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Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).

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Date
2019-09
Authors
Kao, T
Pryer, KM
Freund, FD
Windham, MD
Rothfels, CJ
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Abstract
Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having "farina"-powdery exudates of lipophilic flavonoid aglycones-that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious. In a striking case of convergence, Notholaena standleyi appears to be distantly related to core Notholaena, with several taxa not before associated with Notholaena nested between them. Such conflicts can be due to morphological homoplasy resulting from adaptive convergence or, alternatively, the plastid phylogeny itself might be misleading, diverging from the true species tree due to incomplete lineage sorting, hybridization, or other factors. In this study, we present a species phylogeny for notholaenid ferns, using four low-copy nuclear loci and concatenated data from three plastid loci. A total of 61 individuals (49 notholaenids and 12 outgroup taxa) were sampled, including 31 out of 37 recognized notholaenid species. The homeologous/allelic nuclear sequences were retrieved using PacBio sequencing and the PURC bioinformatics pipeline. Each dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Although we observed several incongruences between the nuclear and plastid phylogenies, our principal results are broadly congruent with previous inferences based on plastid data. By mapping the presence of farina and their biochemical constitutions on our consensus phylogenetic tree, we confirmed that the characters are indeed homoplastic and have complex evolutionary histories. Hybridization among recognized species of the notholaenid clade appears to be relatively rare compared to that observed in other well-studied fern genera.
Type
Journal article
Subject
Chromosomes, Plant
Cell Nucleus
Plastids
Pteridaceae
DNA, Plant
Genetic Markers
Bayes Theorem
Phylogeny
Base Sequence
Gene Dosage
Ploidies
Mexico
Southwestern United States
Biological Evolution
Permalink
https://hdl.handle.net/10161/21745
Published Version (Please cite this version)
10.1016/j.ympev.2019.05.016
Publication Info
Kao, T; Pryer, KM; Freund, FD; Windham, MD; & Rothfels, CJ (2019). Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae). Molecular phylogenetics and evolution, 138. pp. 139-155. 10.1016/j.ympev.2019.05.016. Retrieved from https://hdl.handle.net/10161/21745.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Pryer

Kathleen M. Pryer

Professor of Biology
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