138
F. Marlétaz and Y. Le Parco
Boore JL (2006) The use of genome-level characters for phylogenetic reconstruction. Trends Ecol
Evol 21:439–446
Borchiellini C, Boury-Esnault N, Vacelet J, Le Parco Y (1998) Phylogenetic analysis of the Hsp70
sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between
animals and fungi. Mol Biol Evol 15:647–655
Borchiellini C, Manuel M, Alivon E, Boury-Esnault N, Vacelet J, Le Parco Y (2001) Sponge
paraphyly and the origin of Metazoa. J Evol Biol 14:171–179
Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES,
Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ (2006)
Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
Nature 444:85–88
Collins AG (1998) Evaluating multiple alternative hypotheses for the origin of Bilateria: an
analysis of 18S rRNA molecular evidence. Proc Natl Acad Sci U S A 95:15458–15463
Conway Morris S, Peel JS (1995) Articulated Halkieriids from the Lower Cambrian of North
Greenland and their role in early protostome evolution. Philos Trans Biol Sci 347:305–358
Copley RR, Aloy P, Russell RB, Telford MJ (2004) Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the
idiosyncrasies of Caenorhabditis elegans. Evol Dev 6:164–169
Cuvier G (1817) Le règne animal distribué selon son organisation, pour servir de base à l’hisoire
naturelle des animaux et d’introduction à l’anatomie comparée. Deterville, Paris.
de Queiroz A, Gatesy J (2007) The supermatrix approach to systematics. Trends Ecol Evol 22:
34–41
de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine
G (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:
772–776
Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are
the closest living relatives of vertebrates. Nature 439:965–968
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of
life. Nat Rev Genet 6:361–375
Deutsch JS (2008) Do acoels climb up the “Scale of Beings”?. Evol Dev 10:135–140
Domazet-Loso T, Brajkovic J, Tautz D (2007) A phylostratigraphy approach to uncover the
genomic history of major adaptations in metazoan lineages. Trends Genet 23:533–539
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW,
Obst M, Edgecombe GD, Sorensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen
RM, Wheeler WC, Martindale MQ, Giribet G (2008) Broad phylogenomic sampling improves
resolution of the animal tree of life. Nature 452:745-749
Eernisse DJ, Albert JS, Anderson FE (1992) Annelida and arthropoda are not sister taxa: a
phylogenetic analysis of spiralian metazoan morphology. Syst Biol 41:305–330
Emig CC (1982) The biology of Phoronida. Adv Mar Biol 19:1–89
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively
misleading. Syst Zool 27:401–410
Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988)
Molecular phylogeny of the animal kingdom. Science 239:748–753
Giribet G, Distel DL, Polz M, Sterrer W, Wheeler WC (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 49:539–562
Gould SJ (1977) Ontogeny and phylogeny. Belknap/Harvard, Cambridge, MA.
Gould SJ (2002) The structure of evolutionary theory. Belknap/Harvard, Cambridge, MA.
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies
by maximum likelihood. Syst Biol 52:696–704
Halanych K (2004) The New View of Animal Phylogeny. Annu Rev Ecol Evol Syst 35:
229–256
F. Marlétaz and Y. Le Parco
Boore JL (2006) The use of genome-level characters for phylogenetic reconstruction. Trends Ecol
Evol 21:439–446
Borchiellini C, Boury-Esnault N, Vacelet J, Le Parco Y (1998) Phylogenetic analysis of the Hsp70
sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between
animals and fungi. Mol Biol Evol 15:647–655
Borchiellini C, Manuel M, Alivon E, Boury-Esnault N, Vacelet J, Le Parco Y (2001) Sponge
paraphyly and the origin of Metazoa. J Evol Biol 14:171–179
Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES,
Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ (2006)
Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
Nature 444:85–88
Collins AG (1998) Evaluating multiple alternative hypotheses for the origin of Bilateria: an
analysis of 18S rRNA molecular evidence. Proc Natl Acad Sci U S A 95:15458–15463
Conway Morris S, Peel JS (1995) Articulated Halkieriids from the Lower Cambrian of North
Greenland and their role in early protostome evolution. Philos Trans Biol Sci 347:305–358
Copley RR, Aloy P, Russell RB, Telford MJ (2004) Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the
idiosyncrasies of Caenorhabditis elegans. Evol Dev 6:164–169
Cuvier G (1817) Le règne animal distribué selon son organisation, pour servir de base à l’hisoire
naturelle des animaux et d’introduction à l’anatomie comparée. Deterville, Paris.
de Queiroz A, Gatesy J (2007) The supermatrix approach to systematics. Trends Ecol Evol 22:
34–41
de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine
G (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:
772–776
Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are
the closest living relatives of vertebrates. Nature 439:965–968
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of
life. Nat Rev Genet 6:361–375
Deutsch JS (2008) Do acoels climb up the “Scale of Beings”?. Evol Dev 10:135–140
Domazet-Loso T, Brajkovic J, Tautz D (2007) A phylostratigraphy approach to uncover the
genomic history of major adaptations in metazoan lineages. Trends Genet 23:533–539
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW,
Obst M, Edgecombe GD, Sorensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen
RM, Wheeler WC, Martindale MQ, Giribet G (2008) Broad phylogenomic sampling improves
resolution of the animal tree of life. Nature 452:745-749
Eernisse DJ, Albert JS, Anderson FE (1992) Annelida and arthropoda are not sister taxa: a
phylogenetic analysis of spiralian metazoan morphology. Syst Biol 41:305–330
Emig CC (1982) The biology of Phoronida. Adv Mar Biol 19:1–89
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively
misleading. Syst Zool 27:401–410
Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988)
Molecular phylogeny of the animal kingdom. Science 239:748–753
Giribet G, Distel DL, Polz M, Sterrer W, Wheeler WC (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 49:539–562
Gould SJ (1977) Ontogeny and phylogeny. Belknap/Harvard, Cambridge, MA.
Gould SJ (2002) The structure of evolutionary theory. Belknap/Harvard, Cambridge, MA.
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies
by maximum likelihood. Syst Biol 52:696–704
Halanych K (2004) The New View of Animal Phylogeny. Annu Rev Ecol Evol Syst 35:
229–256