DOI: 10.5061/dryad.gf533
title: Data from: A novel method to infer the origin of polyploids from AFLP data reveals that the Alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy

description: 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- versus
 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
 versus autopolyploid origin with subsequent introgression, remain
 difficult to be distinguished.
description: ITS sequences of the
 Senecio carniolicus aggregateAlignment (in NEXUS
 format) of ITS sequences. Sample names are of the form: Taxon
 acronym*_population number_individual number_clone number*_ploidy level
 (items indicated by an asterisk are not always given). Taxon acronyms are:
 car - S. carniolicus; dis - S. disjunctus; ins - S. insubricus; nor - S.
 noricus. See Table S1 of the paper for further details.Senecio_carniolicus_ITS_sequences.nexConcatenated plastid sequences of the Senecio carniolicus aggregateAlignment (in NEXUS format) of concatenated plastid sequences (1-672: psbD–trnT spacer; 673-1269: rps16–trnK spacer; 1270-2452: petL-psbE spacer; 2453-3382: rpl32–trnL spacer); multi-base pair indels coded as single base pairs for statistical parsimony analysis: see main text for details). Sample names are of the form: Taxon acronym*_population number_individual number_ploidy level (item indicated by an asterisk is not always given). Taxon acronyms are: car - S. carniolicus; dis - S. disjunctus; ins - S. insubricus; nor - S. noricus. See Table S1 of the paper for further details.Senecio_carniolicus_plastid_sequences_coded.nexAFLP data matrix of the Senecio carniolicus aggregateTaxon acronyms are: car - S. carniolicus; dis - S. disjunctus; ins - S. insubricus; nor - S. noricus. See Table S1 of the paper for further details.Senecio_carniolicus_AFLP_Matrix.txtR script for testing scenarios of polyploid origin from AFLP data using Cohen's dInSilicoHybridisation.RPerl scripts to generate in silico AFLP profilesNote: Scripts are compressed in a single zip-file.InSilicoAFLP.zip