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Monophyly of Brachiopods and Phoronids: Reconciliation of Molecular Evidence with Linnaean ClassiŽ Cation (The Subphylum Phoroniformea Nov.) Bernard L

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Monophyly of Brachiopods and Phoronids: Reconciliation of Molecular Evidence with Linnaean ClassiŽ Cation (The Subphylum Phoroniformea Nov.) Bernard L Cohen, B.L. and Stark, S. and Gawthrop, A.B. and Burke, M.E. and Thayer, C.W. (1998) Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa). Proceedings of the Royal Society B: Biological Sciences 265(1395):pp. 475-482. http://eprints.gla.ac.uk/archive/2917/ Glasgow ePrints Service http://eprints.gla.ac.uk Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classi cation (the subphylum Phoroniformea nov.) Bernard L. Cohen University of Glasgow, Institute of Biomedical and Life Sciences, Division of Molecular Genetics, Pontecorvo Building, Anderson College Complex, 56 Dumbarton Road, Glasgow G11 6NU, UK ([email protected]) Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, con¢rm previous indications that in such data, brachiopod and phoronids form a well- supported clade that (on previous evidence) is unambiguously a¤liated with protostomes rather than deuterostomes. Within the brachiopod ^phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inar- ticulates is weakly indicated. Brachiopod ^phoronid monophyly is reconciled with the most recent Linnaean classi¢cation of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell-less forms. Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true, undermines virtually all morphology-based recon- structions of phylogeny made during the past century or more. Keywords: Protostomozoa; Deuterostomozoa; Brachiopoda; Phoronida; 18S rDNA; DNA sequence the phoronid and an inarticulate brachiopod (Glottidia, 1. INTRODUCTION U12647). Like the seminal work in which 18S rDNA The Brachiopoda, Ectoprocta, Phoronida and Pterobran- sequences were ¢rst applied to metazoan molecular chia share a tentacular, ciliated, feeding organ, the lopho- phylogeny (Field et al. 1988), this study relied on a single phore and are sometimes referred to as `lophophorates’ sequence from each phylum. It also included sequence (Emig 1977, 1984, 1997; Hyman 1959). Long-standing errors (Conway Morris et al. 1996; Halanych et al. 1996). controversy over the place of these phyla among Metazoa Lacking the test of phylogenetic congruence provided by (Brusca & Brusca 1990; Eernisse et al. 1992; Nielsen 1995; multiple sequences from each higher taxon, these studies Nielsen et al. 1996; Schram 1991; Willmer 1990) has been ran the risk that some types of sequencing error might go clari¢ed by molecular sequence data, mainly from the undetected and indeed, when a wider sample of brachio- 18S rDNA gene. These data demonstrate that ptero- pod and phoronid sequences was obtained, it became branchs are most closely related to deuterostome hemi- apparent that U12648 from P. `vancouverensis’ did not chordates, but that the other three phyla have clear cluster well with the additional phoronid sequences, two of protostome a¤nities, and they have been assigned to a which had been congruently determined in independent supraphylum, clade-based, assemblage Lophotrochozoa, laboratories (Cohen & Gawthrop 1996, 1997; Mackey et al. along with molluscs and annelids, etc. (Aguinaldo et al. 1996). Moreover, the additional phoronid sequences clus- 1997; Cohen & Gawthrop 1996, 1997; de Rosa et al. 1999; tered preferentially with those of inarticulate, rather than Field et al. 1988; Halanych 1995; Halanych et al. 1995). articulate brachiopods. Thus, the spectre was raised that Protostome a¤nities have been con¢rmed by data from molecular data might indicate phoronids to be diphyletic hox and keratin genes (de Rosa et al. 1999; Erber et al. (Cohen & Gawthrop 1997). However, this ghost was laid 1998), and genetically independent evidence for the by analyses suggesting that U12648 might be a chimaeric protostome a¤nity of brachiopods has come from artefact, perhaps combining 5’-data chie£y from Terebra- analyses of mitochondrial rDNA sequences (Cohen et al. talia with 3’-data from the indicated phoronid (Cohen et al. 1998b) and the complete mitochondrial genome sequence 1998a). Molecular support for phoronid ^brachiopod of Terebratulina retusa (Stechmann & Schlegel 1999). monophyly was also obtained in analyses of 18S align- Molecular phylogenetic data on brachiopod ^phoronid ments that included large numbers of outgroup taxa and relationships developed erratically. The ¢rst report with from which the most variable sites had been removed 18S rDNA sequences from both phyla (Halanych et al. (Cohen & Gawthrop 1996, 1997; Zrzavy et al. 1998). Thus, 1995) presented a tree with 100% bootstrap support for a published 18S sequence analyses demonstrate monophyly sister-group relationship between phoronids (represented of brachiopods and phoronids, the closest relationship by Phoronis `vancouverensis’ GenBank accession U12648) being between phoronids and inarticulate brachiopods. and articulate brachiopods (represented by Terebratalia, This paper reports molecular phylogenetic analyses of U12650) and no support for a close relationship between an enhanced phoronid 18S rDNA data set, which includes Proc. R. Soc. Lond. B (2000) 267, 225^231 225 © 2000 The Royal Society Received 14 September 1999 Accepted 1 November 1999 226 B. L. Cohen Monophyly of brachiopods and phoronids Table 1. Classi¢cation, provenance and identi¢cation of specimens and sequences (Details are given only for previously unreported specimens which, unless otherwise stated, were identi¢ed by the collector (P. australis) or by A. Williams (University of Glasgow), C. H. C. Brunton or S. Long (Natural History Museum, London). The following sequences were retrieved from GenBank and relevant publications are cited in the text: Abyssothyris , AF025928; Eohemithiris , AF025936; Gryphus, AF025940; Megerlia, U08321; Neorhynchia , AF025937; Notosaria, U08335; Terebratulina , U08324; Discina, U08333; Discinisca, U08327; Glottidia pyrimidata; U12647; Lingula adamsi, U08329; Lingula anatina, U08331; Lingula `lingua’, X81631; Neocrania anomala, U08328; Neocrania huttoni, U08334; Phoronis `architecta’, U3627; P. hippocrepia, U08325; Acanthopleura , X70210, Cristatella , AF025947, Glycera, U19519; Pedicellina , U36273; Plumatella, U12649, Clathrina, U42452; P. psammophila, AF025946.) Glasgow GenBank collector genus or binomial accession accession (locality and depth where known) Magellania fragilis D1296 AF202110 T. Brey; 7384’ S, 281’ W Discinisca sp. D1330 AF202444 J. Laudien and C. Lu« ter; Intertidal, Swakopmund, Namibia Glottidia palmeri D1345 AF201744 M Kowalewski and K. Flessa; Baja, CA, USA Phoronis australis D1269 AF202111 B. R. de Forges; 10 m, 21830’ S, 1668 E Phoronis hippocrepia D1257 AF202112 C. C. Emig; Marseilles harbour Phoronis ijimai D1328 AF202113 see } 2 resequencing of P. `vancouverensis’ from newly collected product of the expected size (ca. 1.8 kb) was used to produce a material. This new sequence disagrees with U12648, but double-stranded sequencing template: after de-oiling and agrees at `signature’ sites and clusters closely with all deproteinizing with chloroform, DNA was ethanol-precipitated, other phoronid sequences. redissolved and gel-puri¢ed by electrophoresis (1.0% agarose, in Monophyly of brachiopods and phoronids bears on 1 Tris^borate^EDTA bu¡er, pH 8.3). After ethidium bromide £ interpretations of morphology and the reconciliation of post-staining, the template DNA fragment was recovered from a molecular and Linnaean systematics. The former casts gel slice using Qiagen (Crawley, UK) spin-columns from which doubt on much classical work and the latter leads us to it was eluted with bu¡ered water. Templates were sequenced on propose changes in classi¢cation: the phylum Phoronida both strands with three- to fourfold redundancy using selected is reduced to a subphylum within the Brachiopoda. If terminal and internal primers. Base calls were checked and further data con¢rm the suggestion that phoronids and edited manually using ABI software. Alignment and phylo- craniid inarticulates are monophyletic, it may be neces- genetic analyses were as previously described, except that sary to further reduce phoronids to the class grade and a PAUP*4b2 (Swo¡ord 1997) was used. New sequences have been potential class name is proposed. submitted to GenBank (Benson et al. 1998); accession numbers are given in table 1. 2. MATERIAL AND METHODS (c) Outgroup and ingroup selection (a) Specimens Since brachiopod ^phoronid monophyly had been previously P. `vancouverensis’ was collected by Sea Life Supply, Inc. (Sand found using di¡erent, large alignments (Cohen & Gawthrop City, CA, USA) from pilings of Monterey pier 2, opposite the 1996, 1997; Zrzavy et al. 1998), a smaller one was constructed for west end of Figueroa Street, about 800 ft (250 m) o¡shore and demonstration purposes. This contained
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