A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems

References

• Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Hasegawa M, Okada N. 2006. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol Phylogenet Evol. 38:648–658. doi:10.1016/j.ympev.2005.10.018
   PubMed Web of Science ®Google Scholar
• Aktipis SW, Giribet G. 2010. A phylogeny of Vetigastropoda and other “archaeogastropods”: re-organizing old gastropod clades. Invert Biol. 129:220–240. doi:10.1111/j.1744-7410.2010.00198.x
   Google Scholar
• Aktipis SW, Giribet G. 2012. Testing relationships among the vetigastropod taxa: a molecular approach. J Molluscan Stud. 78:12–27. doi:10.1093/mollus/eyr023
   Web of Science ®Google Scholar
• Aktipis SW, Giribet G, Lindberg DR, Ponder WF. 2008. Gastropoda: an overview and analysis. In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the mollusca. Berkeley: University of California Press; p. 201–237.
   Google Scholar
• Allcock AL, Cooke IR, Strugnell JM. 2011. What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda? Zool J Linnean Soc. 161:573–586. doi:10.1111/j.1096-3642.2010.00656.x
   Web of Science ®Google Scholar
• Ax P. 1999. Das System der Metazoa: ein Lehrbuch der phylogenetischen Systematik. Stuttgart: Fischer Verlag.
   Google Scholar
• Baeumler N, Haszprunar G, Ruthensteiner B. 2011. Development of the excretory system in the polyplacophoran mollusc, Lepidochitona corrugata: the protonephridium. J Morphol. 272:972–986. doi:10.1002/jmor.10964
   PubMed Web of Science ®Google Scholar
• Baeumler N, Haszprunar G, Ruthensteiner B. 2012. Development of the excretory system in a polyplacophoran mollusc: stages in metanephridial system development. Front Zool. 9:23. doi:10.1186/1742-9994-9-23
   PubMed Web of Science ®Google Scholar
• Bartolomaeus T. 1993. Die Leibeshöhlenverhältnisse und Verwandtschaftsbeziehungen der Spiralia. Verhandlungen der Deutschen Zoologischen Gesellschaft. 86:42.
   Google Scholar
• Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, et al. 2013. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol. 69:352–364. doi:10.1016/j.ympev.2013.05.002
   PubMed Web of Science ®Google Scholar
• Bernt M, Braband A, Middendorf M, Misof B, Rota-Stabelli O, Stadler PF. 2013. Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. Mol Phylogenet Evol. 69:320–327. doi:10.1016/j.ympev.2012.09.019
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendor M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319. doi:10.1016/j.ympev.2012.08.023
   PubMed Web of Science ®Google Scholar
• Bonnaud L, Ozouf-Costaz C, Boucher-Rodoni R. 2004. A molecular and karyological approach to the taxonomy of Nautilus. Comptes Rendus Biologies. 327:133–138. doi:10.1016/j.crvi.2003.12.004
   PubMed Web of Science ®Google Scholar
• Boore JL. 2006. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol. 21:439–446.
   PubMed Web of Science ®Google Scholar
• Boore JL, Brown WM. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev. 8:668–674. doi:10.1016/S0959-437X(98)80035-X
   PubMed Web of Science ®Google Scholar
• Boore JL, Medina M, Rosenberg LA. 2004. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol. 21:1492–1503. doi:10.1093/molbev/msh090
   PubMed Web of Science ®Google Scholar
• Brenzinger B, Haszprunar G, Schrödl M. 2013. At the limits of a successful body plan - 3D microanatomy, histology and evolution of Helminthope (Mollusca: Heterobranchia: Rhodopemorpha), the most worm-like gastropod. Front Zool. 10:37. doi:10.1186/1742-9994-10-37
   PubMed Web of Science ®Google Scholar
• Brenzinger B, Padula V, Schrödl M. 2013. Insemination by a kiss? Interactive 3D-microanatomy, biology and systematics of the mesopsammic cephalaspidean sea slug Pluscula cuica Marcus, 1953 from Brazil (Gastropoda: Euopisthobranchia: Philinoglossidae). Organisms Divers Evol. 13:33–54. doi:10.1007/s13127-012-0093-3
   Web of Science ®Google Scholar
• Caron J-B, Scheltema A, Schander C, Rudkin D. 2007. Reply to Butterfield on stem-group worms: fossil lophotrochozoans in the Burgess Shale. BioEssays. 29:200–202. doi:10.1002/bies.20527
   PubMed Web of Science ®Google Scholar
• Caron J-B, Scheltema AH, Schander C, Rudkin D. 2006. A soft-bodied mollusc with radula from the Middle Cambrian Burgess Shale. Nature. 442:159–163. doi:10.1038/nature04894
   PubMed Web of Science ®Google Scholar
• Castro LR, Colgan DJ. 2010. The phylogenetic position of Neritimorpha based on the mitochondrial genome of Nerita melanotragus (Mollusca: Gastropoda). Mol Phylogenet Evol. 57:918–923. doi:10.1016/j.ympev.2010.08.030
   PubMed Web of Science ®Google Scholar
• Chen J-Y, Bottjer DJ, Oliveri P, Dornbos SQ, Gao F, Ruffins S, Chi H, Li C-W, Davidson EH. 2004. Small bilaterian fossils from 40 to 55 million years before the Cambrian. Science. 305:218–222. doi:10.1126/science.1099213
   PubMed Web of Science ®Google Scholar
• Church SH, Ryan JF, Dunn CW. 2014. Automation and evaluation of the SOWH test of phylogenetic topologies with SOWHAT [Internet]. [cited 2014 Oct 2]. Available from: http://biorxiv.org. doi:10.1101/005264
   Google Scholar
• Colgan DJ, Ponder WF, Beacham E, Macaranas J. 2007. Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca). Mol Phylogenet Evol. 42:717–737. doi:10.1016/j.ympev.2006.10.009
   PubMed Web of Science ®Google Scholar
• Conway Morris S, Caron J-B. 2007. Halwaxiids and the early evolution of the lophotrochozoans. Science. 315:1255–1258. doi:10.1126/science.1137187
   PubMed Web of Science ®Google Scholar
• de Vienne DM, Ollier S, Aguileta G. 2012. Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol Biol Evol. 29:1587–1598. doi:10.1093/molbev/msr317
   PubMed Web of Science ®Google Scholar
• Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. TREE. 24:332–340.
   PubMed Web of Science ®Google Scholar
• Doucet-Beaupré H, Breton S, Chapman EG, Blier PU, Bogan AE, Stewart DT, Hoeh WR. 2010. Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA. BMC Evol Biol. 10:50. doi:10.1186/1471-2148-10-50
   PubMed Web of Science ®Google Scholar
• Dreyer H, Steiner G. 2004. The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonodentalium lobatum (Mollusca. Mol Biol Evol. 31:605–617.
   Web of Science ®Google Scholar
• Dreyer H, Steiner G. 2006. The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica–and the first record for a putative ATPase subunit 8 gene in marine bivalves. Front Zool. 3:13. doi:10.1186/1742-9994-3-13
   PubMedGoogle Scholar
• Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745–749. doi:10.1038/nature06614
   PubMed Web of Science ®Google Scholar
• Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. 2011. Higher-level metazoan relationships: recent progress and remaining questions. Organisms Divers Evol. 11:151–172. doi:10.1007/s13127-011-0044-4
   Web of Science ®Google Scholar
• Fallén, CF. 1823. Diptera sveciae. Geomyzides. Berlin. 8 pp.
   Google Scholar
• Gaitán-Espitia JD, Nespolo RF, Opazo JC. 2013. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca): intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura. PloS one. 8:e67299. doi:10.1371/journal.pone.0067299
   PubMed Web of Science ®Google Scholar
• Giribet G. 2008. Bivalvia. In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the mollusca. Berkeley: University of California Press; p. 105–141.
   Google Scholar
• Giribet G, Okusu A, Lindgren AR, Huff SW, Schrodl M, Nishiguchi ML. 2006. Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. Proc Natl Acad Sci. 103:7723–7728. doi:10.1073/pnas.0602578103
   PubMed Web of Science ®Google Scholar
• Grande C, Templado J, Zardoya R. 2008. Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol. 8:61. doi:10.1186/1471-2148-8-61
   PubMed Web of Science ®Google Scholar
• Guralnick R, Smith K. 1999. Historical and biomechanical analysis of integration and dissociation in molluscan feeding, with special emphasis on the true limpets (Patellogastropoda: Gastropoda). J Morphol. 241:175–195. doi:10.1002/(SICI)1097-4687(199908)241:2<175::AID-JMOR7>3.0.CO;2-0
   PubMed Web of Science ®Google Scholar
• Haas W. 1981. Evolution of calcareous hard parts in primitive molluscs. Malacologia. 21:403–418.
   Web of Science ®Google Scholar
• Haeckel EHPA. 1866. Generelle Morphologie der Organismen: allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie. Vol. 2. Berlin: Reimer.
   Google Scholar
• Hallinan NM, Lindberg DR. 2011. Comparative analysis of chromosome counts infers three paleopolyploidies in the Mollusca. Genome Biol Evol. 3:1150–1163. doi:10.1093/gbe/evr087
   PubMed Web of Science ®Google Scholar
• Haszprunar G. 2000. Is the Aplacophora monophyletic? A cladistic point of view. Am Mal Bull. 15:115–130.
   Web of Science ®Google Scholar
• Haszprunar G. 2008. Monoplacophora (Tryblidia). In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the Mollusca. Berkeley: University of California Press; p. 97–104.
   Google Scholar
• Haszprunar G, Ruthensteiner B. 2013. Monoplacophora (Tryblidia) – some unanswered questions. Am Malacological Bull. 31:189–194. doi:10.4003/006.031.0111
   Web of Science ®Google Scholar
• Haszprunar G, Schander C, Halanych KM. 2008. Relationships of higher molluscan taxa. In: Ponder WF, Lindberg DR, editors. Phylogeny and Evolution of the Mollusca. Berkeley: University of California Press; p. 19–32.
   Google Scholar
• Haszprunar G, Wanninger A. 2012. Molluscs. Curr Bio. 22:R510–R514. doi:10.1016/j.cub.2012.05.039
   PubMed Web of Science ®Google Scholar
• Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Roy Soc B. 276:4261–4270.
   PubMed Web of Science ®Google Scholar
• Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254–267. doi:10.1093/molbev/msj030
   PubMed Web of Science ®Google Scholar
• Ivantsov AY. 2009. New reconstruction of Kimberella, problematic Vendian Metazoan. Paleontological J. 43:601–611. doi:10.1134/S003103010906001X
   Web of Science ®Google Scholar
• Ivantsov AY. 2010. Paleontological evidence for the supposed Precambrian occurrence of mollusks. Paleontological J. 44:1552–1559. doi:10.1134/S0031030110120105
   Web of Science ®Google Scholar
• Jackson DJ, McDougall C, Woodcroft B, Moase P, Rose RA, Kube M, Reinhardt R, Rokhsar DS, Montagnani C, Joubert C, et al. 2010. Parallel evolution of nacre building gene sets in molluscs. Mol Biol Evol. 27:591–608. doi:10.1093/molbev/msp278
   PubMed Web of Science ®Google Scholar
• Jenner RA. 2004a. The scientific status of metazoan cladistics: why current research practice must change. Zool Scr. 33:293–310. doi:10.1111/j.0300-3256.2004.00153.x
   Web of Science ®Google Scholar
• Jenner RA. 2004b. When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss. Evol Dev. 6:372–378. doi:10.1111/j.1525-142X.2004.04045.x
   PubMed Web of Science ®Google Scholar
• Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 4:18. doi:10.1186/1471-2148-4-18
   PubMed Web of Science ®Google Scholar
• Jörger KM, Neusser TP, Brenzinger B, Schrödl M. 2014. Exploring the diversity of Mesopsammic Gastropods: how to collect, identify, and delimitate small and elusive Sea Slugs? Am Malacol Bull. 32:290–307.
   Web of Science ®Google Scholar
• Jörger KM, Norenburg JL, Wilson NG, Schrödl M. 2012. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs. BMC Evol Biol. 12:245.
   PubMed Web of Science ®Google Scholar
• Jörger KM, Stöger I, Kano Y, Fukuda H, Knebelsberger T, Schrödl M. 2010. On the origin of Acochlidia and other enigmatic euthyneuran gastropods, with implications for the systematics of Heterobranchia. BMC Evol Biol. 10:323. doi:10.1186/1471-2148-10-323
   PubMed Web of Science ®Google Scholar
• Kano Y, Kimura S, Kimura T, Warén A. 2012. Living Monoplacophora: morphological conservatism or recent diversification? Zool Scr. 41:471–488. doi:10.1111/j.1463-6409.2012.00550.x
   Web of Science ®Google Scholar
• Klussmann-Kolb A, Dinapoli A, Kuhn K, Streit B, Albrecht C. 2008. From sea to land and beyond – New insights into the evolution of euthyneuran Gastropoda (Mollusca). BMC Evol Biol. 8:57. doi:10.1186/1471-2148-8-57
   PubMed Web of Science ®Google Scholar
• Kocot KM. 2013. Recent advances and unanswered questions in deep molluscan phylogenetics. Am Malacological Bull. 31:195–208. doi:10.4003/006.031.0112
   Web of Science ®Google Scholar
• Kocot KM, Cannon JT, Todt C, Citarella MR, Kohn AB, Meyer A, Santos SR, Schander C, Moroz LL, Lieb B, et al. 2011. Phylogenomics reveals deep molluscan relationships. Nature. 477:452–456. doi:10.1038/nature10382
   PubMed Web of Science ®Google Scholar
• Kocot KM, Citarella MR, Moroz LL, Halanych KM. 2013. PhyloTreePruner: a phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evol Bioinform Online. 9:429.
   Web of Science ®Google Scholar
• Kocot KM, Halanych KM, Krug PJ. 2013. Phylogenomics supports Panpulmonata: Opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs. Mol Phylogenet Evol. 69:764–771. doi:10.1016/j.ympev.2013.07.001
   PubMed Web of Science ®Google Scholar
• Kröger B, Vinther J, Fuchs D. 2011. Cephalopod origin and evolution: a congruent picture emerging from fossils, development and molecules. Bioessays. 33:602–613. doi:10.1002/bies.201100001
   PubMed Web of Science ®Google Scholar
• Kück P, Mayer C, Wägele J-W, Misof B. 2012. Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS One. 7:e36593. doi:10.1371/journal.pone.0036593
   PubMed Web of Science ®Google Scholar
• Lartillot N, Philippe H. 2008. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Phil Trans Roy Soc B. 363:1463–1472.
   PubMed Web of Science ®Google Scholar
• Leigh JW, Schliep K, Lopez P, Bapteste E. 2011. Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol. 28:2773–2785. doi:10.1093/molbev/msr110
   PubMed Web of Science ®Google Scholar
• Lemmon AR, Emme SA, Moriarity Lemmon E. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61:727–744. doi:10.1093/sysbio/sys049
   PubMed Web of Science ®Google Scholar
• Lieb B, Todt C. 2008. Hemocyanin in mollusks – A molecular survey and new data on hemocyanin genes in Solenogastres and Caudofoveata. Mol Phylogenet Evol. 49:382–385. doi:10.1016/j.ympev.2008.06.005
   PubMed Web of Science ®Google Scholar
• Lindberg DR. 1988. Heterochrony in gastropods: A neontological view. In: McKinney ML, editors. Heterochrony in evolution. New York: Springer; p. 197–216.
   Google Scholar
• Lindberg DR. 2008. Patellogastropoda, Neritimorpha and Cocculinoidea: the low-diversity gastropod clades. In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the Mollusca. Berkeley: University of California Press; p. 271–296.
   Google Scholar
• Lindberg DR. 2009. Monoplacophorans and the origin and relationships of mollusks. Evol Educ Outreach. 2:191–203. doi:10.1007/s12052-009-0125-4
   Google Scholar
• Lindberg DR, Ponder WF. 1996. An evolutionary tree for the Mollusca: branches or roots? In: Taylor J, editor. Origin and evolutionary radiation of the Mollusca. Oxford: Oxford University Press; p. 67–75.
   Google Scholar
• Lindgren AR, Giribet G, Nishiguchi MK. 2004. A combined approach to the phylogeny of Cephalopoda (Mollusca). Cladistics. 20:454–486. doi:10.1111/j.1096-0031.2004.00032.x
   PubMed Web of Science ®Google Scholar
• López-Giráldez F, Townsend JP. 2011. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol Biol. 11:152. doi:10.1186/1471-2148-11-152
   PubMed Web of Science ®Google Scholar
• Maddison WP, Knowles LL. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst Biol. 55:21–30. doi:10.1080/10635150500354928
   PubMed Web of Science ®Google Scholar
• Maddison WP, Maddison DR. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75 [Internet]. [cited 2014 Oct 2]. Available from: http://mesquiteproject.org
   Google Scholar
• Mallat J, Craig CW, Yoder MJ. 2012. Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol. 64:603–617. doi:10.1016/j.ympev.2012.05.016
   PubMed Web of Science ®Google Scholar
• Mallatt J, Craig CW, Yoder MJ. 2010. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol. 55:1–7. doi:10.1016/j.ympev.2009.09.028
   PubMed Web of Science ®Google Scholar
• Martynov A, Brenzinger B, Hooker Y, Schrodl M. 2011. 3D-anatomy of a new tropical Peruvian nudibranch gastropod species, Corambe mancorensis, and novel hypotheses on dorid gill ontogeny and evolution. J Molluscan Stud. 77:129–141. doi:10.1093/mollus/eyq047
   Web of Science ®Google Scholar
• Martynov A, Schrödl M. 2011. Phylogeny and evolution of corambid nudibranchs (Mollusca: Gastropoda). Zool J Linnean Soc. 163:585–604. doi:10.1111/j.1096-3642.2011.00720.x
   Web of Science ®Google Scholar
• Matz MV, Frank TM, Marshall NJ, Widder EA, Johnsen S. 2008. Giant deep-sea protist produces bilaterian-like traces. Curr Biol. 18:1849–1854. doi:10.1016/j.cub.2008.10.028
   PubMed Web of Science ®Google Scholar
• Medina M, Lal S, Vallès Y, Takaoka TL, Dayrat BA, Boore JL, Gosliner T. 2011. Crawling through time: transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics. Marine Genomics. 4:51–59. doi:10.1016/j.margen.2010.12.006
   PubMed Web of Science ®Google Scholar
• Meyer A, Todt C, Mikkelsen NT, Lieb B. 2010. Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity. BMC Evol Biol. 10:70. doi:10.1186/1471-2148-10-70
   PubMed Web of Science ®Google Scholar
• Meyer A, Witek A, Lieb B. 2011. Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca? Methods Ecol Evol. 2:34–42. doi:10.1111/j.2041-210X.2010.00052.x
   Web of Science ®Google Scholar
• Misof B, Meusemann K, von Reumont BM, Kück P, Prohaska SJ, Stadler PF. 2014. A priori assessment of data quality in molecular phylogenetics. Algorithms Mol Biol. 9:22.
   Web of Science ®Google Scholar
• Monterosato TMA. 1872. Notisie intorno alle conchiglie fossili di Monte Pellegrino e Ficarazzi. Palermo: M. Amenta. pp. 1–44.
   Google Scholar
• Nielsen C, Haszprunar G, Ruthensteiner B, Wanninger A. 2007. Early development of the aplacophoran mollusc Chaetoderma. Acta Zool. 88:231–247. doi:10.1111/j.1463-6395.2007.00270.x
   Web of Science ®Google Scholar
• Nosenko T, Schreiber F, Adamska M, Adamski M, Eitel M, Hammel J, Maldonado M, Müller WE, Schierwater B, Vacelet J, et al. 2013. Deep metazoan phylogeny: when different genes tell different stories. Mol Phylogenet Evol. 67:223–233. doi:10.1016/j.ympev.2013.01.010
   PubMed Web of Science ®Google Scholar
• Otto SP. 2007. The evolutionary consequences of polyploidy. Cell. 131:452–462. doi:10.1016/j.cell.2007.10.022
   PubMed Web of Science ®Google Scholar
• Parkhaev PY. 2008. The early molluscan radiation. In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the Mollusca. Berkeley: University of California Press; p. 33–69.
   Google Scholar
• Passamaneck YJ, Schander C, Halanych KM. 2004. Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences. Mol Phylogenet Evol. 32:25–38. doi:10.1016/j.ympev.2003.12.016
   PubMed Web of Science ®Google Scholar
• Pecoits E, Konhauser KO, Aubet NR, Heaman LM, Veroslavsky G, Stern RA, Gingras MK. 2012. Bilaterian Burrows and Grazing Behavior at >585 Million Years Ago. Science. 336:1693–1696. doi:10.1126/science.1216295
   PubMed Web of Science ®Google Scholar
• Peterson KJ, Cotton JA, Gehling JG, Pisani D. 2008. The Ediacaran emergence of bilaterians: congruence between the genetic and geologic fossil records. Phil Trans Roy Soc London. 363:1435–1443.
   PubMed Web of Science ®Google Scholar
• Peterson KJ, Dietrich MR, McPeek MA. 2009. MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. Bioessays. 31:736–747. doi:10.1002/bies.200900033
   PubMed Web of Science ®Google Scholar
• Peterson KJ, Summons RE, Donoghue PCJ. 2007. Molecular palaeobiology. Palaeontology. 50:775–809. doi:10.1111/j.1475-4983.2007.00692.x
   Web of Science ®Google Scholar
• Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
   PubMed Web of Science ®Google Scholar
• Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, Wrede P, Wiens M, Alié A, Morgenstern B, Manuel M, et al. 2010. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol. 27:1983–1987. doi:10.1093/molbev/msq089
   PubMed Web of Science ®Google Scholar
• Plazzi F, Ribani A, Passamonti M. 2013. The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera. BMC Genomics. 14:409.
   PubMed Web of Science ®Google Scholar
• Ponder W, Lindberg DR. 1997. Towards a phylogeny of gastropod molluscs: an analysis using morphological characters. Zool J Linnean Soc. 119:83–265. doi:10.1111/j.1096-3642.1997.tb00137.x
   Web of Science ®Google Scholar
• Poulsen C. 1967. Fossils from the Lower Cambrian of Bornholm. Danske Videnskabernes Selskab, Matematisk-Fysiske Meddelelser. 36:1–48.
   Google Scholar
• Roure B, Baurain D, Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 30:197–214.
   PubMed Web of Science ®Google Scholar
• Runnegar B, Pojeta J. 1974. Molluscan phylogeny: the paleontological viewpoint. Science. 186:311–317. doi:10.1126/science.186.4161.311
   PubMed Web of Science ®Google Scholar
• Ruthensteiner B, Baeumler N, Barnes DG. 2010. Interactive 3D volume rendering in biomedical publications. Micron. 41:886.e1–886.e17. doi:10.1016/j.micron.2010.03.010
   PubMed Web of Science ®Google Scholar
• Salvini-Plawen L. 1980. A reconsideration of systematics in the Mollusca (phylogeny and higher classification). Malacologia. 19:249–278.
   Web of Science ®Google Scholar
• Salvini-Plawen L. 1990. Origin, phylogeny and classification of the phylum Mollusca. Iberus. 9:1–33.
   Google Scholar
• Salvini-Plawen L. 2006. The significance of the Placophora for molluscan phylogeny. Venus. 65:1–17.
   Google Scholar
• Salvini-Plawen L, Steiner G. 1996. Synapomorphies and plesiomorphies in higher classification of Mollusca. In: Taylor J, editor. Origin and evolutionary radiation of the Mollusca. Oxford: Oxford University Press; p. 29–51.
   Google Scholar
• Sars M. 1859. Om Siphonodentalium vitreum, en ny Slaegt og Art af Dentalidernes Familie. Christiania: Brøgger & Christie. 23 pp.
   Google Scholar
• Scheltema AH. 1993. Aplacophora as Progenetic Aculiferans and the Coelomate Origin of Mollusks as the Sister Taxon of Sipuncula. Biol Bull. 184:57–78. doi:10.2307/1542380
   PubMed Web of Science ®Google Scholar
• Scheltema AH, Kerth K, Kuzirian AM. 2003. Original molluscan radula: comparisons among Aplacophora, Polyplacophora, Gastropoda, and the Cambrian fossil Wiwaxia corrugata. J Morphol. 257:219–245. doi:10.1002/jmor.10121
   PubMed Web of Science ®Google Scholar
• Scherholz M, Redl E, Wollesen T, Todt C, Wanninger A. 2013. Aplacophoran mollusks evolved from ancestors with polyplacophoran-like features. Curr Biol. 23:2130–2134. doi:10.1016/j.cub.2013.08.056
   PubMed Web of Science ®Google Scholar
• Schrödl M, Jörger K, Klussmann-Kolb A, Wilson NG. 2011. Bye bye “Opisthobranchia”! A review on the contribution of mesopsammic sea slugs to euthyneuran systematics. Thalassas. 27:101–112.
   Web of Science ®Google Scholar
• Schrödl M, Jörger K, Wilson NG. 2011. A reply to Medina et al. (2011): crawling through time: transition of snails to slugs dating back to the Paleozoic based on mitochondrial phylogenomics. Marine Genomics. 4:301–303.
   PubMed Web of Science ®Google Scholar
• Schrödl M, Linse K, Schwabe E. 2006. Review on the distribution and biology of Antarctic Monoplacophora, with first abyssal record of Laevipilina antarctica. Polar Biol. 29:721–727. doi:10.1007/s00300-006-0132-7
   Web of Science ®Google Scholar
• Schrödl M, Neusser TP. 2010. Towards a phylogeny and evolution of Acochlidia (Mollusca: Gastropoda: Opisthobranchia). Zool J Linnean Soc. 158:124–154. doi:10.1111/j.1096-3642.2009.00544.x
   Web of Science ®Google Scholar
• Seilacher A, Bose PK, Pflüger F. 1998. Triploblastic animals more than 1 billion years ago: trace fossil evidence from India. Science. 282:80–83. doi:10.1126/science.282.5386.80
   PubMed Web of Science ®Google Scholar
• Sharma PP, González VL, Kawauchi GY, Andrade SCS, Guzmán A, Collins TM, Glover EA, Harper EM, Healy JM, Mikkelsen PM, et al. 2012. Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca). Mol Phylogenet Evol. 65:64–74. doi:10.1016/j.ympev.2012.05.025
   PubMed Web of Science ®Google Scholar
• Shigeno S, Sasaki T, Haszprunar G. 2007. Central nervous system of Chaetoderma japonicum (Caudofoveata, Aplacophora): implications for diversified ganglionic plans in early molluscan evolution. Biol Bull. 213:122–134. doi:10.2307/25066628
   PubMed Web of Science ®Google Scholar
• Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492–508. doi:10.1080/10635150290069913
   PubMed Web of Science ®Google Scholar
• Sigwart JD, Schwabe E, Saito H, Samadi S, Giribet G. 2011. Evolution in the deep sea: a combined analysis of the earliest diverging living chitons (Mollusca: Polyplacophora: Lepidopleurida). Invert Syst. 24:560–572.
   Web of Science ®Google Scholar
• Sigwart JD, Stöger I, Knebelsberger T, Schwabe E. 2013. Chiton phylogeny (Mollusca: Polyplacophora) and the placement of the enigmatic species Choriplax grayi (H. Adams & Angas). Invert Syst. 27:603–621.
   Web of Science ®Google Scholar
• Sigwart JD, Sumner-Rooney LH, Schwabe E, Hess M, Brennan G, Schrödl M. 2014. A new sensory organ in “primitive” molluscs (Polyplacophora: Lepidopleurida), and its context in the nervous system of chitons. Front Zool. 11:7. doi:10.1186/1742-9994-11-7
   PubMed Web of Science ®Google Scholar
• Sigwart JD, Sutton MD. 2007. Deep molluscan phylogeny: synthesis of palaeontological and neontological data. Proc Roy Soc B. 274:2413–2419.
   PubMed Web of Science ®Google Scholar
• Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo D-H, Larsson T, Lv J, Arendt D, et al. 2012. Insights into bilaterian evolution from three spiralian genomes. Nature. 493:526–531. doi:10.1038/nature11696
   PubMed Web of Science ®Google Scholar
• Simison WB, Boore JL. 2008. Molluscan evolutionary genomics. In: Ponder WF, Lindberg DR, editors. Phylogeny and evolution of the Mollusca. Berkeley: University of California Press; p. 447–461.
   Google Scholar
• Simmons MP. 2012. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol Phylogenet Evol. 62:472–484. doi:10.1016/j.ympev.2011.10.017
   PubMed Web of Science ®Google Scholar
• Simone LRL. 2009. Comparative morphology among representatives of main taxa of Scaphopoda and basal protobranch Bivalvia (Mollusca). Papeis Avulsos Zoología. 49:405–457.
   Google Scholar
• Smith MR. 2012. Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula. Proc Roy Soc B. 279:4287–4295.
   PubMed Web of Science ®Google Scholar
• Smith MR, Caron J-B. 2010. Primitive soft-bodied cephalopods from the Cambrian. Nature. 465:469–472. doi:10.1038/nature09068
   PubMed Web of Science ®Google Scholar
• Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 480:364–367. doi:10.1038/nature10526
   PubMed Web of Science ®Google Scholar
• Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. 2013. Corrigendum: resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 493:708–708. doi:10.1038/nature11736
   Web of Science ®Google Scholar
• Sperling EA, Peterson KJ, Pisani D. 2009. Phylogenetic signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol. 26:2261–2274. doi:10.1093/molbev/msp148
   PubMed Web of Science ®Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinform. 22:2688–2690. doi:10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• Steiner G. 1998. Point of View Phylogeny of Scaphopoda (Mollusca) in the light of new anatomical data on the Gadilinidae and some Problematica, and a reply to Reynolds. Zool Scr. 27:73–82. doi:10.1111/j.1463-6409.1998.tb00429.x
   Web of Science ®Google Scholar
• Steiner G. 1999. A new genus and species of the family Anulidentaliidae (Scaphopoda: Dentaliida) and its systematic implications. J Molluscan Stud. 65:151–161. doi:10.1093/mollus/65.2.151
   Web of Science ®Google Scholar
• Steiner G, Dreyer H. 2003. Molecular phylogeny of Scaphopoda (Mollusca) inferred from 18S rDNA sequences: support for a Scaphopoda–Cephalopoda clade. Zool Scr. 32:343–356. doi:10.1046/j.1463-6409.2003.00121.x
   Web of Science ®Google Scholar
• Stöger I, Schrödl M. 2013. Mitogenomics does not resolve deep molluscan relationships (yet?). Mol Phylogenet Evol. 69:376–392. doi:10.1016/j.ympev.2012.11.017
   PubMed Web of Science ®Google Scholar
• Stöger I, Sigwart JD, Kano Y, Knebelsberger T, Marshall BA, Schwabe E, Schrödl M. 2013. An integrative approach supports a new perspective on early molluscan evolution. BioMed Res Int. 2013:1–18.
   Web of Science ®Google Scholar
• Struck TH. 2014. TreSpEx—Detection of misleading signal in phylogenetic reconstructions based on tree information. Evol Bioinform Online. 10:51.
   PubMed Web of Science ®Google Scholar
• Struck TH, Fisse F. 2008. Phylogenetic position of Nemertea derived from phylogenomic data. Mol Biol Evol. 25:728–736. doi:10.1093/molbev/msn019
   PubMed Web of Science ®Google Scholar
• Struck TH, Wey-Fabrizius AR, Golombek A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, et al. 2014. Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of Spiralia. Mol Biol Evol. 31:1833–1849.
   PubMed Web of Science ®Google Scholar
• Sutton MD, Briggs DE, Siveter DJ, Siveter DJ, Sigwart JD. 2012. A Silurian armoured aplacophoran and implications for molluscan phylogeny. Nature. 490:94–97. doi:10.1038/nature11328
   PubMed Web of Science ®Google Scholar
• Sutton MD, Sigwart JD. 2012. A chiton without a foot. Palaeontology. 55:401–411. doi:10.1111/j.1475-4983.2011.01126.x
   Web of Science ®Google Scholar
• Telford MJ, Budd GE. 2011. Invertebrate evolution: bringing order to the molluscan chaos. Curr Biol. 21:964–966. doi:10.1016/j.cub.2011.10.029
   Web of Science ®Google Scholar
• Vinther J. 2009. The canal system in sclerites of Lower Cambrian Sinosachites (Halkieriidae: Sachitida): significance for the molluscan affinities of the sachitids. Palaeontology. 52:689–712. doi:10.1111/j.1475-4983.2009.00881.x
   Web of Science ®Google Scholar
• Vinther J, Sperling EA, Briggs DEG, Peterson KJ. 2012. A molecular palaeobiological hypothesis for the origin of aplacophoran molluscs and their derivation from chiton-like ancestors. Proc Roy Soc B. 279:1259–1268.
   PubMed Web of Science ®Google Scholar
• von Reumont BM, Jenner RA, Wills MA, Dell’Ampio E, Pass G, Ebersberger I, Meyer B, Koenemann S, Iliffe TM, Stamatakis A, et al. 2012. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol. 29:1031–1045. doi:10.1093/molbev/msr270
   PubMed Web of Science ®Google Scholar
• Wägele H, Klussmann-Kolb A. 2005. Opisthobranchia (Mollusca, Gastropoda) – more than just slimy slugs. Shell reduction and its implications on defence and foraging. Front Zool. 2:3–18. doi:10.1186/1742-9994-2-3
   PubMedGoogle Scholar
• Wägele JW, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H. 2009. Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny). Front Zool. 6:12. doi:10.1186/1742-9994-6-12
   PubMed Web of Science ®Google Scholar
• Wägele JW, Mayer C. 2007. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol. 7:147. doi:10.1186/1471-2148-7-147
   PubMed Web of Science ®Google Scholar
• Walcott CD. 1911. Cambrian geology and paleontology. Middle Cambrian annelids. Smithsonian Misc Coll. 57:109–144.
   Google Scholar
• Waller TR. 1998. Origin of the molluscan class Bivalvia and a phylogeny of major groups. In: Johnston PA, Haggard JW, editors. Bivalves: an eon of evolution. Calgary: University of Calgary Press; p. 1–45.
   Google Scholar
• Wanninger A. 2009. Shaping the things to come: ontogeny of lophotrochozoan neuromuscular systems and the Tetraneuralia concept. Biol Bull. 216:293–306.
   PubMed Web of Science ®Google Scholar
• Wanninger A, Haszprunar G. 2001. The expression of an engrailed protein during embryonic shell formation of the tusk-shell, Antalis entalis (Mollusca, Scaphopoda). Evol Dev. 3:312–321. doi:10.1046/j.1525-142X.2001.01034.x
   PubMed Web of Science ®Google Scholar
• Westheide W, Rieger R. 1996. Spezielle Zoologie, Teil 1: Einzeller und wirbellose Tiere. Jena: Gustav Fischer Verlag.
   Google Scholar
• White T, Conrad M, Tseng R, Balayan S, Golding R, de Frias Martins A, Dayrat B. 2011. Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evol Biol. 11:295. doi:10.1186/1471-2148-11-295
   PubMed Web of Science ®Google Scholar
• Williams ST, Foster PG, Littlewood DTJ. 2014. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene. 533:38–47.doi:10.1016/j.gene.2013.10.005
   PubMed Web of Science ®Google Scholar
• Wilson NG, Rouse G, Giribet G. 2010. Assessing the molluscan hypothesis Serialia (Monoplacophora + Polyplacophora) using novel molecular data. Mol Phylogenet Evol. 54:187–193. doi:10.1016/j.ympev.2009.07.028
   PubMed Web of Science ®Google Scholar
• Wingstrand KG. 1985. On the anatomy and relationships of recent Monoplacophora. Galathea Rep. 16:7–94.
   Google Scholar
• Yokobori S-I, Iseto T, Asakawa S, Sasaki T, Shimizu N, Yamagishi A, Oshima T, Hirose E. 2008. Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny. Mol Phylogenet Evol. 47:612–628. doi:10.1016/j.ympev.2008.02.013
   PubMed Web of Science ®Google Scholar
• Yu W. 1984a. Early Cambrian molluscan faunas of Meishucun Stage with special reference to Precambrian-Cambrian boundary. In: Academia sinica, editor. Developments in geoscience, contribution to 27th international geological congress, Moscow. Beijing: Science Press; p. 21–35.
   Google Scholar
• Yu W. 1984b. On merismoconchids. Acta Palaeontologica Sin. 23:432–446. In Chinese with English summary.
   Google Scholar
• Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW. 2014. Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc R Soc Biol Sci. 281: 20141739. doi:10.1098/rspb.2014.1739
   PubMed Web of Science ®Google Scholar
• Zhang Z, Holmer LE, Skovsted CB, Brock GA, Budd GE, Fu D, Zhang X, Shu D, Han J, Liu J, et al. 2013. A sclerite-bearing stem group entoproct from the early Cambrian and its implications. Sci Rep. 3:1066. doi:10.1038/srep01066
   PubMed Web of Science ®Google Scholar