Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification Magnus Lundberg a, * , Mats Töpel b , Bente Eriksen b , Johan A.A. Nylander a , Torsten Eriksson a,c a Department of Botany, Stockholm University, SE-10691, Stockholm, Sweden b Department of Environmental Sciences, Gothenburg University, Box 461, SE-40530, Göteborg, Sweden c Bergius Foundation, Royal Swedish Academy of Sciences, SE-10405, Stockholm, Sweden article info Article history: Received 23 June 2008 Revised 25 February 2009 Accepted 26 February 2009 Available online 5 March 2009 Keywords: Allopolyploidy Fragariinae Incongruence Molecular phylogeny Bayesian convergence diagnostics abstract 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 ribo- somal 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 eval- uated 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 conver- gence diagnostics. Taxonomic implications are discussed for genera such as Alchemilla, Sibbaldianthe, Cha- maerhodos, 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. Ó 2009 Elsevier Inc. All rights reserved. 1. Introduction The importance and detection of hybridisation and its role in species formation have been, and continue to be, major foci in evo- lutionary plant research, notably because hybridisation followed by polyploidisation is suggested to be an important mode of speci- ation among vascular plants. Following hybridisation, alternations at genomic and gene levels occur in the offspring with potential advantages of the polyploid species compared to its diploid pro- genitors. This may be caused by changes of the newly formed hy- brids by reproductive isolation, or by changes in biochemical, physiological and developmental flexibility; changes that are ex- pressed, for example in plant size, flowering time and reproductive output, but also in new combinations of characters (Levin, 1983; Schranz and Osborn, 2000; Song et al., 1995). Speciation through polyploidy was discovered in the beginning of the last century by Winkler (1916) and Winge (1917). To distinguish between the two main types of polyploidy commonly recognised, Kihara and Ono (1926) introduced the terms allopolyploidy (duplication of chromosomes in interspecific hybrids) and autopolyploidy (dupli- cation of chromosomes within a species). Many estimates of the frequency of polyploidy among angio- sperms have been presented. Early estimates, based on chromo- some numbers in related species or arbitrary levels above which species were thought to be polyploid, ranged between 30% and 52% (Müntzing, 1936; Darlington, 1937; Stebbins, 1950; Grant, 1963, 1981). More recent studies based on guard cell sizes suggest that more than 70% of all extant angiosperms are of polyploid ori- gin (Masterson, 1994), and polyploidy has been suggested to be the cause of at least 2–4% of all recent speciation events (Otto and Whitton, 2000), thus suggested to be an important mode of speci- ation (e.g. Mallet, 2007). Such estimates, in particular the older ones, may be rather inaccurate. As an example of the problems in making such estimates, the model plant Arabidopsis thaliana is defined as a functional diploid with a relatively small genome (The Arabidopsis Genome Initiative, 2000). However, results from whole genome sequencing indicates that there have been two or more rounds of genome duplication events in the evolution of that species (Vision et al., 2000; Blanc et al., 2003; Bowers et al., 2003; Simillion et al., 2002). Recent genetic and genomic studies suggest that most or perhaps all angiosperms have undergone one or sev- eral rounds of polyploidisation followed by extensive diploidisa- tion (Wolfe, 2001; Eckhardt, 2001), the evolutionary process where the genomic content of a polyploid species degenerates into a diploid state again. Before molecular methods were developed, polyploid specia- tion was detected by chromosome counts and crossing experi- ments (Grant, 1981). Drawbacks of this method include that it assumes recent polyploidy events and that parental species are ex- tant. More recently, several analyses using molecular data have been developed to detect and reconstruct hybrid speciation, e.g. 1055-7903/$ - see front matter Ó 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2009.02.020 * Corresponding author. Fax: +46 (0)8 165525. E-mail address: Magnus.Lundberg@botan.su.se (M. Lundberg). Molecular Phylogenetics and Evolution 51 (2009) 269–280 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev