Error, signal, and the placement of Ctenophora sister to all other animals

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 18, 2015, Pages 5773-5778

  Whelan, Nathan V ^a   Kocot, Kevin M ^b   Moroz, Leonid L ^c   Halanych, Kenneth M ^a  

^a AUBURN UNIVERSITY   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

Cnidaria; Ctenophora; Metazoa; Phylogenomics; Porifera

Indexed keywords

RIBOSOME PROTEIN; TRANSCRIPTOME;

ARTICLE; BAYESIAN LEARNING; CNIDARIA; CTENOPHORA; MAXIMUM LIKELIHOOD METHOD; MONOPHYLY; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENOMICS; PHYLOGENY; PRIORITY JOURNAL; SYSTEMATIC ERROR; TAXON; ALGORITHM; ANIMAL; BAYES THEOREM; CELL LINEAGE; CLASSIFICATION; EVOLUTION; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; SPONGE (PORIFERA); STATISTICAL MODEL;

ANIMALIA; CNIDARIA; CTENOPHORA (COELENTERATES); METAZOA; PORIFERA;

ALGORITHMS; ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; CELL LINEAGE; CNIDARIA; CTENOPHORA; DATABASES, GENETIC; GENOME; GENOMICS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PORIFERA; RIBOSOMAL PROTEINS; TRANSCRIPTOME;

EID: 84928974643     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1503453112     Document Type: Article

References (57)

1. Dohrmann M, Wörheide G (2013) Novel scenarios of early animal evolution - Is it time to rewrite textbooks? Integr Comp Biol 53(3):503-511.
2. Dellaporta SL, et al. (2006) Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci USA 103(23):8751-8756.
3. Dunn CW, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749.
4. Hejnol A, et al. (2009) Assessing the root of bilaterian animals with scalable phylogenomic models. Proc Biol Sci 276(1802):4261-4270.
5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114.
6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592.
7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell different stories. Mol Phylogenet Evol 67(1):223-233.
8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biol 9(3):e1000602.
9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19(8):706-712.
10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987.
11. Felsenstein J (1978) Cases in which parsimony and compatability methods will be positively misleading. Syst Zool 27(4):401-410.
12. Boussau B, et al. (2014) Strepsiptera, phylogenomics and the long branch attraction problem. PLoS ONE 9(10):e107709.
13. Straub SCK, et al. (2014) Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol 80:169-185.
14. Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46(3):239-257.
15. Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: The beginning of incongruence? Trends Genet 22(4):225-231.
16. Roure B, Baurain D, Philippe H (2013) Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol 30(1):197-214.
17. Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7(Suppl 1):S4.
18. Tavaré S (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci 17:57-86.
19. Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541-562.
20. Altenhoff AM, Dessimoz C (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLOS Comput Biol 5(1):e1000262.
21. Gabaldón T (2008) Large-scale assignment of orthology: Back to phylogenetics? Genome Biol 9(10):235.
22. Borchiellini C, et al. (2001) Sponge paraphyly and the origin of Metazoa. J Evol Biol 14(1):171-179.
23. Sperling EA, Pisani D, Peterson KJ (2007) Poriferan paraphyly and its implications for Precambrian paleobiology. Geol Soc Lond Spec Publ 286:355-368.
24. Sperling EA, Peterson KJ, Pisani D (2009) Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol 26(10):2261-2274.
25. Struck TH (2014) TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information. Evol Bioinform Online 10:51-67.
26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615.
27. van Soest RWM (1984) Deficient Merlia normani Kirkpatrick, 1908, from the Curacao reefs, with a discussion on the phylogenetic interpretation of sclerosponges. Contrib Zool 54(2):211-219.
28. Gazave E, et al. (2012) No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera. Hydrobiologia 687(1):3-10.
29. Dohrmann M, Janussen D, Reitner J, Collins AG, Wörheide G (2008) Phylogeny and evolution of glass sponges (Porifera, Hexactinellida). Syst Biol 57(3):388-405.
30. Voigt O, Adamski M, Sluzek K, Adamska M (2014) Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes. BMC Evol Biol 14(1):230.
31. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3):492-508.
32. Bleidorn C, et al. (2009) On the phylogenetic position of Myzostomida: Can 77 genes get it wrong? BMC Evol Biol 9(1):150.
33. Edwards SV (2009) Natural selection and phylogenetic analysis. Proc Natl Acad Sci USA 106(22):8799-8800.
34. Nesnidal MP, Helmkampf M, Bruchhaus I, El-Matbouli M, Hausdorf B (2013) Agent of whirling disease meets orphan worm: phylogenomic analyses firmly place Myxozoa in Cnidaria. PLoS ONE 8(1):e54576.
35. Ax P (1996) Multicellular Animals: A New Approach to the Phylogenetic Order in Nature (Springer, Berlin).
36. Nielsen C (2008) Six major steps in animal evolution: Are we derived sponge larvae? Evol Dev 10(2):241-257.
37. Srivastava M, et al. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466(7307):720-726.
38. Mah JL, Christensen-Dalsgaard KK, Leys SP (2014) Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology. Evol Dev 16(1):25-37.
39. Osigus H-J, Eitel M, Bernt M, Donath A, Schierwater B (2013) Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 69(2):339-351.
40. Halanych KM (1999) Metazoan phylogeny and the shifting comparative framework. Recent Developments in Comparative Endocrinology and Neurobiology, eds Roubos EW, Wendelaar-Bonga SE, Vaudry H, De Loof A (Shaker, Maastrict, The Netherlands), pp 3-7.
41. Dunn CW, Giribet G, Edgecombe GD, Hejnol A (2014) Animal phylogeny and its evolutionary implications. Annu Rev Ecol Evol Syst 45:371-395.
42. Liebeskind BJ, Hillis DM, Zakon HH (2015) Convergence of ion channel genome content in early animal evolution. Proc Natl Acad Sci USA 112(8):E846-E851.
43. Moroz LL (2015) Convergent evolution of neural systems in ctenophores. J Exp Biol 218(Pt 4):598-611.
44. Halanych KM (2015) The ctenophore lineage is older than sponges? That cannot be right! Or can it? J Exp Biol 218(Pt 4):592-597.
45. Brown T, Howe C, Zhang A, Pyrkosz Q, Brom AB (2012) A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv:1203.4802.
46. Haas BJ, et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8(8):1494-1512.
47. Margulies M, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376-380.
48. Ebersberger I, Strauss S, von Haeseler A (2009) HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 9:157.
49. Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312-1313.
50. R Core Development Team (2014) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria).
51. Telford MJ, et al. (2013) Phylogenomic analysis of echinoderm class relationships supports Asterozoa. Proc Biol Sci 281(1786):20140479.
52. Kück P, Struck TH (2014) BaCoCa - A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions. Mol Phylogenet Evol 70:94-98.
53. Zhong M, et al. (2011) Detecting the symplesiomorphy trap: A multigene phylogenetic analysis of terebelliform annelids. BMC Evol Biol 11(1):369.
54. Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A (2014) Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol 14:82.
55. Thorley JL, Wilkinson M (1999) Testing the phylogenetic stability of early tetrapods. J Theor Biol 200(3):343-344.
56. Smith SA, Dunn CW (2008) Phyutility: A phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24(5):715-716.
57. Shimodaira H, Hasegawa M (2001) CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17(12):1246-1247.