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The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

dc.contributor.author Rothfels, CJ
dc.contributor.author Li, F
dc.contributor.author Sigel, EM
dc.contributor.author Huiet, L
dc.contributor.author Larsson, A
dc.contributor.author Burge, DO
dc.contributor.author Ruhsam, M
dc.contributor.author Deyholos, M
dc.contributor.author Soltis, DE
dc.contributor.author Stewart Jr, CN
dc.coverage.spatial United States
dc.date.accessioned 2015-10-28T20:32:41Z
dc.date.issued 2015-07
dc.identifier http://www.ncbi.nlm.nih.gov/pubmed/26199366
dc.identifier ajb.1500089
dc.identifier.uri https://hdl.handle.net/10161/10798
dc.description.abstract UNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
dc.language eng
dc.publisher Botanical Society of America
dc.relation.ispartof Am J Bot
dc.relation.isversionof 10.3732/ajb.1500089
dc.subject Equisetum
dc.subject codon models
dc.subject curated phylogenomics
dc.subject divergence time dating
dc.subject fern chronogram
dc.subject incomplete lineage sorting
dc.subject low-copy nuclear gene
dc.subject model selection
dc.subject monilophytes
dc.subject transcriptome
dc.subject Base Sequence
dc.subject Biological Evolution
dc.subject DNA, Plant
dc.subject Ferns
dc.subject Gene Dosage
dc.subject Genetic Loci
dc.subject Models, Genetic
dc.subject Molecular Sequence Data
dc.subject Phylogeny
dc.subject Sequence Alignment
dc.subject Sequence Analysis, DNA
dc.subject Transcriptome
dc.title The evolutionary history of ferns inferred from 25 low-copy nuclear genes.
dc.type Journal article
duke.contributor.id Pryer, Kathleen M|0079353
pubs.author-url http://www.ncbi.nlm.nih.gov/pubmed/26199366
pubs.begin-page 1089
pubs.end-page 1107
pubs.issue 7
pubs.organisational-group Biology
pubs.organisational-group Duke
pubs.organisational-group Trinity College of Arts & Sciences
pubs.publication-status Published
pubs.volume 102
dc.identifier.eissn 1537-2197
duke.contributor.orcid Pryer, Kathleen M|0000-0002-9776-6736


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