Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family
Article first published online: 2 APR 2014
© 2014 John Wiley & Sons Ltd
Molecular Ecology Resources
Volume 14, Issue 5, pages 966–975, September 2014
How to Cite
Malé, P.-J. G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., Lhuillier, E., Scotti-Saintagne, C., Tinaut, A. and Chave, J. (2014), Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular Ecology Resources, 14: 966–975. doi: 10.1111/1755-0998.12246
- Issue published online: 12 AUG 2014
- Article first published online: 2 APR 2014
- Accepted manuscript online: 8 MAR 2014 01:29AM EST
- Manuscript Accepted: 22 FEB 2014
- Manuscript Revised: 9 FEB 2014
- Manuscript Received: 30 OCT 2013
- Agence Nationale de la Recherche. Grant Numbers: ANR-10-LABX-25-01, ANR-10-LABX-0041
- Institut des Sciences de l'Evolution. Grant Number: ISEM 2014-021
|men12246-sup-0001FigS1.ps||PS document||745K||Fig. S1 Physical map of the plastid genome (ptDNA) of Licania alba, drawn with the ogdraw software (Lohse et al. 2007).|
|men12246-sup-0002-FigS2.eps||image/eps||8K||Fig. S2 Maximum likelihood phylogenetic trees for eight Chrysobalanaceae species obtained with nonintronic transcribed sequences of plastid genome (panel a), mitochondrial genome (panel b) and nuclear ribosomal region (panel c). Branch lengths are drawn proportional to number of nucleotide substitutions per site, excepted for the branch leading to the outgroup that has been cut for scaling purposes. Bootstrap support values (using raxml) and Bayesian posterior probabilities (from 50% majority-rule consensus trees obtained using mrbayes) are reported when bootstrap values are superior to 70%. Bootstrap values higher than 85% are highlighted in bold. The part of the trees shaded in grey represents outgroups included in these analyses.|
Table S1 Quantity and quality of total DNA used for eight Chrysobalanaceae species and number of reads obtained after sequencing. H. physophora was sequenced on a 12th of a HiSeq 2000 lane whereas the other species were sequenced on a 24th of a HiSeq 2000 lane.
Table S2 Optimal partitioning scheme and best-fit models identified by the partitionfinder software with model choice restricted to models available in raxml for alignments comprising nontranscribed regions (hereafter labelled “nc”). Alpha and the proportion of invariant sites have been estimated using raxml.
Table S3 Optimal partitioning scheme and best-fit models identified by the partitionfinder software with model choice restricted to models available in raxml for alignments comprising only nonintronic transcribed regions. Alpha and the proportion of invariant sites have been estimated using raxml.
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