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Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data
Citation
Johnson, KA and Holland, BR and Heslewood, MM and Crayn, DM, Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data, Molecular Phylogenetics and Evolution, 62, (1) pp. 146-158. ISSN 1055-7903 (2012) [Refereed Article]
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DOI: doi:10.1016/j.ympev.2011.09.011
Abstract
For the predominantly southern hemisphere plant group Styphelioideae (Ericaceae) published sequence datasets of five markers are now available for all except one of the recognised genera. However, severalmarkers are highly incomplete therefore missing data is problematic for producing a genus level phylogeny. We explore the relative utility of supertree and supermatrix approaches for addressing this challenge, and examined the effects of missing data on tree topology and resolution. Although the super-tree approach returned a more conservative hypothesis, overall, both supermatrix and supertree analyses concurred in the topologies they returned. Using multiple genes and a dataset of variably complete taxa we found improved support for the monophyly and position of the tribes and genus level relationships.
However, there was mixed support for the Richeeae tribe appearing one node basal to the Cosmelieae tribe or vice versa. It is probable that this will only be resolved through further sequencing. Our study supports previous findings that the amount of data is more critical than the completeness of the dataset in estimating well-resolved trees. Our results suggest that a ‘‘serendipitous’’ scaffolding approach that includes a mixture of well and poorly sequenced taxa can lead to robust phylogenetic hypotheses.
Item Details
| Item Type: | Refereed Article |
|---|---|
| Keywords: | Bayesian Epacridaceae Maximum likelihood Missing data Matrix Representation with Parsimony Scaffold concept |
| Research Division: | Biological Sciences |
| Research Group: | Evolutionary Biology |
| Research Field: | Phylogeny and Comparative Analysis |
| Objective Division: | Expanding Knowledge |
| Objective Group: | Expanding Knowledge |
| Objective Field: | Expanding Knowledge in the Biological Sciences |
| UTAS Author: | Johnson, KA (Dr Karen Johnson) |
| UTAS Author: | Holland, BR (Associate Professor Barbara Holland) |
| ID Code: | 73456 |
| Year Published: | 2012 |
| Web of Science® Times Cited: | 13 |
| Deposited By: | Geography and Environmental Studies |
| Deposited On: | 2011-10-10 |
| Last Modified: | 2017-10-30 |
| Downloads: | 2 View Download Statistics |
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