A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses.
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.
Pirie
Michael D
MD
Institute for Systematic Botany, University of Zurich, Switzerland. michael.pirie@systbot.uzh.ch
Humphreys
Aelys M
AM
Galley
Chloe
C
Barker
Nigel P
NP
Verboom
G Anthony
GA
Orlovich
David
D
Draffin
Suzy J
SJ
Lloyd
Kelvin
K
Baeza
C Marcelo
CM
Negritto
Maria
M
Ruiz
Eduardo
E
Sanchez
J Hugo Cota
JH
Reimer
Elizabeth
E
Linder
H Peter
HP
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
D017931:DNA Primers; D018742:DNA, Chloroplast; D018744:DNA, Plant