The evolutionary history of ferns inferred from 25 low-copy nuclear genes
2015 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 0032-0919, Vol. 102, no 7, 1089-1107 p.Article in journal (Refereed) Published
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 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 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 similar 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.
Place, publisher, year, edition, pages
2015. Vol. 102, no 7, 1089-1107 p.
codon models, curated phylogenomics, divergence time dating, Equisetum, fern chronogram, incomplete lineage sorting, low-copy nuclear gene, model selection, monilophytes, transcriptome
IdentifiersURN: urn:nbn:se:uu:diva-260632DOI: 10.3732/ajb.1500089ISI: 000358275800008PubMedID: 26199366OAI: oai:DiVA.org:uu-260632DiVA: diva2:847864
FunderSwedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 2006-429, 2010-585
Funding: National Science Foundation OCI-1053575, Natural Sciences and Engineering Research Council [Canada] (PGSD), National Science Foundation [U.S.A.] DEB-1110767 DEB-1145614 DEB-1110775 DEB-1407158, Alberta Ministry of Innovation and Advanced Education, Natural Sciences and Engineering Research Council [Canada] (PDF), Alberta Innovates Technology Futures' Innovates Centers of Research Excellence program, Musea Ventures, BGI-Shenzhen 2015-08-212015-08-212015-08-21Bibliographically approved