Open Access Research article

Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers

Isobel Eyres1, Eftychios Frangedakis12, Diego Fontaneto16, Elisabeth A Herniou3, Chiara Boschetti4, Adrian Carr5, Gos Micklem5, Alan Tunnacliffe4 and Timothy G Barraclough1*

Author Affiliations

1 Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK

2 Present address: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK

3 Institut de Recherche sur la Biologie de l’Insecte, CNRS UMR 7261, Université François-Rabelais, 37200, Tours, France

4 Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK

5 Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom

6 Current address: Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922, Verbania Pallanza, Italy

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BMC Evolutionary Biology 2012, 12:148  doi:10.1186/1471-2148-12-148

Published: 17 August 2012

Additional files

Additional file 1:

Average GC content at the third codon position for sequences belonging to each species. BP=Brachionus plicatilis (monogonont); PF =P. flaviceps; AV=A. vaga; AR=A. ricciae; MQ=M. quadricornifera. Kruskal-Wallis test for variation among species: chi-squared = 41.9, df = 3, p<0.0001.

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Additional file 2:

Model fit comparisons. Model fit comparisons. Log marginal likelihood estimated from posterior samples using Equation (16) in Newton and Raftery (1994) implemented using func.newtonRaftery94_eqn16 [37] in p4 (v0.88; [34]).

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Additional file 3:

Alpha tubulin gene tree based on exon nucleotides including all cloned copies from all bdelloid species sequenced. aLRT support values are shown and the scale bar is in units of substitutions per site.

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Additional file 4:

Alpha tubulin gene tree forAdineta ricciaeincluding cloned and sequenced copies and copies found in the transcriptome. Alpha tubulin gene tree for Adineta ricciae including both cloned and sequenced copies (named ArCopy1 etc.) and the copies found by searching the transcriptome using BLASTN (each named E_Locus followed by a number).

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Additional file 5:

Average dN/dS (Y-axis) obtained by sliding window analysis of the alpha tubulin alignment across classes. Window size = 15, step size = 5. Colours along the x-axis show functional and structural regions: red = alpha helix; blue = beta sheet; green = functional regions (P = interacts with phosphate, ribose = interacts with ribose, others are annotated with their functions). Arrows = codons identified using Bayes empirical Bayes as experiencing divergent selection (position in alignment: 17, 19, 21, 22, 23, 31, 41, 71, 72, 104, 112, 127, 145, 146, 269, 272, 274, 276, 286, 317, 348, 355).

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