Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
- Carl J. Rothfels*,‡,1,
- Anders Larsson‡,2,
- Li-Yaung Kuo‡,3,
- Petra Korall2,
- Wen-Liang Chiou4 and
- Kathleen M. Pryer1
- 1Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708, USA
- 2Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36, Uppsala, Sweden
- 3Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan
- 4Botanical Garden Division, Taiwan Forestry Research Institute, 53 Nan-hai Road, Taipei, 10066, Taiwan
- ↵*Correspondence to be sent to: Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708, USA; E-mail: ; Phone: 919 485 9544.
- Received December 29, 2010.
- Revision received March 20, 2011.
- Revision received August 18, 2011.
- Accepted August 23, 2011.
Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: 1) a long root that reduces apparent levels of support in the ingroup; 2) long ingroup branches subtended by a series of very short backbone internodes (the “ancient rapid radiation” model); and 3) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a dataset of five plastid loci (atpA, atpB, matK, rbcL, trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to datasets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance to the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis and Woodsia. [moderate data; Phycas; phylogeny evaluation; rate heterogeneity; reduced consensus; outgroup rooting; star-tree paradox; Woodsiaceae.]
- outgroup rooting
- moderate data
- phylogeny evaluation
- rate heterogeneity
- reduced consensus
- star-tree paradox
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