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Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes

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Abstract

We estimated the dates of the monocot–dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li–Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot–dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li–Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li–Tanimura method, we propose that monocots branched off from dicots 140–150 Myr ago (late Jurassic–early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous). These estimates indicate that both the monocot–dicot divergence and the core eudicot’s age are older than their respective fossil records.

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Acknowledgements

We thank Robert Friedman for critical comments on an early version of the manuscript and Yoshihiro Matsuoka and Shu-Shin Wu for help with the gene group assignment for the three grasses and other taxa. We also thank the two reviewers’ critical and valuable comments and suggestions. This work was supported in part by National Science Council Grant NSC912311B001103, and Academia Sinica Grant IB91 to S.M.C., and NIH Grant GM30998 to W.H.L.

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Authors and Affiliations

  1. Institute of Botany, Academia Sinica, 128 Sec. 2, Academy Road, Taipei 115, Taiwan

    Shu-Miaw Chaw, Chien-Chang Chang & Hsin-Liang Chen

  2. Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

    Wen-Hsiung Li

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  1. Shu-Miaw Chaw
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  2. Chien-Chang Chang
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  3. Hsin-Liang Chen
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  4. Wen-Hsiung Li
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Correspondence to Shu-Miaw Chaw.

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Chaw, SM., Chang, CC., Chen, HL. et al. Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes . J Mol Evol 58, 424–441 (2004). https://doi.org/10.1007/s00239-003-2564-9

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  • DOI: https://doi.org/10.1007/s00239-003-2564-9

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