title: A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses.
abstract: Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.
authors.affiliation: Institute for Systematic Botany, University of Zurich, Switzerland. michael.pirie@systbot.uzh.ch
authors.forename: Michael D
authors.initials: MD
authors.lastname: Pirie
authors.forename: Aelys M
authors.initials: AM
authors.lastname: Humphreys
authors.forename: Chloe
authors.initials: C
authors.lastname: Galley
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Barker
authors.forename: G Anthony
authors.initials: GA
authors.lastname: Verboom
authors.forename: David
authors.initials: D
authors.lastname: Orlovich
authors.forename: Suzy J
authors.initials: SJ
authors.lastname: Draffin
authors.forename: Kelvin
authors.initials: K
authors.lastname: Lloyd
authors.forename: C Marcelo
authors.initials: CM
authors.lastname: Baeza
authors.forename: Maria
authors.initials: M
authors.lastname: Negritto
authors.forename: Eduardo
authors.initials: E
authors.lastname: Ruiz
authors.forename: J Hugo Cota
authors.initials: JH
authors.lastname: Sanchez
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Reimer
authors.forename: H Peter
authors.initials: HP
authors.lastname: Linder
mesh_terms: D001499:Bayes Theorem; D002467:Cell Nucleus / Q000378:metabolism; D017931:DNA Primers / Q000737:chemistry; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D014644:Genetic Variation; D008957:Models, Genetic; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics*; D016133:Polymerase Chain Reaction; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D018742:DNA, Chloroplast; D018744:DNA, Plant