Corrigendum to "Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing" [Mol. Phylogenet. Evol. 77 (2014) 25-33] doi: 10.1016/j.ympev.2014.04.007;Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing

Molecular Phylogenetics and Evolution

Volumn 77, Issue 1, 2014, Pages 25-33

  Rehm, Peter ^a   Meusemann, Karen ^b,c   Borner, Janus ^a   Misof, Bernhard ^b   Burmester, Thorsten ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

^b ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

^c CSIRO   (Australia)

Author keywords

Arthropoda; Bayesian analyses; Mandibulata; Maximum Likelihood; Myriapoda; Myriochelata

Indexed keywords

TRANSCRIPTION FACTOR CLOCK; TRANSCRIPTOME;

ANIMAL; ARTHROPOD; BAYES THEOREM; CLASSIFICATION; GENETICS; PHYLOGENY;

ANIMALS; ARTHROPODS; BAYES THEOREM; CLOCK PROTEINS; PHYLOGENY; TRANSCRIPTOME;

EID: 84899086165     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.09.002     Document Type: Erratum

References (89)

1. Aguinaldo A.M.A., Turbeville J.M., Linford L.S., Rivera M.C., Garey J.R., Raff R.A., Lake J.A. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997, 387:489-493.
2. Ax P. Das system der Metazoa II. Ein Lehrbuch der phylogenetischen Systematik 1999.
3. Benton M.J., Donoghue P.C. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 2007, 24:26-53.
4. Bitsch C., Bitsch J. Phylogenetic relationships of basal hexapods among the mandibulate arthropods: a cladistic analysis based on comparative morphological characters. Zool. Scr. 2004, 33:511-550.
5. Boore J.L., Collins T.M., Stanton D., Daehler L.L., Brown W.M. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 1995, 376:163-165.
6. Boore J.L., Lavrov D.V., Brown W.M. Gene translocation links insects and crustaceans. Nature 1998, 392:667-668.
7. Bourlat S.J., Juliusdottir T., Lowe C.J., Freeman R., Aronowicz J., Kirschner M., Lander E.S., Thorndyke M., Nakano H., Kohn A.B., Heyland A., Moroz L.L., Copley R.R., Telford M.J. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 2006, 444:85-88.
8. Brewer M.S., Bond J.E. Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding Loci generated using next-generation sequence analyses. PLoS ONE 2013, 8:e79935.
9. Brusca, R.C., Brusca, G.J., 2003. Invertebrates. Sunderland.
10. Cook C.E., Smith M.L., Telford M.J., Bastianello A., Akam M. Hox genes and the phylogeny of the arthropods. Curr. Biol. 2001, 11:759-763.
11. Cox J.C., Ingersoll J.E., Ross S.A. A theory of the term structure of interest rates. Econometrica 1985, 53:385-407.
12. de Rosa R., Grenier J.K., Andreeva T., Cookk C.E., Adoutte A., Akamk M., Carroll S.B., Balavoinek G. Hox genes in brachiopods and priapulids and protostome evolution. Nature 1999, 399:772-776.
13. Dohle W. Sind die Myriapoden eine monophyletische Gruppe? Eine Diskussion der Verwandschaftsbeziehungen der Antennaten. Abh. naturwiss. Ver. Hamburg 1980, 23:45-104.
14. Dong Y., Sun H., Guo H., Pan D., Qian C., Hao S., Zhou K. The complete mitochondrial genome of Pauropus longiramus (Myriapoda: Pauropoda): implications on early diversification of the myriapods revealed from comparative analysis. Gene 2012, 505:57-65.
15. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:699-710.
16. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., Sorensen M.V., Haddock S.H., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
17. Ebersberger I., Strauss S., Haeseler A. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol. Biol. 2009, 9:157.
18. Edgecombe G.D. Morphological data, extant Myriapoda, and the myriapod stem-group. Contrib. Zool. 2004, 73:207-252.
19. Edgecombe G.D. Phylogenetic relationships of Myriapoda. Treatise on Zoology - Anatomy, Taxonomy, Biology. Myriapoda 2011, vol. 1:1-20. Brill, Leiden, The Netherlands.
20. Ertas B., von Reumont B., Wägele J.W., Misof B., Burmester T. Hemocyanin suggests a close relationship of Remipedia and Hexapoda. Mol. Biol. Evol. 2009, 26:2711-2718.
21. Friedrich M., Tautz D. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 1995, 376:165-167.
22. Gai Y.-H., Song D.-X., Sun H.-Y., Zhou K.-Y. Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences. Zool. Sci. 2006, 23:1101-1108.
23. Gai Y.-H., Song D.-X., Sun H.-Y., Yang Q., Zhou K.-Y. The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): extensive gene order rearrangement and evidence in favor of Progoneata. Mol. Phylogenet. Evol. 2008, 49:574-585.
24. García-Machado E., Pempera M., Dennebouy N., Oliva-Suarez M., Mounolou J.C., Monnerot M. Mitochondrial genes collectively suggest the paraphyly of Crustacea with respect to Insecta. J. Mol. Evol. 1999, 49:142-149.
25. Giribet G., Edgecombe G.D. Reevaluating the arthropod tree of life. Annu. Rev. Entomol. 2012, 57:167-186.
26. Giribet G., Ribera C. A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization. Cladistics 2000, 16:204-231.
27. Giribet G., Edgecombe G.D., Wheeler W.C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 2001, 413:157-161.
28. Harvey T.H.P., Butterfield N.J. Sophisticated particle-feeding in a large early Cambrian crustacean. Nature 2008, 452:868-871.
29. Harvey T.H., Velez M.I., Butterfield N.J. Exceptionally preserved crustaceans from western Canada reveal a cryptic Cambrian radiation. Proc. Natl. Acad. Sci. USA 2012, 109:1589-1594.
30. Harzsch S., Müller C.H.G., Wolf H. From variable to constant cell numbers: cellular characteristics of the arthropod nervous system argue against a sister-group relationship of Chelicerata and ''Myriapoda'' but favour the Mandibulata concept. Dev. Genes Evol. 2005, 215:53-68.
31. Heymonds R. Die Entwicklungsgeschichte derr Scolopender. Zool. Stud. 1901, 33:1-244.
32. Holland B., Moulton V. Consensus networks: a method for visualising incompatibilities in collections of trees. Algorithms in Bioinformatics 2003, Springer-Verlag, Berlin, Germany. G. Benson, R. Page (Eds.).
33. Holmes D.S., Bonner J. Preparation, molecular weight, base composition, and secondary structure of giant nuclear ribonucleic acid. Biochemistry 1973, 12:2330-2338.
34. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
35. Hwang U.W., Friedrich M., Tautz D., Park C.J., Kim W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 2001, 413:154-157.
36. Kadner D., Stollewerk A. Neurogenesis in the chilopod Lithobius forficatus suggests more similarities to chelicerates than to insects. Dev. Genes Evol. 2004, 214:367-379.
37. Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 2008, 9:286-298.
38. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., McLnerney J.O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 2006, 6:29.
39. Kraus O. Phylogenetic relationships between higher taxa of tracheate arthropods. Arthropod Relationships 1998, 295-303. Chapman & Hall, London. R.A. Fortey, R.H. Thomas (Eds.).
40. Kück P., Meusemann K. FASconCAT: convenient handling of data matrices. Mol. Phylogenet. Evol. 2010, 56:1115-1118.
41. Kück P., Meusemann K., Dambach J., Thormann B., Reumont B., Wägele J.W., Misof B. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Front. Zool. 2010, 7:10.
42. Kusche K., Burmester T. Diplopod hemocyanin sequence and the phylogenetic position of the Myriapoda. Mol. Biol. Evol. 2001, 18:1566-1573.
43. Kusche K., Ruhberg H., Burmester T. A hemocyanin from the Onychophora and the emergence of respiratory proteins. Proc. Natil. Acad. Sci. USA 2002, 99:10545-10548.
44. 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.
45. Lartillot N., Lepage T., Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25:2286-2288.
46. Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
47. Lepage T., Lawi S., Tupper P., Bryant D. Continuous and tractable models for the variation of evolutionary rates. Math. Biosci. 2006, 199:216-233.
48. Lepage T., Bryant D., Philippe H., Lartillot N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 2007, 24:2669-2680.
49. Loesel R., Nässel D.R., Strausfeld N.J. Common design in a unique midline neuropil in the brains of arthropods. Arthropod. Struct. Dev. 2002, 31:77-91.
50. Mallatt J., Giribet G. Further use of nearly complete, 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol. Phylogenet. Evol. 2006, 40:772-794.
51. Mallatt J.M., Garey J.R., Shultz J.W. Ecdysozoan phylogeny and Bayesian inference. first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 2004, 31:178-191.
52. Meusemann K., Reumont B.M., Simon S., Roeding F., Strauss S., Kück P., Ebersberger I., Walzl M., Pass G., Breuers S., Achter V., Haeseler A., Burmester T., Hadrys H., Wägele J.W., Misof B. A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol. 2010, 27:2451-2464.
53. Misof B., Misof K. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst. Biol. 2009, 58:21-34.
54. Misof B., Meyer B., von Reumont B.M., Kuck P., Misof K., Meusemann K. Selecting informative subsets of sparse supermatrices increases the chance to find correct trees. BMC Bioinformatics 2013, 14:348.
55. Murienne J., Edgecombe G.D., Giribet G. Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol. Phylogenet. Evol. 2010, 57:301-313.
56. Nardi F., Spinsanti G., Boore J.L., Carapelli A., Dallai R., Frati F. Hexapod origins: monophyletic or paraphyletic?. Science 2003, 299:1887-1889.
57. Negrisolo E., Minelli A., Valle G. The mitochondrial genome of the house centipede scutigera and the monophyly versus paraphyly of myriapods. Mol. Biol. Evol. 2004, 21:770-780.
58. Philippe H., Telford M.J. Large-scale sequencing and the new animal phylogeny. Trends Ecol. Evol. 2006, 21:614-620.
59. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W.H., Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 2004, 21:1740-1752.
60. Pisani D., Poling L.L., Lyons-Weiler M., Hedges S.B. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2004, 2:1.
61. Pocock R.I. On the classification of the tracheate Arthropoda. Zool. Anz. 1893, 16:271-275.
62. Podsiadlowski L., Kohlhagen H., Koch M. The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. Mol. Phylogenet. Evol. 2007, 45:251-256.
63. Regier J.C., Shultz J.W., Kambic R.E. Phylogeny of basal hexapod lineages and estimates of divergence times. Ann. Entomol. Soc. Am. 2004, 97:411-419.
64. Regier J.C., Wilson H.M., Shultz J.W. Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes. Mol. Phylogenet. Evol. 2005, 34:147-158.
65. Regier J.C., Shultz J.W., Ganley A.R., Hussey A., Shi D., Ball B., Zwick A., Stajich J.E., Cummings M.P., Martin J.W., Cunningham C.W. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst. Biol. 2008, 57:920-938.
66. Regier J.C., Shultz J.W., Zwick A., Hussey A., Ball B., Wetzer R., Martin J.W., Cunningham C.W. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463:1079-1083.
67. Rehm P., Borner J., Meusemann K., von Reumont B.M., Simon S., Hadrys H., Misof B., Burmester T. Dating the arthropod tree based on large-scale transcriptome data. Mol. Phylogenet. Evol. 2011, 61:880-887.
68. Richter S. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Divers. Evol. 2002, 2:217-237.
69. Roeding F., Hagner-Holler S., Ruhberg H., Ebersberger I., Haeseler A., Kube M., Reinhardt R., Burmester T. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol. Phylogenet. Evol. 2007, 45:942-951.
70. Rota-Stabelli O., Telford M.J. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol. Phylogenet. Evol. 2008, 48:103-111.
71. Rota-Stabelli O., Campbell L., Brinkmann H., Edgecombe G.D., Longhorn S.J., Peterson K.J., Pisani D., Philippe H., Telford M.J. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc. R. Soc. Lond. B. Biol. Sci. 2011, 278:298-306.
72. Rota-Stabelli O., Daley A.C., Pisani D. Molecular timetrees reveal a cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr. Biol. 2013, 23:392-398.
73. Rubinstein C.V., Gerrienne P., de la Puente G.S., Astini R.A., Steemans P. Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytol. 2010, 188:365-369.
74. Ruiz-Trillo I., Paps J., Loukota M., Ribera C., Jondelius U., Bagun J., Riutort M. A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc. Natl. Acad. Sci. USA 2002, 99:11246-11251.
75. Shear W.A., Edgecombe G.D. The geological record and phylogeny of the Myriapoda. Arthropod Struct. Dev. 2010, 39:174-190.
76. Stamatakis A. RAxML-VI-HPC: Maximum Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
77. Steemans P., Herisse A.L., Melvin J., Miller M.A., Paris F., Verniers J., Wellman C.H. Origin and radiation of the earliest vascular land plants. Science 2009, 324:353.
78. Telford M.J. Phylogenomics. Curr. Biol. 2007, 17:R945-R946.
79. Telford M.J., Bourlat S.J., Economou A., Papillon D., Rota-Stabelli O. The evolution of the Ecdysozoa. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008, 363:1529-1537.
80. Thorne J.L., Kishino H., Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 1998, 15:1647-1657.
81. Ungerer P., Scholtz G. The ancestral cleavage pattern of arthropods was not spiral-early development of sea spiders (Arthropoda, Pycnogonidal). J. Morphol. 2008, 269. pp. 1469-1469.
82. von Reumont B.M., Jenner R.A., Wills M.A., Dell'ampio E., Pass G., Ebersberger I., Meyer B., Koenemann S., Iliffe T.M., Stamatakis A., Niehuis O., Meusemann K., Misof B. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol. Biol. Evol. 2012, 29:1031-1045.
83. Waloszek D., Dunlop J.A. A larval sea spider (Arthropoda: Pycnogonida) from the Upper Cambrian 'Orsten' of Sweden, and the phylogenetic position of pycnogonids. Paleontology 2002, 45:421-446.
84. Wheat C.W., Wahlberg N. Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda. Syst. Biol. 2013, 62:93-109.
85. Wilson H.M., Anderson L.I. Morphology and taxonomy of Paleozoic millipedes (Diplopoda: Chilognatha: Archipolypoda) from Scotland. J. Paleontol. 2004, 78:169-184.
86. Wilson K., Cahill V., Ballment E., Benzie J. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: Are malacostracan crustaceans more closely related to insects than to branchiopods?. Mol. Biol. Evol. 2000, 17:863-874.
87. Zhang X.G., Siveter D.J., Waloszek D., Maas A. An epipodite-bearing crown-group crustacean from the Lower Cambrian. Nature 2007, 449:595-598.
88. Zrzavý J., Štys P. The basic body plan of arthropods: insights from evolutionary morphology and developmental biology. J. Evol. Biol. 1997, 10:353-367.
89. Zwick A., Regier J.C., Zwickl D.J. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS ONE 2012, 7:e47450.