Appendix S1 List of material included in this study and haplotype distribution in populations and taxa. Whenever different taxa were growing at the same locality, each taxon was treated as a separate population. Floristic regions in the Nordic countries abbreviated according to Flora Nordica (Jonsell 2004). Taxon abbreviations: alp, D. majalis ssp. alpestris; bal, D. majalis ssp. baltica; bau, D. baumanniana; cam, D. majalis ssp. cambrensis; ela, D. elata; fuc, D. maculata ssp. fuchsii; jun, D. majalis ssp. junialis; lap, D. majalis ssp. lapponica; local allo, local allotetraploids with unclear affiliation; mac, D. maculata ssp. maculata; maj, D. majalis ssp. majalis; nie, D. nieschalkiorum; pra, D. majalis ssp. praetermissa; pur, D. majalis ssp. purpurella; sac, D. maculata ssp. saccifera; sam, D. sambucina; sph, D. majalis ssp. sphagnicola; tra, D. majalis ssp. traunsteineri; urv, D. urvilleana; vir, D. viridis. Question marks denote populations with uncertain taxonomic belonging. The column ‘Genome’ reports gross genome composition and numbers of chromosome complements as described by allozyme data (Hedrén 1996a, b, c, 2001a, 2002b): E, the D. euxina genome; F, the D. maculata s.l. genome; I, the D. incarnata s.l. genome; S, the D. sambucina genome; V, the D. viridis genome; for example, FF represents a diploid within the D. maculata s.l. lineage, FFFF an autotetraploid within the same lineage, and FFII an allotetraploid derived from the D. maculata s.l. and D. incarnata s.l. lineages. The column ‘Haplotypes’ reports haplotypes as defined in Appendix S4 and number of samples within which a particular haplotype has been found. Whenever different haplotypes were found in a population they are separated by semicolons. The column ‘N’ reports the total number of samples analysed within each population.

Appendix S2 Overview of taxa discussed in this study. ‘Genome composition’ report patterns revealed by allozyme analyses.

Appendix S3 Internal primers used for sequencing trnH–trnK in Dactylorhiza.

Appendix S4 Characterization of haplotypes identified in the Dactylorhiza incarnata/maculata complex by means of primer pairs described in Table 1. N, numbers of individuals found with a particular haplotype; Grp, major haplotype group belonging, see Fig. 1 (bau, baumanniana; inc, incarnata; sam, sambucina; vir, viridis); Tax, taxonomic distribution (A, allotetraploids; F, D. maculata ssp. fuchsii; I, D. incarnata s.l.; M, D. maculata ssp. maculata; S, D. sambucina; U, D. urvilleana; V, D. viridis); Area, major distribution area (C, central and southern Europe; N, northern Europe except Scandinavia; S, Scandinavia and the Baltic area). Fragments are given in bp, except at locus 5, which reports number of fragments obtained when cut with RsaI. Haplotypes sorted as ‘odd’ could not be sorted into any of the major haplotype groups (cf. Fig. 1).

Appendix S5 Pairwise FST comparisons between local allotetraploids and putative parental groups. The table also reports frequencies of haplotypes found in the local populations and the frequencies of the same haplotypes found in contrasting groups (in brackets). Significance values report the probability that the groups being compared are not differentiated; ns: not significant; *P < 0.05; **P < 0.01; ***P < 0.001.

Please note: Wiley-Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.

MEC_3965_sm_Appendix1-5.doc166KSupporting info item

Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.