title: A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy.
abstract: Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.|GLORIA Co-ordination, Center for Global Change and Sustainability, University of Natural Resources and Life Sciences Vienna (BOKU) & Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Silbergasse 30/3, Vienna, A-1190, Austria.
authors.forename: Manuela
authors.initials: M
authors.lastname: Winkler
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.
authors.forename: Pedro
authors.initials: P
authors.lastname: Escobar García
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gattringer
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.
authors.forename: Michaela
authors.initials: M
authors.lastname: Sonnleitner
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.|Vienna Institute for Nature Conservation & Analyses, Giessergasse 6/7, Vienna, A-1090, Austria.
authors.forename: Karl
authors.initials: K
authors.lastname: Hülber
authors.affiliation: Institute of Botany, University of Innsbruck, Sternwartestrasse 15, Innsbruck, A-6020, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Schönswetter
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Schneeweiss
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D019659:Asteraceae / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D011123:Polyploidy
chemical_list: D018744:DNA, Plant
keywords: 
  Senecio carniolicus
  ; Amplified Fragment Length Polymorphism; Cohen's d; allopolyploidy; autopolyploidy; in silico polyploidization