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

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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.

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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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Correspondence to S. S. Crawley.

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Online Resource 4 (ESM_4) MP strict consensus tree based on the matK/trnK intron dataset for 51 Caryophyllales taxa (0.3% missing data). Percent bootstrap values greater than 50% are noted on branches

Online Resource 5 (ESM_5) Summary of the MP strict consensus tree based on matK/trnK intron data with expanded taxon sampling (652 taxa with 38% missing data). Percent bootstrap values greater than 50% are noted on branches

Online Resource 6 (ESM_6) ML tree based on the five genomic regions (rbcL, atpB, ndhF, matK, and trnK intron) for 136 Caryophyllales taxa. Percent bootstrap values greater than 50% are noted on branches. (a) Expanded details for the “AAC” and “raphide” clades. (b) Expanded details for the “succulents” clade. (c) Expanded details for the “FTPP” and “carnivorous” clades

Online Resource 7 (ESM_7) MP strict consensus tree based on the dataset of five genomic regions (rbcL, atpB, ndhF, matK, and trnK intron) for 136 taxa (5GR-136; 46% missing data). Percent bootstrap values greater than 50% are noted on branches. (a) The FTPP and carnivorous clades have been collapsed. (b) FTPP and carnivorous clades are expanded

Online Resource 8 (ESM_8) ML tree based on the matK/trnK intron dataset for 51 Caryophyllales taxa. Branch lengths are noted on the branches

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Crawley, S.S., Hilu, K.W. Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: the Caryophyllales (angiosperms). Plant Syst Evol 298, 297–312 (2012). https://doi.org/10.1007/s00606-011-0544-x

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