DOI: 10.5061/dryad.f374gf0
title: Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

description: Background: Polyploidy has played a major role in angiosperm evolution.
 Previous studies have examined polyploid phenotypes in comparison to their
 extant progenitors, but not in context of predicted progenitor phenotypes
 at allopolyploid origin. In addition, differences in the trends of
 polyploid versus diploid evolution have not been investigated. We use
 ancestral character-state reconstructions to estimate progenitor phenotype
 at allopolyploid origin to determine patterns of polyploid evolution
 leading to morphology of the extant species. We also compare trends in
 diploid versus allopolyploid evolution to determine if polyploidy modifies
 floral evolutionary patterns. Results: Predicting the ancestral phenotype
 of a nascent allopolyploid from reconstructions of diploid phenotypes at
 the time of polyploid formation generates different phenotype predictions
 than when extant diploid phenotypes are used, the outcome of which can
 alter conclusions about polyploid evolution; however, most analyses yield
 the same results. Using ancestral reconstructions of diploid floral
 phenotypes indicate that young polyploids evolve shorter, wider corolla
 tubes, but older polyploids and diploids do not show any detectable
 evolutionary trends. Lability of the traits examined (floral shape,
 corolla tube length, and corolla tube width) differs across young and
 older polyploids and diploids. Corolla length is more evolutionarily
 labile in older polyploids and diploids. Polyploids do not display unique
 suites of floral characters based on both morphological and color traits,
 but some suites of characters may be evolving together and seem to have
 arisen multiple times within Nicotiana, perhaps due to the influence of
 pollinators. Conclusions: Young polyploids display different trends in
 floral evolution (shorter, wider corolla tubes, which may result in more
 generalist pollination) than older polyploids and diploids, suggesting
 that patterns of divergence are impacted by the early consequences of
 allopolyploidy, perhaps arising from genomic shock and/or subsequent
 genome stabilization associated with diploidization. Convergent evolution
 in floral morphology and color in Nicotiana can be consistent with
 pollinator preferences, suggesting that pollinators may have shaped floral
 evolution in Nicotiana.
description: ADH alignment
 fileNexus format file for
 ADH gene alignmentADH.nexGLONexus format alignment file for GLOGSNexus format alignment file for GSITSNexus format alignment file for ITSLFY_FLONexus format alignment file for LFY-FLOMADSFULNexus format alignment file for MADSFULNicotiana_all_informationText table for all concatenated genes, including which were present for each taxon and length of each locus.Nicotiana_all_no_homoploidNexus format for concatenated data with all homoploids removed.Nicotiana_all_nexusNexus format alignment of all concatenated lociNicotiana_all.nexNicotiana_all_phyConcatenated alignment file for all loci in .phy format for RAxMLNicotiana_all.phyNicotiana_diploids_onlyNexus format alignment file with only diploids (all polyploids removed).Plastid_genesNexus format alignment file for all plastid loci usedWaxyNexus format alignment file for WAXYADH_bootstrap_support_treeADH best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.ADH_support.treAll_data_support_treeAll concatenated data best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.All_data_support.treAll_no_homoploid_support_treeAll data with homoploids removed best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.All_no_homoploid_support.treDiploids_support_treeDiploids only best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.Diploids_support.treGLO_support_treeGLO best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.GLO_support.treGS_support_treeGS best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.GS_support.treITS_support_treeITS best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.ITS_support.treLFY_support_treeLFY best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.LFY_support.treMADSFUL_support_treeMADSFUL best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.MADSFUL_support.trePlastid_support_treePlastid best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.Plastid_support.treWaxy_support_treeWAXY best maximum likelihood tree from Garli with support values from 1,000 bootstrap replicates at each node.Waxy_support.tre