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POLYPLACOPHORA Figure S1. Majority-Rule Consensus Tree From Dendrochiton gothicus 1 1 Dendrochiton flectens Mopalia muscosa 0,552 Amicula vestita 1 Cryptochiton stelleri Tonicella lokii 1 1 0,999T9onicella lineata Boreochiton beringensis 1 Katharina tunicata Placiphorella sp. A 1 Placiphorella velata 0,9976 “Lepidochitona” beanii 1 0,9997 Nuttallina californica 1 Schizoplax brandtii Cyanoplax cf. caverna 0,9851 Lepidochitona caprearum 1 Lepidochitona cinerea 0,7835 Acanthochitona avicula 0,7829 Choneplax lata 0,7836 Cryptoconchus floridianus 0,5797 Acanthochitona crinita 0,9993 0,7263 Hemiarthrum setulosum Cryptoplax iredalei 0,7836 0,9848 Cryptoplax japonica Nuttallochiton mirandus 0,9974 Plaxiphora albida 0,7836 Plaxiphora biramosa Lorica volvox 0,7212 1 0,8491 Tonicella forbesii 0,7607 Ischnochiton boninensis 0,6577 Chaetopleura apiculata POLYPLACOPHORA Callochiton bouveti 1 Nierstraszella lineata Hanleyella oldroydi Ilyanassa obsoleta 1 1 Bolinus brandaris Haliotis rubra 0.2 Figure S1. Majority-rule consensus tree from the Bayesian analysis of the multilocus amino acid data set. Numbers at nodes are support values from posterior probabilities. Scale bar is in substitutions per site. Dendrochiton gothicus 9 3 100 Dendrochiton flectens Mopalia muscosa 5 5 Amicula vestita 100 4 6 Cryptochiton stelleri Katharina tunicata 8 0 Tonicella lokii 100 Tonicella lineata 6 7 9 3 Boreochiton beringensis Placiphorella sp. A 9 8 Placiphorella velata 7 3 “Lepidochitona” beanii 100 7 1 Nuttallina californica 100 Schizoplax brandtii Cyanoplax cf. caverna 4 3 Lepidochitona caprearum 8 5 Lepidochitona cinerea 5 3 Cryptoconchus floridianus 7 1 9 0 Choneplax lata 9 4 Acanthochitona avicula 5 6 Acanthochitona crinita 6 2 5 8 Hemiarthrum setulosum Cryptoplax iredalei 9 1 7 8 Cryptoplax japonica Nuttallochiton mirandus 7 9 Plaxiphora biramosa 9 9 Plaxiphora albida Tonicella forbesii 4 8 Lorica volvox 9 9 4 9 5 6 Ischnochiton boninensis POLYPLACOPHORA 100 Chaetopleura apiculata Callochiton bouveti Hanleyella oldroydi 7 4 Nierstraszella lineata Ilyanassa obsoleta 100 100 Bolinus brandaris Haliotis rubra 6.0 Figure S2. Maximum likelihood tree from the multilocus nucleotide data set. Numbers at nodes are support values from bootstrap proportions. Scale bar is in substitutions per site. Dendrochiton gothicus 9 3 9 7 Dendrochiton flectens Mopalia muscosa 3 2 Cryptochiton stelleri 9 9 3 3 Amicula vestita Katharina tunicata 6 9 Tonicella lineata 100 Tonicella lokii 6 0 9 4 Boreochiton beringensis Placiphorella sp. A 5 6 9 8 Placiphorella velata Lepidochitona cinerea 9 7 5 9 Lepidochitona caprearum Nuttallina californica 100 “Lepidochitona” beanii 100 Schizoplax brandtii 5 9 Cyanoplax cf. caverna 3 4 Acanthochitona avicula 5 9 5 7 Choneplax lata 3 9 Acanthochitona crinita 3 1 Hemiarthrum setulosum 6 8 Cryptoplax iredalei 7 5 4 3 Cryptoplax japonica Nuttallochiton mirandus Cryptoconchus floridianus 5 7 7 9 5 7 Plaxiphora albida Plaxiphora biramosa Tonicella forbesii 5 4 100 5 3 Lorica volvox 6 4 Ischnochiton boninensis POLYPLACOPHORA 100 Chaetopleura apiculata Callochiton bouveti Nierstraszella lineata 6 9 Hanleyella oldroydi Ilyanassa obsoleta 100 100 Bolinus brandaris Haliotis rubra 0.08 Figure S3. Maximum likelihood tree from the multilocus amino acid data set. Numbers at nodes are support values from bootstrap proportions. Scale bar is in substitutions per site. Dendrochiton flectens 9 6 Dendrochiton gothicus 100 Mopalia muscosa 6 8 Cryptochiton stelleri 4 7 100 Amicula vestita Katharina tunicata 8 4 Tonicella lineata 100Tonicella lokii 7 3 9 2 Boreochiton beringensis Placiphorella sp. A 9 5 Placiphorella velata 6 0 “Lepidochitona” beanii 100 6 3 Nuttallina californica 100 Schizoplax brandtii Cyanoplax cf. caverna 4 1 Lepidochitona caprearum 7 8 Lepidochitona cinerea 7 8 Cryptoconchus floridianus 6 5 Choneplax lata 9 4 9 9 Acanthochitona avicula Acanthochitona crinita 5 7 4 4 Cryptoplax iredalei 7 7 Cryptoplax japonica 9 6 5 4 Hemiarthrum setulosum Nuttallochiton mirandus 6 3 Plaxiphora biramosa 100 Plaxiphora albida Tonicella forbesii 5 3 9 8 5 6 Lorica volvox 2 2 Chaetopleura apiculata POLYPLACOPHORA 8 0 Ischnochiton boninensis Callochiton bouveti Nierstraszella lineata 5 4 Hanleyella oldroydi Ilyanassa obsoleta 100 8 0 Bolinus brandaris Haliotis rubra 7.0 Figure S4. Maximum likelihood tree from the mitochondrial genes (16S, cox1, cob) of the multilocus nucleotide data set. Numbers at nodes are support values from bootstrap proportions. Scale bar is in substitutions per site. Dendrochiton flectens 9 5 9 4 Dendrochiton gothicus Mopalia muscosa 4 8 Cryptochiton stelleri 3 0 9 7 Amicula vestita Katharina tunicata 6 9 Tonicella lineata 100 Tonicella lokii 6 5 9 5 Boreochiton beringensis Placiphorella velata 5 5 9 8 Placiphorella sp. A Lepidochitona cinerea 9 7 5 3 Lepidochitona caprearum Schizoplax brandtii 6 6 Cyanoplax cf. caverna 9 8 Nuttallina californica 100 “Lepidochitona” beanii 4 6 Cryptoconchus floridianus 4 0 4 2 Acanthochitona avicula 5 3 Choneplax lata Acanthochitona crinita 3 6 Cryptoplax iredalei 4 3 5 4 Cryptoplax japonica 5 6 3 6 Hemiarthrum setulosum Nuttallochiton mirandus 7 1 Plaxiphora albida 6 1 Plaxiphora biramosa Lorica volvox 4 9 9 9 6 4 Tonicella forbesii 3 5 Chaetopleura apiculata 4 4 Ischnochiton boninensis POLYPLACOPHORA Callochiton bouveti 7 8 Nierstraszella lineata Hanleyella oldroydi Ilyanassa obsoleta 100 7 8 Bolinus brandaris Haliotis rubra 0.2 Figure S5. Maximum likelihood tree from the mitochondrial genes (16S, cox1, cob) of the multilocus amino acid data set. Numbers at nodes are support values from bootstrap proportions. Scale bar is in substitutions per site. Mopalia muscosa 6 6 Dendrochiton flectens 3 8 Cryptochiton stelleri 4 3 4 5 Katharina tunicata 9 0 Tonicella lineata Placiphorella velata 2 1 Callochiton bouveti 2 5 Hanleyella oldroydi Hemiarthrum setulosum 1 5 6 7 Acanthochitona crinita 2 4 Nierstraszella lineata 2 4 3 3 Plaxiphora albida 2 3 1 8 Cryptoplax japonica Nuttallochiton mirandus POLYPLACOPHORA 8 3 Ischnochiton boninensis 8 6 Lorica volvox Chaetopleura apiculata Ilyanassa obsoleta 100 Bolinus brandaris 8 3 Haliotis rubra 0.05 Figure S6. Maximum likelihood tree from the nuclear genes (18S, 28S) of the multilocus nucleotide data set. Numbers at nodes are support values from.bootstrap proportions Scale bar is in substitutions per site. Note on the Mopalia muscosa 18S sequence (GenBank Acc. No. AY377684) The partial 18S sequence used for Mopalia muscosa (from Okusu et al. 2003) was initially chosen because it covers the same gene region as in the remaining species used here. During the final stages of the review process, detailed phylogenetic analyses of separate cox1 and rrnL genes with expanded taxon sampling suggested that the cox1 and rrnL sequences for the same Mopalia muscosa specimen (voucher MCZ DNA100522) could be from the morphologically similar species Nuttallina fluxa. This raised our concern on the legitimacy of the 18S sequence obtained from the same voucher, but a taxon-dense analysis of available chiton 18S sequences could neither confirm nor reject the correct identity of this sequence. In any case, we repeated our analyses after removing this particular sequence and obtained identical results. Therefore, whether this sequence corresponds to Mopalia muscosa or to Nuttallina fluxa remains undetermined, but our results are robust to the inclusion of this potentially problematic sequence. Literature cited Okusu A, Schwabe E, Eernisse DJ, Giribet G. 2003. Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci. Org Divers Evol 3:281-302. .
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