A new support measure to quantify the impact of local optima in phylogenetic analyses.
KAUST Grant NumberKUS-C1-016-04
Permanent link to this recordhttp://hdl.handle.net/10754/596759
MetadataShow full item record
AbstractPhylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support for each clade. For situations with multiple local optima, we propose p-support which is a clade support measure that shows the impact optima have on a final consensus tree. Our p-support measure is implemented in our PeakMapper software package. We study our approach on two published, large-scale biological tree collections. PeakMapper shows that each data set contains multiple local optima. p-support shows that both datasets contain clades in the majority consensus tree that are only supported by a subset of the local optima. Clades with low p-support are most likely to benefit from further investigation. These tools provide researchers with new information regarding phylogenetic analyses beyond what is provided by other support measures alone.
CitationBrammer, Seung-Jin Sul, Tiffani L. Williams (2011) A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses. EBO: 159. Available: http://dx.doi.org/10.4137/EBO.S7182.
SponsorsThis work was supported by the National Science Foundation under grants DEB-0629849, IIS-0713618, and IIS-1018785.We would like to thank Matthew Gitzendanner, Paul Lewis, and David Soltis for providing us with the tree collections used in this paper. Moreover, this publication is based in part on work supported by Award No. KUS-C1-016-04, made by King Abdullah University of Science and Technology (KAUST).
PublisherLibertas Academica, Ltd.
PubMed Central IDPMC3204936
CollectionsPublications Acknowledging KAUST Support
- Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.
- Authors: Gatesy J, Springer MS
- Issue date: 2014 Nov
- Complete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches.
- Authors: Baker WJ, Savolainen V, Asmussen-Lange CB, Chase MW, Dransfield J, Forest F, Harley MM, Uhl NW, Wilkinson M
- Issue date: 2009 Apr
- Multiple maxima of likelihood in phylogenetic trees: an analytic approach.
- Authors: Chor B, Hendy MD, Holland BR, Penny D
- Issue date: 2000 Oct
- Majority-rule reduced consensus trees and their use in bootstrapping.
- Authors: Wilkinson M
- Issue date: 1996 Mar
- Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1).
- Authors: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Paul M Peterson, Soreng RJ, Paszko B
- Issue date: 2017