsen GH, Martindale MQ: Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proc Nat Acad Sci USA 2006, 103:11195-11200.
- [58]Van Iten H, De Moraes LJ, Simões MG, Marques AC, Collins AG: Reassessment of the phylogenetic position of conulariids (?Ediacaran‐Triassic) within the subphylum medusozoa (phylum cnidaria). J Syst Palaeontol 2006, 4:109-118.
- [59]Dunn CW: Complex colony-level organization of the deep-sea siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) is directionally asymmetric and arises by the subdivision of pro-buds. Dev. Dyn: an official publication of the American Association of Anatomists 2005, 234:835-845.
- [60]Jiménez-Guri E, Philippe H, Okamura B, Holland PWH: Buddenbrockia is a cnidarian worm. Science (New York, N.Y.) 2007, 317:116-118.
- [61]Palmer RA: Symmetry breaking and the evolution of development. Science 2004, 306:828-833.
- [62]Levin M: Left-right asymmetry in embryonic development: a comprehensive review. Mech Develop 2005, 122:3-25.
- [63]Nielsen C: Six major steps in animal evolution: are we derived sponge larvae? Evol Develop 2008, 10:241-257.
- [64]Uchida T: The systematic position of the Stauromedusae. Publ Seto Mar Biol Lab 1972, 20:133-139.
- [65]Werner B: New investigations on systematics and evolution of the class Scyphozoa and the phylum Cnidaria. Publ Seto Mar Biol Lab 1973, 20:35-61.
- [66]Gibbons MJ, Janson LA, Ismail A, Samaai T: Life cycle strategy, species richness and distribution in marine Hydrozoa (Cnidaria: Medusozoa). J Biogeogr 2010, 37:441-448.
- [67]Boero F, Schierwater B, Piraino S: Cnidarian milestones in metazoan evolution. Integr Comp Biol 2007, 47:693-700.
- [68]Beagley CT, Okimoto R, Wolstenholme DR: The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 1998, 148:1091-1108.
- [69]Sinniger F, Pawlowski J: 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, J Coral Reef Studies 2009, 11(1):21-26.
- [70]Van Oppen MJH, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ: The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 2002, 55:1-13.
- [71]Emblem Å, Karlsen BO, Evertsen J, Johansen SD: Mitogenome rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long-term evolving group I intron. Mol Phylogenet Evol 2011, 61:495-503.
- [72]Chen C, Chiou C-Y, Dai C-F, Chen CA: Unique mitogenomic features in the scleractinian family pocilloporidae (scleractinia: astrocoeniina). Marine Biotechnology 2008, 10:538-553.
- [73]Fukami H, Knowlton N: Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs 2005, 24:410-417.
- [74]Flot J-F, Tillier S: The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function. Gene 2007, 401(1–2):80-87.
- [75]Sinniger F, Chevaldonné P, Pawlowski J: Mitochondrial genome of Savalia savaglia (Cnidaria, Hexacorallia) and early metazoan phylogeny. J. Mol. Evol 2007, 64:196-203.
- [76]Van der Ham JL, Brugler MR, France SC: Exploring the utility of an indel-rich, mitochondrial intergenic region as a molecular barcode for bamboo corals (Octocorallia: Isididae). Marine Genomics 2009, 2(3-4):183-192.
- [77]Uda K, Komeda Y, Koyama H, Koga K, Fujita T, Iwasaki N, Suzuki T: Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): Notable differences in gene arrangement. Gene 2011, 476:27-37.
- [78]Brugler MR, France SC: The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): genome structure and putative origins of replication are not conserved among octocorals. J Mol Evol 2008, 67:125-136.
- [79]Beaton MJ, Roger a J, Cavalier-Smith T: Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals. J Mol Evol 1998, 47:697-708.
- [80]Pont-Kingdon G, Okada NA, Macfarlane JL, Beagley CT, Watkins-Sims CD, Cavalier-Smith T, Clark-Walker GD, Wolstenholme DR: 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 1998, 46:419-431.
- [81]Voigt O, Erpenbeck D, Wörheide G: A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata. BMC genomics 2008, 9:350. BioMed Central Full Text
- [82]Signorovitch AY, Buss LW, Dellaporta SL: Comparative genomics of large mitochondria in placozoans. PLoS Genetics 2007, 3(1):e13.
- [83]Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA, Buss LW, Schierwater B: Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci 2006, 103:8751-8756.
- [84]Wang X, Lavrov DV: Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the demospongiae. PLoS ONE 2008, 3:e2723.
- [85]Erpenbeck D, Voigt O, Wörheide G, Lavrov DV: The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE). BMC genomics 2009, 10:591. BioMed Central Full Text
- [86]Lavrov DV: Rapid proliferation of repetitive palindromic elements in mtDNA of the endemic Baikalian sponge Lubomirskia baicalensis. Mol Biol Evol 2010, 27:757-760.
- [87]Lukić-Bilela L, Brandt D, Pojskić N, Wiens M, Gamulin V, Müller WEG: Mitochondrial genome of Suberites domuncula: palindromes and inverted repeats are abundant in non-coding regions. Gene 2008, 412:1-11.
- [88]Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A: Geneious Pro v5.5.6. 2011.
- [89]Suyama M, Torrents D, Bork P: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 2006, 34:W609-W612.
- [90]Philippe H: MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 1993, 21:5264-5272.
- [91]Lartillot N, Philippe H: Computing Bayes factors using thermodynamic integration. Syst Bio 2006, 55:195-207.
- [92]Lartillot N, Philippe H: A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004, 21:1095-1109.
- [93]Ott M, Zola J, Stamatakis A: Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. Proceedings of ACM/IEEE Supercomputing Conference 2007. 2007
- [94]Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 2006, 22:2688-2690.
- [95]Stamatakis A: Phylogenetic models of rate heterogeneity: a high performance computing perspective. Proceedings 20th IEEE International Parallel & Distributed Processing Symposium 2006, 8.
- [96]Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008, 57:758-771.
- [97]Posada D: jModelTest: phylogenetic model averaging. Mol Biol Evol 2008, 25:1253-1256.
- [98]Ronquist F, Teslenko M, Van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012, 61:539-542.
- [99]Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics (Oxford, England) 2001, 17:1246-1247.
- [100]Won J, Rho B, Song J: A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters. Coral Reefs 2001, 20:39-50.
- [101]Swofford DL: PAUP* 4.0. 2002, 42:1-144.