1932

Abstract

In recent years, scientists have made remarkable progress reconstructing the animal phylogeny. There is broad agreement regarding many deep animal relationships, including the monophyly of animals, Bilateria, Protostomia, Ecdysozoa, and Spiralia. This stability now allows researchers to articulate the diminishing number of remaining questions in terms of well-defined alternative hypotheses. These remaining questions include relationships at the base of the animal tree, the position of Xenacoelomorpha, and the internal relationships of Spiralia. Recent progress in the field of animal phylogeny has important implications for our understanding of the evolution of development, morphology, genomes, and other characters. A remarkable pattern emerges—there is far more homoplasy for all these characters than had previously been anticipated, even among many complex characters such as segmentation and nervous systems. The fossil record dates most deep branches of the animal tree to an evolutionary radiation in the early Cambrian with roots in the Late Neoproterozoic.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-ecolsys-120213-091627
2014-11-23
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ecolsys/45/1/annurev-ecolsys-120213-091627.html?itemId=/content/journals/10.1146/annurev-ecolsys-120213-091627&mimeType=html&fmt=ahah

Literature Cited

  1. Adoutte A, Balavoine G, Lartillot N, Lespinet O, Prud'homme B, de Rosa R. 2000. The new animal phylogeny: reliability and implications. Proc. Natl. Acad. Sci. USA 97:94453–56 [Google Scholar]
  2. Antcliffe JB. 2013. Questioning the evidence of organic compounds called sponge biomarkers. Palaeontology 56:5917–25 [Google Scholar]
  3. Ax P. 1995. Das System der Metazoa, Band I Stuttgart, Ger: Fischer
  4. Bartolomaeus T, Ax P. 1992. Protonephridia and Metanephridia—their relation within the Bilateria. J. Zool. Syst. Evol. Res. 30:121–45 [Google Scholar]
  5. Bernt M, Bleidorn C, Braband A, Dambach J, Donath A. et al. 2013. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol. Phylogenet. Evol. 69:2352–64 [Google Scholar]
  6. Bilewitch JP, Degnan SM. 2011. 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. 11:1228 [Google Scholar]
  7. Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J. et al. 2006. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444:711585–88 [Google Scholar]
  8. Campbell LI, Rota-Stabelli O, Edgecombe GD, Marchioro T, Longhorn SJ. et al. 2011. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc. Natl. Acad. Sci. USA 108:3815920–24 [Google Scholar]
  9. Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T. et al. 2010. The dynamic genome of Hydra. Nature 464:7288592–96 [Google Scholar]
  10. Chiodin M, Børve A, Berezikov E, Ladurner P, Martinez P, Hejnol A. 2013. Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads. PLOS ONE 8:2e55499 [Google Scholar]
  11. Cohen PA, Knoll AH, Kodner RB. 2009. Large spinose microfossils in Ediacaran rocks as resting stages of early animals. Proc. Natl. Acad. Sci. USA 106:166519–24 [Google Scholar]
  12. Cunningham JA, Thomas CW, Bengtson S, Kearns SL, Xiao S. et al. 2012. Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians. Proc. R. Soc. B 279:17372369–76 [Google Scholar]
  13. Degnan BM, Leys SP, Larroux C. 2005. Sponge development and antiquity of animal pattern formation. Integr. Comp. Biol. 45:2335–41 [Google Scholar]
  14. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439:7079965–68 [Google Scholar]
  15. Dordel J, Fisse F, Purschke G, Struck TH. 2010. Phylogenetic position of Sipuncula derived from multi-gene and phylogenomic data and its implication for the evolution of segmentation. J. Zool. Syst. Evol. Res. 48:197–207 [Google Scholar]
  16. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE. et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:7188745–49 [Google Scholar]
  17. Dunn CW, Howison M, Zapata F. 2013. Agalma: an automated phylogenomics workflow. BMC Bioinform. 14:330 [Google Scholar]
  18. Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM. et al. 2011. Higher-level metazoan relationships: recent progress and remaining questions. Org. Divers. Evol. 11:2151–72 [Google Scholar]
  19. Eernisse DJ, Albert JS, Anderson FE. 1992. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan morphology. Syst. Biol. 41:3305–30 [Google Scholar]
  20. Ereskovsky AV, Dondua AK. 2006. The problem of germ layers in sponges (Porifera) and some issues concerning early metazoan evolution. Zool. Anz. 245:265–76 [Google Scholar]
  21. Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D. et al. 2011. The Cambrian conondrum: early divergence and later ecological success in the early history of animals. Science 334:60591091–97 [Google Scholar]
  22. Erwin DH, Valentine JW. 2013. The Cambrian Explosion: The Construction of Animal Biodiversity Greenwood Village, CO: Roberts and Company
  23. Fedonkin MA, Simonetta A, Ivantsov AY. 2007. New data on Kimberella, the Vendian mollusc-like organism (White Sea region, Russia): palaeoecological and evolutionary implications. Geol. Soc. Lond. Spec. Publ. 286:1157–79 [Google Scholar]
  24. Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT. et al. 1988. Molecular phylogeny of the animal kingdom. Science 239:4841 Pt. 1748–53 [Google Scholar]
  25. Fromm B, Worren MM, Hahn C, Hovig E, Bachmann L. 2013. Substantial loss of conserved and gain of novel microRNA families in flatworms. Mol. Biol. Evol. 30:122619–28 [Google Scholar]
  26. Funch P, Kristensen RM. 1995. Cycliophora is a new phylum with affinities to Entoprocta and Ectoprocta. Nature 378:711–14 [Google Scholar]
  27. Gaines RR, Briggs DEG, Yuanlong Z. 2008. Cambrian Burgess Shale–type deposits share a common mode of fossilization. Geology 36:10755–58 [Google Scholar]
  28. GIGA Community of Scientists 2014. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. J. Hered. 105:11–18 [Google Scholar]
  29. Giribet G, Distel D, Polz M, Sterrer W, Wheeler W. 2000. Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. Syst. Biol. 49:3539–62 [Google Scholar]
  30. Giribet G, Edgecombe GD. 2012. Reevaluating the arthropod tree of life. Annu. Rev. Entomol. 57:167–86 [Google Scholar]
  31. Giribet G, Sørensen MV, Funch P, Kristensen RM, Sterrer W. 2004. Investigations into the phylogenetic position of Micrognathozoa using four molecular loci. Cladistics 20:11–13 [Google Scholar]
  32. Glenner H, Hansen AJ, Sørensen MV, Ronquist F, Huelsenbeck JP, Willerslev E. 2004. Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach. Curr. Biol. 14:181644–49 [Google Scholar]
  33. Golombek A, Tobergte S, Nesnidal MP, Purschke G, Struck TH. 2013. Mitochondrial genomes to the rescue—Diurodrilidae in the myzostomid trap. Mol. Phylogenet. Evol. 68:2312–26 [Google Scholar]
  34. Grotzinger JP, Fike DA, Fischer WW. 2011. Enigmatic origin of the largest-known carbon isotope excursion in earth's history. Nat. Geosci. 4:5285–92 [Google Scholar]
  35. Haeckel E. 1866. Generelle Morphologie der Organismen. Allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenztheorie Berlin: Georg Reimer
  36. Halanych KM. 2004. The new view of animal phylogeny. Annu. Rev. Ecol. Evol. Syst. 35:229–56 [Google Scholar]
  37. Halanych KM, Bacheller JD, Aguinaldo AM, Liva SM, Hillis DM, Lake JA. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267:52041641–43 [Google Scholar]
  38. Hankeln T, Wey-Fabrizius AR, Herlyn H, Witek A, Weber M. et al. 2014. Phylogeny of platyzoan taxa based on molecular data. Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis JW Wägele, T Bartolomaeus 105–26 Berlin: De Gruyter [Google Scholar]
  39. Hannibal RL, Patel NH. 2013. What is a segment?. EvoDevo 4:135 [Google Scholar]
  40. Hejnol A, Martindale MQ. 2009. The mouth, the anus, and the blastopore—open questions about questionable openings. Animal Evolution: Genomes, Fossils, and Trees MJ Telford, DTJ Littlewood 33–40 Oxford, UK: Oxford Univ. Press [Google Scholar]
  41. Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW. et al. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B 276:16774261–70 [Google Scholar]
  42. Helm C, Bernhart SH, Siederdissen CH, Nickel B. 2012. Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Mol. Phylogenet. Evol. 64:198–203 [Google Scholar]
  43. Herranz M, Boyle MJ, Pardos F, Neves RC. 2014. Comparative myoanatomy of Echinoderes (Kinorhyncha): a comprehensive investigation by CLSM and 3D reconstruction. Front. Zool. 11:131 [Google Scholar]
  44. Holland LZ, Carvalho JOE, Escriva H, Laudet V, Schubert M. et al. 2013. Evolution of bilaterian central nervous systems: a single origin?. EvoDevo 4:127 [Google Scholar]
  45. Holland ND. 2003. Early central nervous system evolution: an era of skin brains?. Nat. Rev. Neurosci. 4:8617–27 [Google Scholar]
  46. Huldtgren T, Cunningham JA, Yin C, Stampanoni M, Marone F. et al. 2011. Fossilized nuclei and germination structures identify Ediacaran “animal embryos” as encysting protists. Science 334:60631696–99 [Google Scholar]
  47. Jager M, Chiori R, Alié A, Dayraud C, Quéinnec E, Manuel M. 2010. New insights on ctenophore neural anatomy: immunofluorescence study in Pleurobrachia pileus (Müller 1776). J. Exp. Zool. 316B:3171–87 [Google Scholar]
  48. Jondelius U, Ruiz Trillo I, Baguñà J, Riutort M. 2002. The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zool. Scr. 31:2201–15 [Google Scholar]
  49. Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S, Lavrov DV. 2012. Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biol. Evol. 4:11–12 [Google Scholar]
  50. Koch M, Quast B, Bartolomaeus T. 2014. Coeloms and nephridia in annelids and arthropods. Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis JW Wägele, T Bartolomaeus 173–284 Berlin: De Gruyter [Google Scholar]
  51. Kocot KM, Cannon JT, Todt C, Citarella MR, Kohn AB. et al. 2011. Phylogenomics reveals deep molluscan relationships. Nature 477:7365452–56 [Google Scholar]
  52. Kouchinsky A, Bengtson S, Runnegar B, Skovsted C, Steiner M, Vendrasco M. 2012. Chronology of Early Cambrian biomineralization. Geol. Mag. 149:221–51 [Google Scholar]
  53. Kristensen RM, Niilonen T. 1982. Structural studies on Diurodrilus Remane (Diurodrilidae fam.n.), with description of Diurodrilus westheidei sp.n. from the Arctic interstitial meiobenthos, W. Greenland. Zool. Scr. 11:11–12 [Google Scholar]
  54. Ladurner P, Rieger R. 2000. Embryonic muscle development of Convoluta pulchra (Turbellaria–Acoelomorpha, Platyhelminthes). Dev. Biol. 222:2359–75 [Google Scholar]
  55. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:172286–88 [Google Scholar]
  56. Lavrov DV. 2007. Key transitions in animal evolution: a mitochondrial DNA perspective. Integr. Comp. Biol. 47:5734–43 [Google Scholar]
  57. Lavrov DV, Pett W, Voigt O, Wörheide G, Forget L. et al. 2013. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA editing, and a novel genetic code. Mol. Biol. Evol. 30:4865–80 [Google Scholar]
  58. Lee MSY, Soubrier J, Edgecombe GD. 2013. Rates of phenotypic and genomic evolution during the Cambrian Explosion. Curr. Biol. 23:1889–95 [Google Scholar]
  59. Lemmon EM, Lemmon AR. 2013. High-throughput genomic data in systematics and phylogenetics. Annu. Rev. Ecol. Evol. Syst. 44:99–121 [Google Scholar]
  60. Leys SP, Riesgo A. 2011. Epithelia, an evolutionary novelty of metazoans. J. Exp. Zool. 318:6438–47 [Google Scholar]
  61. Liu P, Xiao S, Yin C, Chen S, Zhou C, Li M. 2014. Ediacaran acanthomorphic acritarchs and other microfossils from chert nodules of the Upper Doushantuo Formation in the Yangtze Gorges area, South China. J. Paleontol. 88:sp721–139 [Google Scholar]
  62. Love GD, Grosjean E, Stalvies C, Fike DA, Grotzinger JP. et al. 2009. Fossil steroids record the appearance of Demospongiae during the Cryogenian Period. Nature 457:7230718–21 [Google Scholar]
  63. Lowe CJ. 2008. Molecular genetic insights into deuterostome evolution from the direct-developing hemichordate Saccoglossus kowalevskii. Philos. Trans. R. Soc. B 363:14961569–78 [Google Scholar]
  64. Lundin K. 1998. The epidermal ciliary rootlets of Xenoturbella bocki (Xenoturbellida) revisited: new support for a possible kinship with the Acoelomorpha (Platyhelminthes). Zool. Scr. 27:3263–70 [Google Scholar]
  65. Mah JL, Christensen-Dalsgaard KK, Leys SP. 2014. Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology. Evol. Dev. 16:125–37 [Google Scholar]
  66. Marlétaz F, Martin E, Perez Y, Papillon D, Caubit X. et al. 2006. Chaetognath phylogenomics: a protostome with deuterostome-like development. Curr. Biol. 16:15R577–78 [Google Scholar]
  67. Martindale MQ. 2004. Investigating the origins of triploblasty: ‘mesodermal’ gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa). Development 131:102463–74 [Google Scholar]
  68. Maslakova SA, Martindale MQ, Norenburg JL. 2004. Vestigial prototroch in a basal nemertean, Carinoma tremaphoros (Nemertea; Palaeonemertea). Evol. Dev. 6:4219–26 [Google Scholar]
  69. Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H. et al. 2006. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr. Biol. 16:15R575–76 [Google Scholar]
  70. Maxwell EK, Ryan JF, Schnitzler CE, Browne WE, Baxevanis AD. 2012. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 13:1714 [Google Scholar]
  71. Medina M, Collins AG, Silberman JD, Sogin ML. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc. Natl. Acad. Sci. USA 98:179707–12 [Google Scholar]
  72. Mendivil Ramos O, Barker D, Ferrier DEK. 2012. Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Curr. Biol. 22:201951–56 [Google Scholar]
  73. Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP. et al. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature 510:7503109–14 [Google Scholar]
  74. Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I. et al. 2013. New phylogenomic data support the monophyly of Lophophorata and an ectoproct-phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol. Biol. 13:253 [Google Scholar]
  75. Neves RC, Bailly X, Leasi F, Reichert H, Sørensen MV, Kristensen RM. 2013. A complete three-dimensional reconstruction of the myoanatomy of Loricifera: comparative morphology of an adult and a Higgins larva stage. Front. Zool. 10:119 [Google Scholar]
  76. Nielsen C, Scharff N, Eibye-Jacobsen D. 1996. Cladistic analyses of the animal kingdom. Biol. J. Linn. Soc. 57:4385–410 [Google Scholar]
  77. Northcutt RG. 2012. Evolution of centralized nervous systems: two schools of evolutionary thought. Proc. Natl. Acad. Sci. USA 109:Suppl. 110626–33 [Google Scholar]
  78. Nosenko T, Schreiber F, Adamska M, Adamski M, Eitel M. et al. 2013. Deep metazoan phylogeny: when different genes tell different stories. Mol. Phylogenet. Evol. 67:1223–33 [Google Scholar]
  79. Ogino K, Tsuneki K, Furuya H. 2010. Unique genome of dicyemid mesozoan: highly shortened spliceosomal introns in conservative exon/intron structure. Gene 449:1–270–76 [Google Scholar]
  80. Osigus H-J, Eitel M, Bernt M, Donath A, Schierwater B. 2013a. Mitogenomics at the base of Metazoa. Mol. Phylogenet. Evol. 69:2339–51 [Google Scholar]
  81. Osigus H-J, Eitel M, Schierwater B. 2013b. Chasing the urmetazoon: striking a blow for quality data?. Mol. Phylogenet. Evol. 66:551–57 [Google Scholar]
  82. Pani AM, Mullarkey EE, Aronowicz J, Assimacopoulos S, Grove EA, Lowe CJ. 2013. Ancient deuterostome origins of vertebrate brain signalling centres. Nature 483:7389289–94 [Google Scholar]
  83. Papillon D. 2004. Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome. Mol. Biol. Evol. 21:112122–29 [Google Scholar]
  84. Paps J, Baguñà J, Riutort M. 2009. Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc. R. Soc. B 276:16601245–54 [Google Scholar]
  85. Perez Y, Müller CHG, Harzsch S. 2014. The Chaetognatha: an anarchistic taxon between Protostomia and Deuterostomia. Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis JW Wägele, T Bartolomaeus 49–78 Berlin: De Gruyter [Google Scholar]
  86. Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ. et al. 2011. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: insight from mtDNA and the nuclear genome. Mitochondrial DNA 22:130–42 [Google Scholar]
  87. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H. et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:7333255–58 [Google Scholar]
  88. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C. et al. 2009. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19:8706–12 [Google Scholar]
  89. Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:51246–53 [Google Scholar]
  90. Philippe H, Telford MJ. 2006. Large-scale sequencing and the new animal phylogeny. Trends Ecol. Evol. 21:11614–20 [Google Scholar]
  91. Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ. et al. 2010. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol. Biol. Evol. 27:91983–87 [Google Scholar]
  92. Pisani D, Carton R, Campbell LI, Akanni WA, Mulville E, Rota-Stabelli O. 2013. An overview of arthropod genomics, mitogenomics, and the evolutionary origins of the arthropod proteome. Arthropod Biology and Evolution: Molecules, Development, Morphology A Minelli, G Boxshall, G Fusco 41–61 Heidelberg, Ger: Springer-Verlag [Google Scholar]
  93. Porter SM. 2007. Seawater chemistry and early carbonate biomineralization. Science 316:58291302 [Google Scholar]
  94. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J. et al. 2007. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:583486–94 [Google Scholar]
  95. Reitzel AM, Pang K, Ryan JF, Mullikin JC, Martindale MQ. et al. 2011. Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?. EvoDevo 2:13 [Google Scholar]
  96. Richter S, Loesel R, Purschke G, Schmidt-Rhaesa A, Scholtz G. et al. 2010. Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Front. Zool. 7:129 [Google Scholar]
  97. Rieger RM. 1980. A new group of interstitial worms, Lobatocerebridae nov. fam. (Annelida) and its significance for metazoan phylogeny. Zoomorphologie 95:141–84 [Google Scholar]
  98. Rokas A, Carroll SB. 2006. Bushes in the tree of life. PLOS Biol. 4:11e352 [Google Scholar]
  99. Ruppert EE. 1991. Introduction to the aschelminth phyla: a consideration of mesoderm, body cavities, and cuticle. Microscopic Anatomy of Invertebrates Volume 4: Aschelminthes, ed. FW Harrison, EE Ruppert 1–17 New York: Wiley-Liss [Google Scholar]
  100. Ruppert EE. 1994. Evolutionary origin of the vertebrate nephron. Am. Zool. 34:542–53 [Google Scholar]
  101. Ruppert EE, Smith PR. 1988. The functional-organization of filtration nephridia. Biol. Rev. Camb. Philos. Soc. 63:2231–58 [Google Scholar]
  102. Ryan JF, Pang K. Mullikin JC, Martindale MQ, Baxevanis AD. NISC Comparative Sequencing Program 2010. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. EvoDevo 1:19 [Google Scholar]
  103. Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT. et al. 2013. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342:61641242592 [Google Scholar]
  104. Sarrazin AF, Peel AD, Averof M. 2012. A segmentation clock with two-segment periodicity in insects. Science 336:6079338–41 [Google Scholar]
  105. Schmidt-Rhaesa A. 2008. The Evolution of Organ Systems Oxford, UK: Oxford Univ. Press
  106. Schmidt-Rhaesa A. 2013. Gastrotricha, Cycloneuralia and Gnathifera: general history and phylogeny. Handbook of Zoology: Gastrotricha, Cycloneuralia and Gnathifera Volume 1 Nematomorpha, Priapulida, Kinorhyncha, Loricifera A Schmidt-Rhaesa 1–10 Berlin: De Gruyter [Google Scholar]
  107. Schmidt-Rhaesa A, Rothe BH. 2014. Brains in Gastrotricha and Cycloneuralia—a comparison. Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis JW Wägele, T Bartolomaeus 93–104 Berlin: De Gruyter [Google Scholar]
  108. Scholtz G. 2002. The Articulata hypothesis—or what is a segment?. Org. Divers. Evol. 2:3197–215 [Google Scholar]
  109. Schram FR. 1991. Cladistic analysis of metazoan phyla and the placement of fossil problematica. The Early Evolution of Metazoa and the Significance of Problematic Taxa AM Simonetta, S Conway Morris 35–46 Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  110. Scimone ML, Srivastava M, Bell GW, Reddien PW. 2011. A regulatory program for excretory system regeneration in planarians. Development 138:204387–98 [Google Scholar]
  111. Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K. et al. 2011. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 476:7360320–23 [Google Scholar]
  112. Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS. et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:7377364–67 [Google Scholar]
  113. Sørensen MV, Giribet G. 2006. A modern approach to rotiferan phylogeny: combining morphological and molecular data. Mol. Phylogenet. Evol. 40:2585–608 [Google Scholar]
  114. Sperling EA, Petersen KJ, Pisani D. 2009. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol. Biol. Evol. 26:2261–74 [Google Scholar]
  115. Sperling EA, Peterson KJ, Laflamme M. 2010. Rangeomorphs, Thectardis (Porifera?) and dissolved organic carbon in the Ediacaran oceans. Geobiology 9:124–33 [Google Scholar]
  116. Sperling EA, Vinther J. 2010. A placozoan affinity for Dickinsonia and the evolution of late Proterozoic metazoan feeding modes. Evol. Dev. 12:2201–9 [Google Scholar]
  117. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U. et al. 2008. The Trichoplax genome and the nature of placozoans. Nature 454:7207955–60 [Google Scholar]
  118. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA. et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:7307720–26 [Google Scholar]
  119. Stach T. 2008. Chordate phylogeny and evolution: a not so simple three-taxon problem. J. Zool. 276:2117–41 [Google Scholar]
  120. Stöger I, Schrödl M. 2013. Mitogenomics does not resolve deep molluscan relationships (yet?). Mol. Phylogenet. Evol. 69:2376–92 [Google Scholar]
  121. Storch V. 1991. Priapulida. Microscopic Anatomy of Invertebrates Volume 4 Aschelminthes FW Harrison, EE Ruppert 333–50 New York: Wiley-Liss [Google Scholar]
  122. Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW. et al. 2013. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4:2325 [Google Scholar]
  123. Suzuki TG, Ogino K, Tsuneki K, Furuya H. 2010. Phylogenetic analysis of dicyemid mesozoans (phylum Dicyemida) from innexin amino acid sequences: Dicyemids are not related to Platyhelminthes. J. Parasitol. 96:3614–25 [Google Scholar]
  124. Tang F, Bengtson S, Wang Y, Wang X-L, Yin C-Y. 2011. Eoandromeda and the origin of Ctenophora. Evol. Dev. 13:5408–14 [Google Scholar]
  125. Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM. et al. 2013. miRNAs: small genes with big potential in metazoan phylogenetics. Mol. Biol. Evol. 30:112369–82 [Google Scholar]
  126. Tessmar-Raible K. 2007. The evolution of neurosecretory centers in bilaterian forebrains: insights from protostomes. Semin. Cell Dev. Biol. 18:4492–501 [Google Scholar]
  127. Thomson RC, Plachetzki DC, Mahler DL, Moore BR. 2014. A critical appraisal of the use of microRNA data in phylogenetics. Proc. Natl. Acad. Sci. USA. 111:35E3659–68 [Google Scholar]
  128. Torruella G, Derelle R, Paps J, Lang BF, Roger AJ. et al. 2012. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol. Biol. Evol. 29:2531–44 [Google Scholar]
  129. Vallès Y, Halanych KM, Boore JL. 2008. Group II introns break new boundaries: presence in a bilaterian's genome. PLOS ONE 3:1e1488 [Google Scholar]
  130. Vannier J, Calandra I, Gaillard C, Zylinska A. 2010. Priapulid worms: pioneer horizontal burrowers at the Precambrian-Cambrian boundary. Geology 38:8711–14 [Google Scholar]
  131. Wallberg A, Thollesson M, Farris J, Jondelius U. 2004. The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling. Cladistics 20:6558–78 [Google Scholar]
  132. Weigert A, Helm C, Meyer M, Nickel B, Arendt D. et al. 2014. Illuminating the base of the annelid tree using transcriptomics. Mol. Biol. Evol. 31:1391–401 [Google Scholar]
  133. Wey-Fabrizius AR, Herlyn H, Rieger B, Rosenkranz D, Witek A. et al. 2014. Transcriptome data reveal syndermatean relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage. PLOS ONE 9:2e88618 [Google Scholar]
  134. Witek A, Herlyn H, Ebersberger I, Mark Welch DB, Hankeln T. 2009. Support for the monophyletic origin of Gnathifera from phylogenomics. Mol. Phylogenet. Evol. 53:31037–41 [Google Scholar]
  135. Wörheide G, Dohrmann M, Erpenbeck D, Larroux C, Maldonado M. et al. 2012. Deep phylogeny and evolution of sponges (phylum Porifera). Adv. Mar. Biol. 61:1–78 [Google Scholar]
  136. Worsaae K, Rouse GW. 2008. Is Diurodrilus an annelid?. J. Morphol. 269:121426–55 [Google Scholar]
  137. Xiao S, Laflamme M. 2009. On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota.. Trends Ecol. Evol. 24:131–40 [Google Scholar]
  138. Xiao S, Zhang Y, Knoll AH. 1998. Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite. Nature 391:6667553–58 [Google Scholar]
  139. Yin L, Zhu M, Knoll AH, Yuan X, Zhang J, Hu J. 2007. Doushantuo embryos preserved inside diapause egg cysts. Nature 446:661–63 [Google Scholar]
  140. Zrzavý J, Mihulka S, Kepka P, Bezděk A, Tietz D. 1998. Phylogeny of the metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics 14:3249–85 [Google Scholar]
/content/journals/10.1146/annurev-ecolsys-120213-091627
Loading
/content/journals/10.1146/annurev-ecolsys-120213-091627
Loading

Data & Media loading...

Supplemental Material

Supplementary Data

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error