DOI: 10.5061/dryad.573pm
title: Data from: Polyploidisation and geographic differentiation drive diversification in a European high mountain plant group (Doronicum clusii aggregate, Asteraceae)

description: Range shifts (especially during the Pleistocene), polyploidisation and
 hybridization are major factors affecting high-mountain biodiversity. A
 good system to study their role in the European high mountains is the
 Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s.,
 D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp.
 calcareum) are differentiated geographically, ecologically (basiphilous
 versus silicicolous) and/or via their ploidy levels (diploid versus
 tetraploid). Here, we use DNA sequences (three plastid and one nuclear
 spacer) and AFLP fingerprinting data generated for 58 populations to infer
 phylogenetic relationships, origin of polyploids—whose ploidy level was
 confirmed by chromosomally calibrated DNA ploidy level estimates—and
 phylogeographic history. Taxonomic conclusions were informed, among
 others, by a Gaussian clustering method for species delimitation using
 dominant multilocus data. Based on molecular data we identified three
 lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii)
 silicicolous tetraploid D. stiriacum in the eastern Alps (outside the
 range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous
 diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp.
 calcareum (northeastern Alps); each taxon was identified as distinct by
 the Gaussian clustering, but the separation of D. glaciale subsp.
 calcareum and D. glaciale subsp. glaciale was not stable, supporting their
 taxonomic treatment as subspecies. Carpathian and Alpine populations of D.
 stiriacum were genetically differentiated suggesting phases of vicariance,
 probably during the Pleistocene. The origin (autopolyploid versus
 allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp.
 calcareum was genetically and morphologically weakly separated from D.
 glaciale subsp. glaciale but exhibited significantly higher genetic
 diversity and rarity. This suggests that the more widespread D. glaciale
 subsp. glaciale originated from D. glaciale subsp. calcareum, which is
 restricted to a prominent Pleistocene refugium previously identified in
 other alpine plant species.
description: AFLP matrix for
 Doronicum clusii aggregate (Asteraceae)AFLP data matrix (as
 comma separated file) of the Doronicum clusii aggregate (Asteraceae).
 Sample names have the following format: Taxon name_population
 number_individual number.Doronicum_clusii_aggregate_AFLP_matrix.csvAlignment of original cpDNA sequences of the Doronicum clusii aggregate (Asteraceae)Alignment (in fasta format) of three concatenated cpDNA regions of the Doronicum clusii aggregate (Asteraceae). The three regions are: ndhF-rpl32 intergenic spacer (positions 1-1099); rpl32-trnL(UAG) intergenic spacer (positions 1100-1959); 3'rps16-5'trnK(UUU) intergenic spacer (positions 1960-2883). Sample names have the following format: Taxon name_population number_individual number.Doronicum_clusii_aggregate_cpDNA_alignment_original_sequences.fasAlignment of coded cpDNA sequences of the Doronicum clusii aggregate (Asteraceae)Alignment (in fasta format) of three concatenated cpDNA regions, coded for TCS analysis, of the Doronicum clusii aggregate (Asteraceae). The three regions are: ndhF-rpl32 intergenic spacer (positions 1-1057); rpl32-trnL(UAG) intergenic spacer (positions 1058-1914); 3'rps16-5'trnK(UUU) intergenic spacer (positions 1915-2776). Sample names have the following format: Taxon name_population number_individual number.Doronicum_clusii_aggregate_cpDNA_alignment_coded.fasDoronicum_clusii_aggregate_ITS_alignmentAlignment (in fasta format) of nuclear ITS sequences of the Doronicum clusii aggregate (Asteraceae). Sample names have the following format: Taxon name_population number_individual number_clone number (clone numbers only for some individuals).