a) RT - ASTRAL 91/0.7 decumbens Eualchemilla - lobed 66/— Alchemilla heptagona 91/0.97 Alchemilla glabra 90/— Alchemilla japonica 1 Eualchemilla - dissected Alchemilla indivisa coalescent unit 90/— * 0.10 Alchemilla mollis Aphanes ‘lobed’ clade −0.21/0.29/0.99 100/0.84 * Alchemilla flabellata Alchemilla xanthochlora 100/0.94 Eualchemilla Lachemilla * Alchemilla plicata 0.62/0.17/0.99 Alchemilla lapeyrousii Alchemilla fissa Afromilla 99/0.63 75/— Alchemilla splendens Farinopsis salesoviana 0.023/0.87/0.98 * Alchemilla subsericea Alchemilla alpina ‘dissected’ clade * Alchemilla pentaphyllea 0.98/0/1 * 43/— Aphanes sp. “patagonica” Aphanes sp. “boliviana” 1/—/1 47/— * Aphanes cotopaxiensis * Aphanes * Aphanes microcarpa * Aphanes australis 1/—/1 * Alchemilla fischeri 99/— Alchemilla cryptantha 11/1 100/— Alchemilla kiwuensis Alchemilla ellenbeckii 0.18/0.66/0.99 99/0.61 * Alchemilla schizophylla * Alchemilla hildebrandtii 73/— Alchemilla rutenbergii * Alchemilla colura * Alchemilla woodii * Alchemilla elongata Afromilla Alchemilla johnstonii 2/0.92 * Alchemilla microbetula Alchemilla haumanii 97/— Alchemilla stuhlmannii Alchemilla triphylla * 98/— * Alchemilla subnivalis 1/—/1 * Alchemilla argyrophylla Alchemilla roccatii 100/0.95 Lachemilla moritziana Alchemilla s.l. * Lachemilla aphanoides * Lachemilla standleyi 1/—/1 42/— * Lachemilla procumbens 93/1 Lachemilla hirta Lachemilla sibbaldiifolia * * Lachemilla jamesonii * Lachemilla vulcanica 95/1 Lachemilla andina 95/— Lachemilla pringlei Lachemilla velutina 94/1 Lachemilla llanganatensis * 79/— Lachemilla hispidula 99/0.97 * Lachemilla galioides Lachemilla nivalis Lachemilla * 76/— Lachemilla angustata 100/— Lachemilla polylepis * Lachemilla equisetiformis * Lachemilla ramosissima * Lachemilla verticillata 1/—/1 * Lachemilla tanacetifolia * Lachemilla erodiifolia Lachemilla mandoniana 60/— * * Lachemilla pinnata * Lachemilla diplophylla * Lachemilla barbata * Lachemilla pectinata 100/0.97 Lachemilla orbiculata Farinopsis salesoviana * Sibbaldianthe adpressa * * Sibbaldianthe bifurca Pie chart key Sibbaldia procumbens Fragariinae Comarum palustre Discordant * Fragaria vesca (main alternative) * Drymocallis glandulosa Drymocallis arguta * Discordant * * Chamaerhodos erecta (remaining Concordant * Dasiphora fruticosa Potaninia mongolica alternatives) Potentilla indica 0.03 Sanguisorba menziesii substitution per site Uninformative + Missing Rosa woodsii

Figure S1. Maximum likelihood phylogeny of Alchemilla s.l. inferred from RAxML analysis of the concatenated 1,894-nuclear gene supermatrix from the ‘rooted ingroup’ (RT) orthologs. Bootstrap support (BS) and Local posterior probability (LLP) are shown above branches. Nodes with full support (BS= 100/LLP= 100) are noted with an asterisk (*). Em dashes (—) denoted alternative topology compared to the ASTRAL species tree. Quartet Sampling (QS) scores for major clades are shown below branches. QS scores in blue indicate strong support and red scores indicate weak support. QS scores: Quartet concordance/Quartet differential/Quartet informativeness. Pie charts for major clades represent the proportion of exon ortholog trees that support that clade (blue), the proportion that support the main alternative bifurcation (green), the proportion that support the remaining alternatives (red), and the proportion (conflict or support) that have < 50% bootstrap support plus missing data (gray). Branch lengths are in number of substitutions per site (scale bar on the bottom). Inset: a) Summary ASTRAL species inferred from 1,894 nuclear gene trees from the RT orthologs. LLP and QS are shown above and below the branch that differ from the RAxML tree. Branch lengths are in coalescent units. 0.79 Alchemilla heptagona 0.69 Alchemilla decumbens 1 Alchemilla glabra 1 Alchemilla japonica 0.94 Alchemilla plicata 0.41 Alchemilla lapeyrousii Alchemilla flabellata lobed clade 1 0.99 Alchemilla xanthochlora Eualchemilla 1 1 Alchemilla indivisa 0.99 Alchemilla mollis Alchemilla splendens 0.76 Alchemilla fissa 1 Alchemilla subsericea 1 Alchemilla alpina dissected clade Alchemilla pentaphyllea 1 0.77 Aphanes cotopaxiensis 0.4 Aphanes sp “patagonica” 1 Aphanes sp “boliviana” 1 Aphanes occidentalis 1 1 Aphanes microcarpa Aphanes australis Aphanes Aphanes arvensis 1 Alchemilla cryptantha 0.48 Alchemilla fischeri 0.99 Alchemilla kiwuensis 0.52 0.57 Alchemilla ellenbeckii 1 Alchemilla johnstonii 0.72 Alchemilla microbetula 1 Alchemilla schizophylla 0.5 1 Alchemilla hildebrandtii Alchemilla rutenbergii 0.92 Afromilla

Alchemilla haumanii .l. s 1 Alchemilla woodii 1 Alchemilla colura 1 Alchemilla elongata 1 Alchemilla stuhlmannii Alchemilla subnivalis 0.99 Alchemilla 1 Alchemilla argyrophylla 1 Alchemilla triphylla iinae Alchemilla roccatii r 1 Lachemilla hirta aga 0.79 Lachemilla procumbens r 1 F 0.5 Lachemilla sibbaldiifolia 1 Lachemilla aphanoides 1 Lachemilla moritziana Lachemilla standleyi 1 1 Lachemilla vulcanica 1 Lachemilla jamesonii 1 Lachemilla andina Lachemilla pringlei 0.86 Lachemilla velutina 0.99 1 Lachemilla llanganatensis 0.94 Lachemilla hispidula 1 Lachemilla nivalis 0.94 Lachemilla galioides Lachemilla 1 0.51 Lachemilla angustata 0.99 Lachemilla polylepis 1 Lachemilla verticillata 1 1 Lachemilla ramosissima Lachemilla equisetiformis 1 Lachemilla tanacetifolia 0.98 Lachemilla erodiifolia 1 1 Lachemilla mandoniana Lachemilla pinnata 0.59 1 Lachemilla barbata Lachemilla diplophylla 0.98 1 Lachemilla orbiculata 1 Lachemilla pectinata Farinopsis salesoviana 1 Sibbaldianthe bifurca 1 Sibbaldianthe adpressa Sibbaldia procumbens 1 Fragaria vesca 1 Comarum palustre 1 Drymocallis glandulosa 1 1 Drymocallis arguta 1 Chamaerhodos erecta 1 Dasiphora fruticosa Potaninia mongolica Potentilla indica Sanguisorba menziesii Rosa woodsii

1 coalescent unit

Figure S2. ASTRAL-Pro species trees of Alchemilla s.l. inferred from 923 multi-labeled homolog trees. Local posterior probability (LLP) are shown next to nodes. Branch lengths are in coalescent units (scale bar on the bottom) 142/721 Alchemilla heptagona 93/841 0.07 Alchemilla decumbens 127/867 0.05 Alchemilla glabra 74/880 0.04 Alchemilla japonica 0.04 90/893 Alchemilla plicata 0.04 125/903 Alchemilla lapeyrousii lobed 0.04 116/702 Alchemilla flabellata 352/887 clade 0.05 0.05 Alchemilla xanthochlora 255/883 444/591 Alchemilla indivisa 0.05 0.17 97/878 Alchemilla mollis

0.05 Alchemilla splendens Eualchemilla 502/857 Alchemilla fissa 0.09 323/563 Alchemilla subsericea dissected 402/755 0.15 Alchemilla alpina 0.13 Alchemilla pentaphyllea clade 557/772 54/453 Aphanes cotopaxiensis 0.16 112/571 0.15 Aphanes sp “patagonica” 483/364 0.20 Aphanes sp “boliviana” 0.49 399/498 Aphanes occidentalis Aphanes 0.47 814/44 496/129 Aphanes microcarpa 0.82 0.70 Aphanes australis Aphanes arvensis 216/740 Alchemilla cryptantha 60/867 0.06 Alchemilla fischeri 76/897 0.03 Alchemilla kiwuensis 0.03 649/766 43/917 Alchemilla ellenbeckii 0.20 −0.03 261/711 Alchemilla johnstonii 64/916 0.08 Alchemilla microbetula 0.03 285/587 Alchemilla schizophylla 33/916 390/698 0.12 Alchemilla hildebrandtii 0.03 0.11 Alchemilla rutenbergii 125/917 Afromilla

Alchemilla haumanii .l.

0.03 s 334/597 Alchemilla woodii 396/753 0.12 Alchemilla colura 0.10 694/748 Alchemilla elongata 0.13 149/640 Alchemilla stuhlmannii 214/812 0.06 Alchemilla subnivalis

Alchemilla 148/842 0.04 Alchemilla argyrophylla 145/893 0.04 Alchemilla triphylla 0.04 iinae Alchemilla roccatii r 555/381 Lachemilla hirta aga 107/782 0.31 Lachemilla procumbens r 912/20 F 0.05 0.95 49/893 Lachemilla sibbaldiifolia 0.03 143/619 Lachemilla aphanoides 133/790 0.06 Lachemilla moritziana 0.04 Lachemilla standleyi 166/906 0.04 358/524 Lachemilla vulcanica 219/761 0.15 Lachemilla jamesonii 131/829 0.07 Lachemilla andina 68/877 0.05 Lachemilla pringlei 0.04 Lachemilla velutina 157/906 124/522 Lachemilla llanganatensis 0.04 149/696 0.07 Lachemilla hispidula 210/738 0.06 Lachemilla nivalis 111/833 0.06 Lachemilla galioides Lachemilla 508/427 89/872 0.04 Lachemilla angustata 0.39 0.04 132/883 Lachemilla polylepis 0.04 315/812 Lachemilla verticillata 0.05 787/414 150/556 Lachemilla ramosissima 0.35 0.07 Lachemilla equisetiformis 202/673 Lachemilla tanacetifolia 164/776 0.08 Lachemilla erodiifolia 282/810 0.06 226/698 Lachemilla mandoniana 95/878 0.07 0.18 Lachemilla pinnata 0.04 170/876 Lachemilla barbata 0.05 178/900 Lachemilla diplophylla 0.04 328/671 Lachemilla orbiculata 289/692 0.11 Lachemilla pectinata 0.17 Farinopsis salesoviana 881/22 Sibbaldianthe bifurca 416/432 0.91 Sibbaldianthe adpressa 0.33 Sibbaldia procumbens 676/234 Fragaria vesca 0.51 119/682 0.13 Comarum palustre 881/16 Drymocallis glandulosa 587/191 300/548 0.93 Drymocallis arguta 0.67 489/396 0.26 Chamaerhodos erecta 0.28 654/174 Dasiphora fruticosa 0.67 Potaninia mongolica Potentilla indica Sanguisorba menziesii Rosa woodsii

Figure S3. ASTRAL-Pro ASTRAL species trees cladogram of Alchemilla s.l. inferred from 923 multi-labeled homolog trees. Local posterior probability (LLP) are shown next to nodes. Numbers above branches indicate the number of gene trees concordant/conflicting with that node in the species tree. Numbers below the branches are the Internode Certainty All (ICA) score. 92 Lachemilla sibbaldiifolia 64 Lachemilla moritziana 100 Lachemilla pringlei 100 Lachemilla aphanoides 60 Lachemilla standleyi 100 Lachemilla velutina 100 Lachemilla procumbens 100 Lachemilla hirta 100 Lachemilla jamesonii 100 Lachemilla vulcanica 100 Lachemilla andina 98 Lachemilla equisetiformis 100 100 Lachemilla ramosissima Lachemilla polylepis 100 Lachemilla verticillata Lachemilla Lachemilla pectinata 100 100 Lachemilla orbiculata 100 Lachemilla hispidula 100 Lachemilla galioides 100 Lachemilla nivalis 100 Lachemilla angustata 100 Lachemilla llanganatensis 1/—/1 100 Lachemilla erodiifolia 100 Lachemilla barbata 100 Lachemilla diplophylla Lachemilla mandoniana 100 100 Lachemilla pinnata Lachemilla tanacetifolia 100 Alchemilla rutenbergii 100 Alchemilla hildebrandtii 20 Alchemilla schizophylla 100 Alchemilla elongata 19 0.99/0/0.99 Alchemilla johnstonii 50 Alchemilla cryptantha 61 Alchemilla kiwuensis 100 39 Alchemilla fischeri Alchemilla colura 100 Alchemilla woodii Afromilla 100 92 Alchemilla ellenbeckii 100 Alchemilla triphylla 100 Alchemilla subnivalis 100 Alchemilla stuhlmannii 100 0.98/0/1 Alchemilla argyrophylla 100 Alchemilla roccatii Alchemilla microbetula 100 Alchemilla s.l. 100 Alchemilla haumanii 67 Alchemilla fissa 1/—/1 58 Alchemilla flabellata Alchemilla plicata 92 100 Alchemilla japonica

87 Alchemilla indivisa Alchemilla mollis 66 lobed clade 100 Alchemilla glabra 0.95/0.25/0.92 62 Alchemilla decumbens 21 Alchemilla xanthochlora Eualchemilla 25 Alchemilla splendens 100 Alchemilla lapeyrousii 100 100 1/—/1 Alchemilla heptagona Alchemilla subsericea 100 Alchemilla alpina dissected clade 100 75 Alchemilla pentaphyllea 0.8/0.43/0.88 1/—/1 78 Aphanes cotopaxiensis 62 Aphanes sp “boliviana” 100 100 Aphanes sp “patagonica” 100 Aphanes occidentalis Aphanes 90 Aphanes australis 1/—/1 100 Aphanes arvensis 100 Aphanes microcarpa Farinopsis salesoviana Comarum palustre 100 Sibbaldianthe adpressa Fragariinae Sibbaldianthe bifurca 100 60 Sibbaldia procumbens 100 Drymocallis arguta 100 Drymocallis glandulosa 100 100 100 Potaninia mongolica Dasiphora fruticosa Chamaerhodos erecta 100 Fragaria vesca Potentilla indica Sanguisorba menziesii 0.003 substitution per site Rosa woodsii

Figure S4. Maximum likelihood phylogeny of Alchemilla s.l. inferred from RAxML analysis of partial plastomes. Bootstrap support (BS) is shown above branches in black. Quartet Sampling (QS) scores for major clades are shown below branches. QS scores in blue indicate strong support and red scores indicate weak support. QS scores: Quartet concordance/Quartet differential/Quartet informativeness. Branch lengths are in number of substitutions per site (scale bar on the bottom). MO RT

Alchemilla heptagona Alchemilla decumbens 1/868 − 1/250 Alchemilla decumbens 1/868 − 1/250 Alchemilla heptagona 1/868 − 1/250 0.1 / 0.4 Alchemilla japonica 1/868 − 1/250 0.1 / 0.4 Alchemilla glabra 0.1 / 0.4 0.1 / 0.4 Alchemilla glabra 1/868 − 0 Alchemilla japonica 1/868 − 0 Alchemilla plicata 0.1 / 0 Alchemilla indivisa 0.1 / 0 3/868 − 0 Alchemilla mollis Eualchemilla − Alchemilla mollis lobed 5/868 − 1/250 0.3 / 0 Alchemilla flabellata 0.6 / 0.4 Alchemilla indivisa lobed clade 2/868 − 1/250 clade Alchemilla xanthochlora 0.2 / 0.4 Alchemilla xanthochlora 2/868 − 0 2/868 − 0 0.2 / 0 Alchemilla flabellata Alchemilla plicata 5/868 − 1/250 0.2 / 0 7/868 − 1/250 0.6 / 0.4 Alchemilla lapeyrousii Alchemilla lapeyrousii 2/868 − 0 0.8 / 0.4 0.2 / 0 Alchemilla splendens Alchemilla fissa Eualchemilla Alchemilla fissa 71/868 − 13/250 Alchemilla splendens 8.2 / 5.2 Aphanes cotopaxiensis Alchemilla subsericea dissected 12/868 − 4/250 Aphanes sp “patagonica” 2/868 − 0 Alchemilla alpina 0.2 / 0 clade 1.4 / 1.6 Aphanes sp “boliviana” Alchemilla pentaphyllea 1/868 − 0 Aphanes occidentalis Aphanes 173/868 − 39/250 Aphanes sp “patagonica” 0.1 / 0 Aphanes australis 19.9 / 15.6 Aphanes sp “boliviana” 216/868 − 46/250 8/868 − 0 1/868 − 1/250 24.9 / 18.4 0.9 / 0 0.1 / 0.4 Aphanes microcarpa Aphanes cotopaxiensis 1/868 − 0 Aphanes arvensis Aphanes occidentalis 0.1 / 0 Aphanes Aphanes microcarpa Alchemilla alpina Eualchemilla − 8/868 − 0 1/868 − 1/250 2/868 − 0 Alchemilla subsericea 0.9 / 0 0.1 / 0.4 Aphanes australis 0.2 / 0 Alchemilla pentaphyllea dissected clade Aphanes arvensis Alchemilla ellenbeckii Alchemilla fischeri Alchemilla kiwuensis Alchemilla cryptantha Alchemilla fischeri Alchemilla kiwuensis 344/868 − 86/250 344/868 − 86/250 Alchemilla cryptantha 39.6 / 34.4 Alchemilla ellenbeckii 39.6 / 34.4 Alchemilla hildebrandtii Alchemilla schizophylla Alchemilla schizophylla Alchemilla hildebrandtii Alchemilla rutenbergii Alchemilla rutenbergii Alchemilla johnstonii Alchemilla colura Alchemilla microbetula Alchemilla woodii Afromilla Afromilla

Alchemilla elongata .l. Alchemilla haumanii .l. s s Alchemilla woodii Alchemilla johnstonii Alchemilla colura Alchemilla microbetula 34/868 − 8/250 Alchemilla elongata 34/868 − 8/250 Alchemilla haumanii 3.9 / 3.2 3.9 / 3.2 Alchemilla stuhlmannii 1/868 − 1/250 Alchemilla stuhlmannii Alchemilla subnivalis 0.1 / 0.4 Alchemilla triphylla Alchemilla Alchemilla 1/868 − 1/250 Alchemilla argyrophylla Alchemilla subnivalis 0.1 / 0.4 Alchemilla triphylla Alchemilla argyrophylla iinae r Alchemilla roccatii Alchemilla roccatii iinae r Lachemilla aphanoides Lachemilla moritziana aga r Lachemilla standleyi Lachemilla aphanoides aga r F 810/868 − 215/250

810/868 − 215/250 F Lachemilla moritziana Lachemilla standleyi 93.3 / 86.0 93.3 / 86.0 Lachemilla sibbaldiifolia 1/868 − 1/250 Lachemilla procumbens 1/868 − 1/250 Lachemilla hirta 0.1 / 0.4 Lachemilla hirta 0.1 / 0.4 Lachemilla procumbens Lachemilla sibbaldiifolia 17/868 − 3/250 17/868 − 3/250 Lachemilla vulcanica Lachemilla jamesonii 2.0 / 1.2 2.0 / 1.2 Lachemilla jamesonii Lachemilla vulcanica Lachemilla andina Lachemilla andina 2/868 − 1/250 Lachemilla pringlei 2/868 − 1/250 Lachemilla pringlei 0.2 / 0.4 0.2 / 0.4 Lachemilla velutina Lachemilla velutina Lachemilla hispidula Lachemilla llanganatensis 11/868 − 3/250 2/868 − 2/250 11/868 − 3/250 2/868 − 2/250 0.2 / 0.8 1.3 / 1.2 0.2 / 0.8 Lachemilla llanganatensis 1.3 / 1.2 Lachemilla hispidula Lachemilla nivalis Lachemilla galioides 1/868 − 1/250 Lachemilla galioides Lachemilla 1/868 − 1/250 Lachemilla nivalis Lachemilla 0.1 / 0.4 12/868 − 2/250 0.1 / 0.4 12/868 − 2/250 Lachemilla angustata Lachemilla angustata 1.4 / 0.8 1.4 / 0.8 Lachemilla verticillata Lachemilla polylepis Lachemilla polylepis Lachemilla equisetiformis 230/868 − 46/250 Lachemilla ramosissima 230/868 − 46/250 Lachemilla ramosissima 26.5 / 18.4 Lachemilla equisetiformis 26.5 / 18.4 Lachemilla verticillata Lachemilla tanacetifolia Lachemilla tanacetifolia Lachemilla erodiifolia Lachemilla erodiifolia 8/868 − 4/250 Lachemilla mandoniana 8/868 − 4/250 Lachemilla mandoniana 0.9 / 1.6 Lachemilla pinnata 0.9 / 1.6 Lachemilla pinnata Lachemilla barbata Lachemilla diplophylla Lachemilla diplophylla Lachemilla barbata Lachemilla pectinata Lachemilla pectinata 37/868 − 11/250 Lachemilla orbiculata 37/868 − 11/250 Lachemilla orbiculata 4.3 / 4.4 Farinopsis salesoviana 4.3 / 4.4 Farinopsis salesoviana 1/868 − 0 Sibbaldianthe adpressa 1/868 − 0 Sibbaldianthe adpressa 28/868 − 9/250 1/868 − 1/250 0.1 / 0 Sibbaldianthe bifurca 28/868 − 9/250 1/868 − 1/250 0.1 / 0 Sibbaldianthe bifurca 3.2 / 3.6 3.2 / 3.6 0.1 / 0.4 0.1 / 0.4 Sibbaldia procumbens Sibbaldia procumbens Comarum palustre Comarum palustre 95/868 − 20/250 Fragaria vesca 95/868 − 20/250 Fragaria vesca 10.9 / 8.0 10.9 / 8.0 1/868 − 0 Drymocallis arguta 1/868 − 0 Drymocallis glandulosa 0.1 / 0 Drymocallis glandulosa 0.1 / 0 Drymocallis arguta 3/868 − 1/250 Chamaerhodos erecta 3/868 − 1/250 Chamaerhodos erecta 0.3 / 0.4 0.3 / 0.4 1/868 − 0 Dasiphora fruticosa 1/868 − 0 Dasiphora fruticosa 0.1 / 0 Potaninia mongolica 0.1 / 0 Potaninia mongolica Potentilla indica Potentilla indica Sanguisorba menziesii Sanguisorba menziesii Rosa woodsii Rosa woodsii

Figure S5. a) Maximum likelihood cladogram of Alchemilla s.l. inferred from RAxML analysis of the concatenated 910-nuclear gene supermatrix from the ‘monophyletic outgroup’ (MO) orthologs with gene duplication estimates from the subclade orthogroup tree topology approach. b) Maximum likelihood cladogram of Alchemilla s.l. inferred from RAxML analysis of the concatenated 1,894-nuclear gene supermatrix from the ‘rooted ingroup’ (RT) orthologs with gene duplication estimates from the subclade orthogroup tree topology approach. Numbers below branches denote gene duplication counts when using all exon homologs (868) and only one exon homolog per gene (250). Numbers above branches denote gene duplication percentages when using all exons and only one exon per gene. Missing label nodes denote bipartitions without gene duplication. MO RT

Eualchemilla - lobed Eualchemilla - lobed Aphanes Eualchemilla - dissected Eualchemilla - dissected Aphanes Eualchemilla - lobed Eualchemilla - lobed Afromilla Afromilla Lachemilla Lachemilla Farinopsis salesoviana Farinopsis salesoviana Other Fragariinae/Outgroups Other Fragariinae/Outgroups

Figure S6. Optimal multi-labeled trees from GRAMPA analyses using ‘monophyletic outgroup’ (MO) and ‘rooted ingroup’ (RT) ortholog species trees. Red branches denote the allopolyploid origin of the 'lobed' clade of Eualchemilla. MO cpDNA

Eualchemilla - lobed Eualchemilla - dissected Aphanes Eualchemilla - lobed Eualchemilla - dissected Aphanes Afromilla Afromilla Lachemilla Lachemilla Farinopsis salesoviana Eualchemilla - dissected Sibbaldia Eualchemilla - lobed Sibbaldianthe Aphanes Comarum Afromilla Fragaria Lachemilla Eualchemilla - lobed Farinopsis salesoviana Aphanes Comarum Eualchemilla - dissected Sibbaldia Afromilla Sibbaldianthe Lachemilla Dasiphora Farinopsis salesoviana Potaninia mongolica Sibbaldia Drymocallis Sibbaldianthe Chamaerhodos Drymocallis Fragaria Chamaerhodos Outgroups Dasiphora Potaninia mongolica Outgroups

Figure S7. Optimal summarized multi-labeled trees from GRAMPA analyses using searches constrained to the crown node of Alchemilla s.l. on the ‘monophyletic outgroup’ (MO) and cpDNA species trees. Orange branches denote the allopolyploid origin of the clade composed of Alchemilla s.l., Farinopsis, Sibbaldianthe, and Sibbaldia (MO) or the autopolyploid origin Alchemilla s.l. (cpDNA). a) MO

Aphanes − only Afromilla − only Eualchemilla-dissected − only Eualchemilla-lobed − only Lachemilla − only

Aphanes Afromilla Eualchemilla - dissected Eualchemilla - lobed Lachemilla Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Sibbaldia Sibbaldia Sibbaldia Sibbaldia Sibbaldia Sibbaldianthe Sibbaldianthe Sibbaldianthe Sibbaldianthe Sibbaldianthe Comarum Comarum Comarum Comarum Comarum Fragaria Fragaria Fragaria Fragaria Fragaria Aphanes Afromilla Eualchemilla - dissected Eualchemilla - lobed Lachemilla Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Sibbaldia Sibbaldia Sibbaldia Sibbaldia Sibbaldia Sibbaldianthe Sibbaldianthe Sibbaldianthe Sibbaldianthe Sibbaldianthe Other Fragariinae/Outgroups Other Fragariinae/Outgroups Other Fragariinae/Outgroups Other Fragariinae/Outgroups Other Fragariinae/Outgroups

b) cpDNA

Aphanes − only Afromilla − only Eualchemilla-dissected − only Eualchemilla-lobed − only Lachemilla − only

Aphanes Afromilla Eualchemilla - dissected Eualchemilla - lobed Lachemilla Farinopsis salesoviana Afromilla Eualchemilla - dissected Eualchemilla - lobed Lachemilla Other Fragariinae/Outgroups Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Farinopsis salesoviana Other Fragariinae/Outgroups Other Fragariinae/Outgroups Other Fragariinae/Outgroups Other Fragariinae/Outgroups

Figure S8. Optimal summarized multi-labeled trees from GRAMPA analyses using individual major clades Alchemilla s.l. on the ‘monophyletic outgroup’ (MO) and cpDNA species trees. Orange branches denote the allopolyploid events (MO) or autopolyploid events (cpDNA).

a) Alchemilla_alpina_2n=120 Alchemilla_fissa_2n=145−156 Alchemilla_mollis_2n=102−106 Alchemilla_xanthochlora_2n=103 Sibbaldia_parviflora_2n=14 Sibbaldianthe_adpressa_2n=14 Sibbaldianthe_bifurca_2n=56 Comarum_palustre_2n=28−64 Fragaria_vesca_2n=14 Dasiphora_glabra_2n=14 Chamaerhodos_erecta_2n=14 Drymocallis_arguta_2n=14 Potaninia_mongolica_2n=14 3 4 3 3 4 5 3 0.4 3 3 3 2 3 4 2 2 3 2 2 0.3 2 3 2 2 2 2 2 0.2 Density Density Density Density Density Density Density Density Density Density Density Density 1 2 Density 1 1 1 1 1 1 1 1 1 1 1 0.1

0 0 0 0 0 0 0 0 0.0 0 0 0 0 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3 Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks b) Alchemilla_alpina_2n=120 Alchemilla_fissa_2n=145−156 Alchemilla_mollis_2n=102−106 Alchemilla_xanthochlora_2n=103 Sibbaldia_parviflora_2n=14 Sibbaldianthe_adpressa_2n=14 Sibbaldianthe_bifurca_2n=28 Comarum_palustre_2n=28−64 Fragaria_vesca_2n=14 Dasiphora_fruticosa_2n=14 Chamaerhodos_erecta_2n=14 Drymocallis_arguta_2n=14 Potaninia_mongolica_2n=14 3 5 12 12.5 4 10.0 6 4 4 7.5 7.5 4 7.5 10.0 9 9 7.5 3 3 2 3 4 3 5.0 7.5 5.0 6 5.0 2 5.0 6 2 2 Density Density Density Density Density Density Density Density Density 2 Density 5.0 Density Density Density 2 1 2.5 2.5 2.5 1 1 3 2.5 3 1 1 2.5

0 0 0 0 0 0.0 0.0 0 0 0.0 0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks Ks c) Alchemilla_alpina_2n=120 Alchemilla_fissa_2n=145−156 Alchemilla_mollis_2n=102−106 Alchemilla_xanthochlora_2n=103 Sibbaldia_parviflora_2n=14 Sibbaldianthe_adpressa_2n=14 Sibbaldianthe_bifurca_2n=28 Comarum_palustre_2n=28−64 Fragaria_vesca_2n=14 Dasiphora_fruticosa_2n=14 Chamaerhodos_erecta_2n=14 Drymocallis_arguta_2n=14 Potaninia_mongolica_2n=14 0.4 0.4 0.8 0.3 0.3 0.6 0.3 0.6 0.75 0.6 0.3 0.6 0.75 0.3 0.3 0.6 0.2 0.2 0.4 0.2 0.4 0.50 0.4 0.2 0.4 0.50 0.2 0.2 0.4 Density Density Density Density Density Density Density Density Density Density Density Density Density 0.2 0.1 0.1 0.1 0.2 0.25 0.2 0.1 0.2 0.1 0.1 0.2 0.25

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00 0.00 0.0 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 −4 −3 −2 −1 0 1 log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks) log(Ks)

Figure S9. Distribution of synonymous distance among gene pairs (Ks) plots for four species of Eualchemilla and nine species of other genera in Fragariinae. Alchemilla alpina belongs to the 'dissected' clade, and A. fissa, A. mollis, and A. xanthochlora belong to the Lobe clade. Reported known chromosome numbers for each species as noted next to the species name. a) Plots using normal Ks distances. b) Plots using log-transformed Ks distances. c) Plots using normal Ks distances between 0 and 0.5. Red lines denote peaks inferred using a mixture model that are unique for each species or shared among Eualchemilla. Blue lines denote significant peaks from ancestral angiosperm-share whole genome duplication.

Table S1. Main characteristics of majors clades of Alchemilla s.l.

Characters Eualchemilla Afromilla Lachemilla Aphanes Life cycle Perennial Perennial Perennial Annual or biannual Rosette-forming herbs, prostrate Rosette-forming herbs, trailing Rosette-forming herbs, trailing herbs, often with woody herbs, prostrate herbs, or dwarf herbs, procumbent herbs, Habit rootstock shrubs subshrubs, or dwarf shrubs Slender ascending herbs

Lobed, dissected, pinnate, bi- morphology Lobed to dissected Lobed to dissected pinnate, appendaged and whorled Dissected Number of species ca. 900 ca. 70 ca. 65 ca. 20 Sub-Saharan and Madagascar, Mountains of the Neotropics, Holarctic, with and a center of with a diversity center in the especially diverse in the high- Temperate regions of the world, diversity in the mountains of temperate climate regions like elevation grasslands of northern with a center of diversity in the Distribution Central Europe. mountains South America. western Mediterranean Four stamens inserted on the Four stamens inserted on the outer Two stamens inserted on the One stamens inserted on the inner Stamens outer side of the disc side of the disc inner side of the disc side of the disc Octoploid to decaploid (data Diploid to dodecaploid (mostly Ploidy (n =8) Octoploid to 24-ploid available for only two species) polyploid) Diploid and tetraploid Apomixis Autonomous Present (mechanism unknown) Autonomous Pseudogamous Table S2. List of species and vouchers used in this study. SRA accesion Section/clade within Species number Collection number Herbarium Major group major group Notes Alchemilla johnstonii Oliv. B. Gehrke 364 ZT Afromilla Sect. Geraniifoliae Alchemilla roccatii Cort. B. Gehrke 365 ZT Afromilla Sect. Geraniifoliae Alchemilla haumanii Rothm. B. Gehrke 204 ZT Afromilla Sect. Grandifoliae Alchemilla colura Hilliard B. Gehrke 464 ZT Afromilla Sect. Longicaules Alchemilla cryptantha Steud. ex A.Rich. B. Gehrke 306 ZT Afromilla Sect. Longicaules Alchemilla ellenbeckii Engl. B. Gehrke 104 ZT Afromilla Sect. Longicaules Alchemilla elongata Eckl. & Zeyh. B. Gehrke 446 ZT Afromilla Sect. Longicaules Alchemilla fischeri Engl. B. Gehrke 018 ZT Afromilla Sect. Longicaules Alchemilla kiwuensis Engl. B. Gehrke 057 ZT Afromilla Sect. Longicuales Alchemilla woodii Kuntze B. Gehrke 453 ZT Afromilla Sect. Longicuales Alchemilla argyrophylla Oliv. SRR6667468 W. Rauh T139 M Afromilla Sect. Parvifoliae Alchemilla microbetula T.C.E.Fr. B. Gehrke 360 ZT Afromilla Sect. Parvifoliae Alchemilla hildebrandtii Engl. B. Gehrke 258 ZT Afromilla Sect. Schizophyllae Alchemilla rutenbergii O.Hoffm. B. Gehrke 253 ZT Afromilla Sect. Schizophyllae Alchemilla schizophylla Bak. B. Gehrke 282 ZT Afromilla Sect. Schizophyllae Alchemilla stuhlmannii Engl. B. Gehrke 363 ZT Afromilla Sect. Subcuneatifoliae Alchemilla subnivalis Bak. B. Gehrke 362 ZT Afromilla Sect. Subcuneatifoliae Alchemilla triphylla Rothm. B. Gehrke 361 ZT Afromilla Sect. Subcuneatifoliae Alchemilla alpina L. SL 11498 ZT Eualchemilla - Dissected clade Sect. Alpinae Alchemilla pentaphyllea L. J. Kadereit & M. Lauterbach 201252 JGU Eualchemilla - Dissected clade Sect. Pentaphylleae Alchemilla subsericea Reut. P. Frost-Olsen 11984 AAU Eualchemilla - Dissected clade Sect. Glaciales Alchemilla decumbens Buser B. Gehrke 662 ZT Eualchemilla - Lobed clade Sect. Decumbentes Alchemilla fissa Gunth. & Schumm. P. Frost-Olsen 8240 AAU Eualchemilla - Lobed clade Sect. Calycinae Alchemilla flabellata Buser P. Frost-Olsen 11859 AAU Eualchemilla - Lobed clade Sect. Flabellatae Alchemilla glabra Neygenf. P. Frost-Olsen 12658 AAU Eualchemilla - Lobed clade Sect. Coriaceae Alchemilla heptagona Juz. P. Frost-Olsen 6999 AAU Eualchemilla - Lobed clade Sect. Ultravulgares Alchemilla indivisa Formánek ex Rothm. P. Frost-Olsen 3383 AAU Eualchemilla - Lobed clade Sect. Erectae Alchemilla japonica Nakai & H.Hara B. Dichore 1986 GOET Eualchemilla - Lobed clade Sect. Plicatae Alchemilla lapeyrousii Buser P. Frost-Olsen 10029 AAU Eualchemilla - Lobed clade Sect. Pubescentes Alchemilla mollis (Buser) Rothm. SRR6667455 D.F. Morales-Briones 687 ID Eualchemilla - Lobed clade Sect. Erectae Alchemilla plicata Buser P. Frost-Olsen 11575 AAU Eualchemilla - Lobed clade Sect. Plicatae Alchemilla splendens Christ P. Frost-Olsen 7587 AAU Eualchemilla - Lobed clade Sect. Splendentes Alchemilla xanthochlora Rothm. Lippert s.n. M Eualchemilla - Lobed clade Sect. Alchemilla Aphanes arvensis L. Bot. Garden Zürich s.n. ZT Aphanes Sect. Inaequidentatae Aphanes australis Rydb. SRR6667469 D.C. Tank 1107 ID Aphanes Sect. Inaequidentatae Aphanes cotopaxiensis Romol. & Frost-Olsen D.F. Morales-Briones et al. 276 ID Aphanes Sect. Inaequidentatae Aphanes microcarpa (Boiss. & Reut.) Rothm. L. Koepke 201000524-1 OSU Aphanes Sect. Inaequidentatae Aphanes occidentalis (Nutt.) Rydb. D.F. Morales-Briones & D. Caetano 579 ID Aphanes Sect. Inaequidentatae Aphanes sp. "boliviana" D.F. Morales-Briones et al. 291 ID Aphanes Sect. Inaequidentatae Aphanes spᵃ Aphanes sp. "patagonica" Marticoerena et al. 941 CONC Aphanes Sect. Inaequidentatae Aphanes neglectaᵃ Lachemilla orbiculata (Ruiz & Pav.) Rydb. SRR6667480 D.F. Morales-Briones et al. 108 QCA Lachemilla Orbiculate Lachemilla pectinata (Kunth) Rothm. SRR6667481 D.F. Morales-Briones & K. Romoleroux 161 QCA Lachemilla Orbiculate Lachemilla barbata (C.Presl) Rothm. SRR6667472 D.F. Morales-Briones & S. Uribe-Convers 229 ID Lachemilla Pinnate Lachemilla diplophylla (Diels) Rothm. SRR6667473 D.F. Morales-Briones & E. Morales-Checa 30 QCA Lachemilla Pinnate Lachemilla erodiifolia (Wedd.) Rothm. SRR6667470 D.F. Morales-Briones & K. Romoleroux 119 QCA Lachemilla Pinnate Lachemilla mandoniana (Wedd.) Rothm. SRR6667482 D.F. Morales-Briones et al. 112 QCA Lachemilla Pinnate Lachemilla pinnata (Ruiz & Pav.) Rothm. SRR6667484 D.F. Morales-Briones et al. 113 QCA Lachemilla Pinnate Lachemilla tanacetifolia Rothm. SRR6667464 D.F. Morales-Briones et al. 122 QCA Lachemilla Pinnate Lachemilla andina (L.M.Perry) Rothm. SRR6667466 D.F. Morales-Briones & K. Romoleroux 162 QCA Lachemilla Tripartite Lachemilla aphanoides (Mutis ex L.f.) Rothm. SRR6667467 D.F. Morales-Briones et al. 115 QCA Lachemilla Tripartite Lachemilla hirta (L.M.Perry) Rothm. SRR6667475 D.F. Morales-Briones & K. Romoleroux 118 QCA Lachemilla Tripartite Lachemilla jamesonii (L.M.Perry) Rothm. SRR6667476 K. Romoleroux et al. 4684 QCA Lachemilla Tripartite Lachemilla moritziana Dammer D.F. Morales-Briones & S. Uribe-Convers 427 ID Lachemilla Tripartite Lachemilla pringlei Rydb. D.F. Morales-Briones & P. Tenorio-Lezama 595 ID Lachemilla Tripartite Lachemilla procumbens (Rose) Rydb. SRR6667461 K. Romoleroux et al. 5011 QCA Lachemilla Tripartite Lachemilla sibbaldiifolia (Kunth) Rydb. D.F. Morales-Briones & P. Tenorio-Lezama 599 ID Lachemilla Tripartite Lachemilla standleyi (L.M.Perry) Rothm. K. Romoleroux et al. 5005 QCA Lachemilla Tripartite Lachemilla velutina (S.Watson) Rydb. D.F. Morales-Briones & P. Tenorio-Lezama 607 ID Lachemilla Tripartite Lachemilla vulcanica (Schltdl. & Cham.) Rydb. SRR6667486 D.F. Morales-Briones et al. 117 QCA Lachemilla Tripartite Lachemilla angustata Romol. K. Romoleroux et al.1562 QCA Lachemilla Verticillate Lachemilla equisetiformis (Trevir.) Rothm. Muller 91-28 MSB Lachemilla Verticillate Lachemilla galioides (Benth.) Rothm. SRR6667474 K. Romoleroux et al. 4699 QCA Lachemilla Verticillate Lachemilla hispidula (L.M.Perry) Rothm. SRR6667478 D.F. Morales-Briones & K. Romoleroux 110 QCA Lachemilla Verticillate Lachemilla llanganatensis Romol. D.F. Morales-Briones et al. 63 QCA Lachemilla Verticillate Lachemilla nivalis (Kunth) Rothm. SRR6667483 K. Romoleroux et al. 4580 QCA Lachemilla Verticillate Lachemilla polylepis (Wedd.) Rothm. SRR6667485 P. Sklenář 12207 QCA Lachemilla Verticillate Lachemilla ramosissima (Rothm.) Rothm. Aristeguieta 3882 NY Lachemilla Verticillate Lachemilla verticillata (Fielding & Gardner) Rothm. SRR6667457 K. Romoleroux et al. 5007 QCA Lachemilla Verticillate Chamaerhodos erecta (L.) Bunge R.L. Hartman & B.E Nelson 54641 ID Fragariinae N/A Comarum palustre L. J. Duemmel et al. 29-08 ID Fragariinae N/A Dasiphora fruticosa (L.) Rydb. H.E. Marx & D. Daly 2013-209 ID Fragariinae N/A Drymocallis arguta (Pursh) Rydb. J.F. Smith 8736 ID Fragariinae N/A Drymocallis glandulosa (Lindl.) Rydb. A. Liston 1373 OSC Fragariinae N/A Farinopsis salesoviana (Stephan) Chrtek & Soják B. Bartholomew et al. 8364 MO Fragariinae N/A Fragaria vesca L. Genome v1.1 Shulaev, et. al 2010 Fragariinae N/A Potaninia mongolica Maxim. L. Yingxin & Z. Xiufu 93039 MO Fragariinae N/A Sibbaldia procumbens L. H.E. Marx & Z. Klos 2012-041 ID Fragariinae N/A Sibbaldianthe adpressa (Bunge) Juz. И.M. Kpachoбopoв 320 MO Fragariinae N/A Sibbaldianthe bifurca (L.) Kurtto & T.Erikss. D.E. Boufford et al. 29796 MO Fragariinae N/A Potentilla indica (Andrews) Th.Wolf A. Liston 1363 OSC Outgroup N/A Rosa woodsii Lindl. A. Liston 1360 OSC Outgroup N/A Sanguisorba menziesii Rydb. A. Liston 1342 OSC Outgroup N/A ᵃName in alignment and tree files Table S3. Plastomes used for assembly and phylogenetic inference. Species GenBank accession Reference Chamaerhodos erectaᵃ KY420001 Zhang et al., 2017 Dasiphora fruticosaᵃ KY420016 Zhang et al., 2017 Drymocallis glandulosaᵃ KY420015 Zhang et al., 2017 Farinopsis salesovianaᵃ KY420034 Zhang et al., 2017 Fragaria vescaᵃ JF345175 Shulaev et al., 2011 Lachemilla pectinataᵇ KY419937 Zhang et al., 2017 Potaninia mongolicaᵃ KY419959 Zhang et al., 2017 Potentilla indicaᵃ KY420014 Zhang et al., 2017 Rosa lichiangensisᵇ KY419934 Zhang et al., 2017 Sanguisorba officinalisᵇ KY419975 Zhang et al., 2017 Sibbaldia procumbensᵃ KY419935 Zhang et al., 2017 Sibbaldianthe sericeaᵇ KY419993 Zhang et al., 2017 ᵃUsed for plastome assembly and phylogenetic inference. ᵇUsed only for plastome assembly. Tables S4. List of species used for synonymous distance among gene pairs (Ks) plots. Ploidy (n = 8 in Section/clade Alchemilla; n = 7 in within major Species rest of Fragariinae) Major group group Source Accesion number Alchemilla alpina 2n = 120 Eualchemilla Dissected clade Xiang et al. 2017 Alchemilla fissa 2n = 145–156 Eualchemilla Lobed clade Xiang et al. 2017 Alchemilla mollis 2n = 102–106 Eualchemilla Lobed clade Unpublished SAMN14517905 Alchemilla xanthocholora 2n = 103 Eualchemilla Lobed clade Unpublished SAMN14517906 Chamaerhodos erecta 2n = 14 Fragariinae N/A Xiang et al. 2017 Comarum palustre 2n = 28–64 Fragariinae N/A Xiang et al. 2017 Dasiphora glabra 2n = 14 Fragariinae N/A Xiang et al. 2017 Drymocallis arguta 2n = 14 Fragariinae N/A Xiang et al. 2017 Fragaria vesca 2n = 14 Fragariinae N/A Shulaev, et. al 2010 Phytozome - Genome v1.1 Potaninia mongolica 2n = 14 Fragariinae N/A Xiang et al. 2017 Sibbaldia parviflora 2n = 14 Fragariinae N/A Xiang et al. 2017 Sibbaldianthe bifurca 2n = 56 Fragariinae N/A Xiang et al. 2017 Sibbaldianthe adpressa 2n = 14 Fragariinae N/A Xiang et al. 2017 Table S5. HybPiper assembly statistics Number of exons Number of exons Number of exons Number of exons with sequences > with sequences > with sequences > with sequences > Number of exons Number of Percent reads Number of exons Number of exons Number of exons 25% of the target 50% of the target 75% of the target 150% of the target with paralog Species Number of reads reads on target on target with reads with contigs with sequences length length length length warnings Alchemilla_alpina 524,481 358,784 68.4% 926 862 860 857 849 821 3 370 Alchemilla_argyrophylla 9,423,799 2,302,455 24.4% 930 909 906 905 889 863 0 686 Alchemilla_colura 2,339,559 1,659,277 70.9% 930 919 916 916 909 895 0 623 Alchemilla_cryptantha 4,234,959 3,104,915 73.3% 930 927 924 924 915 891 2 671 Alchemilla_decumbens 1,718,446 1,080,216 62.9% 932 914 909 907 895 864 2 572 Alchemilla_ellenbeckii 2,234,479 1,633,354 73.1% 933 923 919 918 912 890 0 662 Alchemilla_elongata 3,384,889 2,452,689 72.5% 931 924 921 919 911 888 2 655 Alchemilla_fischeri 2,371,539 1,681,160 70.9% 932 925 921 919 911 891 1 654 Alchemilla_fissa 168,831 108,950 64.5% 923 695 692 688 671 632 0 66 Alchemilla_flabellata 743,681 473,981 63.7% 923 887 881 880 865 834 2 458 Alchemilla_glabra 2,295,784 1,556,467 67.8% 929 921 915 914 904 880 1 579 Alchemilla_haumanii 2,234,226 1,608,164 72.0% 927 920 915 914 908 888 1 617 Alchemilla_heptagona 1,856,644 1,210,799 65.2% 925 918 912 910 905 881 1 585 Alchemilla_hildebrandtii 484,180 326,667 67.5% 928 870 867 865 856 826 1 470 Alchemilla_indivisa 1,734,141 1,107,718 63.9% 929 915 910 909 902 876 1 575 Alchemilla_japonica 2,217,591 1,514,768 68.3% 930 921 916 915 909 882 0 583 Alchemilla_johnstonii 3,378,617 2,400,151 71.0% 930 925 924 921 915 899 0 645 Alchemilla_kiwuensis 1,709,266 1,186,794 69.4% 929 912 909 906 902 886 1 601 Alchemilla_lapeyrousii 1,096,905 691,343 63.0% 933 895 891 887 874 848 2 477 Alchemilla_microbetula 4,323,618 3,122,993 72.2% 933 927 923 923 918 897 0 642 Alchemilla_mollis 10,805,273 4,148,516 38.4% 930 919 915 911 902 886 1 746 Alchemilla_pentaphyllea 1,931,279 1,257,408 65.1% 929 918 916 916 908 876 4 619 Alchemilla_plicata 473,046 309,663 65.5% 929 860 856 855 845 818 0 384 Alchemilla_roccatii 3,508,263 2,523,772 71.9% 933 927 924 924 917 895 0 630 Alchemilla_rutenbergii 1,781,618 1,268,216 71.2% 932 921 919 919 912 891 1 595 Alchemilla_schizophylla 770,984 530,610 68.8% 930 899 898 896 885 855 1 541 Alchemilla_splendens 881,924 569,639 64.6% 928 891 890 884 869 835 4 437 Alchemilla_stuhlmannii 501,136 335,671 67.0% 926 888 887 885 869 846 1 428 Alchemilla_subnivalis 1,852,807 1,225,895 66.2% 929 923 920 920 910 879 0 581 Alchemilla_subsericea 2,400,286 1,636,676 68.2% 929 921 918 918 909 882 2 579 Alchemilla_triphylla 573,770 374,779 65.3% 928 883 882 880 871 846 1 428 Alchemilla_woodii 657,131 444,252 67.6% 930 887 886 882 868 842 0 497 Alchemilla_xanthochlora 952,341 671,634 70.5% 929 914 911 908 899 871 0 541 Aphanes_arvensis 2,637,012 1,690,388 64.1% 900 875 871 864 853 821 0 256 Aphanes_australis 15,601,983 3,760,913 24.1% 902 848 843 840 833 813 0 152 Aphanes_cotopaxiensis 402,741 232,904 57.8% 892 825 821 818 804 780 0 124 Aphanes_microcarpa 467,018 277,304 59.4% 905 830 825 823 810 786 0 120 Aphanes_occidentalis 1,643,973 1,081,203 65.8% 884 859 851 847 838 814 0 133 Aphanes_sp "boliviana" 651,401 390,319 59.9% 897 838 834 831 819 800 0 128 Aphanes_sp "patagonica" 3,576,077 2,484,557 69.5% 902 867 860 854 846 823 0 143 Chamaerhodos_erecta 2,384,006 1,808,610 75.9% 938 926 926 926 925 922 0 29 Comarum_paluste 1,436,708 1,173,401 81.7% 938 937 937 936 936 932 0 388 Dasiphora_fruticosa 965,137 743,804 77.1% 939 938 938 938 938 934 0 48 Drymocallis_arguta 3,183,973 2,585,201 81.2% 939 939 939 939 939 934 0 32 Drymocallis_glandulosa 1,805,073 562,801 31.2% 939 927 927 927 921 900 0 10 Farinopsis_salesoviana 2,831,516 2,428,596 85.8% 939 939 939 937 927 906 0 429 Lachemilla_andina 11,120,534 4,403,408 39.6% 929 919 915 915 909 892 0 628 Lachemilla_angustata 2,107,992 1,682,792 79.8% 931 919 915 911 899 873 1 475 Lachemilla_aphanoides 18,547,039 7,933,424 42.8% 933 921 913 913 911 903 2 654 Lachemilla_barbata 23,347,654 9,207,955 39.4% 932 923 917 917 910 904 1 653 Lachemilla_diplophylla 13,925,112 5,978,669 42.9% 930 917 914 913 907 898 0 638 Lachemilla_equisetiformis 455,469 343,612 75.4% 929 883 881 877 860 822 0 302 Lachemilla_erodiifolia 8,525,733 3,441,532 40.4% 928 915 912 910 906 896 1 645 Lachemilla_galioides 8,234,295 3,333,021 40.5% 930 908 904 904 899 888 1 651 Lachemilla_hirta 14,748,363 6,391,178 43.3% 930 918 915 915 910 900 3 625 Lachemilla_hispidula 8,337,125 3,367,380 40.4% 928 914 912 912 906 895 1 619 Lachemilla_jamesonii 10,935,704 4,421,523 40.4% 931 917 914 914 909 892 2 644 Lachemilla_llanganatensis 529,599 344,731 65.1% 928 887 883 882 878 858 1 409 Lachemilla_mandoniana 7,238,811 2,537,702 35.1% 931 908 906 906 902 888 1 624 Lachemilla_moritziana 501,013 319,142 63.7% 933 880 878 877 871 851 1 336 Lachemilla_nivalis 7,912,741 2,643,787 33.4% 925 905 902 902 897 888 1 604 Lachemilla_orbiculata 9,159,390 3,519,420 38.4% 927 913 910 909 905 893 0 625 Lachemilla_pectinata 13,747,010 5,885,754 42.8% 930 918 917 917 914 900 1 692 Lachemilla_pinnata 21,402,835 7,412,832 34.6% 930 921 916 916 912 901 0 641 Lachemilla_polylepis 14,256,485 4,708,023 33.0% 929 917 915 915 909 901 1 637 Lachemilla_pringlei 613,473 418,391 68.2% 928 889 887 886 881 865 0 410 Lachemilla_procumbens 8,827,483 3,277,780 37.1% 928 910 906 906 902 889 0 618 Lachemilla_ramosissima 1,629,249 1,313,895 80.6% 934 919 914 909 899 873 1 460 Lachemilla_sibbaldiifolia 645,613 445,494 69.0% 929 902 898 898 889 874 1 406 Lachemilla_standleyi 3,039,388 2,329,689 76.6% 929 926 921 919 908 890 1 501 Lachemilla_tanacetifolia 5,333,257 2,323,802 43.6% 929 908 905 905 897 882 0 647 Lachemilla_velutina 655,979 453,092 69.1% 925 901 896 896 891 873 0 445 Lachemilla_verticillata 9,252,744 4,020,526 43.5% 932 916 913 912 906 897 1 652 Lachemilla_vulcanica 9,285,254 4,015,561 43.2% 932 915 911 911 907 892 1 641 Potaninia_mongolica 2,828,344 2,419,418 85.5% 938 933 932 932 930 923 0 63 Potentilla_indica 4,917,501 1,534,558 31.2% 939 925 925 925 921 890 1 96 Rosa_woodsii 4,510,487 1,057,848 23.5% 939 933 933 933 928 902 0 28 Sanguisorba_menziesii 3,033,042 648,547 21.4% 939 901 900 899 882 844 1 122 Sibbaldia_procumbens 538,539 426,339 79.2% 936 933 933 933 933 931 0 32 Sibbaldianthe_adpressa 1,455,531 1,269,404 87.2% 936 935 934 934 931 921 1 30 Sibbaldianthe_bifurca 2,801,305 2,416,512 86.3% 936 936 936 936 935 923 0 117 Table S6. MO and RT orthologs statistics. Number of Percentage of MO Number of RT Percentage of RT Species MO orthologs orthologs (total 914) orthologs orthologs (total 1906) Alchemilla_alpina 396 43.3% 712 37.4% Alchemilla_argyrophylla 614 67.2% 1250 65.6% Alchemilla_colura 582 63.7% 1170 61.4% Alchemilla_cryptantha 604 66.1% 1234 64.7% Alchemilla_decumbens 485 53.1% 902 47.3% Alchemilla_ellenbeckii 615 67.3% 1244 65.3% Alchemilla_elongata 605 66.2% 1234 64.7% Alchemilla_fischeri 590 64.6% 1224 64.2% Alchemilla_fissa 252 27.6% 408 21.4% Alchemilla_flabellata 431 47.2% 812 42.6% Alchemilla_glabra 510 55.8% 927 48.6% Alchemilla_haumanii 570 62.4% 1182 62.0% Alchemilla_heptagona 503 55.0% 930 48.8% Alchemilla_hildebrandtii 481 52.6% 965 50.6% Alchemilla_indivisa 487 53.3% 896 47.0% Alchemilla_japonica 518 56.7% 949 49.8% Alchemilla_johnstonii 583 63.8% 1207 63.3% Alchemilla_kiwuensis 554 60.6% 1159 60.8% Alchemilla_lapeyrousii 441 48.2% 850 44.6% Alchemilla_microbetula 607 66.4% 1239 65.0% Alchemilla_mollis 589 64.4% 1060 55.6% Alchemilla_pentaphyllea 516 56.5% 933 49.0% Alchemilla_plicata 398 43.5% 745 39.1% Alchemilla_roccatii 580 63.5% 1206 63.3% Alchemilla_rutenbergii 573 62.7% 1163 61.0% Alchemilla_schizophylla 536 58.6% 1069 56.1% Alchemilla_splendens 431 47.2% 802 42.1% Alchemilla_stuhlmannii 467 51.1% 964 50.6% Alchemilla_subnivalis 563 61.6% 1154 60.5% Alchemilla_subsericea 496 54.3% 932 48.9% Alchemilla_triphylla 477 52.2% 967 50.7% Alchemilla_woodii 497 54.4% 1004 52.7% Alchemilla_xanthochlora 480 52.5% 883 46.3% Aphanes_arvensis 453 49.6% 639 33.5% Aphanes_australis 444 48.6% 619 32.5% Aphanes_cotopaxiensis 424 46.4% 598 31.4% Aphanes_microcarpa 428 46.8% 599 31.4% Aphanes_occidentalis 441 48.2% 618 32.4% Aphanes_sp "boliviana" 433 47.4% 608 31.9% Aphanes_sp "patagonica" 450 49.2% 630 33.1% Chamaerhodos_erecta 737 80.6% 759 39.8% Comarum_palustre 773 84.6% 830 43.5% Dasiphora_fruticosa 748 81.8% 773 40.6% Drymocallis_arguta 756 82.7% 777 40.8% Drymocallis_glandulosa 747 81.7% 764 40.1% Farinopsis_salesoviana 849 92.9% 933 49.0% Fragaria_vesca 715 78.2% 740 38.8% Lachemilla_andina 720 78.8% 1309 68.7% Lachemilla_angustata 653 71.4% 1180 61.9% Lachemilla_aphanoides 721 78.9% 1295 67.9% Lachemilla_barbata 726 79.4% 1285 67.4% Lachemilla_diplophylla 731 80.0% 1301 68.3% Lachemilla_equisetiformis 542 59.3% 976 51.2% Lachemilla_erodiifolia 699 76.5% 1261 66.2% Lachemilla_galioides 725 79.3% 1346 70.6% Lachemilla_hirta 722 79.0% 1294 67.9% Lachemilla_hispidula 711 77.8% 1307 68.6% Lachemilla_jamesonii 734 80.3% 1330 69.8% Lachemilla_llanganatensis 592 64.8% 1087 57.0% Lachemilla_mandoniana 694 75.9% 1225 64.3% Lachemilla_moritziana 549 60.1% 1014 53.2% Lachemilla_nivalis 702 76.8% 1283 67.3% Lachemilla_orbiculata 695 76.0% 1240 65.1% Lachemilla_pectinata 736 80.5% 1335 70.0% Lachemilla_pinnata 720 78.8% 1281 67.2% Lachemilla_polylepis 727 79.5% 1324 69.5% Lachemilla_pringlei 604 66.1% 1073 56.3% Lachemilla_procumbens 712 77.9% 1270 66.6% Lachemilla_ramosissima 646 70.7% 1154 60.5% Lachemilla_sibbaldiifolia 598 65.4% 1072 56.2% Lachemilla_standleyi 662 72.4% 1195 62.7% Lachemilla_tanacetifolia 730 79.9% 1319 69.2% Lachemilla_velutina 629 68.8% 1097 57.6% Lachemilla_verticillata 734 80.3% 1347 70.7% Lachemilla_vulcanica 732 80.1% 1335 70.0% Potaninia_mongolica 737 80.6% 761 39.9% Sibbaldia_procumbens 703 76.9% 744 39.0% Sibbaldianthe_adpressa 717 78.4% 752 39.5% Sibbaldianthe_bifurca 725 79.3% 762 40.0% Potentilla_indica 849 92.9% N/A N/A Rosa_woodsii 913 99.9% N/A N/A Sanguisorba_menziesii 860 94.1% N/A N/A