Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

Rothfels, Carl J

Larsson, Anders

Kuo, Li-Yaung

Korall, Petra

Chiou, Wen-Liang

Pryer, Kathleen M

2020-12-01T21:08:35Z

2020-12-01T21:08:35Z

2012-05

2020-12-01T21:08:33Z

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: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and 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 data sets 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 of 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.

sys001

1063-5157

1076-836X

https://hdl.handle.net/10161/21788

eng

Oxford University Press (OUP)

Systematic biology

10.1093/sysbio/sys001

Ferns

Bayes Theorem

Phylogeny

Genes, Plant

Molecular Sequence Data

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

Journal article

Pryer, Kathleen M|0000-0002-9776-6736

490

509

3

Trinity College of Arts & Sciences

Biology

Duke Science & Society

Duke

Initiatives

Institutes and Provost's Academic Units

Staff

Published

61