Open Access Highly Accessed Research article

Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset

Per Alström1*, Sebastian Höhna2, Magnus Gelang3, Per GP Ericson3 and Urban Olsson4

Author Affiliations

1 Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden

2 Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden

3 Department of Vertebrate Zoology, and Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden

4 Department of Zoology, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden

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BMC Evolutionary Biology 2011, 11:352  doi:10.1186/1471-2148-11-352

Published: 5 December 2011

Additional files

Additional file 1:

Cytochrome b gene tree. Majority rule (50%) consensus tree of Cettiidae based on mitochondrial cytochrome b sequences, inferred by Bayesian inference. All available sequences (including all subspecies) were included. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00.

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Additional file 2:

ODC gene tree. Majority rule (50%) consensus tree of Cettiidae based on nuclear ornithine decarboxylase introns 6 and 7 and exons 7 and parts of 6 and 8 (ODC) sequences, inferred by Bayesian inference. All available sequences (including all subspecies) were included. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00.

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Additional file 3:

Myoglobin gene tree. Majority rule (50%) consensus tree of Cettiidae based on nuclear myoglobin intron 2 sequences, inferred by Bayesian inference. All available sequences (including all subspecies) were included. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00.

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Additional file 4:

GAPDH gene tree. Majority rule (50%) consensus tree of Cettiidae based on nuclear nuclear glyceraldehyde-3-phosphodehydrogenase intron 11 (GAPDH) sequences, inferred by Bayesian inference. All available sequences (including all subspecies) were included. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00.

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Additional file 5:

Tree of Cettiidae based on concatenated sequences - all taxa, unpartitioned analysis. Majority rule (50%) consensus tree of Cettiidae based on concatenated nuclear ODC, myoglobin and GAPDH and mitochondrial cytochrome b sequences, inferred by unpartitioned Bayesian inference. All available sequences (including all subspecies) were included. Generic affinity according to traditional taxonomy (Dickinson, 2003) indicated by different colour shadings. The three species for which only cytochrome b is available are in red. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00. A red § indicates a clade with marked difference compared to partitioned analysis (Figure 1).

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Additional file 6:

Tree of Cettiidae based on concatenated sequences - complete data, partitioned analysis. Majority rule (50%) consensus tree of Cettiidae based on concatenated nuclear ODC, myoglobin and GAPDH and mitochondrial cytochrome b sequences, inferred by Bayesian inference, analysed in four partitions. Only individuals for which all sequences were available were included (cf. Figure 1). Generic affinity according to traditional taxonomy [12] indicated by different colour shadings. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00. The outgroups (Alauda arvensis and Mirafra javanica in Alaudidae and Orthotomus sepium, O. sutorius and Prinia familiaris in Cisticolidae) have been pruned from the tree.

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Additional file 7:

Phylogeny of Cettiidae. Inferred by *BEAST. Only individuals for which all loci were available were included (cf. Figure 3). All loci had independent substitution models; and a relaxed clock prior was applied ("Full jModelTest relaxed"). Generic affinity according to traditional taxonomy [12] is indicated by different colour shadings. Values in parentheses after names are the number of individuals included. Posterior probabilities are indicated at the nodes; an asterisk represents posterior probability 1.00.

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Additional file 8:

List of samples (in alphabetical order), with GenBank accession numbers.

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