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Systematics and polyploid evolution in Potentilleae (Rosaceae)
Stockholm University, Faculty of Science, Department of Botany.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis comprises studies of the phylogenetic relationships in the flowering plant clade Potentilleae in Rosaceae. The relationships were elucidated by using DNA sequence data from the nuclear genome as well as from the plastid genome. In particular, the focus of the studies was the investigation of allopolyploidy, i.e. speciation as a result of hybridization and subsequent chromosome doubling. A phylogenetic method was used for identifying allopolyploidy through comparison of trees resulting from the analyses of different DNA sequences. Five sub-clades were investigated. First, both the sister clades that together contain all of Potentilleae: Fragariinae and Potentilla. Secondly, three subclades of Fragariinae, namely Alchemilla in wide sense, Sibbaldia and relatives, and Fragaria. The aim was to unravel the phylogenetic relationships, including instances of allopolyploidy. Classification issues were discussed in relation to the phylogenetic results. The split between Potentilla (=Potentillinae) and Fragariinae received better support than in previous studies. The phylogeny of Fragariinae was found to be consistent with classifying ten genera: Alchemilla in wide sense (incl. Aphanes and Lachemilla), Comarum, Sibbaldia, Sibbaldianthe, Sibbaldiopsis, Chamaerhodos, Drymocallis, Dasiphora, Potaninia, Fragaria, and also including a few orphan Potentilla species. The segregated genera Ivesia, Horkelia, Horkeliella and Duchesnea were found to be nested within Potentilla, corroborating earlier studies, while the segregated genus Argentina (P. anserina and close relatives) showed an ambiguous position. Plastid and nuclear (ribosomal) phylogenies were compared and incongruences were detected as potential instances of allopolyploid speciation. Five strongly supported incongruences were detected in Fragariinae and four of them were considered to be potentially caused by allopolyploidy. In addition, five supported incongruences were found in Potentilla. Alchemilla in the wide sense was found to contain four major clades, African Alchemilla, Eurasian Alchemilla, Lachemilla and Aphanes. Both Lachemilla and Aphanes were nested within Alchemilla and it was suggested that the name Alchemilla should be used in the wide sense, i.e. including both the genera Lachemilla and Aphanes. The genus Sibbaldia as commonly classified was shown to be polyphyletic in five different places in Potentilleae. Three Sibbaldia clades ended up in Fragariinae and two in Potentilla. A phylogeny of Fragaria, based on a nuclear low/single copy DNA region was estimated. The gene copy phylogeny was used to construct a reticulate tree hypothesizing allopolyploid speciation events. The evolution of Fragaria was shown to have been shaped by polyploidy.

Place, publisher, year, edition, pages
Stockholm: Department of Botany, Stockholm University , 2011. , 28 p.
Keyword [en]
Potentilleae, Fragariinae, Potentilla, Sibbaldia, Fragaria, Alchemilla, systematics, phylogeny, polyploidy, autopolyploidy, allopolyploidy, reticulate evolution
National Category
Biological Systematics
Research subject
Plant Systematics
Identifiers
URN: urn:nbn:se:su:diva-53967ISBN: 978-91-7447-227-1OAI: oai:DiVA.org:su-53967DiVA: diva2:392234
Public defence
2011-05-20, föreläsningssalen, Botanicum, Lilla Frescativägen 5, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.Available from: 2011-04-28 Created: 2011-01-25 Last updated: 2011-04-26Bibliographically approved
List of papers
1. Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification
Open this publication in new window or tab >>Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification
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2009 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 51, no 2, 269-280 p.Article in journal (Refereed) Published
Abstract [en]

Potential events of allopolyploidy may be indicated by incongruences between separate phylogenies based on plastid and nuclear gene sequences. We sequenced two plastid regions and two nuclear ribosomal regions for 34 ingroup taxa in Fragariinae (Rosaceae), and six outgroup taxa. We found five well supported incongruences that might indicate allopolyploidy events. The incongruences involved Aphanes arvensis, Potentilla miyabei, Potentilla cuneata, Fragaria vesca/moschata, and the Drymocallis clade. We evaluated the strength of conflict and conclude that allopolyploidy may be hypothesised in the four first cases. Phylogenies were estimated using Bayesian inference and analyses were evaluated using convergence diagnostics. Taxonomic implications are discussed for genera such as Alchemilla, Sibbaldianthe, Chamaerhodos, Drymocallis and Fragaria, and for the monospecific Sibbaldiopsis and Potaninia that are nested inside other genera. Two orphan Potentilla species, P. miyabei and P. cuneata are placed in Fragariinae. However, due to unresolved topological incongruences they are not reclassified in any genus.

National Category
Biological Sciences Biological Systematics
Research subject
Systematic Botany
Identifiers
urn:nbn:se:su:diva-34698 (URN)doi:10.1016/j.ympev.2009.02.020 (DOI)000265812000012 ()
Available from: 2010-01-11 Created: 2010-01-11 Last updated: 2011-04-26Bibliographically approved
2. Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)
Open this publication in new window or tab >>Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Several naturally occurring hybrids in Potentilla (Rosaceae) have been reported, but no molecular evidence has so far been available to test these hypotheses of hybridization. We have compared a nuclear and a chloroplast gene tree to identify topological incongruences that may indicate hybridization events in the genus. Furthermore, the monophyly and phylogenetic position of the proposed segregated genera Argentina, Ivesia and Horkelia have been tested. The systematic signal from the two morphological characters, style- and anther shape, has also been investigated by ancestral state reconstruction, to elucidate how well these characters concur with the results of the molecular phylogenies. Six major clades, Anserina, Alba, Fragarioides, Reptans, ivesioid Potentilleae and Argentea, have been identified within genus Potentilla. The ivesioid Potentilleae (Horkelia, Ivesia and Horkeliella) form a monophyletic group nested within Potentilla. Furthermore, the origin of the proposed segregated genus Argentina (the Anserina clade) is uncertain but not in conflict with a new generic status of the group. We also found style morphology to be an informative character that reflects the phylogenetic relationships within Potentilla. Four well supported incongruences were found between the nuclear and the chloroplast phylogenies, where the involved taxa were polyploids. However, further investigations using low copy molecular markers are required to infer the phylogeny of these species and to test the hypothesis of hybrid origin.

Keyword
Allopolyploidy, Potentilla, molecular phylogeny, Rosaceae, hybridization
National Category
Biological Systematics
Research subject
Systematic Botany
Identifiers
urn:nbn:se:su:diva-56686 (URN)
Available from: 2011-04-26 Created: 2011-04-20 Last updated: 2011-04-26Bibliographically approved
3. Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification
Open this publication in new window or tab >>Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification
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2008 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 47, 1030-1044 p.Article in journal (Refereed) Published
Abstract [en]

Alchemilla (the lady’s mantles) is a well known but inconspicuous group in the Rosaceae, notable for its ornamental leaves and pharmaceutical properties. The systematics of Alchemilla has remained poorly understood, most likely due to confusion resulting from apomixis, polyploidisation and hybridisation, which are frequently observed in the group, and which have led to the description of a large number of (micro-) species. A molecular phylogeny of the genus, including all sections of Alchemilla and Lachemilla as well as five representatives of Aphanes, based on the analysis of the chloroplast trnL–trnF and the nuclear ITS regions is presented here. Gene phylogenies reconstructed from the nuclear and chloroplast sequence data were largely congruent. Limited conflict between the data partitions was observed with respect to a small number of taxa. This is likely to be the result of hybridisation/introgression or incomplete lineage sorting. Four distinct clades were resolved, corresponding to major geographical division and life forms: Eurasian Alchemilla, annual Aphanes, South American Lachemilla and African Alchemilla. We argue for a wider circumscription of the genus Alchemilla, including Lachemilla and Aphanes, based on the morphology and the phylogenetic relationships between the different clades.

Keyword
Alchemilla, Lachemilla, Aphanes, Alchemillinae, Rosaceae, Molecular phylogeny, Generic delimitation, Apomixis
National Category
Biological Sciences Biological Systematics
Research subject
Plant Systematics
Identifiers
urn:nbn:se:su:diva-36223 (URN)10.1016/j.ympev.2008.03.004 (DOI)000257128900013 ()
Available from: 2010-01-22 Created: 2010-01-22 Last updated: 2011-04-26Bibliographically approved
4. Sibbaldia – a molecular phylogenetic study of a polyphyletic genus in Rosaceae
Open this publication in new window or tab >>Sibbaldia – a molecular phylogenetic study of a polyphyletic genus in Rosaceae
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Using DNA sequence data from nuclear ribosomal ITS in combination with plastid trnLF spacer and trnL intron data we show that Sibbaldia is a polyphyletic assemblage. It falls into five separate clades of Potentilleae, three within Fragariinae, and two within Potentilla (Potentillinae sensu Soják). In the main, our phylogenetic results agree with the findings by Soják (2008) which were based on anther structure. Four of our sampled Sibbaldia species remain in Sibbaldia, one [adpressa] is classified in Sibbaldianthe, one species [perpusilloides] is considered to represent an undescribed genus in Fragariinae, one [micropetala] is nested within the Potentilla anserina clade, and four species belong in a basal clade of Potentilla. Sibbaldiopsis is very close to Sibbaldia, and its single species should be named Sibbaldiopsis retusa (O.F. Müller) T. Erikss. and M. Lundberg.

Keyword
Sibbaldia, Potentilleae, Fragariinae, polyphyly, taxonomy, phylogeny, Bayesian inference, convergence diagnostics
National Category
Biological Systematics
Research subject
Systematic Botany
Identifiers
urn:nbn:se:su:diva-56687 (URN)
Available from: 2011-04-26 Created: 2011-04-20 Last updated: 2011-04-26Bibliographically approved
5. New insights into polyploid evolution in Fragaria (Rosaceae) based on the single/low copy nuclear intergenic region RGA1-Subtilase
Open this publication in new window or tab >>New insights into polyploid evolution in Fragaria (Rosaceae) based on the single/low copy nuclear intergenic region RGA1-Subtilase
(English)Manuscript (preprint) (Other academic)
Abstract [en]

A phylogenetic study of the genus Fragaria (Rosaceae) was performed based on the nuclear low/singlecopy intergenic region between the two genes Resistance Gene Analogue 1 (RGA1) and Subtilase(Subt). Potential diploid progenitors of the polyploid Fragaria species were detected and autopolyploid species were distinguished from allopolyploid. Our analyses indicate nine separate events of polyploidization in the evolution of Fragaria, of which three are of autopolyploid and six are of allopolyploid origin. Three tetraploid Fragaria have a probable autopolyploid origin, while a fourth one is most likely an allopolyploid. Fragaria nipponica is the diploid progenitor of autotetraploid F. tibetica, a diploid of the F. nipponica lineage is the progenitor of autotetraploid F. gracilis and F. vesca or more likely F. mandshurica is the diploid progenitor of autotetraploid F. orientalis. The progenitorsof the allotetraploid F. corymbosa are a diploid of the F. nipponica lineage and a diploid sister to the F.nipponica lineage. The hexaploid F. moschata originated after two events of allopolyploidization. First,a hybridization event involving the two diploids F. vesca and F. viridis took place, resulting in an undescribed allotetraploid and secondly, this allotetraploid hybridized with a diploid of the F. iinumae lineage. The octoploid lineage that gave rise to the two species F. virginiana and F. chiloensis was formed after an allopolyploidization event between F. moschata and a diploid of the F. iinumae lineage.The decaploid F. iturupensis originated after an allopolyploidization event between the octoploid lineage and a diploid of the F. iinumae lineage. The potential new species, formerly known as F.virginiana ssp. platypetala, originated after an allopolyploidization event between F. virginiana and a diploid Fragaria basally placed in our phylogeny, close to F. daltoniana.

Keyword
Fragaria, polyploid speciation, allopolyploidy, autopolyploidy, single/low copy gene, phylogenetics, reticulate evolution
National Category
Biological Systematics
Research subject
Systematic Botany
Identifiers
urn:nbn:se:su:diva-56685 (URN)
Available from: 2011-04-26 Created: 2011-04-20 Last updated: 2011-04-26Bibliographically approved

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