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Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
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2012 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, 490-509 p.Article in journal (Refereed) Published
Abstract [en]

Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to data sets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance of the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.

Place, publisher, year, edition, pages
2012. Vol. 61, no 3, 490-509 p.
Keyword [en]
Moderate data, outgroup rooting, Phycas, phylogeny evaluation, rate heterogeneity, reduced consensus, star-tree paradox, Woodsiaceae
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-174717DOI: 10.1093/sysbio/sys001ISI: 000303336200009OAI: oai:DiVA.org:uu-174717DiVA: diva2:528688
Available from: 2012-05-28 Created: 2012-05-25 Last updated: 2015-01-23Bibliographically approved
In thesis
1. Systematics of Woodsia: Ferns, bioinformatics and more
Open this publication in new window or tab >>Systematics of Woodsia: Ferns, bioinformatics and more
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Ferns are one of the three main clades of vascular plants. They have few easily studied morphological characters, reflected in a historically unstable classification. The fern genus Woodsia is known to have a complex evolutionary history including numerous polyploid taxa and hybrids. It is a cosmopolitan group of small rock loving ferns mainly found in montane areas.

This thesis aims at analyzing the patterns of diploid and polyploid evolution in Woodsia and to resolve and classify the relationships of Woodsiaceae and the other families in the large fern clade Eupolypods II.

The Eupolypods II family relationships were inferred with DNA sequences from 81 specimens representing all major lineages. This resulted in the first well supported phylogeny of this clade and revealed Woodsiaceae to be non-monophyletic. The genera previously placed in this family were reclassified into five new or resurrected families. Swedish fern genera that have changed family classification are Woodsia (hällebräknar), now in the monogeneric family Woodsiaceae, Athyrium (majbräknar), now  in Athyriaceeae and Cystopteris (stenbräknar) and Gymnocarpium (ekbräknar) now in Cystopteridaceae.

To analyze the evolution of Woodsia, phylogenies were produced from five plastid and two nuclear regions sequenced from 188 specimens. The results show that most taxa in Woodsia are polyploid. Polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young and many of the polyploid taxa seem to have formed multiple times. The results also address several taxonomic and biogeographic questions.

In the process of the work we made methodological advancements and developed 20 new low copy nuclear marker regions as well as a software pipeline for finding primers in transcriptome datasets. The alignment editor software AliView was developed for handling the increasing size datasets in a user friendly way.

In conclusion this thesis provides new insights into the complexities of the evolution of a fern genus in which much of the diversity is accommodated in young species formed through polyploidization. It provides a framework of phylogenetic relationships at different levels that both answers long standing questions and generates new ones.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 36 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1182
ferns, Eupolypods II, Woodsia, phylogeny, biogeography, polyploidy, polyploid speciation, classification, alignment
National Category
Biological Systematics
Research subject
Biology with specialization in Systematics
urn:nbn:se:uu:diva-232233 (URN)978-91-554-9040-9 (ISBN)
Public defence
2014-10-31, Lindahlsalen, Norbyvägen 18B, Uppsala, 10:00 (English)
Swedish Research Council Formas, 2006-429 and 2010-585
Available from: 2014-10-10 Created: 2014-09-15 Last updated: 2015-01-23

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