Evaluating Hypotheses of Basal Animal Phylogeny Using Complete Sequences of Large and Small Subunit rRNA

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2001-08, Vol.98 (17), p.9707-9712
Main Authors: Medina, Mónica, Collins, Allen G., Silberman, Jeffrey D., Sogin, Mitchell L.
Format: Article
Language:English
Subjects:
Animal Population Groups - classification
Animal Population Groups - genetics
Animalia
Animals
Aplysia - genetics
Bilateria
Biological Sciences
Brackish
Cnidaria
Cnidaria - classification
Cnidaria - genetics
Ctenophora
Datasets
Demospongia
Echinodermata - genetics
Evolution
Evolution, Molecular
Freshwater
Fungi
Fungi - classification
Fungi - genetics
Genes
Hexactinellida
Marine
Metazoa
Microorganisms
Models, Biological
Molecular Sequence Data
Phylogenetics
Phylogeny
Platyhelminths - genetics
Polymerase Chain Reaction
Porifera
Porifera - genetics
Ribonucleic acid
RNA
RNA, Fungal - genetics
RNA, Ribosomal - genetics
rRNA
Sequence Alignment
Sequence Analysis, RNA
Sequence Homology, Nucleic Acid
Silicea
Species Specificity
Sponges
Taxa
Topology
Urochordata - genetics
Xenopus laevis - genetics
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Summary:We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.171316998