Phylogenomic resolution of the hemichordate and echinoderm clade

Current Biology

Volumn 24, Issue 23, 2014, Pages 2827-2832

  Cannon, Johanna T ^a,b,e   Kocot, Kevin M ^a,c,e   Waits, Damien S ^a   Weese, David A ^a,d   Swalla, Billie J ^e   Santos, Scott R ^a   Halanych, Kenneth M ^a,e  

^a AUBURN UNIVERSITY   (United States)

^b SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d GEORGIA COLLEGE AND STATE UNIVERSITY   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASTEROIDEA; ASTEROZOA; CHORDATA; ECHINODERMATA; ECHINOIDEA; ENTEROPNEUSTA; HEMICHORDATA; OPHIUROIDEA; OTUS; PTEROBRANCHIA; PTYCHODERA FLAVA; PTYCHODERIDAE; RHABDOPLEURIDA; SACCOGLOSSUS KOWALEVSKII; SOMASTEROIDEA; STEREOBALANUS CANADENSIS; STRONGYLOCENTROTUS PURPURATUS;

TRANSCRIPTOME;

ANIMAL; CHORDATA; CLASSIFICATION; EVOLUTION; GENETICS; INVERTEBRATE CHORDATA; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BIOLOGICAL EVOLUTION; CHORDATA; CHORDATA, NONVERTEBRATE; LIKELIHOOD FUNCTIONS; PHYLOGENY; TRANSCRIPTOME;

EID: 84919665052     PISSN: 09609822     EISSN: 18790445     Source Type: Journal    
DOI: 10.1016/j.cub.2014.10.016     Document Type: Article

References (44)

1. K.M. Halanych The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data Mol. Phylogenet. Evol. 4 1995 72 76
2. S.J. Bourlat, T. Juliusdottir, C.J. Lowe, R. Freeman, J. Aronowicz, M. Kirschner, E.S. Lander, M. Thorndyke, H. Nakano, and A.B. Kohn Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida Nature 444 2006 85 88
3. F.D. Brown, A. Prendergast, and B.J. Swalla Man is but a worm: chordate origins Genesis 46 2008 605 613
4. B.J. Swalla, and A.B. Smith Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives Philos. Trans. R. Soc. Lond. B Biol. Sci. 363 2008 1557 1568
5. C.B. Cameron, J.R. Garey, and B.J. Swalla Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla Proc. Natl. Acad. Sci. USA 97 2000 4469 4474
6. J.T. Cannon, A.L. Rychel, H. Eccleston, K.M. Halanych, and B.J. Swalla Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts Mol. Phylogenet. Evol. 52 2009 17 24
7. J.T. Cannon, B.J. Swalla, and K.M. Halanych Hemichordate molecular phylogeny reveals a novel cold-water clade of harrimaniid acorn worms Biol. Bull. 225 2013 194 204
8. D. Janies Phylogenetic relationships of extant echinoderm classes Can. J. Zool. 79 2001 1232 1250
9. D. Pisani, R. Feuda, K.J. Peterson, and A.B. Smith Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships Mol. Phylogenet. Evol. 62 2012 27 34
10. D.T.J. Littlewood, A.B. Smith, K.A. Clough, and R.H. Emson The interrelationships of the echinoderm classes: morphological and molecular evidence Biol. J. Linn. Soc. Lond. 61 1997 409 438
11. A.B. Smith Deuterostomes in a twist: the origins of a radical new body plan Evol. Dev. 10 2008 493 503
12. F. Delsuc, H. Brinkmann, D. Chourrout, and H. Philippe Tunicates and not cephalochordates are the closest living relatives of vertebrates Nature 439 2006 965 968
13. H. Philippe, H. Brinkmann, R.R. Copley, L.L. Moroz, H. Nakano, A.J. Poustka, A. Wallberg, K.J. Peterson, and M.J. Telford Acoelomorph flatworms are deuterostomes related to Xenoturbella Nature 470 2011 255 258
14. C.B. Cameron A phylogeny of the hemichordates based on morphological characters Can. J. Zool. 83 2005 196 215
15. C.E. Mitchell, M.J. Melchin, C.B. Cameron, and J. Maletz Phylogenetic analysis reveals that Rhabdopleura is an extant graptolite Lethaia 46 2013 34 56
16. M.J. Telford, C.J. Lowe, C.B. Cameron, O. Ortega-Martinez, J. Aronowicz, P. Oliveri, and R.R. Copley Phylogenomic analysis of echinoderm class relationships supports Asterozoa Proc. Biol. Sci. 281 2014 20140479
17. T.D. O'Hara, A.F. Hugall, B. Thuy, and A. Moussalli Phylogenomic resolution of the class ophiuroidea unlocks a global microfossil record Curr. Biol. 24 2014 1874 1879
18. Meyer, B., Meusemann, K., and Misof, B. (2010). MARE v0.1.2-rc. http://mare.zfmk.de/.
19. K.M. Kocot, M.R. Citarella, L.L. Moroz, and K.M. Halanych PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics Evol. Bioinform. Online 9 2013 429 435
20. K.M. Kocot, J.C. Cannon, and K.M. Halanych Elucidating animal phylogeny R. DeSalle, B. Schierwater, Key Transitions in Animal Evolution 2010 CRC Press Enfield 15 33
21. K.J. Peterson, Y.-H. Su, M.I. Arnone, B. Swalla, and B.L. King MicroRNAs support the monophyly of enteropneust hemichordates J. Exp. Zoolog. B Mol. Dev. Evol. 320 2013 368 374
22. R.C. Thomson, D.C. Plachetzki, D.L. Mahler, and B.R. Moore A critical appraisal of the use of microRNA data in phylogenetics Proc. Natl. Acad. Sci. USA 111 2014 E3659 E3668
23. K.J. Osborn, L.A. Kuhnz, I.G. Priede, M. Urata, A.V. Gebruk, and N.D. Holland Diversification of acorn worms (Hemichordata, Enteropneusta) revealed in the deep sea Proc. Biol. Sci. 279 2012 1646 1654
24. N.D. Holland, L.A. Kuhnz, and K.J. Osborn Morphology of a new deep-sea acorn worm (class Enteropneusta, phylum Hemichordata): a part-time demersal drifter with externalized ovaries J. Morphol. 273 2012 661 671
25. K.J. Osborn, A.V. Gebruk, A. Rogacheva, and N.D. Holland An externally brooding acorn worm (Hemichordata, Enteropneusta, Torquaratoridae) from the Russian arctic Biol. Bull. 225 2013 113 123
26. J.-B. Caron, S.C. Morris, and C.B. Cameron Tubicolous enteropneusts from the Cambrian period Nature 495 2013 503 506
27. K.M. Halanych, J.T. Cannon, A.R. Mahon, B.J. Swalla, and C.R. Smith Modern Antarctic acorn worms form tubes Nat. Commun. 4 2013 2738
28. B.S. McCauley, E.P. Wright, C. Exner, C. Kitazawa, and V.F. Hinman Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms Evodevo 3 2012 17
29. M. Byrne, Y. Nakajima, F.C. Chee, and R.D. Burke Apical organs in echinoderm larvae: insights into larval evolution in the Ambulacraria Evol. Dev. 9 2007 432 445
30. R. Mooi, and B. David What a new model of skeletal homologies tells us about asteroid evolution Am. Zool. 40 2000 326 339
31. C.J. Lowe Molecular genetic insights into deuterostome evolution from the direct-developing hemichordate Saccoglossus kowalevskii Philos. Trans. R. Soc. Lond. B Biol. Sci. 363 2008 1569 1578
32. M. Nomaksteinsky, E. Röttinger, H.D. Dufour, Z. Chettouh, C.J. Lowe, M.Q. Martindale, and J.-F. Brunet Centralization of the deuterostome nervous system predates chordates Curr. Biol. 19 2009 1264 1269
33. V.B. Morris Early development of coelomic structures in an echinoderm larva and a similarity with coelomic structures in a chordate embryo Dev. Genes Evol. 222 2012 313 323
34. J. Forment, F. Gilabert, A. Robles, V. Conejero, F. Nuez, and J.M. Blanca EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration BMC Bioinformatics 9 2008 5
35. Brown, C.T., Howe, A., Zhang, Q., Pyrkosz, A.B., and Brom, T.H. (2012). A reference-free algorithm for computational normalization of shotgun sequencing data. ArXiv, arXiv:1203.4802. http://arxiv.org/abs/1203.4802.
36. M.G. Grabherr, B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, and Q. Zeng Full-length transcriptome assembly from RNA-Seq data without a reference genome Nat. Biotechnol. 29 2011 644 652
37. I. Ebersberger, S. Strauss, and A. von Haeseler HaMStR: profile hidden markov model based search for orthologs in ESTs BMC Evol. Biol. 9 2009 157
38. K.M. Kocot, J.T. Cannon, C. Todt, M.R. Citarella, A.B. Kohn, A. Meyer, S.R. Santos, C. Schander, L.L. Moroz, B. Lieb, and K.M. Halanych Phylogenomics reveals deep molluscan relationships Nature 477 2011 452 456
39. K. Katoh, K. Kuma, H. Toh, and T. Miyata MAFFT version 5: improvement in accuracy of multiple sequence alignment Nucleic Acids Res. 33 2005 511 518
40. B. Misof, and K. Misof A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion Syst. Biol. 58 2009 21 34
41. A. Stamatakis RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 22 2006 2688 2690
42. D. Darriba, G.L. Taboada, R. Doallo, and D. Posada ProtTest 3: fast selection of best-fit models of protein evolution Bioinformatics 27 2011 1164 1165
43. H. Shimodaira An approximately unbiased test of phylogenetic tree selection Syst. Biol. 51 2002 492 508
44. N. Lartillot, N. Rodrigue, D. Stubbs, and J. Richer PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment Syst. Biol. 62 2013 611 615