Supplementary data:
Gaps, an elusive source of phylogenetic information
Kumar Saurabh1,2, Barbara R Holland1,3, Gillian C Gibb1,4 and David Penny1
1, IMBS/IFS, Massey University, Palmerston North, New Zealand
2, Department of Biotechnology, Indian Institute of Technology Guwahati, India
3, School of Mathematics and Physics, University of Tasmania, Hobart, Australia
4, Institut des Sciences de l'Evolution, Université Montpellier II, France
Details of the datasets
The β-fibrinogen intron 7 sequence data comes from Hackett et al. (2008) and is ~1kb in
length. The β-fibrinogen intron 7 gap data was calculated from these sequences. The RAG1
exons (~1kb) are from Paton et al. (2003), and exclude Dromas as a con-familial species was
not available. The mt exons come from Paton and Baker (2006) and are ~11kb. For the
mitochondrial data set, Catharacta replaced Dromas, Nycticryphes semicollaris replaced
Rostulata, but there was no con-familial data available for Phegornis (F)
References
Drummond A.J., Ashton B., Buxton S., Cheung M., Cooper A., Heled J., Kearse M., Moir R.,
Stones-Havas S., Sturrock S., Thierer T., Wilson A. 2010. Geneious v5.3, Available from
http://www.geneious.com
Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L.,
Cox W.A., Han K.-L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore
W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri,T. 2008. A phylogenomic study of
birds reveals their evolutionary history. Science 320:1763-1768.
Paton T.A., Baker A.J. 2006. Sequences from 14 mitochondrial genes provide a well-supported
phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree. Mol. Phyl.
Evol. 39:657-667.
Paton T.A., Baker A.J., Groth J.G., Barrowclough G.F. 2003. RAG-1 sequences resolve
phylogenetic relationships within Charadriiform birds. Mol. Phylog. Evol. 29: 268-278.
Figure S1. Differences in alignments of -fibrinogen intron 7 between MUSCLE, T-Coffee, Clustal and MAFFT for the Scolopaci; graphical
representation using Geneious (Drummond et al. 2010). For easier visualisation, the alignment has been stripped of all identical columns and
four gaps were manually introduced to align the alignments from different programmes. Pale grey regions represent the consensus, differences
are highlighted as red (A), green (T), blue (C) and orange (G). Ambiguities are magenta, and gaps are shown as thin lines in grey (consensus) or
black (disagreement)