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Positive selection on panpulmonate mitogenomes provide new clues on adaptations to terrestrial life

Version 3 2016-08-11, 18:26
Version 2 2016-08-02, 08:05
Version 1 2016-08-01, 12:59
Posted on 2016-08-11 - 18:26 authored by Pedro E. Romero
This fileset consists of the data used in the article "Positive selection on panpulmonate mitogenomes provide new clues on adaptations to terrestrial life" (Romero, Weigand and Pfenninger), accepted in BMC Evolutionary Biology.

Additional File 8. Sequence identifiers in the alignments, gene partitions for the concatenated dataset (9711 nt.) and for the concatenated dataset without the third position (6474 nt.).

Additional File 9. Nexus alignment with the information to run MrBayes.

Additional File 10. Phylip file of the concatenated nucleotide dataset (9711 nt.)

Additional File 11. Phylip file of the concatenated nucleotide dataset (first and second positions, 6474 nt.), used for tree reconstruction in RAxML.

Additional File 12. Partition information to run RAxML.

Additional File 13. cob amino acid alignment of the molluscan mitogenomic dataset without the outgroup. Position 151 corresponds to a Proline (P) in the first sequence (a4: Bulla).

Additional File 14. nad5 amino acid alignment of the molluscan mitogenomic dataset without the outgroup. Position 474 corresponds to a Serine (S) in the first sequence (a5: Chromodoris).

Additional File 15. cob amino acid alignment from Garvin et al. [17]. Position 158 corresponds to an Aspartate (D) in the first sequence (Anguilla).

Additional File 16. nad5 amino acid alignment from Garvin et al. [17]. Position 540 corresponds to a Threonine (T) in the first sequence (Anguilla).

Additional File 17. cob amino acid alignment of the terrestrial snails and the data from Garvin et al. [17]. Position 151 in the molluscan alignment is homologous to position 158 in the vertebrate alignment. This corresponds to a phenylalanine (F) in the first terrestrial sequence (Aegista). The final position in the merged alignment is 159 because of a gap insertion.

Additional File 18. nad5 amino acid alignment of the terrestrial snails and the data from Garvin et al. [17]. Position 474 in the molluscan alignment is homologous to position 540 in the vertebrate alignment. This corresponds to an isoleucine (I) in the first terrestrial sequence (Aegista). The final position in the merged alignment is 527 because of several gap insertions.

Additional File 19. Bayesian tree obtained in MrBayes.

Additional File 20. Maximum likelihood tree obtained in RAxML.

Additional File 21. cob codon alignment for PAML.

Additional File 22. nad5 codon alignment for PAML.

Additional File 23. PAML control file.



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