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Botany 2015 Colloquium: Phylogenomics and the 1000 plants (1KP) initiative

Rothfels, Carl [1], Li, Fay-Wei [2], Sigel, Erin M. [3], Huiet, Layne [4], Larsson, Anders [5], Graham, Sean W. [6], Wong, Gane Ka-Shu [7], Pryer, Kathleen M. [8].

Curated phylogenomics and the first single-copy nuclear phylogeny of the ferns.

Molecular phylogenetic investigations over the past two decades have revolutionized our understanding of fern phylogeny; however, the vast majority of these studies used only plastid data. Through the efforts of the 1KP project, nuclear data from a broad sample of ferns are available for the first time, providing the opportunity to independently assess established plastid-based phylogenetic hypotheses. Here we adopt a “curated phylogenomics” approach that combines broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35,877 bp), and applies rigorous alignment inference, orthology inference, and model selection. This approach proved effective at inferring a strongly supported phylogeny, while being arguably less sensitive to systematic biases than would a truly genome-scale analysis. Our phylogeny is broadly congruent with previous inferences from plastid data, but also provides novel insights. In particular, we find strong support for horsetails as sister to the rest of ferns, marattioid ferns as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypod ferns. Our divergence-time analyses provide the first temporal framework for fern evolution that includes broad representation of both eusporangiate and leptosporangiate lineages, and reveal that the extant fern orders diverged prior to ~200 million years ago. Finally, our species-tree inferences are congruent with analyses of the concatenated data, but with generally lower support. Instances where species-tree support values are proportionally higher than expected involve relationships that were well supported by smaller plastid datasets. This result suggests that deep coalescence is reducing support from the concatenated nuclear data and highlights the fact that data characteristics as well as data quantity need to be considered in phylogenetic studies.


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1 - University of California, Berkeley, University Herbarium and Dept. of Integrative Biology, Berkeley, CA, 94720-2465, USA
2 - Duke University, Biology, Durham, NC, 27708, USA
3 - National Museum of Natural History, Smithsonian Institution, Department of Botany, Washington DC, DC, 20013, USA
4 - Duke University, Biology, Box 90338, Durham, NC, 27708, USA
5 - Evolutionary Biology Centre, Uppsala University, Department of Organismal Biology, Uppsala, Sweden
6 - University of British Columbia, Department of Botany, Vancouver, BC, V6J3S7, Canada
7 - University of Alberta, Biological Sciences; Medicine (Gastroenterology), CW405 Biological Sciences, Edmonton, AB, T6G 2E9, Canada
8 - Duke University, Science Drive, Durham, NC, 27708-0338, USA

Keywords:
codon models
curated phylogenomics
deep coalescence
divergence time
Equisetum
fern chronogram
incomplete lineage sorting
model selection
moderate data
monilophytes
single-copy nuclear gene
taxon sampling.

Presentation Type: Colloquium Presentations
Session: C1
Location: Salon 4/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 10:30 AM
Number: C1011
Abstract ID:616
Candidate for Awards:None


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