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Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data
journal contribution
posted on 2023-05-17, 08:26 authored by Karen JohnsonKaren Johnson, Barbara HollandBarbara Holland, Heslewood, MM, Crayn, DMFor 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.
History
Publication title
Molecular Phylogenetics and EvolutionVolume
62Pagination
146-158ISSN
1055-7903Department/School
School of Geography, Planning and Spatial SciencesPublisher
Academic PressPlace of publication
3251 Riverport Ln, Maryland Heights, MO 63043 USARights statement
The definitive version is available at http://www.sciencedirect.comRepository Status
- Restricted