Taxon · 2011 · 37 citations · 44 references
Life SciencesBotanyPlant SciencesPhylogeneticsPlant TaxonomySystematicsBryophyte PhylogenyEvolutionary RelationshipsMolecular PhylogenyPhylogenetic Tree ReconstructionPlant PhylogenyTaxonomic ClassificationPhylogenetic DelimitationPhylogenetic Species DelimitationPhylogenetic Taxonomy
Abstract Phylogenetic relationships within Silene sect. Physolychnis are investigated using DNA sequences from two low‐copy nuclear regions and three plastid regions. We expand the circumscription of Physolychnis to include also Siberian and Eurasian taxa, with S . zawadzkii and S . uralensis as delimiters of the section. Two main clades are identified within Physolychnis , the Siberian S . ajanensis group and an Asian/American clade. Several taxa, previously classified to sect. Odontopetalae , sect. Occidentales , and sect. Morrisonmontanae , are shown to belong to the Asian/American clade, which otherwise corresponds to Bocquet's (1969) circumscription of sect. Physolychnis . Silene sect. Physolychnis also includes several additional, mainly Asian taxa (e.g., S . davidii , S . seoulensis , S . keiskei , S . viscosa , S . quadriloba , and homoeologues from S . songarica , S . firma , and S . tolmatchevii ). Several putative allopolyploids are identified, in several cases stemming from crosses between the two main clades. The two allotetraploids S . involucrata and S . sachalinensis , although morphologically and geographically distinct, have indistinguishable ancestries.
44
MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar · Nucleic Acids Research · 2004 · 46.5K citations · Full text
MRBAYES: Bayesian inference of phylogenetic trees
John P. Huelsenbeck, Fredrik Ronquist · Bioinformatics · 2001 · 22.2K citations · Full text
MODELTEST: testing the model of DNA substitution.
David Posada, Keith A. Crandall · Bioinformatics · 1998 · 20.1K citations
Base-Calling of Automated Sequencer Traces Using<i>Phred.</i> I. Accuracy Assessment
Brent Ewing, LaDeana Hillier, Michael C. Wendl et al. · Genome Research · 1998 · 7K citations · Full text