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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses
Molecular Phylogenetics and Evolution, Volume 48, No. 3, Year 2008
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Description
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. © 2008 Elsevier Inc. All rights reserved.
Authors & Co-Authors
Pirie, Michael David
Switzerland, Zurich
Universität Zürich
Humphreys, Aelys M.
Switzerland, Zurich
Universität Zürich
Galley, Chloé A.
Switzerland, Zurich
Universität Zürich
Barker, Nigel Paul
South Africa, Grahamstown
Rhodes University
Verboom, George Anthony
South Africa, Cape Town
University of Cape Town
Orlovich, David
New Zealand, Dunedin
University of Otago
Draffin, Suzy J.
New Zealand, Dunedin
University of Otago
Lloyd, Kelvin M.
New Zealand, Dunedin
Landcare Research, Dunedin
Baeza, Carlos Marcelo
Chile, Biobio
Universidad de Concepcion
Negritto, María A.
Chile, Biobio
Universidad de Concepcion
Ruiz, Eduardo A.
Chile, Biobio
Universidad de Concepcion
Sanchez, J. Hugo Cota
Canada, Saskatoon
University of Saskatchewan
Reimer, Elizabeth
Canada, Saskatoon
University of Saskatchewan
Linder, Hans Peter
Switzerland, Zurich
Universität Zürich
Statistics
Citations: 77
Authors: 14
Affiliations: 7
Identifiers
Doi:
10.1016/j.ympev.2008.05.030
ISSN:
10557903
e-ISSN:
10959513
Research Areas
Cancer
Genetics And Genomics