Plant Systematics and Evolution

, Volume 298, Issue 2, pp 297–312 | Cite as

Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: the Caryophyllales (angiosperms)

Original Article

Abstract

Density of taxon sampling and number/kind of characters are central to achieving the ultimate goals in phylogenetic reconstruction: tree robustness and improved accuracy. In molecular phylogenetics, DNA sequence repositories such as GenBank are potential sources for expanding datasets in two dimensions, taxa and characters, to the level of “supermatrices.” However, the issue of missing characters/genomic regions is generally considered a major impediment to this endeavor. We used here the angiosperm order Caryophyllales to systematically address the impact of missing data when expanding taxon sampling and number of characters in phylogenetic reconstruction. Our analyses show that expansion of taxon sampling by ~13-fold resulted in improved phylogenetic assessment of the Caryophyllales despite up to 38% missing data. Expanding number of characters in the dataset by allowing for up to 100-fold increase in amount of missing data and inclusion of entries with about 40% missing genomic regions did not negatively impact tree structure or robustness, but to the contrary improved both. These results are timely regarding the ongoing efforts to achieve detailed assessment of the tree of life.

Keywords

Caryophyllales Angiosperm Missing data Taxon sampling Phylogenetics 

Notes

Acknowledgments

The authors thank J. Gordon Burleigh for his contributions to this manuscript; and D. and P. Soltis, S. Brockington, and M. Moore, as well as the Missouri Botanical Garden and the Royal Botanic Garden at Kew for providing DNA samples for several taxa. We thank M. Barthet for help in designing a primer, A. Hinckle for helping with specimen collection, S. Newman for assistance in laboratory work, and A. Ferraioli for assistance with figures. We also thank two anonymous reviewers for their comments and suggestions. This work is part of the AToL-Angiosperm project supported by grants from the National Science Foundation, USA (EF-043105 and REU-477683 3) to K.W.H.

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© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Department of Biological SciencesVirginia TechBlacksburgUSA

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