Fig. 1

Examples of rare allele, intermediate allele in a gSNP locus and complicated and dSNP locus. Dot indicates identical nucleotide compared to ortholog (A. lyrata sequence relative to the alignment of A. thaliana). The numbers above the ortholog sequence denote nucleotide positions in the sequence. Fixed sites between haplotypes at rare or intermediate alleles are shown in grey shadow. a An example of a rare haplotype in gSNP locus is located at 18433043 (chr. 1). b An intermediate allele is shown in gSNP locus which is at 24321799 (chr. 1). c An example used as a complex locus that holds two distinct haplotypes of both a rare allele (light grey shadow) and an intermediate allele (dark grey shadow) is located at 4826763 (chr. 1). d An example of a dSNP locus is at 10095832 (chr. 1). Only part of the accessions within each haplotype is displayed in all examples