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

dc.contributor.author Rothfels, Carl J
dc.contributor.author Larsson, Anders
dc.contributor.author Kuo, Li-Yaung
dc.contributor.author Korall, Petra
dc.contributor.author Chiou, Wen-Liang
dc.contributor.author Pryer, Kathleen M
dc.date.accessioned 2020-12-01T21:08:35Z
dc.date.available 2020-12-01T21:08:35Z
dc.date.issued 2012-05
dc.identifier sys001
dc.identifier.issn 1063-5157
dc.identifier.issn 1076-836X
dc.identifier.uri https://hdl.handle.net/10161/21788
dc.description.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.
dc.language eng
dc.publisher Oxford University Press (OUP)
dc.relation.ispartof Systematic biology
dc.relation.isversionof 10.1093/sysbio/sys001
dc.subject Ferns
dc.subject Bayes Theorem
dc.subject Phylogeny
dc.subject Genes, Plant
dc.subject Molecular Sequence Data
dc.title Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.
dc.type Journal article
duke.contributor.id Rothfels, Carl J|0389798
duke.contributor.id Pryer, Kathleen M|0079353
dc.date.updated 2020-12-01T21:08:33Z
pubs.begin-page 490
pubs.end-page 509
pubs.issue 3
pubs.organisational-group Trinity College of Arts & Sciences
pubs.organisational-group Biology
pubs.organisational-group Duke Science & Society
pubs.organisational-group Duke
pubs.organisational-group Initiatives
pubs.organisational-group Institutes and Provost's Academic Units
pubs.organisational-group Staff
pubs.publication-status Published
pubs.volume 61
duke.contributor.orcid Pryer, Kathleen M|0000-0002-9776-6736


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