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Multi-Gene Analyses of the Phylogenetic Relationships Among the Mollusca, Annelida, and Arthropoda Donald J

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Multi-Gene Analyses of the Phylogenetic Relationships Among the Mollusca, Annelida, and Arthropoda Donald J Zoological Studies 47(3): 338-351 (2008) Multi-Gene Analyses of the Phylogenetic Relationships among the Mollusca, Annelida, and Arthropoda Donald J. Colgan1,*, Patricia A. Hutchings2, and Emma Beacham1 1Evolutionary Biology Unit, The Australian Museum, 6 College St. Sydney, NSW 2010, Australia 2Marine Invertebrates, The Australian Museum, 6 College St., Sydney, NSW 2010, Australia (Accepted October 29, 2007) Donald J. Colgan, Patricia A. Hutchings, and Emma Beacham (2008) Multi-gene analyses of the phylogenetic relationships among the Mollusca, Annelida, and Arthropoda. Zoological Studies 47(3): 338-351. The current understanding of metazoan relationships is largely based on analyses of 18S ribosomal RNA ('18S rRNA'). In this paper, DNA sequence data from 2 segments of 28S rRNA, cytochrome c oxidase subunit I, histone H3, and U2 small nuclear (sn)RNA were compiled and used to test phylogenetic relationships among the Mollusca, Annelida, and Arthropoda. The 18S rRNA data were included in the compilations for comparison. The analyses were especially directed at testing the implication of the Eutrochozoan hypothesis that the Annelida and Mollusca are more closely related than are the Annelida and Arthropoda and at determining whether, in contrast to analyses using only 18S rRNA, the addition of data from other genes would reveal these phyla to be monophyletic. New data and available sequences were compiled for up to 49 molluscs, 33 annelids, 22 arthropods, and 27 taxa from 15 other metazoan phyla. The Porifera, Ctenophora, and Cnidaria were used as the outgroup. The Annelida, Mollusca, Entoprocta, Phoronida, Nemertea, Brachiopoda, and Sipuncula (i.e., all studied Lophotrochozoa except for the Bryozoa) formed a monophyletic clade with maximum likelihood bootstrap support of 81% and a Bayesian posterior probability of 0.66 when all data were analyzed. The clade was also formed (including 1 arthropod, a symphylan) when only genes other than 18S rRNA were analyzed. Two molluscan genera with long branch lengths (Nautilus and Philippia) were removed from the Lophotrochozoa in the maximum-parsimony analyses of all data. The Ecdysozoa (comprised of the Kinorhyncha, Priapula, Nematoda, Onychophora, Tardigrada, and Arthropoda) was included in a clade with the Chaetognatha (with maximum-likelihood support of 80% and a Bayesian probability of 0.57) using the total data. This clade except the symphylan had a Bayesian probability of 0.66 when 18S r DNA data were excluded. The reciprocal separation of the Annelida and Mollusca was generally supported where this could be resolved. The monophyly of the Annelida was contradicted only by the inclusion of the Sipuncula and Brachiopoda and the exclusion of Owenia. Molluscan monophyly was contradicted by the anomalous placement of Nautilus and/or Philippia, but these taxa were never placed in the Annelida. http://zoolstud.sinica.edu.tw/Journals/47.3/338.pdf Key words: Phylogenetics, Lophotrochozoa, Eutrochozoa, Ecdysozoa, Basal Annelida. The widespread use of 18S ribosomal RNA is not universally held (Ghiselin 1988, Eernisse et (“18S rRNA”) data in molecular phylogenetics al. 1992, Eernisse 1997), it is widely reported in has presented major challenges to prevailing invertebrate textbooks (e.g., Brusca and Brusca views of evolutionary relationships among 2003). Analyses of 18S rRNA data suggest 3 metazoan phyla. The Arthropoda and Annelida major changes. First, the Annelida is more closely have traditionally been regarded as being closely related to the Mollusca and some other minor phyla related based on morphological data (Willmer (the Sipuncula, Nemertea, and Echiura) than to the 1990, Wägele et al. 1999, Wägele and Misof 2001, Arthropoda. The group containing these phyla was Scholtz 2002, Nielsen 2003). Although this view named the Eutrochozoa (Ghiselin 1988). Second, * To whom correspondence and reprint requests should be addressed. E-mail:[email protected] 338 Colgan et al. - Relationships among Arthropods, Annelids, and Molluscs 339 the Eutrochozoa together with lophophorate phyla optimization showed support for the ecdysozoan (Phoronida, Brachiopoda, and Ectoprocta) and the hypothesis only under some parameter settings. Entoprocta form a group that Halanych et al. (1995) Often, nematodes were placed basally in the named the Lophotrochozoa. Third, the Arthropoda Metazoa. Lophotrochozoans were poorly resolved forms part of a clade of molting animals including into phyla and were also paraphyletic with respect the Nematoda, Nematomorpha, Kinorhyncha, to a group containing arthropods, priapulids, and Priapula, Gastrotricha, and Loricifera. This was chordates (Giribet 2003). The investigation of the proposed by Aguinaldo et al. (1997) who named it sodium-potassium ATPase α subunit by Anderson the Ecdysozoa. et al. (2004) included no annelids. Sequences Although these suggestions have been from this gene have subsequently been collected widely adopted, further study is required in some for a single annelid, Hirudo medicinalis (Kusche et areas. As reviewed below in the "Introduction" al. 2005), that was found to be the sister group to and“Discussion”, evidence for the suggestions the 2 flatworms rather than the 7 ecdysozoan taxa from other molecular and morphological data is in that study. supportive, but cannot by itself be considered Three multigene studies of metazoan conclusive. Second, 18S rRNA analyses do relationships including multiple eutrochozoan not indicate reciprocal monophylies of the and ecdysozoan taxa are available. Mallat and major eutrochozoan phyla. In studies including Winchell (2002) and Passamaneck and Halanych substantial numbers of both the Annelida and (2006) included 18S rRNA and 28S rRNA, while Mollusca, neither has been recovered as a Giribet (2003) included 18S rRNA, myosin II, monophyletic group (Giribet and Ribera 1998, histone H3, and elongation factor I alpha. If the Halanych 1998, Winnepenninckx et al. 1998, Chaetognatha was excluded, the Ecdysozoa and Passamaneck and Halanych 2006). In the largest Lophotrochozoa were both robustly supported , compilations of 18S rRNA data, the Annelida and in Mallatt and Winchell s analysis (2002). The Mollusca broadly intermingle (Giribet et al. 2000, Ecdysozoa and Lophotrochozoa were both Peterson and Eernisse 2001). monophyletic in the maximum-likelihood and Evidence from single genes other than 18S Bayesian analyses (with high support) of rRNA in favor of the respective monophyly of the Passamaneck and Halanych (2006) when trees , Eutrochozoa, Lophotrochozoa, and Ecdysozoa were rooted on the deuterostomes. Giribet s mostly comes from 28S rRNA. Mallat and Winchell analyses (2003) do not support the monophyly of (2002) included data comprising 2348 aligned the Lophotrochozoa or Eutrochozoa. Assuming bases of this gene from 9 lophotrochozoans equal costs for gap extensions, transitions, and and 5 ecdysozoans. Their analyses supported transversions, the Mollusca plus Phoronida was the monophyly of the molting clade if the (non- the sister group to a clade containing 2 main molting) arrow-worm Sagitta (Chaetognatha) was lineages, the Ecdysozoa and a combination of the excluded. Within the Lophotrochozoa, 2 annelids Nemertea, Sipuncula, Annelida, and Chordata. and an echiuran were shown as the sister group With transversion costs set to twice that of other to a clade comprising a mollusc, a phoronid, and a changes, the Nematoda became basal in the brachiopod. Passamaneck and Halanych (2006) Metazoa, and the Arthropoda was recovered as analyzed 2370 aligned bases from 6 molluscan, the sister group of a clade divided into a group 6 annelidan, and 3 ecdysozoan taxa and found containing the Nemertea, Platyhelminthes, and that the Ecdysozoa, Mollusca, and Annelida were Mollusca, and one containing the Annelida, respectively monophyletic, with the latter 2 phyla in Phoronida, and Chordata. a clade exclusive of the former. A number of studies based on large numbers A study of myosin II by Ruiz-Trillo et al. of genes but small taxon numbers and not (2002) found support for the Ecdysozoa including both annelid and molluscan taxa have (with Deuterostomia as its sister group) and tested implications of the Ecdysozoa hypothesis. Lophotrochozoa (with 17 taxa included) Some, e.g., Stuart and Barry (2004) and Dopazo including the Annelida (4 taxa) as a sister group and Dopazo (2005), support the hypothesis while to the Mollusca (3 taxa). The Mollusca and others reject it (Blair et al. 2002, Philip et al. Deuterostomia were well supported, but support for 2005). Philippe et al. (2005) include 1 composite the other taxa was low. Re-analysis of an extended representative“annelid”and“mollusc”in their dataset“basically extracted”from the data of Ruiz- compiled dataset comprised of 146 genes and Trillo et al. (2002) by Giribet (2003) using direct 49 taxa. The Ecdysozoa could be recovered 340 Zoological Studies 47(3): 338-351 (2008) in analyses of this set if only“slowly evolving” a relatively small number of outgroups. In the genes were included, some taxa were omitted, present case, there are effectively a large number and the Cnidaria was used as the sole outgroup. of species-level outgroups for each phylum. Otherwise, the Platythelminthes and Nematoda Potentially, this should allow better estimation of were shown as sister taxa. character states in the phylum stem groups and a The investigation reported here was possible improvement in the placement of the root. conducted to test whether genes other than 18S rRNA support a closer relationship
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