Special Issue: Genotyping by Sequencing
The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing
Article first published online: 2 APR 2013
© 2013 John Wiley & Sons Ltd
Special Issue: GENOTYPING BY SEQUENCING IN ECOLOGICAL AND CONSERVATION GENOMICS
Volume 22, Issue 11, pages 2986–3001, June 2013
How to Cite
Jones, J. C., Fan, S., Franchini, P., Schartl, M. and Meyer, A. (2013), The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Molecular Ecology, 22: 2986–3001. doi: 10.1111/mec.12269
- Issue published online: 30 MAY 2013
- Article first published online: 2 APR 2013
- Manuscript Accepted: 15 JAN 2013
- Manuscript Revised: 10 JAN 2013
- Manuscript Received: 30 JUN 2012
- Deutsche Forschungsgemeinschaft (DFG)
- University of Konstanz
- University of Würzburg
Fig. S1 Number of raw reads obtained per individual for each of the 29 species in this analysis.
Fig. S2 Coverage obtained per individual. Due to the low number of reads achieved for X. evelynae, individual samples for this species were combined for further analyses.
Fig. S3 SNP matrix size found when different numbers of maximum mismatches (5 or 8) and minimum number of species (15, 20 or 25) are implemented.
Fig. S4 Phylogenetic estimations using ML with different maximum mismatches and minimum number of species (the following order is shown at each node when estimations differed from bootstrap values of 100—m5, sp15; m5, sp20; m5, sp25; m8, sp15; m8, sp20; m8, sp25). *indicates a different topology at that node; in the clemenciae clade, X. monticolus and X. clemenciae were found to be the most derived species using one of six matrices. In the northern platyfish clade, X. couchianus and X. gordoni were found to be the most derived using two of six matrices. These estimations were less well supported than the topology found using the majority of the SNP matrices.
Table S1 Overview of RAD raw data and experimental setup. Individual raw read data, read data retained after quality control, library number (multiplexing design) and sequencing platform.
Table S2 Proportion of missing data at all parameters analysed in this study where maximum and minimum numbers are calculated for the ingroup taxa (see also Fig. S4).
Table S3 Estimated time of origin of the major Xiphophorus clades including mean and 95% confidence interval values (see also Methods).
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