TreeBASE Search-Analyses for study 11476

@ARTICLE{TreeBASE2Ref19750, author = {Hanna Weiss-Schneeweiss and Cordula Bl?ch and Barbara Turner and Jose L Villasenor and Tod F. Stuessy and Gerald M. Schneeweiss}, title = {The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)}, year = {2011}, keywords = {allopolyploidy, chromosome evolution, fluorescence in situ hybridisation, genome size, phylogeny, rDNA}, doi = {10.1111/j.1558-5646.2011.01424.x}, url = {http://}, pmid = {}, journal = {Evolution}, volume = {}, number = {}, pages = {}, abstract = {Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra- and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting the presence of processes counterbalancing genome reduction. Patterns of ribosomal DNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.} }

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Analyses for Study 11476

Citation title: "The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)".

Study name: "The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)".

This study is part of submission 11466 (Status: Published).

Analyses

Analysis 1

Analysis details

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Notes

Input data

1 Input object(s)

Analysis step

Bayesian Analysis ITS --

Output data

1 Output object(s)

Analysis 2

Analysis details

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1 Input object(s)

Analysis step

Maximum parsimony analysis ITS --

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

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1 Input object(s)

Analysis step

Bayesian Analysis plastid data --

Step details

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Commands
charset trnk = 1-174 1696-1958; charset matK_1st2ndpos = 175-1695\3 176-1695\3; charset matK_3rdpos = 177-1695\3; charset psba = 1959-2431; [in charset psba positions 73-108 (i.e. in the combined alignment positions 2027-2061) have been reverted] partition favored = 4 : trnk, matK_1st2ndpos, matK_3rdpos, psba; set partition = favored; prset applyto =(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=1 rates=gamma; prset applyto =(2) statefreqpr=dirichlet(1,1,1,1); lset applyto=(2) nst=1 rates=gamma; prset applyto =(3) statefreqpr=dirichlet(1,1,1,1); lset applyto=(3) nst=2 rates=gamma; Prset applyto =(4) statefreqpr=dirichlet (1,1,1,1); lset nst=2 rates=gamma ngammacat=6; mcmc ngen=5000000 nruns=4 samplefreq=1000;

Output data

1 Output object(s)

Analysis 4

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1 Input object(s)

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Maximum parsimony analysis cpDNA data --

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1 Output object(s)

Analysis 5

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1 Input object(s)

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Bayesian Analysis 5S spacer data --

Output data

1 Output object(s)

Analysis 6

Analysis details

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1 Input object(s)

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Maximum parsimony analysis 5S spacer data --

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1 Output object(s)

Analysis 7

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1 Input object(s)

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Bayesian Analysis pgiCI data --

Step details

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Software used

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Commands
charset exon = 87-147 270-336 474-530 624-677; charset intron = 1-86 148-269 337-473 531-623 678-739; partition favored = 2 : exon, intron; set partition = favored; prset applyto =(1) statefreqpr=dirichlet (1,1,1,1); lset applyto =(1) nst=2 rates =gamma ngammacat=6; prset applyto =(2) statefreqpr=dirichlet (1,1,1,1); lset applyto =(2) nst=6 rates =gamma ngammacat=6; mcmc ngen=5000000 nruns=4 samplefreq=1000;

Output data

1 Output object(s)

Analysis 8

Analysis details

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1 Input object(s)

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Maximum parsimony analysis pgiCI data --

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1 Output object(s)

Analysis 9

Analysis details

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1 Input object(s)

Analysis step

Bayesian Analysis pgiCII data --

Step details

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Software used

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charset exon = 101-161 270-336 448-504 598-651; charset intron = 1-100 162-269 337-447 505-597 652-715; partition favored = 2 : exon, intron; set partition = favored; prset applyto =(1) statefreqpr=dirichlet (1,1,1,1); lset applyto =(1) nst=2 rates =gamma ngammacat=6; prset applyto =(2) statefreqpr=dirichlet (1,1,1,1); lset applyto =(2) nst=6 rates =gamma ngammacat=6; mcmc ngen=5000000 nruns=4 samplefreq=1000;

Output data

1 Output object(s)

Analysis 10

Analysis details

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1 Input object(s)

Analysis step

Maximum parsimony analysis pgiCII data --

Output data