Table 1.
Material and gene sequences used
| Species | Taxonomic group (base chromosome number) | 2n | x | GenBank accession ID | Voucher ID |
|---|---|---|---|---|---|
| Viola congesta | sect. Andinium (x = 7) | -- | 2x | a: GU289564; b: GU289615 | Marcussen 641 (O) |
| Viola biflora | sect. Chamaemelanium (x = 6) | 2n = 12 | 2x | a: GU289574; b: GU289625 | Marcussen 775 (O) |
| Viola brevistipulata | sect. Chamaemelanium (x = 6) | 2n = 12 | 2x | a: GU289575; b: GU289626, GU289627 | Marcussen 803 (O) |
| Viola canadensis | sect. Chamaemelanium (x = 6) | 2n = 12, 24 | 4x | aa: GU289576; ba: GU289637 | Marcussen 802 (O) |
| Viola nuttallii | sect. Chamaemelanium (x = 6) | 2n = 24 | 4x | a: GU289577, GU289578, GU289579; b: GU289628, GU289629 | Marcussen 801 (O) |
| Viola pubescens | sect. Chamaemelanium (x = 6) | 2n = 12 | 2x | a: GU289580; b: GU289630 | Marcussen 637 (O) |
| Viola maculata | sect. Chilenium | -- | 8x | a: GU289570, GU289571, GU289572, GU289573; b: GU289616, GU289617, (GU289618b), GU289619 | Marcussen 804 (O) |
| Viola banksii | sect. Erpetion | -- | 8x-10x | a: GU289565, GU289566, GU289567c, GU289568c, (GU289569b); b: (GU289620c), GU289621, GU289622b, GU289623, GU289624 | Marcussen 630 (O) |
| Viola bicolor | sect. Melanium | 2n = 34 | 12x? | a: GU289603, GU289604, GU289605c, GU289606b, GU289607c, GU289608b | Marcussen 743 (O) |
| Viola calcarata | sect. Melanium | 2n = 20 | 12x? | a: GU289609, GU289610, GU289611, GU289612c, GU289613, GU289614 | Marcussen 672 (O) |
| Viola dirimliensis | sect. Melanium | 2n = 8 | 8x? | a: GU289599, GU289600, GU289601, GU289602c | Marcussen 650 (O) |
| Viola epipsila | sect. Viola (x = 10, 12) | 2n = 24 | 4x | a: GU289587, GU289588; b: GU289635b | Marcussen 661 (O) |
| Viola hirta | sect. Viola (x = 10, 12) | 2n = 20 | 4x | a: GU289581, GU289582 | Marcussen 682 (O) |
| Viola mirabilis | sect. Viola (x = 10, 12) | 2n = 20 | 4x | a: GU289583, GU289584; b: GU289631 | Marcussen 683 (O) |
| Viola selkirkii | sect. Viola (x = 10, 12) | 2n = 24 | 4x | a: GU289589, GU289590; b: GU289634b | Marcussen 698 (O) |
| Viola spathulata | sect. Viola (x = 10, 12) | -- | 8x? | a: GU289593, GU289594, GU289595b, GU289596b, GU289597, GU289598; b: GU289636b | Marcussen 670 (O) |
| Viola uliginosa | sect. Viola (x = 10, 12) | 2n = 20 | 4x | a: GU289585, GU289586; b: GU289632 | Marcussen 662 (O) |
| Viola verecunda | sect. Viola (x = 10, 12) | 2n = 24 | 4x | a: GU289591, GU289592; b: GU289633 | Marcussen 697 (O) |
| Allexis batangae | Violaceae (outgroup) | -- | 2x | a: GU289562; b: GU289563c | Bos 4241 (UPS) |
| Anchietea parvifolia | Violaceae (outgroup) | -- | 2x | GU289559c | Myndel Pedersen 13944 (UPS) |
| Corynostylis arborea | Violaceae (outgroup) | -- | 2x | GU289560 | Asplund 14509 (UPS) |
| Cubelium concolor (= Hybanthus concolor) | Violaceae (outgroup) | 2n = 48 | 2x | GU289561 | Pläck & Bodin s.n. (UPS) |
| Hybanthus enneaspermus | Violaceae (outgroup) | 2n = 16, 32 | 2x | GU289558 | unknown 2001-05-13 (UPS) |
| Rinorea ilicifolia | Violaceae (outgroup) | -- | 2x | GU289557 | Friis et al. 2445 (UPS) |
| Populus trichocarpa | Salicaceae (outgroup) | 2n = 38 | -- | a: DT509274; b: CV227572 | -- |
| Manihot esculenta | Euphorbiaceae (outgroup) | 2n = 36, 54, 72 | -- | a: DV448133; b: (CK652029) | -- |
| Euphorbia esula | Euphorbiaceae (outgroup) | 2n = 20, 48-60 | -- | DV145650 | -- |
Taxa used in this study, with respective GenBank accessions for DNA sequences and voucher information. For each taxon systematic affinity (sections within Viola for ingroup, and families within Malpighiales for outgroup), chromosome counts (2n, where available), and putative ploidal levels (x, inferred from the NRPD2/E2 data), are indicated. GenBank accession IDs are sorted by paralog (a and b), and by homoeolog (ascending numbers); gene copies excluded from phylogenetic analysis, because they were considered too short for reliable analysis, are put in brackets. Note that NRPD2/E2-a and NRPD2/E2-b are arbitrary labels, and that NRPD2/E2-a and NRPD2/E2-b in Euphorbiaceae, Salicaceae and Violaceae are not orthologous to each other. Herbarium acronyms for voucher specimen deposition (i.e., O, U) follow Holmgren and Holmgren [50].
a the secondarily duplicated gene copies in Viola canadensis differed only in 3 (NRPD2/E2-a) and 8 (NRPD2/E2-b) substitutions, and their respective consensuses were used as single sequences in the analyses
b partial sequence (exon 6 to exon 7); PCR 1 failed (see Figure 1)
c partial sequence (exon 5 to intron 6); PCR 2 failed (see Figure 1)