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

dc.contributor.author

Rothfels, CJ

dc.contributor.author

Li, F

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Sigel, EM

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Huiet, L

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Larsson, A

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Burge, DO

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Ruhsam, M

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Deyholos, M

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Soltis, DE

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Stewart Jr, CN

dc.coverage.spatial

United States

dc.date.accessioned

2015-10-28T20:32:41Z

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2015-07

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.identifier

http://www.ncbi.nlm.nih.gov/pubmed/26199366

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ajb.1500089

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1537-2197

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https://hdl.handle.net/10161/10798

dc.language

eng

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Botanical Society of America

dc.relation.ispartof

Am J Bot

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10.3732/ajb.1500089

dc.subject

Equisetum

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codon models

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curated phylogenomics

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divergence time dating

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fern chronogram

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incomplete lineage sorting

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low-copy nuclear gene

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model selection

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monilophytes

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transcriptome

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Base Sequence

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Biological Evolution

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DNA, Plant

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Ferns

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Gene Dosage

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Genetic Loci

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Models, Genetic

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Molecular Sequence Data

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Phylogeny

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Sequence Alignment

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Sequence Analysis, DNA

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Transcriptome

dc.title

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

dc.type

Journal article

duke.contributor.orcid

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

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

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