Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.
Abstract
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.
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https://hdl.handle.net/10161/21788Published Version (Please cite this version)
10.1093/sysbio/sys001Publication Info
Rothfels, Carl J; Larsson, Anders; Kuo, Li-Yaung; Korall, Petra; Chiou, Wen-Liang;
& Pryer, Kathleen M (2012). Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid
radiation of eupolypod II ferns. Systematic biology, 61(3). pp. 490-509. 10.1093/sysbio/sys001. Retrieved from https://hdl.handle.net/10161/21788.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Kathleen M. Pryer
Professor of Biology

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