Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

Abouheif, Ehab; Zardoya, Rafael; Meyer, Axel

doi:10.1007/pl00006397

Cited by 154 publications

(93 citation statements)

References 47 publications

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“…Parsimony analysis resulted in 17 equally most-parsimonious trees (¢gure 1). The analysis under maximum likelihood yielded a very low maximumlikelihood estimate of the shape parameter of the gamma distribution (0.27), con¢rming previous studies (Abouheif et al 1998;Martin et al 2000) and the importance of taking between-site rate variation into account in phylogenetic analyses of the 18S rRNA gene with this method.…”

Section: Resultssupporting

confidence: 79%

On the origin of the Hirudinea and the demise of the Oligochaeta

Martin

2001

Proc. R. Soc. Lond. B

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The phylogenetic relationships of the Clitellata were investigated with a data set of published and new complete 18S rRNA gene sequences of 51 species representing 41 families. Sequences were aligned on the basis of a secondary structure model and analysed with maximum parsimony and maximum likelihood. In contrast to the latter method, parsimony did not recover the monophyly of Clitellata. However, a close scrutiny of the data suggested a spurious attraction between some polychaetes and clitellates. As a rule, molecular trees are closely aligned with morphology-based phylogenies. Acanthobdellida and Euhirudinea were reconciled in their traditional Hirudinea clade and were included in the Oligochaeta with the Branchiobdellida via the Lumbriculidae as a possible link between the two assemblages. While the 18S gene yielded a meaningful historical signal for determining relationships within clitellates, the exact position of Hirudinea and Branchiobdellida within oligochaetes remained unresolved. The lack of phylogenetic signal is interpreted as evidence for a rapid radiation of these taxa. The placement of Clitellata within the Polychaeta remained unresolved. The biological reality of polytomies within annelids is suggested and supports the hypothesis of an extremely ancient radiation of polychaetes and emergence of clitellates.

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Section: Resultssupporting

confidence: 79%

On the origin of the Hirudinea and the demise of the Oligochaeta

Martin

2001

Proc. R. Soc. Lond. B

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“…However, this sequence alone is unable to resolve the inter-relationships of most lophotrochozoan, protostome phyla with strong support (e.g. Adoutte and Philippe 1993;Abouheif et al 1998). (2) Nuclear-encoded, large subunit rDNA (23S or LSU rDNA), because complete sequences have recently been found to add usefully to the resolution of protostome phyla .…”

Section: Sequences Data-editing and Alignmentmentioning

confidence: 99%

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

Cohen

Weydmann

2005

Organisms Diversity & Evolution

137

113

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Concatenated SSU (18S) and partial LSU (28S) sequences ($2 kb) from 12 ingroup taxa, comprising 2 phoronids, 2 members of each of the craniid, discinid, and lingulid inarticulate brachiopod lineages, and 4 rhynchonellate, articulate brachiopods (2 rhynchonellides, 1 terebratulide and 1 terebratellide) were aligned with homologous sequences from 6 protostome, deuterostome and sponge outgroups (3964 sites). Regions of potentially ambiguous alignment were removed, and the resulting data (3275 sites, of which 377 were parsimony-informative and 635 variable) were analysed by parsimony, and by maximum and Bayesian likelihood using objectively selected models. There was no base composition heterogeneity. Relative rate tests led to the exclusion (from most analyses) of the more distant outgroups, with retention of the closer pectinid and polyplacophoran (chiton). Parsimony and likelihood bootstrap and Bayesian clade support values were generally high, but only likelihood analyses recovered all brachiopod indicator clades designated a priori. All analyses confirmed the monophyly of (brachiopods+phoronids) and identified phoronids as the sister-group of the three inarticulate brachiopod lineages. Consequently, a revised Linnean classification is proposed in which the subphylum Linguliformea comprises three classes: Lingulata, 'Phoronata' (the phoronids), and 'Craniata' (the current subphylum Craniiformea). Divergence times of all nodes were estimated by regression from node depths in non-parametrically rate-smoothed and other chronograms, calibrated against palaeontological data, with probable errors not less than 50 My. Only three predicted brachiopod divergence times disagree with palaeontological ages by more than the probable error, and a reasonable explanation exists for at least two. Pruning long-branched ingroups made scant difference to predicted divergence time estimates. The palaeontological age calibration and the existence of Lower Cambrian fossils of both main brachiopod clades together indicate that initial genetic divergence between brachiopod and molluscan (chiton) lineages occurred well before the Lower Cambrian, suggesting that much divergence between metazoan phyla took place in the Proterozoic.

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“…In part owing to the improvement not only due to denser taxonomic sampling, but also due to a systematic selection of the slowest evolving representatives of the majority of animal phyla, a consensus rapidly emerged, reducing the diversity of Bilateria into three main clades: Deuterostomia, Lophotrochozoa (Halanych et al 1995) and Ecdysozoa (Aguinaldo et al 1997). The statistical support for most of the nodes was nevertheless non-significant (Philippe et al 1994;Abouheif et al 1998), thus preventing any firm conclusions.…”

Section: Introduction (A) the Limits Of Morphologymentioning

confidence: 99%

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Lartillot

Piégay

2008

Phil. Trans. R. Soc. B

167

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Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.

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Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

Cited by 154 publications

References 47 publications

On the origin of the Hirudinea and the demise of the Oligochaeta

On the origin of the Hirudinea and the demise of the Oligochaeta

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

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