DOI: 10.5061/dryad.jc754
title: Data from: From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)

description: Allopolyploidisation acounts for a significant fraction of speciation
 events in many eukaryotic lineages. However, existing phylogenetic and
 dating methods require tree-like topologies and are unable to handle the
 network-like phylogenetic relationships of lineages containing
 allopolyploids. No explicit framework has so far been established for
 evaluating competing network topologies, and few attempts have been made
 to date phylogenetic networks. We used a four-step approach to generate a
 dated polyploid species network for the cosmopolitan angiosperm genus
 Viola L. (Violaceae Batch.). The genus contains ca 600 species and both
 recent (neo-) and more ancient (meso-) polyploid lineages distributed over
 16 sections. First, we obtained DNA sequences of three low-copy nuclear
 genes and one chloroplast region, from 42 species representing all 16
 sections. Second, we obtained fossil-calibrated chronograms for each
 nuclear gene marker. Third, we determined the most parsimonious
 multilabelled genome tree and its corresponding network, resolved at the
 section (not the species) level. Reconstructing the ‘correct’ network for
 a set of polyploids depends on recovering all homoeologs, i.e. all
 subgenomes, in these polyploids. Assuming the presence of Viola subgenome
 lineages that were not detected by the nuclear gene phylogenies (‘ghost
 subgenome lineages’), significantly reduced the number of inferred
 polyploidisation events. We identified the most parsimonious network
 topology from a set of five competing scenarios differing in the
 interpretation of homoeolog extinctions and lineage sorting, based on (1)
 fewest possible ghost subgenome lineages, (2) fewest possible
 polyploidisation events, and (3) least possible deviation from expected
 ploidy as inferred from available chromosome counts of the involved
 polyploid taxa. Finally, we estimated the homoploid and polyploid
 speciation times of the most parsimonious network. Homoploid speciation
 times were estimated by coalescent analysis of gene tree node ages.
 Polyploid speciation times were estimated by comparing branch lengths and
 speciation rates of lineages with and without ploidy shifts. Our analyses
 recognise Viola as an old genus (crown age 31 Ma) whose evolutionary
 history has been profoundly affected by allopolyploidy. Between 16 and 21
 allopolyploidisations are necessary to explain the diversification of the
 16 major lineages (sections) of Viola, suggesting that allopolyploidy has
 accounted for a high percentage – between 67% and 88% – of the speciation
 events at this level. The theoretical and methodological approaches
 presented here for (1) constructing networks and (2) dating speciation
 events within a network, have general applicability for phylogenetic
 studies of groups where allopolyploidisation has occurred. They make
 explicit use of a hitherto underexplored source of ploidy information from
 chromosome counts to help resolve phylogenetic cases where incomplete
 sequence data hampers network inference. Importantly, the coalescent-based
 method used herein circumvents the assumption of tree-like evolution
 required by most techniques for dating speciation events.
description: S_Files_140901Supplementary Files - appendices 1-2, figures S1-S11, tables S1-S6S_BEAST_GPI_calBEAST phylogeny for GPI - calibrated analysis - FigTree tree fileS_BEAST_GPI_calBEAST phylogeny for GPI - calibrated analysis - XML input fileS_BEAST_GPI_uncalBEAST phylogeny for GPI - uncalibrated analysis - FigTree tree fileS_BEAST_NRPD2a_calBEAST phylogeny for NRPD2a - calibrated analysis - FigTree tree fileS_BEAST_NRPD2a_calBEAST phylogeny for NRPD2a - calibrated analysis - XML input fileS_BEAST_NRPD2a_uncalBEAST phylogeny for NRPD2a - uncalibrated analysis - FigTree tree fileS_BEAST_SDH_calBEAST phylogeny for SDH - calibrated analysis - FigTree tree fileS_BEAST_SDH_calBEAST phylogeny for SDH - calibrated analysis - XML input fileS_BEAST_SDH_uncalBEAST phylogeny for SDH - uncalibrated analysis - FigTree tree fileS_BEAST_trnLFBEAST phylogeny for trnL-trnF - FigTree tree fileS_BEAST_trnLFBEAST phylogeny for trnL-trnF - XML input fileS_BUGS_homoploidBUGS script for estimation of homoploid speciation times - TXT fileS_BUGS_polyploidBUGS script for estimation of polyploid speciation times - TXT fileS_MrB_8cp_geneMrBayes phylogeny for 8 chloroplast regions - NEXUS input fileS_MrB_8cp_geneMrBayes phylogeny for 8 chloroplast regions - FigTree tree fileS_MrB_GPIMrBayes phylogeny for GPI - NEXUS input fileS_MrB_GPIMrBayes phylogeny for GPI - FigTree tree fileS_MrB_NRPD2aMrBayes phylogeny for NRPD2a - NEXUS input fileS_MrB_NRPD2aMrBayes phylogeny for NRPD2a - FigTree tree fileS_MrB_SDHMrBayes phylogeny for SDH - NEXUS input fileS_MrB_SDHMrBayes phylogeny for SDH - FigTree tree fileS_MrB_trnLFMrBayes phylogeny for trnL-trnF - NEXUS input fileS_MrB_trnLFMrBayes phylogeny for trnL-trnF - FigTree tree file