Organisms Diversity & Evolution

, Volume 16, Issue 2, pp 419–426 | Cite as

New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics

Review

Abstract

The science of phylogenetics, and specially the subfield of molecular systematics, has grown exponentially not only in the amount of publications and general interest, but also especially in the amount of genetic data available. Modern phylogenomic analyses use large genomic and transcriptomic resources, yet a comprehensive molecular phylogeny of animals, including the newest types of data for all phyla, remains elusive. Future challenges need to address important issues with taxon sampling—especially for rare and small animals—orthology assignment, algorithmic developments, and data storage and to figure out better ways to integrate information from genomes and morphology in order to place fossils more precisely in the animal tree of life. Such precise placement will also aid in providing more accurate dates to major evolutionary events during the evolution of our closest kingdom.

Keywords

Genomics Transcriptomics Metazoan phylogeny New animal phylogeny Fossils Tip dating Total evidence dating 

References

  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 U S A, 97(9), 4453–4456.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Aguinaldo, A. M. A., Turbeville, J. M., Lindford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., et al. (1997). Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387, 489–493.CrossRefPubMedGoogle Scholar
  3. Altenhoff, A. M., Schneider, A., Gonnet, G. H., & Dessimoz, C. (2011). OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res, 39, D289–D294. doi:10.1093/Nar/Gkq1238.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Andrade, S. C. S., Montenegro, H., Strand, M., Schwartz, M., Kajihara, H., Norenburg, J. L., et al. (2014). A transcriptomic approach to ribbon worm systematics (Nemertea): resolving the Pilidiophora problem. Mol Biol Evol, 31(12), 3206–3215. doi:10.1093/molbev/msu253.CrossRefPubMedGoogle Scholar
  5. Andrade, S. C. S., Novo, M., Kawauchi, G. Y., Worsaae, K., Pleijel, F., Giribet, G., et al. (2015). Articulating “archiannelids”: phylogenomics and annelid relationships, with emphasis on meiofaunal taxa. Molecular Biology and Evolution, doi: 10.1093/molbev/msv157.
  6. Arcila, D., Pyron, R. A., Tyler, J. C., Ortí, G., & Betancur-R, R. (2015). An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol, 82, 131–145. doi:10.1016/j.ympev.2014.10.011.CrossRefPubMedGoogle Scholar
  7. Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., et al. (2013). Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1), 10. doi:10.1186/2047-217X-2-10.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Burleigh, J. G., Alphonse, K., Alverson, A. J., Bik, H. M., Blank, C., Cirranello, A. L., et al. (2013). Next-generation phenomics for the Tree of Life. PLoS Currents Tree of Life, 5, doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733.
  9. Cannon, J. T., Kocot, K. M., Waits, D. S., Weese, D. A., Swalla, B. J., Santos, S. R., et al. (2014). Phylogenomic resolution of the hemichordate and echinoderm clade. Curr Biol, 24(23), 2827–2832. doi:10.1016/j.cub.2014.10.016.CrossRefPubMedGoogle Scholar
  10. Carranza, S., Baguñà, J., & Riutort, M. (1997). Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences. Mol Biol Evol, 14(5), 485–497.CrossRefPubMedGoogle Scholar
  11. Cavalier-Smith, T. (1998). A revised six-kingdom system of life. Biol Rev, 73, 203–266.CrossRefPubMedGoogle Scholar
  12. Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439(7079), 965–968.CrossRefPubMedGoogle Scholar
  13. Donoghue, M. J., Doyle, J. J., Gauthier, J., Kluge, A. G., & Rowe, T. (1989). The importance of fossils in phylogeny reconstruction. Annu Rev Ecol Syst, 20, 431–460.CrossRefGoogle Scholar
  14. Dopazo, H., Santoyo, J., & Dopazo, J. (2004). Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics, 20(Suppl 1), I116–I121.CrossRefPubMedGoogle Scholar
  15. Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., et al. (2008). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452(7188), 745–749. doi:10.1038/nature06614.CrossRefPubMedGoogle Scholar
  16. Dunn, C. W., Howison, M., & Zapata, F. (2013). Agalma: an automated phylogenomics workflow. BMC Bioinformatics, 14, 330. doi:10.1186/1471-2105-14-330.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Dunn, C. W., Giribet, G., Edgecombe, G. D., & Hejnol, A. (2014). Animal phylogeny and its evolutionary implications. Annu Rev Ecol Evol Syst, 45(1), 371–395. doi:10.1146/annurev-ecolsys-120213-091627.CrossRefGoogle Scholar
  18. Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D. W., Fass, J., et al. (2011). Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res, 21(12), 2224–2241. doi:10.1101/Gr.126599.111.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Ebersberger, I., Strauss, S., & von Haeseler, A. (2009). HaMStR: profile hidden Markov model based search for orthologs in ESTs. BMC Evol Biol, 9, 157. doi:10.1186/1471-2148-9-157.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Edgecombe, G. D., Giribet, G., Dunn, C. W., Hejnol, A., Kristensen, R. M., Neves, R. C., et al. (2011). Higher-level metazoan relationships: recent progress and remaining questions. Organisms, Diversity & Evolution, 11, 151–172. doi:10.1007/s13127-011-0044-4.
  21. Egger, B., Lapraz, F., Tomiczek, B., Müller, S., Dessimoz, C., Girstmair, J., et al. (2015). A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms. Curr Biol, 25(10), 1347–1353. doi:10.1016/j.cub.2015.03.034.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Eisen, J. A., & Fraser, C. M. (2003). Phylogenomics: intersection of evolution and genomics. Science, 300(5626), 1706–1707. doi:10.1126/science.1086292.CrossRefPubMedGoogle Scholar
  23. Fernández, R., & Giribet, G. (2015). Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida). Royal Society Open Science, 2(6), 150065. doi:10.1098/rsos.150065.
  24. Fernández, R., Hormiga, G., & Giribet, G. (2014). Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers. Curr Biol, 24(15), 1772–1777. doi:10.1016/j.cub.2014.06.035.CrossRefPubMedGoogle Scholar
  25. Garwood, R. J., Sharma, P. P., Dunlop, J. A., & Giribet, G. (2014). A new stem-group Palaeozoic harvestman revealed through integration of phylogenetics and development. Curr Biol, 24, 1–7. doi:10.1016/j.cub.2014.03.039.CrossRefGoogle Scholar
  26. Gatesy, J., & O’Leary, M. A. (2001). Deciphering whale origins with molecules and fossils. TRENDS in Ecology and Evolution, 16, 562–570.Google Scholar
  27. Giribet, G. (2008). Assembling the lophotrochozoan (=spiralian) tree of life. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, 1513–1522.Google Scholar
  28. Giribet, G. (2010). A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. Acta Zoologica (Stockholm), 91, 11–19. doi:10.1111/j.1463-6395.2009.00420.x.
  29. Giribet, G. (2015). Morphology should not be forgotten in the era of genomics—a phylogenetic perspective. Zool Anz, 256, 96–103. doi:10.1016/j.jcz.2015.01.003.CrossRefGoogle Scholar
  30. Giribet, G., Carranza, S., Baguñà, J., Riutort, M., & Ribera, C. (1996). First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Mol Biol Evol, 13(1), 76–84.CrossRefPubMedGoogle Scholar
  31. Giribet, G., Distel, D. L., Polz, M., Sterrer, W., & Wheeler, W. C. (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(3), 539–562.Google Scholar
  32. González, V. L., Andrade, S. C. S., Bieler, R., Collins, T. M., Dunn, C. W., Mikkelsen, P. M., et al. (2015). A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proc R Soc B Biol Sci, 282(1801), 20142332. doi:10.1098/rspb.2014.2332.CrossRefGoogle Scholar
  33. Halanych, K. M. (2004). The new view of animal phylogeny. Annu Rev Ecol Evol Syst, 35, 229–256.CrossRefGoogle Scholar
  34. Halanych, K. M. (2015). The ctenophore lineage is older than sponges? That cannot be right! Or can it? J Exp Biol, 218(Pt 4), 592–597. doi:10.1242/jeb.111872.CrossRefPubMedGoogle Scholar
  35. Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M. A., Liva, S. M., Hillis, D. M., & Lake, J. A. (1995). Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science, 267(5204), 1641–1643.CrossRefPubMedGoogle Scholar
  36. Hausdorf, B., Helmkampf, M., Meyer, A., Witek, A., Herlyn, H., Bruchhaus, I., et al. (2007). Spiralian phylogenomics supports the resurrection of Bryozoa comprising ectoprocta and entoprocta. Mol Biol Evol, 24(12), 2723–2729. doi:10.1093/molbev/msm214.CrossRefPubMedGoogle Scholar
  37. Hejnol, A., Obst, M., Stamatakis, A. M. O., Rouse, G. W., Edgecombe, G. D., et al. (2009). Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society B: Biological Sciences, 276, 4261–4270. doi:10.1098/rspb.2009.0896.
  38. Helmkampf, M., Bruchhaus, I., & Hausdorf, B. (2008). Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept. Proc R Soc B Biol Sci, 275(1645), 1927–1933. doi:10.1098/rspb.2008.0372.CrossRefGoogle Scholar
  39. Jondelius, U., Ruiz-Trillo, I., Baguñà, J., & Riutort, M. (2002). The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zool Scr, 31, 201–215.CrossRefGoogle Scholar
  40. Kocot, K. M., Cannon, J. T., Todt, C., Citarella, M. R., Kohn, A. B., Meyer, A., et al. (2011). Phylogenomics reveals deep molluscan relationships. Nature, 447, 452–456. doi:10.1038/nature10382.CrossRefGoogle Scholar
  41. Kocot, K. M., Halanych, K. M., & Krug, P. J. (2013). Phylogenomics supports Panpulmonata: opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs. Mol Phylogenet Evol, 69(3), 764–771. doi:10.1016/j.ympev.2013.07.001.CrossRefPubMedGoogle Scholar
  42. Kück, P., & Struck, T. H. (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. doi:10.1016/j.ympev.2013.09.011.CrossRefPubMedGoogle Scholar
  43. Kvist, S., & Siddall, M. E. (2013). Phylogenomics of Annelida revisited: a cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data. Cladistics, 29(4), 435–448. doi:10.1111/cla.12015.CrossRefGoogle Scholar
  44. 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. doi:10.1093/Sysbio/Syt022.CrossRefPubMedGoogle Scholar
  45. Laumer, C. E., Bekkouche, N., Kerbl, A., Goetz, F., Neves, R. C., Sørensen, M. V., et al. (2015a). Spiralian phylogeny informs the evolution of microscopic lineages. Curr Biol, 25(15), 2000–2006. doi:10.1016/j.cub.2015.06.068.CrossRefPubMedGoogle Scholar
  46. Laumer, C. E., Hejnol, A., & Giribet, G. (2015b). Nuclear genomic signals of the “microturbellarian” roots of platyhelminth evolutionary innovation. eLife, 4, e05503. doi:10.7554/eLife.05503.CrossRefGoogle Scholar
  47. Lemer, S., Kawauchi, G. Y., Andrade, S. C. S., González, V. L., Boyle, M. J., & Giribet, G. (2015). Re-evaluating the phylogeny of Sipuncula through transcriptomics. Mol Phylogenet Evol, 83, 174–183. doi:10.1016/j.ympev.2014.10.019.CrossRefPubMedGoogle Scholar
  48. Lopez, J. V., Bracken-Grissom, H., Collins, A. G., Collins, T., Crandall, K., Distel, D., et al. (2014). The global invertebrate genomics alliance (GIGA): developing community resources to study diverse invertebrate genomes. J Hered, 105(1), 1–18. doi:10.1093/jhered/est084.CrossRefGoogle Scholar
  49. López-Giráldez, F., Moeller, A. H., & Townsend, J. P. (2013). Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. Biomed Research International, 2013, 621604. doi:10.1155/2013/621604.
  50. Marlétaz, F., Martin, E., Perez, Y., Papillon, D., Caubit, X., Lowe, C. J., et al. (2006). Chaetognath phylogenomics: a protostome with deuterostome-like development. Curr Biol, 16(15), R577–R578.CrossRefPubMedGoogle Scholar
  51. Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., et al. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science, 346(6210), 763–767. doi:10.1126/science.1257570.CrossRefPubMedGoogle Scholar
  52. Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., et al. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature, 510(7503), 109–114. doi:10.1038/nature13400.CrossRefPubMedPubMedCentralGoogle Scholar
  53. Murienne, J., Edgecombe, G. D., & Giribet, G. (2010). Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol Phylogenet Evol, 57, 301–313. doi:10.1016/j.ympev.2010.06.022.CrossRefPubMedGoogle Scholar
  54. Nesnidal, M. P., Helmkampf, M., Bruchhaus, I., & Hausdorf, B. (2010). Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol Biol Evol, 27(9), 2095–2104. doi:10.1093/molbev/msq097.CrossRefPubMedGoogle Scholar
  55. Nesnidal, M. P., Helmkampf, M., Meyer, A., Witek, A., Bruchhaus, I., Ebersberger, 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. doi:10.1186/1471-2148-13-253.CrossRefPubMedPubMedCentralGoogle Scholar
  56. Neves, R. C., Kristensen, R. M., & Wanninger, A. (2009). Three-dimensional reconstruction of the musculature of various life cycle stages of the cycliophoran Symbion americanus. J Morphol, 270(3), 257–270. doi:10.1002/jmor.10681.CrossRefPubMedGoogle Scholar
  57. Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., et al. (2013). Deep metazoan phylogeny: when different genes tell different stories. Mol Phylogenet Evol, 67(1), 223–233. doi:10.1016/j.ympev.2013.01.010.CrossRefPubMedGoogle Scholar
  58. Novacek, M. J. (1992). Fossils as critical data for phylogeny. In M. J. Novacek & Q. D. Wheeler (Eds.), Extinction and phylogeny (1st ed., pp. 46–88). New York: Columbia University Press.Google Scholar
  59. Oakley, T. H., Wolfe, J. M., Lindgren, A. R., & Zaharoff, A. K. (2013). Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement, and pancrustacean phylogeny. Mol Biol Evol, 30(1), 215–233. doi:10.1093/molbev/mss216.CrossRefPubMedGoogle Scholar
  60. Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., et al. (2012). Best practices for justifying fossil calibrations. Syst Biol, 61(2), 346–359.CrossRefPubMedPubMedCentralGoogle Scholar
  61. Peterson, K. J., & Eernisse, D. J. (2001). Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evolution & Development, 3(3), 170–205.Google Scholar
  62. Philippe, H., Lartillot, N., & Brinkmann, H. (2005). Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protostomia. Mol Biol Evol, 22(5), 1246–1253.CrossRefPubMedGoogle Scholar
  63. Philippe, H., Brinkmann, H., Martinez, P., Riutort, M., & Baguñà, J. (2007). Acoel flatworms are not Platyhelminthes: evidence from phylogenomics. PLoS One, 2, e717.CrossRefPubMedPubMedCentralGoogle Scholar
  64. Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., et al. (2009). Phylogenomics revives traditional views on deep animal relationships. Curr Biol, 19, 1–17. doi:10.1016/j.cub.2009.02.052.CrossRefGoogle Scholar
  65. Philippe, H., Brinkmann, H., Copley, R. R., Moroz, L. L., Nakano, H., Poustka, A. J., et al. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470(7333), 255–258. doi:10.1038/nature09676.CrossRefPubMedPubMedCentralGoogle Scholar
  66. Pick, K. S., Philippe, H., Schreiber, F., Erpenbeck, D., Jackson, D. J., Wrede, P., et al. (2010). Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol, 27(9), 1983–1987. doi:10.1093/molbev/msq089.CrossRefPubMedPubMedCentralGoogle Scholar
  67. Pyron, R. A. (2011). Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol, 60(4), 466–481.CrossRefPubMedGoogle Scholar
  68. Pyron, R. A. (2015). Post-molecular systematics and the future of phylogenetics. Trends Ecol Evol, 30(7), 384–389. doi:10.1016/j.tree.2015.04.016.CrossRefPubMedGoogle Scholar
  69. Regier, J. C., Shultz, J. W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., et al. (2010). Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463, 1079–1083. doi:10.1038/nature08742.CrossRefPubMedGoogle Scholar
  70. Ruiz-Trillo, I., Riutort, M., Littlewood, D. T. J., Herniou, E. A., & Baguñà, J. (1999). Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes. Science, 283(5409), 1919–1923.CrossRefPubMedGoogle Scholar
  71. Ryan, J. F., Pang, K., Schnitzler, C. E., Nguyen, A. D., Moreland, R. T., Simmons, D. K., et al. (2013). The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science, 342(6164), 1242592. doi:10.1126/science.1242592.CrossRefPubMedPubMedCentralGoogle Scholar
  72. Sharma, P. P., & Giribet, G. (2014). A revised dated phylogeny of the arachnid order Opiliones. Front Genet, 5, 255. doi:10.3389/fgene.2014.00255.PubMedPubMedCentralGoogle Scholar
  73. Sharma, P. P., Kaluziak, S., Pérez-Porro, A. R., González, V. L., Hormiga, G., Wheeler, W. C., et al. (2014). Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal. Mol Biol Evol, 31(11), 2963–2984. doi:10.1093/molbev/msu235.
  74. Sigwart, J. D., & Lindberg, D. R. (2015). Consensus and confusion in molluscan trees: evaluating morphological and molecular phylogenies. Syst Biol, 64(3), 384–395. doi:10.5061/dryad.b4m2c.CrossRefPubMedPubMedCentralGoogle Scholar
  75. Smith, S., Wilson, N. G., Goetz, F., Feehery, C., Andrade, S. C. S., Rouse, G. W., et al. (2011). Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature, 480, 364–367. doi:10.1038/nature10526.CrossRefPubMedGoogle Scholar
  76. Srivastava, M., Mazza-Curll, K. L., van Wolfswinkel, J. C., & Reddien, P. W. (2014). Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling. Curr Biol, 24(10), 1107–1113. doi:10.1016/j.cub.2014.03.042.CrossRefPubMedGoogle Scholar
  77. Stamatakis, A. (2014a). ExaBayes user’s manual.Google Scholar
  78. Stamatakis, A. (2014b). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313. doi: 10.1093/bioinformatics/btu033.
  79. Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., et al. (2015). Big Data: astronomical or genomical? PLoS Biol, 13(7), e1002195. doi:10.1371/journal.pbio.1002195.CrossRefPubMedPubMedCentralGoogle Scholar
  80. Struck, T. H., Paul, C., Hill, N., Hartmann, S., Hösel, C., Kube, M., et al. (2011). Phylogenomic analyses unravel annelid evolution. Nature, 471(7336), 95–98. doi:10.1038/nature09864.CrossRefPubMedGoogle Scholar
  81. Struck, T. H., Wey-Fabrizius, A. R., Golombek, A., Hering, L., Weigert, A., Bleidorn, C., et al. (2014). Platyzoan paraphyly based on phylogenomic data supports a non-coelomate ancestry of Spiralia. Mol Biol Evol, 31(7), 1833–1849. doi:10.1093/molbev/msu143.CrossRefPubMedGoogle Scholar
  82. Struck, T. H., Golombek, A., Weigert, A., Franke, F. A., Westheide, W., Purschke, G., et al. (2015). The evolution of annelids reveals two adaptive routes to the interstitial realm. Current Biology, 25(15), 1993–1999, doi:10.1016/j.cub.2015.06.007.
  83. Telford, M. J., Lowe, C. J., Cameron, C. B., Ortega-Martinez, O., Aronowicz, J., Oliveri, P., et al. (2014). Phylogenomic analysis of echinoderm class relationships supports Asterozoa. Proc R Soc B Biol Sci, 281(1786), 20140479. doi:10.1098/rspb.2014.0479.CrossRefGoogle Scholar
  84. von Reumont, B. M., & Wägele, J. W. (2014). Advances in molecular phylogeny of crustaceans in the light of phylogenomic data. In J. W. Wägele & T. Bartholomaeus (Eds.), Deep metazoan phylogeny: the backbone of the tree of life. New insights from analyses of molecules, morphology, and theory of data analysis (pp. 385–398). Berlin/Boston: De Gruyter.Google Scholar
  85. Wanninger, A. (2015). Morphology is dead—long live morphology! Integrating MorphoEvoDevo into molecular EvoDevo and phylogenomics. Frontiers in Ecology and Evolution, 3, 54. doi:10.3389/fevo.2015.00054.
  86. Weigert, A., Helm, C., Meyer, M., Nickel, B., Arendt, D., Hausdorf, B., et al. (2014). Illuminating the base of the annelid tree using transcriptomics. Mol Biol Evol, 31(6), 1391–1401. doi:10.1093/molbev/msu080.CrossRefPubMedGoogle Scholar
  87. Wheeler, W. C., Cartwright, P., & Hayashi, C. Y. (1993). Arthropod phylogeny: a combined approach. Cladistics, 9(1), 1–39.CrossRefGoogle Scholar
  88. Wheeler, W. C., Giribet, G., & Edgecombe, G. D. (2004). Arthropod systematics. The comparative study of genomic, anatomical, and paleontological information. In J. Cracraft & M. J. Donoghue (Eds.), Assembling the Tree of Life (pp. 281–295). New York: Oxford University Press.Google Scholar
  89. Whelan, N. V., Kocot, K. M., Moroz, L. L., & Halanych, K. M. (2015). Error, signal, and the placement of Ctenophora sister to all other animals. Proc Natl Acad Sci U S A, 112(18), 5773–5778. doi:10.1073/pnas.1503453112.CrossRefPubMedPubMedCentralGoogle Scholar
  90. Wood, H. M., Matzke, N. J., Gillespie, R. G., & Griswold, C. E. (2013). Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Syst Biol, 62(2), 264–284. doi:10.1093/sysbio/sys092.CrossRefPubMedGoogle Scholar
  91. Zapata, F., Wilson, N. G., Howison, M., Andrade, S. C. S., Jörger, K. M., Schrödl, M., et al. (2014). Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc R Soc B Biol Sci, 281, 20141739. doi:10.1101/007039.CrossRefGoogle Scholar
  92. Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., et al. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385.CrossRefPubMedPubMedCentralGoogle Scholar
  93. Zrzavý, J., Mihulka, S., Kepka, P., Bezdek, A., & Tietz, D. (1998). Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics, 14(3), 249–285.CrossRefGoogle Scholar

Copyright information

© Gesellschaft für Biologische Systematik 2015

Authors and Affiliations

  1. 1.Museum of Comparative Zoology & Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUSA

Personalised recommendations