Publications within the SPP 1174

Bernhard Hausdorf, Martin Helmkampf, Achim Meyer, Alexander Witek, Holger Herlyn, Iris Bruchhaus, Thomas Hankeln,Torsten H. Struck and Bernhard Lieb. "Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta", Molecular Biology and Evolution,

Ebersberger, I., Gube, M.. Strauss, S. Kupczok, A., Eckart, M., Voigt, K., Kothe, E., and von Haeseler, A.. "A stable backbone for the fungi", submitted,

Guido Fritzsch, Manja U. Boehme, Mike Thorndyke,Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln, Peter F. Stadler. "A PCR Survey of Xenoturbella bocki Hox Genes", JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL),

Harzsch S, Wanninger A. "Evolution of invertebrate nervous systems: the Chaetognatha as a case study", Acta Zoologica, in press

Misof, B and Misof K. "A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments: A More Objective Means of Data Exclusion ", Systematic Biology, May 20, 2009, 58(1)

Ebersberger, I., Strauss, S., and von Haeseler, A.. "HaMStR: Profile Hidden Markov Model Based Search for Orthologs in ESTs", BMC Evolutionary Biology, 8 July 2009, 9(157) PubMed Id: 19586527 [View at PubMed]

Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, Baurain D. "Resolving difficult phylogenetic questions: why more sequences are not enough.", PLoS Biol., 2011 Mar, 9(3), e1000602. PubMed Id: 21423652 [View at PubMed]

Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, Wrede P, Wiens M, Alie A, Morgenstern B, Manuel M, Worheide G. "Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.", Mol. Biol. Evol., 2010 Sep, 27(9), 1983-7. PubMed Id: 20378579 [View at PubMed]

Nguyen MA, Klaere S, von Haeseler A. "MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment.", Molecular biology and evolution, 2010 Jul PubMed Id: 20643866 [View at PubMed]

Koestler T, von Haeseler A, Ebersberger I. "FACT: Functional annotation transfer between proteins with similar feature architectures.", BMC bioinformatics, 2010 Aug, 11(1), 417. PubMed Id: 20696036 [View at PubMed]

Kupczok A, Schmidt HA, von Haeseler A. "Accuracy of phylogeny reconstruction methods combining overlapping gene data sets.", Algorithms Mol Biol, 2010 , 5, 37. PubMed Id: 21134245 [View at PubMed]

Rothe, B.H. and Schmidt-Rhaesa, A.. "The structure of the nervous system in Tubiluchus troglodytes (Priapulida)", Invertebrate Biology, 2010, 129, 39-58.

Rieger V, Perez Y, Mueller CHG, Lipke E, Sombke A, Hansson BS, Harzsch S . "Immunohistochemical analysis and 3D reconstruction of the cephalic nervous system in Chaetognatha: insights into an early bilaterian brain? ", Invertebrate Biology, 2010, 129(1), 77-104.

Rothe, B.H. and Schmidt-Rhaesa, A. . "Oregodasys cirratus, a new species of Gastrotricha (Macrodasyida) from Tenerife (Canary Islands), with a description of the muscular and nervous system", Meiofauna Marina, 2010, 17

von Reumont BM, Meusemann K, Szucsich NU, DellAmpio E, Gowri-Shankar V, Bartel D, Simon S, Letsch HO, Stocsits RR, Luan YX, Waegele JW, Pass G, Hadrys H, Misof B. "Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships", BMC Evol. Biol., 2009 May, 9(1), 119. PubMed Id: 19473484 [View at PubMed]

Comandi S, Carapelli A, Podsiadlowski L, Nardi F, Frati F. "The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.", Gene, 2009 Mar PubMed Id: 19285124 [View at PubMed]

Bleidorn C, Podsiadlowski L, Zhong M, Eeckhaut I, Hartmann S, Halanych KM, Tiedemann R. "On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?", BMC Evol. Biol., 2009 Jul, 9(1), 150. PubMed Id: 19570199 [View at PubMed]

Witek A, Herlyn H, Ebersberger I, Mark Welch DB, Hankeln T. "Support for the monophyletic origin of Gnathifera from phylogenomics.", Mol. Phylogenet. Evol., 2009 Aug PubMed Id: 19654049 [View at PubMed]

Ertas B, von Reumont BM, Waegele JW, Misof B, Burmester T. "Hemocyanin suggests a close relationship of Remipedia and Hexapoda.", Mol. Biol. Evol., 2009 Aug PubMed Id: 19692666 [View at PubMed]

Roeding F, Borner J, Kube M, Klages S, Reinhardt R, Burmester T. "A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator).", Mol. Phylogenet. Evol., 2009 Aug PubMed Id: 19695333 [View at PubMed]

Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Worheide G, Manuel M. "Phylogenomics Revives Traditional Views on Deep Animal Relationships.", Curr. Biol., 2009 Apr PubMed Id: 19345102 [View at PubMed]

Mwinyi A, Meyer A, Bleidorn C, Lieb B, Bartolomaeus T, Podsiadlowski L. "Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida.", BMC Genomics, 2009 , 10, 27. PubMed Id: 19149868 [View at PubMed]

Erpenbeck D, Voigt O, Worheide G, Lavrov DV. "The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE).", BMC Genomics, 2009 , 10, 591. PubMed Id: 20003196 [View at PubMed]

Suschenko D, Purschke G . "Ultrastructure of pigmented adult eyes in errant polychaetes (Annelida) - implications for annelid evolution.", Zoomorphology , 2009, 128, 75-96.

Rothe, B.H. and Schmidt-Rhaesa, A. "Architecture of the nervous system in two Dactylopodola species (Gastrotricha, Macrodasyida)", Zoomorphology, 2009, 128, 227-246.

Harzsch S, Mueller CHG, Rieger V, Perez Y, Sintoni S, Sardet C, Hansson B. "Fine structure of the ventral nerve centre and interspecific identification of individual neurons in the enigmatic Chaetognatha", Zoomorphology, 2009, 128(1), 53-73.

Bleidorn C, Lanterbecq D, Eeckhaut I, Tiedemann R. "A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum", Development, Genes and Evolution, 2009, 219, 211-216.

Bleidorn C. "Lophotrochozoan relationships and parasites. A snap-shot.", Parasite, 2008 Sep, 15(3), 329-32. PubMed Id: 18814703 [View at PubMed]

Brenneis G, Ungerer P, Scholtz G. "The chelifores of sea spiders (Arthropoda, Pycnogonida) are the appendages of the deutocerebral segment.", Evol. Dev., 2008 Nov-Dec, 10(6), 717-24. PubMed Id: 19021742 [View at PubMed]

Zhong M, Struck TH, Halanych KM. "Phylogenetic information from three mitochondrial genomes of Terebelliformia (Annelida) worms and duplication of the methionine tRNA.", Gene, 2008 Jun, 416(1-2), 11-21. PubMed Id: 18439769 [View at PubMed]

Masta SE, Klann AE, Podsiadlowski L. "A comparison of the mitochondrial genomes from two families of Solifugae (Arthropoda: Chelicerata): Eremobatidae and Ammotrechidae.", Gene, 2008 Jul, 417(1-2), 35-42. PubMed Id: 18456437 [View at PubMed]

Helmkampf M, Bruchhaus I, Hausdorf B. "Multigene analysis of lophophorate and chaetognath phylogenetic relationships.", Mol. Phylogenet. Evol., 2008 Jan, 46(1), 206-14. PubMed Id: 17937996 [View at PubMed]

Podsiadlowski L, Braband A, Mayer G. "The Complete Mitochondrial Genome of the Onychophoran Epiperipatus biolleyi Reveals a Unique Transfer RNA Set and Provides Further Support for the Ecdysozoa Hypothesis.", Mol. Biol. Evol., 2008 Jan, 25(1), 42-51. PubMed Id: 17934206 [View at PubMed]

Voigt O, Erpenbeck D, Worheide G. "Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera.", BMC Evol. Biol., 2008 Feb, 8(1), 69. PubMed Id: 18304338 [View at PubMed]

Worheide G. "A hypercalcified sponge with soft relatives: Vaceletia is a keratose demosponge.", Mol. Phylogenet. Evol., 2008 Feb, 47(1), 433-438. PubMed Id: 18321733 [View at PubMed]

Pirow R, Buchen I, Richter M, Allmer C, Nunes F, Guensel A, Heikens W, Lamkemeyer T, von Reumont BM, Hetz SK. "Cationic composition and acid-base state of the extracellular fluid, and specific buffer value of hemoglobin from the branchiopod crustacean Triops cancriformis.", J. Comp. Physiol. B, Biochem. Syst. Environ. Physiol., 2008 Dec PubMed Id: 19066911 [View at PubMed]

Witek A, Herlyn H, Meyer A, Boell L, Bucher G, Hankeln T. "EST based phylogenomics of Syndermata questions monophyly of Eurotatoria.", BMC Evol. Biol., 2008 Dec, 8(1), 345. PubMed Id: 19113997 [View at PubMed]

Struck TH, Nesnidal MP, Purschke G, Halanych KM. "Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa).", Mol. Phylogenet. Evol., 2008 Aug, 48(2), 628-45. PubMed Id: 18572419 [View at PubMed]

Helmkampf M, Bruchhaus I, Hausdorf B. "Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept.", Proc. Biol. Sci., 2008 Aug, 275(1645), 1927-33. PubMed Id: 18495619 [View at PubMed]

Struck TH, Fisse F. "Phylogenetic position of Nemertea derived from phylogenomic data.", Mol. Biol. Evol., 2008 Apr, 25(4), 728-36. PubMed Id: 18222945 [View at PubMed]

Baecker, H., Fanenbruck, M., Waegele, J.W. "A forgotten homology supporting the monophyly of Tracheata: the subcoxa of insects and myriapods", Zoologischer Anzeiger, 2008, 247, 185-207.

Rothe, B.H. and Schmidt-Rhaesa, A.. "Variation in the nervous system in three species of the genus Turbanella (Gastrotricha, Macrodasyida)", Meiofauna Marina, 2008, 16, 175-184.

Lanterbecq D, Bleidorn C, Michel S, Eeckhaut I. "Locomotion and fine structure of parapodia in Myzostoma cirriferum (Myzostomida)", Zoomorphology, 2008, 127(1), 59-68.

Fahrein K, Talarico G, Braband A, Podsiadlowski L. "The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida.", BMC Genomics, 2007 Oct, 8(1), 386. PubMed Id: 17961221 [View at PubMed]

Podsiadlowski L, Kohlhagen H, Koch M. "The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla.", Mol. Phylogenet. Evol., 2007 Oct, 45(1), 251-60. PubMed Id: 17764978 [View at PubMed]

Jackson, D.J., Macis, L., Reitner, J., Degnan, B.M., Worheide, G.. "Sponge Paleogenomics Reveals an Ancient Role for Carbonic Anhydrase in Skeletogenesis", Science, 2007 Jun, 316, 1893-1895. PubMed Id: 17540861 [View at PubMed]

Heuer CM, Loesel R. "Immunofluorescence analysis of the internal brain anatomy of Nereis diversicolor (Polychaeta, Annelida).", 2007 Dec PubMed Id: 18071754 [View at PubMed]

Roeding F, Hagner-Holler S, Ruhberg H, Ebersberger I, von Haeseler A, Kube M, Reinhardt R, Burmester T. "EST sequencing of Onychophora and phylogenomic analysis of Metazoa.", Mol. Phylogenet. Evol., 2007 Dec, 45(3), 942-51. PubMed Id: 17933557 [View at PubMed] [Suppl. Material]

Bleidorn C, Eeckhaut I, Podsiadlowski L, Schult N, McHugh D, Halanych KM, Milinkovitch MC, Tiedemann R. "Mitochondrial genome and nuclear sequence data support myzostomida as part of the annelid radiation.", Mol. Biol. Evol., 2007 Aug, 24(8), 1690-701. PubMed Id: 17483114 [View at PubMed]

Harzsch S, Mueller CH. "A new look at the ventral nerve centre of Sagitta: implications for the phylogenetic position of Chaetognatha (arrow worms) and the evolution of the bilaterian nervous system.", Front. Zool., 2007 , 4, 14. PubMed Id: 17511857 [View at PubMed] [Suppl. Material]

Waegele JW, Mayer C. "Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects.", BMC Evol. Biol., 2007 , 7, 147. PubMed Id: 17725833 [View at PubMed]

Struck TH, Schult N, Kusen T, Hickman E, Bleidorn C, McHugh D, Halanych KM. "Annelid phylogeny and the status of Sipuncula and Echiura.", BMC Evol. Biol., 2007 , 7, 57. PubMed Id: 17411434 [View at PubMed]

Struck TH. "Data congruence, paedomorphosis and salamanders.", Front. Zool., 2007 , 4, 22. PubMed Id: 17974010 [View at PubMed]

Halanych, KM, Cox, LN, Struck, TH. "A brief review of holopelagic annelids. ", Integrative and Comparative Biology , 2007, 47, 872-879.

Worheide, G., Erpenbeck, D.. "DNA taxonomy of sponges - progress and perspectives", Journal of the Marine Biological Society of the United Kingdom, 2007, 87, 1629-1633.

Erpenbeck, D., List-Armitage, S., Alvarez, B., Degnan, B.M., Worheide, G., Hooper, J.N.. "The systematics of Raspailiidae (Demospongiae: Poecilosclerida: Microcionina) re-analysed with a ribosomal marker", Journal of the Marine Biological Society of the United Kingdom, 2007, 87, 1571-1576.

Erpenbeck, D., Cleary, D.F.R., Voigt, O., Nichols, S.A., Degnan, B.M., Hooper, J.N.A., Worheide, G.. "Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA", Journal of the Marine Biological Society of the United Kingdom, 2007, 87, 1607-1614.

Erpenbeck, D., Worheide, G.. "On the molecular phylogeny of sponges (Porifera). In: Zhang, Z.-Q., and Shear, W.A. (Eds.), Linnaeus Tercentenary: Progress in Invertebrate Taxonomy", Zootaxa, 2007, 1668, 107-126.

Erpenbeck, D., Nichols, S.A., Voigt, O., Dohrmann, M., Hooper, J.N.A., Worheide, G. . "Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches - case studies with diploblast LSU", Journal of Molecular Evolution, 2007, 64, 543-557.

Purschke G, Arendt D, Hausen H, Mueller MC. "Photoreceptor cells and eyes in Annelida.", Arthropod structure & development, 2006 Dec, 35(4), 211-30. PubMed Id: 18089072 [View at PubMed]

Podsiadlowski L, Braband A. "The complete mitochondrial genome of the sea spider Nymphon gracile (Arthropoda: Pycnogonida).", BMC Genomics, 2006 , 7, 284. PubMed Id: 17087824 [View at PubMed]

Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelsson, Detlef Bernhard and Martin Schlegel. "The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis", Theory Biosci., 10 May 2007, 126(1), 35-42.

Wilkens V, Purschke G. "Central nervous system and sense organs with special reference to photoreceptor-like sensory elements in Polygordius appendiculatus (Annelida), an interstitial polychaete with uncertain phylogenetic affinities.", Inv. Biol., 2009 , 128, 46-64 .