This is a ReadMe file to Alignment files.zip. Alignments have been numbered (1-11) as in manuscript. Note that the coding region of PHYA locus includes both no. 5 and no. 6 fragments. Locus specific haplotypes have been inferred from the genotypes using the PHASE algorithm (Stephens et al. 2001; Stephens and Donnelly 2003). In fragment 1, "N" (sites 227-236) are missing sites compared to A. thaliana reference sequence. In fragment 5-6, there is missing sequence information (sites 2171-2216) in some samples in the Plech population. In fragment 7, the sequence data is missing (329 and 444) in the Plech population. Indels have been marked with gap symbol (-).