4 Phylogeny of Animals
139
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:
1641–1643
Hausdorf B, Helmkampf M, Meyer A, Witek A, Herlyn H, Bruchhaus I, Hankeln T, Struck
TH, Lieb B (2007) Spiralian phylogenomics supports the resurrection of Bryozoa comprising
Ectoprocta and Entoprocta. Mol Biol Evol 24:2723–2729
Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana.
Hordijk W, Gascuel O (2005) Improving the efficiency of SPR moves in phylogenetic tree search
methods based on maximum likelihood. Bioinformatics 21:4338–4347
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and
its impact on evolutionary biology. Science 294:2310–2314
Hyman LH (1940–1967) The invertebrates. McGraw-Hill, New York.
Hyman LH (1959) The invertebrates, Vol. 5. Smaller Coelomate groups. McGraw-Hill, New York
Irimia M, Maeso I, Penny D, Garcia-Fernandez J, Roy SW (2007) Rare coding sequence changes
are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol 24:1604–1607
Jeffery WR, Strickler AG, Yamamoto Y (2004) Migratory neural crest-like cells form body
pigmentation in a urochordate embryo. Nature 431:696–699
Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: the beginning of incongruence?. Trends Genet 22:225–231
Jenner RA (2000) Evolution of animal body plans: the role of metazoan phylogeny at the interface
between pattern and process. Evol Dev 2:208–221
Jenner RA (2001) Bilaterian phylogeny and uncritical recycling of morphological data sets. Syst
Biol 50:730–742
Jenner RA (2004) Libbie Henrietta Hyman (1888–1969): from developmental mechanics to the
evolution of animal body plans. J Exp Zoolog B Mol Dev Evol 302:413–423
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press,
Cambridge.
Lake JA (1990) Origin of the Metazoa. Proc Natl Acad Sci U S A 87:763–766
Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the
animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7(Suppl 1):S4
Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the
amino-acid replacement process. Mol Biol Evol 21:1095–1109
Lartillot N, Philippe H (2008) Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci 363:1463–1472
Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918–1922
Littlewood DT, Olson PD, Telford MJ, Herniou EA, Riutort M (2001) Elongation factor 1-alpha
sequences alone do not assist in resolving the position of the acoela within the metazoa. Mol
Biol Evol 18:437–442
Lynch M (2007) The origins of genome architecture. Sinauer, Sunderland.
Mallatt J, Winchell CJ (2002) Testing the new animal phylogeny: first use of combined largesubunit and small-subunit rRNA gene sequences to classify the protostomes. Mol Biol Evol
19:289–301
Marcus E (1958) On the evolution of the animal phyla. Quart Rev Biol 33:24–58
Marlétaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco
Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians.
Genome Biol 9:R94
Marlétaz F, Martin E, Perez Y, Papillon D, Caubit X, Lowe CJ, Freeman B, Fasano L, Dossat C,
Wincker P, Weissenbach J, Le Parco Y (2006) Chaetognath phylogenomics: a protostome with
deuterostome-like development. Curr Biol 16:R
Martindale MQ (2005) The evolution of metazoan axial properties. Nat Rev Genet 6:917–927
Martindale MQ, Henry JQ (1999) Intracellular fate mapping in a basal metazoan, the ctenophore
Mnemiopsis leidyi, reveals the origins of mesoderm and the existence of indeterminate cell
lineages. Dev Biol 214:243–257
139
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:
1641–1643
Hausdorf B, Helmkampf M, Meyer A, Witek A, Herlyn H, Bruchhaus I, Hankeln T, Struck
TH, Lieb B (2007) Spiralian phylogenomics supports the resurrection of Bryozoa comprising
Ectoprocta and Entoprocta. Mol Biol Evol 24:2723–2729
Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana.
Hordijk W, Gascuel O (2005) Improving the efficiency of SPR moves in phylogenetic tree search
methods based on maximum likelihood. Bioinformatics 21:4338–4347
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and
its impact on evolutionary biology. Science 294:2310–2314
Hyman LH (1940–1967) The invertebrates. McGraw-Hill, New York.
Hyman LH (1959) The invertebrates, Vol. 5. Smaller Coelomate groups. McGraw-Hill, New York
Irimia M, Maeso I, Penny D, Garcia-Fernandez J, Roy SW (2007) Rare coding sequence changes
are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol 24:1604–1607
Jeffery WR, Strickler AG, Yamamoto Y (2004) Migratory neural crest-like cells form body
pigmentation in a urochordate embryo. Nature 431:696–699
Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: the beginning of incongruence?. Trends Genet 22:225–231
Jenner RA (2000) Evolution of animal body plans: the role of metazoan phylogeny at the interface
between pattern and process. Evol Dev 2:208–221
Jenner RA (2001) Bilaterian phylogeny and uncritical recycling of morphological data sets. Syst
Biol 50:730–742
Jenner RA (2004) Libbie Henrietta Hyman (1888–1969): from developmental mechanics to the
evolution of animal body plans. J Exp Zoolog B Mol Dev Evol 302:413–423
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press,
Cambridge.
Lake JA (1990) Origin of the Metazoa. Proc Natl Acad Sci U S A 87:763–766
Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the
animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7(Suppl 1):S4
Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the
amino-acid replacement process. Mol Biol Evol 21:1095–1109
Lartillot N, Philippe H (2008) Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci 363:1463–1472
Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918–1922
Littlewood DT, Olson PD, Telford MJ, Herniou EA, Riutort M (2001) Elongation factor 1-alpha
sequences alone do not assist in resolving the position of the acoela within the metazoa. Mol
Biol Evol 18:437–442
Lynch M (2007) The origins of genome architecture. Sinauer, Sunderland.
Mallatt J, Winchell CJ (2002) Testing the new animal phylogeny: first use of combined largesubunit and small-subunit rRNA gene sequences to classify the protostomes. Mol Biol Evol
19:289–301
Marcus E (1958) On the evolution of the animal phyla. Quart Rev Biol 33:24–58
Marlétaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco
Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians.
Genome Biol 9:R94
Marlétaz F, Martin E, Perez Y, Papillon D, Caubit X, Lowe CJ, Freeman B, Fasano L, Dossat C,
Wincker P, Weissenbach J, Le Parco Y (2006) Chaetognath phylogenomics: a protostome with
deuterostome-like development. Curr Biol 16:R
Martindale MQ (2005) The evolution of metazoan axial properties. Nat Rev Genet 6:917–927
Martindale MQ, Henry JQ (1999) Intracellular fate mapping in a basal metazoan, the ctenophore
Mnemiopsis leidyi, reveals the origins of mesoderm and the existence of indeterminate cell
lineages. Dev Biol 214:243–257