Integrative Animal Biology Fenton/Campbell/Dumont/Owen

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1 Integrative Animal Biology Fenton/Campbell/Dumont/Owen Chapter 3: The Phylogeny of Animal Groups Reference List Aguinaldo, A. M. A., & Lake, A. A. (1998). Evolution of the multicellular animals. American Zoologist, 38, Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., et al. (1997). Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387, Andrew, D. R. (2011). A new view of insect crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics. Arthropod Structure & Development, 40 (3), Baguñà, J., & Riutort, M. (2004). Molecular phylogeny of the Platyhelminthes. Canadian Journal of Zoology, 82 (2), Ball, E. E., Hayward, D. C., Saint, R., et al. (2004). A simple plan cnidarians and the origins of developmental mechanisms. Genetics, 5 (8), Bleidorn, C. (2008). Lophotrochozoan relationships and parasites: A snap-shot. Parasite, 15, Borchiellini, C., Chombard, C., Manuel, M., et al. (2004). Molecular phylogeny of Demospongiae: Implications for classification and scenarios of character evolution. Molecular Phylogenetics and Evolution, 32 3), Bourlat, S. J., Nielsen, C., Economou, A. D., et al. (2008). Testing the new animal phylogeny: A phylum level molecular analysis of the animal kingdom. Molecular Phylogenetics and Copyright 2014 Nelson Education Ltd. 1

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3 12), Dohrmann, M., Janussen, D., Reitner, J., et al. (2008). Phylogeny and evolution of glass sponges (Porifera, Hexactinellida). Systematic Biology, 5 7(3), Dunlop, J. A. (2010). Geological history and phylogeny of Chelicerata. Arthropod Structure & Development, 39, Dunn, C. W., Hejnol, A., Matus, D. Q., et al. (2008). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, Edgecombe, G. D. (2010). Arthropod phylogeny: An overview from the perspectives of morphology, molecular data and the fossil record. Arthropod Structure & Development, 39, Egger, B., Steinke, D., Tarui, H., et al. (2009). To be or not to be a flatworm: The acoel controversy. PLoS ONE, 4 (5), e5502. Ehlers, U. (1991). Comparative morphology of statocysts in the plathelminthes and the xenoturbellida. Hydrobiologia, 227, Ertas, B., von Reumont, B. M., Wagele, J. W., et al. (2009). Hemocyanin suggests a close relationship of Remipedia and Hexapoda. Molecular Biology and Evolution, 26 (12), Ewer, J. (2011). How the ecdysozoan changed its coat. PLoS Biol., 3 (10), 349. Frand, A. R., Russel, S., & Ruvkun, G. (2005). Functional genomic analysis of C. elegans molting. PLoS Biol., 3 (10), e312. Fuchs, J., Iseto, T., Hirose, M., et al. (2010). The first internal molecular phylogeny of the animal phylum Entoprocta (Kamptozoa). Molecular Phylogenetics and Evolution, 56 (1), Copyright 2014 Nelson Education Ltd. 3

4 Fuchs, J., Obst, M., & Sundberg, P. (2009). The first comprehensive molecular phylogeny of Bryozoa (Ectoprocta) based on combined analyses of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution, 52 (1), Fussmann, G. F. (2010). Rotifers: Excellent subjects for the study of macro- and microevolutionary change. Hydrobiologia, 662 (1), Garcia-Varela, M., & Nadler, S. A. (2006). Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences. Molecular Phylogenetics and Evolution, 40 (1), Garey, J. R., Schmidt-Rhaesa, A., Near, T. J., et al. (1998). The evolutionary relationships of rotifers and acanthocephalans. Hydrobiologia, 387/388, Garey, J. R., Near, T. J., Nonnemacher, M. R., et al. (1996). Molecular evidence for Acanthocephala as a subtaxon of Rotifera. Journal of Molecular Evolution, 43, Giribet, G. (2000). A review of arthropod phylogeny: New data based on ribosomal DNA sequences and direct character optimization. Cladistics, 16 (2), Giribet, G., Distel, D. L., Pol, M., et al. (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. Systematic Biology, 49(3), Giribet, G., Dunn, C. W., Edgecombe, G. D., et al. (2007). A modern look at the animal tree of life. Zootaxa, 1668, Giribet, G., & Edgecombe, G. D. (2010). Reevaluating the arthropod tree of life. Annual Review of Entomology, 57, ( ). Giribet, G., Sørensen, M. V., Funch, P., et al. (2004). Investigations into the phylogenetic Copyright 2014 Nelson Education Ltd. 4

5 position of micrognathozoa using four molecular loci. Cladistics, 20, Grimaldi, D. A. (2010). 400 million years on six legs: On the origin and early evolution of Hexapoda. Arthropod Structure & Development, 39, Grimaldi, D. A. (2010). Fossil record and phylogeny of the Arthropoda Introduction. Arthropod Structure & Development, 39, Haug, J. T., Waloszek, D., Haug, C., et al. (2010). High-level phylogenetic analysis using developmental sequences: The Cambrian Martinssonia elongata, Musacaris gerdgeyeri gen. et sp. nov. and their position in early crustacean evolution. Arthropod Structure & Development, 39, Hausdorf, B., Helmkampf, M., Nesnidal, M. P., et al. (2010). Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida). Molecular Phylogenetics and Evolution, 55 (3), Helmkampf, M., Bruchhaus, I., & Hausdorf, B. (2008). Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept. Proceedings of the Royal Society of London, Series B: Biological Sciences, 275 (1645), Herlyn, H., Piskurek, O., Schmitz, J. U., et al. (2003). The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rdna sequences. Molecular Phylogenetics and Evolution, 26, Jenner, R. A. (2010). Higher-level crustacean phylogeny: Consensus and conflicting hypotheses. Arthropod Structure & Development, 39, Kim, W., & Cunningham, C. W. (1999). A new perspective on lower metazoan relationships from 18S rdna sequences. Molecular Biology and Evolution, 16 (3), Copyright 2014 Nelson Education Ltd. 5

6 King, N., Westbrook, M. J., Young, S. L., et al. (2008). The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature, 451 (7180), Kocot, K. M., Cannon, J. T., Todt, C., et al. (2011). Phylogenomics reveals deep molluscan relationships. Nature, 477 (7365), Koenemann, S., Jenner, R. A., Hoenemann, M., et al. (2010). Arthropod phylogeny revisited, with a focus on crustacean relationships. Arthropod Structure & Development, 39, Larsson, K., & Jondelius, U. (2008). Phylogeny of Catenulida and support for Platyhelminthes. Organisms Diversity & Evolution, 8 (5), Lavrov, D. V., Brown, W. M., & Boore, J. L. (2004). Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society of London, Series B: Biological Sciences., 271 (1538), Lieberman, B. S., & Karim, T. S. (2010). Tracing the trilobite tree from the root to the tips: A model marriage of fossils and phylogeny. Arthropod Structure & Development, 39, Littlewood, D. T. J., Rohde, K., & Clough, K. A. (1999). The interrelationships of all major groups of Platyhelminthes: Phylogenetic evidence from morphology and molecules. Biological Journal of the Linnean Society, 66, Lockyer, A. E., Olson, P. D., & Littlewwod, D. T. J. (2003). Utility of complete large and small subunit rrna genes in resolving the phylogeny of the Neodermata (Platyhelminthes): Implications and a review of the cercomer theory. Biological Journal of the Linnean Society, 78, Maldonado, M. (2004). Choanoflagellates, choanocytes, and animal multicellularity. Copyright 2014 Nelson Education Ltd. 6

7 Invertebrate Biology, 123 (1), Mallatt, J., & Winchell, C. J. (2007). Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star. Molecular Phylogenetics and Evolution, 43 (3), Mark Welch, D. B. (2005). Bayesian and maximum likelihood analyses of rotifer acanthocephalan relationships. Hydrobiologia, 546, Martindale, M. Q., Finnerty, J. R., & Henry, J. Q. (2002). The Radiata and the evolutionary origins of the bilaterian body plan. Molecular Phylogenetics and Evolution, 24, Maxmen, A. (2011). A can of worms. Nature, 470, Meusemann, K., von Reumont, B. M., Simon, S., et al. (2010). A phylogenomic approach to resolve the arthropod tree of life. Molecular Biology and Evolution, 27 (11), Mwinyi, A., Bailly, X., Bourlat, S. J.,et al. (2010). The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evolutionary Biology, 10 (1), 309. Neuhaus, B., & Higgins, R. P. (2002). Ultrastructure, biology, and phylogenetic relationships of Kinorhyncha1. Integrative and Comparative Biology, 42, Nichols, S., & Worheide, G. (2005). Sponges: New views of old animals. Integrative and Comparative Biology, 45, Nielsen, C. (2010). After all: Xenoturbella is an acoelomorph! Evolution & Development, 12 (3), Passamaneck, Y., & Halanych, K. M. (2006). Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of lophophorate polyphyly. Molecular Phylogenetics and Evolution, 40 (1), Copyright 2014 Nelson Education Ltd. 7

8 Perseke, M., Hankeln, H., Weich, B., et al. (2007). The mitochondrial DNA of Xenoturbella bocki: Genomic architecture and phylogenetic analysis. Theory in Biosciences, 126 (1), Petrov, N. B., Pegova, A. N., Manylov, O. G., et al. (2007). Molecular phylogeny of Gastrotricha on the basis of a comparison of the 18S rrna genes: Rejection of the hypothesis of a relationship between Gastrotricha and Nematoda. Molecular Biology, 41 (3), Philippe, H., Brinkmann, H., Copley, R. R., et al. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470 (7333), Philippe, H., Derelle, R., Lopez, P., et al. (2009). Phylogenomics revives traditional views on deep animal relationships. Current Biology, 19 (8), Pick, K. S., Philippe, H., Schreiber, F., et al. (2010). Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Molecular Biology and Evolution, 27 (9), Podar, M. (2001). A molecular phylogenetic framework for the phylum Ctenophora using 18S rrna Genes. Molecular Phylogenetics and Evolution, 21 (2), Regier, J. C., Shultz, J. W., Zwick, A., et al. (2010). Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463, Regier, J. C., Wilson, H. M., & Shultz, J. W. (2005). Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes. Molecular Phylogenetics and Evolution, 34 (1), Rieger, R. M., & Tyler, S. (1995). Sister-group relationship of Gnathostomulida and Rotifera Acanthocephala. Invertebrate Biology, 114 (2), Rota-Stabelli, O., Campbell, L., Brinkmann, H., et al. (2011). A congruent solution to arthropod Copyright 2014 Nelson Education Ltd. 8

9 phylogeny: Phylogenomics, micrornas and morphology support monophyletic Mandibulata. Proceedings of the Royal Society of London, Series B: Biological Sciences, 278 (1703), Rota-Stabelli, O., Kayal, E., Gleeson, D., et al. (2010). Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biology and Evolution, 2, Schierwater, B., Eitel, M., Jakob, W., et al. (2009). Concatenated analysis sheds light on early metazoan evolution and fuels a modern Urmetazoon hypothesis. PLoS Biol, 7 (1), Shear, W. A. (1992). End of the Uniramia taxon. Nature, 359, Shultz, J. R.. W., & Regier, J. C. (2000). Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proceedings of the Royal Society of London, Series B: Biological Sciences, 267, Sigwart, J. D., & Sutton, M. D. (2007). Deep molluscan phylogeny: Synthesis of palaeontological and neontological data. Proceedings of the Royal Society of London, Series B: Biological Sciences, 274 (1624), Smith, A. B. (2004). Deuterostome phylogeny and the interpretation of problematic fossil echinoderms., page in Heinzeller, T., & Nebelsick, J.H., Echinoderms. München: CRC Press Sperling, E. A., Peterson, K. J., & Pisani, D. (2009). Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Molecular Biology and Evolution, 26 (10), Strausfeld, N. J., & Andrew, D. R. (2011). A new view of insect crustacean relationships I. Copyright 2014 Nelson Education Ltd. 9

10 Inferences from neural cladistics and comparative neuroanatomy. Arthropod Structure & Development, 40 (3), Struck, T. H., & Fisse, F. (2008). Phylogenetic position of Nemertea derived from phylogenomic data. Molecular Biology and Evolution, 25 (4), Struck, T. H., Paul, C., Hill, N., et al. (2011). Phylogenomic analyses unravel annelid evolution. Nature, 47 1(7336), Struck, T. H., Schult, N., Kusen, T., et al. (2007). Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evolutionary Biology, 5 (57), Stys, P., & Zrzavy, J. (1994). Phylogeny and classification of extant Arthropoda: Review of hypotheses and nomenclature. European Journal of Entomology, 91, Swalla, B. J., Cameron, C. B., Corley, L. S., et al. (2000). Urochordates are monophyletic within the deuterostomes. Systematic Biology, 49 (1), Telford, M. J. (2009). Animal evolution: Once upon a time. Current Biology, 19 (8), R Tzertzinis, G., Egaña, A. L., Palli, S. R., et al. (2010). Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Neglected Tropical Diseases, 4(3), e625. Wallberg, A., Thollesson, M., Farris, J. S., et al. (2004). The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling. Cladistics, 20, Wetzer, R., & Pentcheff, N. D. (2006). Insects are crustaceans [Poster]., Los Angeles: Natural History Museum of Los Angeles County, Twentieth Annual Bug Fair. Witek, A., Herlyn, H., Ebersberger, I., et al. (2009). Support for the monophyletic origin of Gnathifera from phylogenomics. Molecular Phylogenetics and Evolution, 53 (3), Copyright 2014 Nelson Education Ltd. 10

11 Wood, T. S., & Lore, M. (2005). The higher phylogeny of phylactolaemate bryozoans inferred from 18S ribosomal DNA sequences In Moyano, H. I., Cancino, J. M. and Wyse- Jackson, P.N. (PDF). In: Bryozoan Studies 2004: Proceedings of the 13th International Bryozoology Association. pp London: Taylor & Francis Group. Zhong, J., Zhang, J., Mukwaya, E., et al. (2009). Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data. Journal of Genetics and Genomics, 36 (3), Copyright 2014 Nelson Education Ltd. 11