Plant Systematics and Evolution

, Volume 298, Issue 2, pp 297–312

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

Original Article

DOI: 10.1007/s00606-011-0544-x

Cite this article as:
Crawley, S.S. & Hilu, K.W. Plant Syst Evol (2012) 298: 297. doi:10.1007/s00606-011-0544-x


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.


CaryophyllalesAngiospermMissing dataTaxon samplingPhylogenetics

Supplementary material

606_2011_544_MOESM1_ESM.doc (78 kb)
Supplementary material 1 (DOC 77 kb)
606_2011_544_MOESM2_ESM.doc (220 kb)
Supplementary material 2 (DOC 220 kb)
606_2011_544_MOESM3_ESM.doc (538 kb)
Supplementary material 3 (DOC 537 kb)
606_2011_544_MOESM4_ESM.eps (1 mb)
Supplementary material 4 (EPS 1050 kb)
606_2011_544_MOESM5_ESM.eps (487 kb)
Supplementary material 5 (EPS 487 kb)
606_2011_544_MOESM6_ESM.eps (1.1 mb)
Supplementary material 6 (EPS 1142 kb)
606_2011_544_MOESM7_ESM.eps (1.1 mb)
Supplementary material 7 (EPS 1166 kb)
606_2011_544_MOESM8_ESM.eps (1.2 mb)
Supplementary material 8 (EPS 1219 kb)
606_2011_544_MOESM9_ESM.eps (1.8 mb)
Supplementary material 9 (EPS 1869 kb)
606_2011_544_MOESM10_ESM.eps (1.2 mb)
Supplementary material 10 (EPS 1206 kb)
606_2011_544_MOESM11_ESM.tiff (2.9 mb)
Supplementary material 11 (TIFF 2931 kb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Department of Biological SciencesVirginia TechBlacksburgUSA