DOI: 10.5061/dryad.8d820
title: Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)

description: The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae,
 comprise the closest relatives of the arctic-alpine model plant S.
 oppositifolia and have a centre of diversity in the central and southern
 European mountain ranges. A multitude of taxa has been described and
 taxonomic concepts vary among different treatments. Using amplified
 fragment length polymorphism (AFLP) fingerprinting we show that some taxa
 indeed form strongly supported genetic entities best recognized on the
 species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana,
 S. speciosa), while others (S. murithiana, S. paradoxa) are not
 genetically divergent at all. Saxifraga oppositifolia s. s. is
 phylogenetically incoherent. Plastid DNA sequence data show very limited
 congruence with the predominantly nuclear-derived AFLPs. Several
 co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s.
 s., S. retusa) share the same set of haplotypes. In the widespread species
 S. oppositifolia and S. retusa, highly divergent haplotype lineages were
 discovered, which exhibit a geographic rather than taxonomic structure.
 Recent and ancient hybridization and/or lineage sorting are likely
 responsible for the strong incongruence between data derived from nuclear
 and plastid genomes. Hybridization, which is known to occur among almost
 all taxa of this group when growing in sympatry, seems, however,
 insufficient to break down species barriers.
description: Plastid DNA sequences of
 Saxifraga oppositifolia s.l.Combined alignment of
 plastid DNA sequences (psbA-trnH, trnT-trnF) of Saxifraga oppositifolia
 s.l. The alignment was created using BioEdit. First column: individual
 name containing population number and taxon abbreviation (aug = S. retusa
 subsp. augustana, bif = S. biflora subsp. biflora, ble = S. oppositifolia
 subsp. blepharophylla, opp = S. oppositifolia subsp. oppositifolia, par =
 S. oppositifolia subsp. paradoxa, rud = S. oppositifolia subsp.
 rudolphiana, ret = S. retusa subsp. retusa, spe = S. oppositifolia subsp.
 speciosa), second column: aligned sequences.SaxOppSL_plastidSeqs_alignment.txtAFLP matrix of Saxifraga oppositifolia s.l.Manually scored AFLP matrix of Saxifraga oppositifolia s.l. using DAx (Van Mierlo Software Consultancy, Eindhoven) with non-reproducible and homogeneous fragments removed. AFLP data were generated following the procedure of Vos et al. (1995) with the modifications described by Schönswetter et al. (2009) using three primer combinations for selective PCR (fluorescent dyes in brackets) EcoRI (6-FAM)-ACA/MseI-CAC, EcoRI (VIC)-AGG/MseI-CTC, EcoRI (NED)-ACC/MseI-CAG. First column: individual name containing population number and taxon abbreviation (aug = S. retusa subsp. augustana, bif = S. biflora subsp. biflora, ble = S. oppositifolia subsp. blepharophylla, opp = S. oppositifolia subsp. oppositifolia, par = S. oppositifolia subsp. paradoxa, rud = S. oppositifolia subsp. rudolphiana, ret = S. retusa subsp. retusa, spe = S. oppositifolia subsp. speciosa), other columns: 0/1 matrix.SaxOppSL_AFLP_matrix.txt