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Systematics of Woodsia: Ferns, bioinformatics and more
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
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.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1182
Keyword [en]
ferns, Eupolypods II, Woodsia, phylogeny, biogeography, polyploidy, polyploid speciation, classification, alignment
National Category
Biological Systematics
Research subject
Biology with specialization in Systematics
Identifiers
URN: urn:nbn:se:uu:diva-232233ISBN: 978-91-554-9040-9 (print)OAI: oai:DiVA.org:uu-232233DiVA: diva2:747587
Public defence
2014-10-31, Lindahlsalen, Norbyvägen 18B, Uppsala, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council Formas, 2006-429 and 2010-585
Available from: 2014-10-10 Created: 2014-09-15 Last updated: 2015-01-23
List of papers
1. Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
Open this publication in new window or tab >>Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
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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.

Keyword
Moderate data, outgroup rooting, Phycas, phylogeny evaluation, rate heterogeneity, reduced consensus, star-tree paradox, Woodsiaceae
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-174717 (URN)10.1093/sysbio/sys001 (DOI)000303336200009 ()
Available from: 2012-05-28 Created: 2012-05-25 Last updated: 2017-12-07Bibliographically approved
2. A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales)
Open this publication in new window or tab >>A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales)
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2012 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 61, no 3, 515-533 p.Article in journal (Refereed) Published
Abstract [en]

We present a family-level classification for the eupolypod II clade of leptosporangiate ferns, one of the two major lineages within the Eupolypods, and one of the few parts of the fern tree of life where family-level relationships were not well understood at the time of publication of the 2006 fern classification by Smith & al. Comprising over 2500 species, the composition and particularly the relationships among the major clades of this group have historically been contentious and defied phylogenetic resolution until very recently. Our classification reflects the most current available data, largely derived from published molecular phylogenetic studies. In comparison with the five-family (Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae, Woodsiaceae) treatment of Smith & al., we recognize 10 families within the eupolypod II clade. Of these, Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae have the same composition as treated by Smith & al. Woodsiaceae, which Smith & al. acknowledged as possibly non-monophyletic in their treatment, is circumscribed here to include only Woodsia and its segregates; the other "woodsioid" taxa are divided among Athyriaceae, Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and Hemidictyaceae. We provide circumscriptions for each family, which summarize their morphological, geographical, and ecological characters, as well as a dichotomous key to the eupolypod II families. Three of these families-Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae-were described in the past year based on molecular phylogenetic analyses; we provide here their first morphological treatment.

Keyword
Athyriaceae, Diplaziopsis, ferns, Rhachidosorus, taxonomy, Woodsiaceae
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-177615 (URN)000305439100003 ()
Available from: 2012-07-17 Created: 2012-07-17 Last updated: 2017-12-07Bibliographically approved
3. Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns
Open this publication in new window or tab >>Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns
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2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 10, e76957- p.Article in journal (Refereed) Published
Abstract [en]

Background: Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. Principal Findings: We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. Conclusions: The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-210575 (URN)10.1371/journal.pone.0076957 (DOI)000325552200089 ()
Available from: 2013-11-13 Created: 2013-11-11 Last updated: 2017-12-06Bibliographically approved
4. AliView: a fast and lightweight alignment viewer and editor for large data sets
Open this publication in new window or tab >>AliView: a fast and lightweight alignment viewer and editor for large data sets
2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 22, 3276-3278 p.Article in journal (Refereed) Published
Abstract [en]

Summary: AliView is an alignment viewer and editor designed tomeet the requirements of next generation sequencing era phyloge-netic datasets. AliView handles alignments of unlimited size in theformats most commonly used, i.e. Fasta, Phylip, Nexus, Clustal andMSF. The intuitive graphical interface makes it easy to inspect, sort,delete, merge and realign sequences as part of the manual filteringprocess of large data sets. AliView also works as an easy to usealignment editor for small as well as large data sets.Availability: AliView is released as open-source software under theGNU General Public License, version 3.0 (GPLv3), and is availableat GitHub (www.github.com/AliView). The program is cross-platformand extensively tested on Linux, Mac OS X and Windows systems.Downloads and help are available at http://ormbunkar.se/aliviewContact: anders.larsson@ebc.uu.seSupplementary information:

National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:uu:diva-232231 (URN)10.1093/bioinformatics/btu531 (DOI)000344774600022 ()
Funder
Swedish Research Council Formas, 2006-429 and 2010-585
Available from: 2014-09-15 Created: 2014-09-15 Last updated: 2017-12-05Bibliographically approved
5. Phylogeny of Woodsia (Woodsiaceae): recent speciation through polyploidization is common in old diploid stock.
Open this publication in new window or tab >>Phylogeny of Woodsia (Woodsiaceae): recent speciation through polyploidization is common in old diploid stock.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Woodsia is a genus of small tufted ferns growing in rocky habitats. It is widely distributed in temperate and montane regions of the world. Through previous cytological studies and allozyme work it is known to have a complex evolutionary history and includes numerous polyploid taxa and hybrids. We present here for the first time detailed phylogenetic analyses of a wide range of taxa within Woodsia, including samples from many chromosome-counted specimens. Five plastid (atpA, atpB, matK, rbcL and trnG-R) and two nuclear (pgiC and RPA2) regions have been used from an ingroup of 188 samples representing 36 taxa and six hybrids. In a complementary expanded analysis the polyploid speciation frequency is estimated within the 10 families most closely related to Woodsiaceae (the Eupolypods II). Woodsia is monophyletic if the often segregated genera Protowoodsia, Cheilanthopsis and Hymenocystis are included. The genus comprises two major well-supported clades, one including the circumboreal and most of the Asian species, and the other including all American and the remaining Asian species. The split between these clades is estimated to 45 Ma. Woodsia × abbae is a remarkable triploid hybrid between members of these two clades. Most taxa in Woodsia are polyploid and polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young. Some of the polyploid taxa, such as W. alpina and W. obtusa, seem to have been formed multiple times. The Eupolypod II study agrees with the Woodsia study in showing a high proportion of polyploids with a polyploid speciation rate of 46%. Old polyploid lineages are rare. The circumboreal species do not form a monophyletic group and are nested among various Asian species, whereas the "American clade" is monophyletic and nested among Asian species. Within the American clade W. montevidensis has its main distribution in South America, but also has made a recent leap to Southern Africa and Madagascar.

Keyword
biogeography, chromosome numbers, Eupolypods II, hybrids, nuclear and plastid DNA, polyploid speciation
National Category
Botany
Research subject
Biology with specialization in Systematics
Identifiers
urn:nbn:se:uu:diva-232232 (URN)
Funder
Formas, 2006-429 and 2010-585
Available from: 2014-09-15 Created: 2014-09-15 Last updated: 2015-01-23

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