DOI: 10.6084/m9.figshare.3122023
title: Data from: Rocha et al. (2016) The evolutionary history of Trachylepis skinks from the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biological Journal of the Linnean Society, in press.

description: Data from: Rocha et al. (2016) The evolutionary history of <i>Trachylepis </i>skinks from the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. <i>Biological Journal of the Linnean Society, in press.</i><br>alignment files used for phylogenetic analyses, networks, summary statistics, etc. the different versions of the phase inferences are given. see main ms and file descriptions bellow.<br><b>FILE TITLE:</b> trachylepis_cytb_haps.nex<b>DESCRIPTION:</b> nexus file of haplotypes of cytochrome-b used to phylogenetic analysis (Figure 2). Full dataset can be obtained from genbank with acession nrs provided in manuscript (Table S1)<br><b>FILE TITLE:</b> trachylepis_cytb_PLs.nex<b>DESCRIPTION: </b>nexus file of sequences of cytochrome-b used to the networks on Fig2A.<br><b>FILE TITLE: </b>trachylepis_cytb_MAsW.nex<b>DESCRIPTION:</b> nexus file of sequences of cytochrome-b used to the networks on Fig2B.<br><b>FILE TITLE: </b>trachylepis_cmos_phased8N.phy<b>DESCRIPTION: </b>phylip file used for cmos network construction. Please note comment lines inside with info on seq id's. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction, summary statistics, and IMa analysis.<br><b>FILE TITLE:</b> trachylepis_rag2_phased8N.phy<b>DESCRIPTION:</b> phylip file used for rag2 network construction. Please note comment lines inside with info on seq id's. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction, summary statistics, and IMa analysis.<b><br></b><b>FILE TITLE: </b>trachylepis_reln_phased8N.phy<b>DESCRIPTION:</b> phylip file used for reln network construction. Please note comment lines inside with info on seq id's. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction, summary statistics, and IMa analysis.<br><b>FILE TITLE: </b>trachylepis_mc1R_phased8N.phy<b>DESCRIPTION:</b> phylip file used for mc1r network construction. Please note comment lines inside with info on seq id's. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction, summary statistics, and IMa analysis.<br><b>FILE TITLE: </b>trachylepis_pdc_phased8N.phy<b>DESCRIPTION: </b>phylip file used for pdc network construction. Please note comment lines inside with info on seq id's. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction, summary statistics, and IMa analysis.<br><br><b>FILE TITLE: </b>phased_amb_for_ebsp.zip<b>DESCRIPTION:</b> phylip files (nuclear genes alignments) used for ebsp analyses, where positions whose phases were resolved with &lt; 0.8 posterior probability are coded with IUPAC ambiguity codes. Please find two folders, each with alignments for each species. Use for analyses presented in Figure 5 D and E.