Chloroplast DNA <i>trn</i>L/F suprahaplotype networks of the <i>Arabidopsis arenosa</i> species complex.

<p>The sizes of the circles indicate the relative frequency of a suprahaplotype. Geographic regions, taxonomic entities, and cytotypes are indicated with the same colours as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone-0042691-g002" target="_blank">Figure 2</a>. A: Visualization according to geographic regions. B: Visualization according to taxonomy. <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is marked with an asterisk. C: Visualization according to ploidal level.</p

(a) Regional genetic differentiation and (b) genetic differentiation according to taxonomy, based on AFLP and chloroplast DNA sequence data (<i>trn</i>L/F suprahaplotypes).

<p>Sample size (<i>n</i>), Nei's gene diversity (<i>H_E</i>), proportion of variable markers (FP), and nucleotide diversity (<i>π</i>) with standard deviation are provided. For <i>trn</i>L/F suprahaplotypes effective genetic diversity according to Gregorius (<i>V_a</i>) is additionally displayed. The following seven geographic regions were considered: (1) Balkan Peninsula (Balk), (2) Carpathians (Carp), (3) unglaciated Eastern and Southeastern Alps (UnglaESEAlps), (4) glaciated Eastern Alps (GlaEAlps), (5) glaciated Western Alps (GlaWAlps), (6) unglaciated Central Europe (UnglaCentrEur), and (7) glaciated northern Europe (GlaNEur). <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is integrated within <i>A. arenosa</i> subsp. <i>arenosa</i>. <i>Arabidopsis nitida</i> was omitted from the analyses, as it was represented by one (AFLPs) and three (<i>trn</i>L/F suprahaplotypes) accession(s) only.</p

Principal Component Analysis of AFLP data from the <i>Arabidopsis arenosa</i> species complex.

<p>Each symbol represents an individual. A: Visualization according to geographic regions. The following seven geographic regions were considered: (1) Balkan Peninsula (Balk), (2) Carpathians (Carp), (3) unglaciated Eastern and Southeastern Alps (UnglaESEAlps), (4) glaciated Eastern Alps (GlaEAlps), (5) glaciated Western Alps (GlaWAlps), (6) unglaciated Central Europe (UnglaCentrEur), and (7) glaciated northern Europe (GlaNEur). These regions are illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone-0042691-g001" target="_blank">Figure 1</a>. B: Visualization according to taxonomy. <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is marked with an asterisk. C: Visualization according to ploidal level. Data lacking ploidal level estimates are marked in grey.</p

Distribution of accessions from the <i>Arabidopsis arenosa</i> species complex investigated.

<p>Maximal glaciation and mountain glaciers of the LGM are drawn according to Ehlers and Gibbard <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Ehlers1" target="_blank">[32]</a>. The borders of the seven geographic regions are indicated (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691.s001" target="_blank">Table S1</a>, where the affiliation of each accession to one of these regions is listed). A: Visualization according to taxonomy. Seven entities are distinguished: <i>A. arenosa</i> subsp. <i>arenosa</i>, <i>A. arenosa</i> subsp. <i>borbasii</i>, <i>A. carpatica</i>, <i>A. neglecta</i>, <i>A. nitida</i>, and <i>A. petrogena</i>, following Měsíček <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Msek1" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Msek2" target="_blank">[18]</a> and Kolník <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Kolnk1" target="_blank">[19]</a>, and <i>Arabidopsis arenosa</i> var. <i>intermedia</i> from the Alps. B: Visualization according to ploidal level (diploids and tetraploids). Ploidal level estimates were only available for a subset of accessions. C: Visualization according to chloroplast DNA suprahaplotypes.</p

Taxonomy, ploidal level, and geographic distribution of the various taxa of the <i>Arabidopsis arenosa</i> species complex (for details refer to the text).

<p>Several taxa are awaiting taxonomic recognition (indicated with nom. prov.).</p

ITS alignment

Alignment of Arabidopsis ITS types

Arabidopsis Microsatellite data

Microsatellite input data (STRUCTURE) set for seven loci. Accession codes refer to the respective accession list. Missing data "-9". In the second row numbers 1-23 indicates taxa (taxon identifyer as used in accession list

Accession data

Accession list with detailed information on origin, DNA data, cytogenetic data and inferences and haplotype definition