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

Carl J. Rothfels, Fay Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, C. Neal Stewart, Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude Walker Depamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. StevensonSean W. Graham, Gane K.S. Wong, Kathleen M. Pryer

Research output: Contribution to journalArticle

72 Citations (Scopus)

Abstract

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 fi rst 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 35 877 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 fi nd 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.

Original languageEnglish (US)
Pages (from-to)1089-1107
Number of pages19
JournalAmerican journal of botany
Volume102
Issue number7
DOIs
StatePublished - Jul 1 2015

Fingerprint

Ferns
fern
ferns and fern allies
History
history
Phylogeny
gene
Genes
phylogeny
genes
Plastids
plastid
Dennstaedtiaceae
plastids
Equisetales
Marattiales
divergence
Embryophyta
phylogenetics
loci

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science

Cite this

Rothfels, C. J., Li, F. W., Sigel, E. M., Huiet, L., Larsson, A., Burge, D. O., ... Pryer, K. M. (2015). The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American journal of botany, 102(7), 1089-1107. https://doi.org/10.3732/ajb.1500089
Rothfels, Carl J. ; Li, Fay Wei ; Sigel, Erin M. ; Huiet, Layne ; Larsson, Anders ; Burge, Dylan O. ; Ruhsam, Markus ; Deyholos, Michael ; Soltis, Douglas E. ; Stewart, C. Neal ; Shaw, Shane W. ; Pokorny, Lisa ; Chen, Tao ; Depamphilis, Claude Walker ; DeGironimo, Lisa ; Chen, Li ; Wei, Xiaofeng ; Sun, Xiao ; Korall, Petra ; Stevenson, Dennis W. ; Graham, Sean W. ; Wong, Gane K.S. ; Pryer, Kathleen M. / The evolutionary history of ferns inferred from 25 low-copy nuclear genes. In: American journal of botany. 2015 ; Vol. 102, No. 7. pp. 1089-1107.
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abstract = "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 fi rst 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 35 877 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 fi nd 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.",
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Rothfels, CJ, Li, FW, Sigel, EM, Huiet, L, Larsson, A, Burge, DO, Ruhsam, M, Deyholos, M, Soltis, DE, Stewart, CN, Shaw, SW, Pokorny, L, Chen, T, Depamphilis, CW, DeGironimo, L, Chen, L, Wei, X, Sun, X, Korall, P, Stevenson, DW, Graham, SW, Wong, GKS & Pryer, KM 2015, 'The evolutionary history of ferns inferred from 25 low-copy nuclear genes', American journal of botany, vol. 102, no. 7, pp. 1089-1107. https://doi.org/10.3732/ajb.1500089

The evolutionary history of ferns inferred from 25 low-copy nuclear genes. / Rothfels, Carl J.; Li, Fay Wei; Sigel, Erin M.; Huiet, Layne; Larsson, Anders; Burge, Dylan O.; Ruhsam, Markus; Deyholos, Michael; Soltis, Douglas E.; Stewart, C. Neal; Shaw, Shane W.; Pokorny, Lisa; Chen, Tao; Depamphilis, Claude Walker; DeGironimo, Lisa; Chen, Li; Wei, Xiaofeng; Sun, Xiao; Korall, Petra; Stevenson, Dennis W.; Graham, Sean W.; Wong, Gane K.S.; Pryer, Kathleen M.

In: American journal of botany, Vol. 102, No. 7, 01.07.2015, p. 1089-1107.

Research output: Contribution to journalArticle

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T1 - The evolutionary history of ferns inferred from 25 low-copy nuclear genes

AU - Rothfels, Carl J.

AU - Li, Fay Wei

AU - Sigel, Erin M.

AU - Huiet, Layne

AU - Larsson, Anders

AU - Burge, Dylan O.

AU - Ruhsam, Markus

AU - Deyholos, Michael

AU - Soltis, Douglas E.

AU - Stewart, C. Neal

AU - Shaw, Shane W.

AU - Pokorny, Lisa

AU - Chen, Tao

AU - Depamphilis, Claude Walker

AU - DeGironimo, Lisa

AU - Chen, Li

AU - Wei, Xiaofeng

AU - Sun, Xiao

AU - Korall, Petra

AU - Stevenson, Dennis W.

AU - Graham, Sean W.

AU - Wong, Gane K.S.

AU - Pryer, Kathleen M.

PY - 2015/7/1

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N2 - 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 fi rst 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 35 877 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 fi nd 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.

AB - 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 fi rst 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 35 877 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 fi nd 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.

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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO et al. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American journal of botany. 2015 Jul 1;102(7):1089-1107. https://doi.org/10.3732/ajb.1500089