Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).
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 articleSubject
Chromosomes, PlantCell Nucleus
Plastids
Pteridaceae
DNA, Plant
Genetic Markers
Bayes Theorem
Phylogeny
Base Sequence
Gene Dosage
Ploidies
Mexico
Southwestern United States
Biological Evolution
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https://hdl.handle.net/10161/21745Published Version (Please cite this version)
10.1016/j.ympev.2019.05.016Publication 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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Kathleen M. Pryer
Professor of Biology

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