DOI: 10.5061/dryad.ts73227
title: Data from: Is the incidence of survival in interior Pleistocene refugia (nunataks) underestimated? Phylogeography of the high mountain plant Androsace alpina (Primulaceae) in the European Alps revisited

description: Temperate mountain ranges such as the European Alps have been strongly
 affected by the Pleistocene glaciations. Glacial advances forced biota
 into refugia, which were situated either at the periphery of mountain
 ranges or in their interior. Whereas in the Alps peripheral refugia have
 been repeatedly and congruently identified, support for the latter
 scenario, termed “nunatak hypothesis”, is still limited and no general
 pattern is recognizable yet. Here, we test the hypothesis of nunatak
 survival for species growing in the high-alpine to subnival zones on
 siliceous substrate using the cushion plant Androsace alpina
 (Primulaceae), endemic to the European Alps, as our model species. To this
 end, we analysed AFLP and plastid DNA sequence data obtained from a dense
 and range-wide sampling. Both AFLPs and plastid sequence data identified
 the southwestern-most population as the most divergent one. AFLP data did
 not allow for discrimination of interior and peripheral populations, but
 rather identified two to three longitudinally separated major gene pools.
 In contrast, in the eastern half of the Alps several plastid haplotypes of
 regional or local distribution in interior ranges – the Alpine periphery
 mostly harboured a widespread haplotype – were indicative for the presence
 of interior refugia. Together with evidence from other Alpine plant
 species this study shows that in the eastern Alps silicicolous species of
 open habitats in the alpine and subnival zone survived, also or
 exclusively so, in interior refugia. As the corresponding genetic
 structure may be lost in mostly nuclear-derived, rapidly homogenising
 marker systems such as AFLPs or RAD sequencing tags, markers not prone to
 homogenization, as is the case for plastid sequences (Sanger-sequenced or
 extracted from an NGS data set) will continue to be important for
 detecting older, biogeographically relevant patterns.
description: AFLP data set of
 Androsace alpina (Primulaceae)Data matrix (samples
 times locus); samples are abbreviated as AA-XX-Y, where AA is the species
 acronym, XX is the population number (the same as used in the manuscript),
 and Y is the individual numberAndrosace_alpina_AFLP_data.txtConcatenated plastid sequences of Androsace alpine (Primulaceae)DNA sequences in fasta format; samples are abbreviated as alp-popXX-Y, where alp is the species acronym, popXX is the population number (the same as used in the manuscript), and Y is the individual numberAndrosace_alpina_plastid_sequences_combined.fasAndrosace_alpina_plastid_sequences_combined_TCS_codedDNA sequences in fasta format, where inversions and indels spanning more than one nucleotide are re-coded to single base pair columns (for statistical parsimony analysis in TCS treating gaps as fifth base); samples are abbreviated as alp-popXX-Y, where alp is the species acronym, popXX is the population number (the same as used in the manuscript), and Y is the individual number