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Figure S1. Maximum Likelihood Phylogeny of Alchemilla S.L

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Figure S1. Maximum Likelihood Phylogeny of Alchemilla S.L a) RT - ASTRAL 91/0.7 Alchemilla 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 occidentalis Aphanes * Aphanes microcarpa * Aphanes australis 1/—/1 Aphanes arvensis * 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
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