4 Phylogeny of Animals
141
Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving
incongruence in molecular phylogenies. Nature 425:798–804
Roy SW, Gilbert W (2005) Resolution of a deep animal divergence by the pattern of intron
conservation. Proc Natl Acad Sci U S A 102:4403–4408
Roy SW, Irimia M (2008) Rare genomic characters do not support Coelomata: intron loss/gain.
Mol Biol Evol 25:620–623
Ruiz-Trillo I, Riutort M, Littlewood DT, Herniou EA, Baguna J (1999) Acoel flatworms: earliest
extant bilaterian Metazoans, not members of Platyhelminthes. Science 283:1919–1923
Schubert M, Escriva H, Xavier-Neto J, Laudet V (2006) Amphioxus and tunicates as evolutionary
model systems. Trends Ecol Evol 21:269–277
Scotland RW, Olmstead RG, Bennett JR (2003) Phylogeny reconstruction: the role of morphology.
Syst Biol 52:539–548
Shubin N, Tabin C, Carroll S (1997) Fossils, genes and the evolution of animal limbs. Nature
388:639–648
Siewing R (1976) Probleme und neuere Erkenntnisse in der Großsystematik der Wirbellosen. Verh
Dtsch Zool Ges 70:59–83
Stach T, Winter J, Bouquet JM, Chourrout D, Schnabel R (2008) Embryology of a planktonic
tunicate reveals traces of sessility. Proc Natl Acad Sci U S A 105:7229–7234
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Struck TH, Fisse F (2008) Phylogenetic position of Nemertea derived from phylogenomic data.
Mol Biol Evol 23:2058–2071
Swofford DL (1990) PAUP: Phylogenetic analysis using parsimony, Version 3.0. Illinois Natural
History Survey, Champaign
Tautz D (2004) Segmentation. Dev Cell 7:301–312
Telford MJ, Holland PW (1993) The phylogenetic affinities of the chaetognaths: a molecular
analysis. Mol Biol Evol 10:660–676
Valentine JW (1997) Cleavage patterns and the topology of the metazoan tree of life. Proc Natl
Acad Sci U S A 94:8001–8005
Wagner GP (2007) The developmental genetics of homology. Nat Rev Genet 8:473–479
Wanninger A, Koop D, Bromham L, Noonan E, Degnan BM (2005) Nervous and muscle system
development in Phascolion strombus (Sipuncula). Dev Genes Evol 215:509–518
Willmer P (1990) Invertebrates relationships: patterns in animal evolution. Cambrige University
Press, Cambridge
Winchell CJ, Sullivan J, Cameron CB, Swalla BJ, Mallatt J (2002) Evaluating hypotheses of
deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data.
Mol Biol Evol 19:762–776
Wolf YI, Rogozin IB, Koonin EV (2004) Coelomata and not Ecdysozoa: evidence from genomewide phylogenetic analysis. Genome Res 14:29–36
Zheng J, Rogozin IB, Koonin EV, Przytycka TM (2007) Support for the Coelomata clade
of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol
24:2583–2592
141
Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving
incongruence in molecular phylogenies. Nature 425:798–804
Roy SW, Gilbert W (2005) Resolution of a deep animal divergence by the pattern of intron
conservation. Proc Natl Acad Sci U S A 102:4403–4408
Roy SW, Irimia M (2008) Rare genomic characters do not support Coelomata: intron loss/gain.
Mol Biol Evol 25:620–623
Ruiz-Trillo I, Riutort M, Littlewood DT, Herniou EA, Baguna J (1999) Acoel flatworms: earliest
extant bilaterian Metazoans, not members of Platyhelminthes. Science 283:1919–1923
Schubert M, Escriva H, Xavier-Neto J, Laudet V (2006) Amphioxus and tunicates as evolutionary
model systems. Trends Ecol Evol 21:269–277
Scotland RW, Olmstead RG, Bennett JR (2003) Phylogeny reconstruction: the role of morphology.
Syst Biol 52:539–548
Shubin N, Tabin C, Carroll S (1997) Fossils, genes and the evolution of animal limbs. Nature
388:639–648
Siewing R (1976) Probleme und neuere Erkenntnisse in der Großsystematik der Wirbellosen. Verh
Dtsch Zool Ges 70:59–83
Stach T, Winter J, Bouquet JM, Chourrout D, Schnabel R (2008) Embryology of a planktonic
tunicate reveals traces of sessility. Proc Natl Acad Sci U S A 105:7229–7234
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Struck TH, Fisse F (2008) Phylogenetic position of Nemertea derived from phylogenomic data.
Mol Biol Evol 23:2058–2071
Swofford DL (1990) PAUP: Phylogenetic analysis using parsimony, Version 3.0. Illinois Natural
History Survey, Champaign
Tautz D (2004) Segmentation. Dev Cell 7:301–312
Telford MJ, Holland PW (1993) The phylogenetic affinities of the chaetognaths: a molecular
analysis. Mol Biol Evol 10:660–676
Valentine JW (1997) Cleavage patterns and the topology of the metazoan tree of life. Proc Natl
Acad Sci U S A 94:8001–8005
Wagner GP (2007) The developmental genetics of homology. Nat Rev Genet 8:473–479
Wanninger A, Koop D, Bromham L, Noonan E, Degnan BM (2005) Nervous and muscle system
development in Phascolion strombus (Sipuncula). Dev Genes Evol 215:509–518
Willmer P (1990) Invertebrates relationships: patterns in animal evolution. Cambrige University
Press, Cambridge
Winchell CJ, Sullivan J, Cameron CB, Swalla BJ, Mallatt J (2002) Evaluating hypotheses of
deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data.
Mol Biol Evol 19:762–776
Wolf YI, Rogozin IB, Koonin EV (2004) Coelomata and not Ecdysozoa: evidence from genomewide phylogenetic analysis. Genome Res 14:29–36
Zheng J, Rogozin IB, Koonin EV, Przytycka TM (2007) Support for the Coelomata clade
of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol
24:2583–2592