Rerooting the rDNA gene tree reveals phoronids to be 'brachiopods without shells'; dangers of wide taxon samples in metazoan phylogenetics (Phoronida; Brachiopoda)

Zoological Journal of the Linnean Society

Volumn 167, Issue 1, 2013, Pages 82-92

  Cohen, Bernard L ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Lophophorates; Lophotrochozoa; Metazoa; Systematics

Indexed keywords

ANIMALIA; BRACHIOPODA; LOPHOPHORATA; LOPHOTROCHOZOA; METAZOA; MOLLUSCA; PHORONIFORMEA;

EID: 84872596144     PISSN: 00244082     EISSN: 10963642     Source Type: Journal    
DOI: 10.1111/j.1096-3642.2012.00869.x     Document Type: Article

References (67)

1. Andrade SCS, Strand M, Schwartz M, Chend H, Kajihara H, von Döhren J, Sung S, Junoy J, Thiel M, Norenburg JL, Turbeville JM, Giribet G, Sundberg P. 2012. Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea. Cladistics 28: 141-159.
2. Balthasar U. 2004. Shell structure, ontogeny and affinities of the Lower Cambrian bivalved problematic fossil Mickwitzia muralensis Walcott, 1913. Lethaia 37: 381-400.
3. Balthasar U, Butterfield NJ. 2009. Early Cambrian 'soft-shelled'brachiopods as possible stem-group phoronids. Acta Palaeontolgica Polonica 54: 307-314.
4. Brinkmann H, Philippe H. 1999. Archea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Molecular Biology and Evolution 16: 817-825.
5. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552.
6. Cohen BL. 2000. Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.). Proceedings of the Royal Society, London, Series B 267: 225-231.
7. Cohen BL. 2007. The brachiopod genome. In: Selden PA, ed. Treatise on invertebrate paleontology. Part H6 (Supplement), Brachiopoda (revised). Lawrence, KS: Geological Society of America and University of Kansas Press, 2356-2372.
8. Cohen BL, Gawthrop AB. 1996. Brachiopod molecular phylogeny. In: Copper P, Jin J, eds. Brachiopods: proceedings of the third international brachiopod congress, Sudbury, Ontario. 1995. Rotterdam: Balkema, 73-80.
9. Cohen BL, Gawthrop AB. 1997. The brachiopod genome. In: Kaesler RL, ed. Treatise on invertebrate paleontology. Part H1, Brachiopoda, revised. Lawrence: Geological Society of America and University of Kansas Press, 189-211.
10. Cohen BL, Gawthrop AB, Cavalier-Smith T. 1998. Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences. Philosophical Transactions of the Royal Society, B 353: 2039-2061.
11. Cohen BL, Long SL, Saito M. 2008. Living craniids: preliminary molecular evidence of their inter-relationships. Fossils and Strata 54: 283-287.
12. Cohen BL, Weydmann A. 2005. Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the Early Cambrian. Organisms, Diversity & Evolution 5: 253-273.
13. Conway Morris S, Peel JS. 1995. Articulated halkierids from the Lower Cambrian of North Greenland and their role in early protostome evolution. Philosophical Transactions of the Royal Society, B 347: 305-358.
14. Cooper GA. 1977. Brachiopods from the Caribbean Sea and adjacent waters. Coral Gables: University of Miami Press, 1-211.
15. Davidson E, Levin M. 2005. Gene regulatory networks. Proceedings of the National Academy of Sciences, Washington 102: 20063-20066.
16. Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H. 2004. The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils. Proceedings of the National Academy of Sciences, USA 101: 15386-15391.
17. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. Plos Biology 4: e88.
18. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-750.
19. Endo K, Ozawa T, Kojima S. 2001. Nuclear and mitochondrial gene sequences reveal unexpected genetic heterogeneity among northern Pacific populations of the brachiopod Lingula anatina. Marine Biology 139: 105-112.
20. Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. 2011. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334: 1091-1097.
21. Farris JS, Albert VA, Källersjö M, Lipscomb D, Kluge AG. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
22. Felsenstein J. 2004. Inferring phylogenies. Sunderland: Sinauer Associates, MA1-664.
23. Freudenstein JV, Davis JI. 2010. Branch support via resampling: an empirical study. Cladistics 26: 1-14.
24. Halanych K. 1995. The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data. Molecular Phylogenetics and Evolution 4: 72-76.
25. Hausdorf B, Helmkampf M, Nesnidal MP, Bruchhaus I. 2010. Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida). Molecular Phylogenetics and Evolution 55: 1121-1127. 10.1016/j.ympev.2009.12.022.
26. Hillis DM, Moritz C, Mable BK, eds. 1996. Molecular systematics, 1-655. Sunderland, MA: Sinauer Associates.
27. Holmer LE, Skovsted CB, Larsson C, Brock GA, Zhang Z. 2011. First record of a bivalved larval shell in Early Cambrian tomotiids and its phylogenetic significance. Palaeontology 54: 235-239.
28. Holmer LE, Skovsted CB, Williams A. 2002. A stem group brachiopod from the Lower Cambrian-support for a Micrina (halkieriid) ancestry. Palaeontology 45: 875-882.
29. Huelsenbeck JP, Bollback JP, Levine AM. 2002. Inferring the root of a phylogenetic tree. Systematic Biology 51: 32-43.
30. Huson DH. 1998. SplitsTree: analysing and visualizing evolutionary data. Bioinformatics 14: 68-73.
31. Kaesler RL, ed. 19972007. Treatise on invertebrate paleontology. Brachiopoda, Parts H1-5, revised. Boulder, CO and Lawrence, KS: Geological Society of America and University of Kansas.
32. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
33. Lee DE, Brunton CHC. 2001. Novocrania, new name for the genus Neocrania Lee and Brunton, 1986 (Brachiopoda, Craniida); preoccupied by Neocrania Davis, 1978 (Insecta, Lepidoptera). Bulletin of the Natural History Museum (Geology Series) 57: 1-5.
34. Maddison DR, Maddison WP. 2001. MacClade 4: Analysis of phylogeny and character evolution, version 4.02. Sunderland, MA: Sinauer Associates.
35. Maddison WP, Donoghue MJ, Maddison DR. 1984. Outgroup analysis and parsimony. Systematic Zoology 33: 83-103.
36. Mallatt J, Craig CW, Yoder MJ. 2010. Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Molecular Phylogenetics and Evolution 55: 1-17.
37. Mallatt J, Craig CW, Yoder MJ. 2012. Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis. Molecular Phylogenetics and Evolution 63: 604-617.
38. Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B. 2010. Compositional heterogeneity and phylogenomic inference of metazoan relationships. Molecular Biology and Evolution 27: 2095-2104.
39. Nixon KC, Carpenter JM. 1993. On outgroups. Cladistics 9: 413-426.
40. Paps J, Baguna J, Riutort M. 2009. Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proceedings of the Royal Society, B 276: 1245-1254.
41. Passamaneck Y, Halanych KM. 2006. Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly. Molecular Phylogenetics and Evolution 40: 20-28.
42. Philippe H, Delsuc F, Brinkmann H. 2005. Phylogenomics. Annual Review of Ecology and Systematics 36: 541-562.
43. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808.
44. Posada D, Crandall KP. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
45. Ronquist FR, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
46. Ronquist FR, Huelsenbeck J, Teslenko M. 2011. Draft MrBayes version 3.2 manual: tutorials and model summaries, version 15 November 2011. Distributed with the software. Available at: http//:brahms.biology.rochester.edu/software.html.
47. Rosenfeld JA, Payne A, DeSalle R. 2012. Random roots and lineage sorting. Molecular Phylogenetics and Evolution 64: 12-20.
48. Sanderson MJ, Thorne JL, Wikstrom N, Bremer K. 2004. Molecular evidence on plant divergence times. American Journal of Botany 9: 1656-1665.
49. Santagata S, Cohen BL. 2009. Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1. Zoological Journal of the Linnean Society 157: 34-50. 10.1111/j.1096-3642.2009.00531.x.
50. Siddall ME. 2010. Unringing a bell: metazoan phylogenomics and the partition bootstrap. Cladistics 26: 444-452. 10.1111/j.1096-0031.2009.00295.x.
51. Simmons MP. 2000. A fundamental problem with amino-acid sequence characters for phylogenetic analysis. Cladistics 16: 274-282.
52. Simmons MP, Freudenstein JV. 2002. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics 18: 354-365.
53. Sinsheimer JS, Little RJA, Lake JA. 2012. Rooting trees without outgroups: EP rooting. Genome Biology and Evolution. doi: 10.1093/gbe/evs047.
54. Skovsted CB, Brock GA, Paterson JR, Holmer LE, Budd GE. 2008. The scleritome of Eccentrotheca from the Lower Cambrian of South Australia: lophophorate affinities and implications for tommotiid phylogeny. Geology 36: 171-174.
55. Smith AB. 1994. Rooting molecular trees: problems and strategies. Biological Journal of the Linnean Society 51: 279-292.
56. Sperling E, Pisani D, Peterson KJ. 2011. Molecular palaeobiological insights into the origin of the Brachiopoda. Evolution & Development 13: 290-303.
57. Stumpf MPH, Porter MA. 2012. Critical truths about power laws. Science 335: 665-666.
58. Swofford DL, 1998. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods), version 4.0. Sinauer Associates, Sunderland Massachusetts.
59. Telford ML, Littlewood DTJ, eds. 2009. Animal evolution: genomes, fossils, and trees, 1-245. Oxford: Oxford University Press.
60. Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51: 689-702.
61. Watrous LE, Wheeler QD. 1981. The out-group comparison method of character analysis. Systematic Zoology 30: 1-11.
62. Wiens JJ, Morrill MC. 2011. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Systematic Biology 60: 719-731. doi: 10.1093/sybio/syr025.
63. Williams A, Carlson SJ, Brunton CHC. 1997. Linguliformea. In: Kaesler RL, ed. Treatise on invertebrate paleontology. Part H2, Brachiopoda, revised. Lawrence: Geological Society of America and University of Kansas Press, 30-157.
64. Williams A, James MA, Emig CC, Mackay S, Rhodes MC. 1997. Anatomy. In: Kaesler RL, ed. Treatise on invertebrate paleontology. Part H1, Brachiopoda, revised. Lawrence: Geological Society of America and University of Kansas Press, 7-188.
65. Williams A, Carlson SJ, Brunton CHC, Holmer L, Popov L. 1996. A supra-ordinal classification of the Brachiopoda. Philosophical Transactions of the Royal Society, B 351: 1171-1193.
66. Williams A, Cusack M, Buckman JO, Stachel T. 1998. Siliceous tablets in the larval shells of apatitic discinid brachiopods. Science 279: 2094-2096.
67. Zimmer RL. 1991. Phoronida. In: Giese AC, Pearse JS, Pearse VB, eds. Reproduction of marine invertebrates. Pacific Grove, CA: Boxwood Press, 2-45.