FIGURE S1.- Polymorphism and divergence at the CAD locus for A. halleri, A. l.
petraea, and A. thaliana. Each sequence is labelled according to the name of the
corresponding individual (as indicated in Table 1) followed by the letter a or b to
designate each allele of an individual. The A. thaliana sequence was obtained from
GenBank (accession no. Z31715). Positions are numbered according to the entire
alignment; for insertions-deletions more than 1 bp long, the first and last affected
nucleotides are indicated; nucleotide polymorphisms located within an indel region
are indicated in square brackets. The nine classes of mutations described in the text
(see also Table 8) are indicated as FH, FP and FO (Sfhal, Sfpet and Sfout, respectively),
XH, XP and XO (Sxhal , Sxpet, and Sxout respectively), A1, A2 and AS (Sfhalxpet, Sfpetxhal,
and Sshared, respectively), with MH indicating multiple hit events (insertion-deletions
not included). Synonymous and nonsynonymous polymorphisms are indicated as S
and N, respectively; polymorphic sites with more than two variants can exhibit both
types; an asterisk indicates a position in a complex codon. Black boxes indicate
coding regions. A dash indicates a gap, and a dot indicates the same nucleotide as the
first sequence.
FIGURE S2.- Polymorphism and divergence at the CHI locus for A. halleri, A. l.
petraea, and A. thaliana. Annotation is as in Figure S1 except for A. thaliana.
Although only one A. thaliana sequence is shown (GenBank accession no. AJ287299
corresponding to ecotype Can-0; KUITTINEN and AGUADÉ 2000), the alignment was
performed using all sequences in KUITTINEN and AGUADÉ (2000). Blank zones
indicate missing data.
FIGURE S3.- Polymorphism and divergence at the CHS locus within and between A.
halleri, A. l. petraea, A. l. lyrata, and A. thaliana. Annotation is as in Figure S1
except that the A. thaliana sequences are newly reported sequences. There are two
rows categorizing the 9 classes of mutations: one row for the comparison of A. l.
petraea and A. l. lyrata, with A. thaliana as the outgroup, and one row for the
comparison of A. l. petraea and A. halleri with A. thaliana as the outgroup. In the A.
l. petraea/A. l. lyrata comparison, FL and XL refer to Sflyr and Sxlyr, respectively, and
A1 and A2 refer to Sflyrxpet, Sfpetxlyr, respectively. In the A. l. petraea/A. l. halleri
comparison, all abbreviations are the same as in Figure S1. Blank zones indicate
missing data.
FIGURE S4.- Polymorphism and divergence at the DFR locus for A. halleri, A. l.
petraea, and A. thaliana. Annotation is as in Figure S1. The A. thaliana sequence
used was obtained from GenBank (accession no. M86359). Blank zones indicate
missing data.
FIGURE S5.- Polymorphism and divergence at the F3H locus for A. halleri, A. l.
petraea, and A. thaliana. Annotation is as in Figure S2. Although only one A.
thaliana sequence is shown (GenBank accession no. AJ295587 corresponding to
ecotype COND; AGUADÉ 2001), the alignment was performed using all sequences in
AGUADÉ (2001). Polymorphisms exclusive to A. thaliana are not shown, except for
those (indicated as #) in sites variable in the presented dataset.
FIGURE S6.- Polymorphism and divergence at the FAH1 locus for A. halleri, A. l.
petraea, and A. thaliana. Annotation is as in Figure S2. Although only one A.
thaliana sequence is shown (GenBank accession no. AJ295572 corresponding to
ecotype RUB-1; AGUADÉ 2001), the alignment was performed using all sequences in
AGUADÉ (2001). Polymorphisms exclusive to A. thaliana are not shown, except for
those (indicated as #) in sites variable in the presented dataset.
FIGURE S7.-Polymorphism and divergence at the GS locus for A. halleri, A. l. petraea,
A. l. lyrata, and A. thaliana. Annotation is as in Figure S3, except that the A. thaliana
ecotype Columbia sequence corresponds to GenBank accession number AC002333.
FIGURE S8.- Polymorphism and divergence at the MAM-L locus for A. halleri, A. l.
petraea, A. l. lyrata, and A. thaliana. Annotation is as in Figure S3, except that the A.
thaliana ecotype Columbia sequence corresponds to GenBank Accession number
AB006708. All remaining A. thaliana MAM-L sequences were provided by Jürgen
Kroymann (unpublished data).