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

Despite the evolutionary and ecological relevance of different modes of polyploid origin, these have 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- versus allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen’s d of distances between in silico generated polyploids 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, 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. This may suggest that the tetraploid species has two independent origins, but the alternative hypothesis of an autopolyploid origin with subsequent introgression from the second diploid species cannot be excluded. Altogether, identifying the best among alternative scenarios using Cohen’s d can be straightforward, but particular scenarios, such as allopolyploid origin versus autopolyploid origin with subsequent introgression, remain difficult to be distinguished.