Supplementary Appendix for

The Origin and Early Evolution of the Legumes are a Complex

Paleopolyploid Phylogenomic Tangle closely associated with the

Cretaceous-Paleogene (K-Pg) Boundary

Authors: Erik J.M. Koenen1*, Dario I. Ojeda2,3, Royce Steeves4,5, Jérémy Migliore2, Freek Bakker6, Jan J. Wieringa7, Catherine Kidner8,9, Olivier Hardy2, R. Toby Pennington8,10, Patrick S. Herendeen11, Anne Bruneau4 and Colin E. Hughes1

1 Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland 2 Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium 3 Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway 4 Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada 5 Fisheries & Oceans Canada, Gulf Fisheries Center, 343 Université Ave, Moncton, NB E1C 5K4, Canada 6 Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands 7 Naturalis Biodiversity Center, Leiden, Darwinweg 2, 2333 CR, Leiden, The Netherlands 8 Royal Botanic Gardens, 20a Inverleith Row, Edinburgh EH3 5LR, U.K. 9School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, UK 10 Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, U.K. 11 Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL 60022, U.S.A.

* Correspondence to be sent to: Zollikerstrasse 107, CH-8008, Zurich, Switzerland; phone: +41 (0)44 634 84 16; email: [email protected]. Methods S1. Discussion on fossils used for calibrating divergence time analyses.

Non-legume Eudicot Fossils

These were taken from Magallon et al. (2015) and are thoroughly discussed in the supplementary information of that article. The numbers listed in Table 1 are the same numbers as used in the Supplementary Information Methods 1 of Magallon et al. (2015). We have followed their fossil placements although our more limited taxon sampling means that some minimum ages are placed on deeper nodes. The only exception is the stem node of

Fagales (calibration X14), which was here calibrated using the oldest fossil prior used by Xing et al. (2014). All minimum ages were updated to the latest version of the Geologic Time Scale

(v. 4.0; Gradstein et al., 2012).

Legume Fossils

The selection of legume fossils used here for calibrating the divergence time estimation analyses differs from previous legume time tree studies (Lavin et al., 2005; Bruneau et al.,

2008; Simon et al., 2009), both in the placement of fossils as well as in the minimum ages that some of these fossils represent. Calibrations Q2 and Z are used for the first time here.

Calibrations A, D, F, G, I2, M2 and Q are labelled according to the schemes of Bruneau et al.

(2008) and/or Simon et al. (2009), and differences from previous studies are discussed here.

Other fossils used by Bruneau et al. (2008) and/or Simon et al. (2009) are not used here because of our sparser taxon sampling.

2 First, we did not fix the crown age of the family, which is critical as it is the most important node for which we want to estimate the age. The oldest definitive legume fossil, a fossil wood from the Early Paleocene of Patagonia (Brea et al., 2008), is used to set a minimum age on the stem node of the family at 63.5 Ma (calibration A, same node as in

Bruneau et al. (2008) and Simon et al. (2009), but a new fossil and minimum age). This calibration is probably not very informative because of the long stem of the family, but it is included for completeness. The oldest crown group fossil, bipinnate leaves from the Late

Paleocene of Colombia (Wing et al., 2009; Herrera et al., submitted), is placed on the stem node of Caesalpinioideae with a minimum age of 58 Ma (calibration Z), a new calibration that has not been used in previous studies. This calibration renders the calibration of the stem of

Papilionoideae (which is sister to Caesalpinioideae), with fossil flowers of Barnebyanthus buchananensis from the Paleocene-Eocene boundary at 56 Ma (Crepet & Herendeen, 1992), redundant.

We find the interpretation of some Early and Middle Eocene fossils, that were used in previous studies to calibrate lineages within crown group Cercidoideae and Detarioideae

(Bruneau et al., 2008; Simon et al., 2009) to be problematic. Bruneau et al. (2008: Table 3) already pointed out the large discrepancy in age estimates of Detarioideae between calibrated and non-calibrated analyses. Given that this subfamily has a very long stem lineage (Figs 2 & 3), placing Early to Middle Eocene fossils within the crown group would require very high inferred substitution rates along the stem lineage, while at the same time implying a relatively low substitution rate for the Detarioideae crown group lineages (see

Results). Cercidoideae are also subtended by a long stem lineage, leading to similar, although less severe substitution rate discrepancies than in Detarioideae. We investigate and test this with molecular clock analyses with fixed local clocks, as described below. Here, we

3 discuss the interpretation of these fossils as either stem or crown relatives and how we have calibrated lineages from subfamilies Cercidoideae and Detarioideae.

Bauhinia-like bilobed leaves from the Eocene of Tanzania (c. 46 Ma) (Jacobs &

Herendeen, 2004) were used by Bruneau et al. (2008) and Simon et al. (2009) to calibrate the stem lineage of Bauhinia s.l.. This leaf type is highly characteristic for Cercidoideae and therefore the fossil is certainly representative of the subfamily. However, even though this type of leaf is not found in Cercis, which has been found to be sister to the rest of the genera in the subfamily (Bruneau et al., 2008; Wang et al., 2018), it may not provide a strong apomorphy for crown group Cercidoideae. Leaves in Bauhinia s.l. are variously bifoliolate, bilobed or entire, implying that entire leaves like those of Cercis have evolved multiple times independently, leading to homoplasy. This means that the bilobed leaves may have been present in the most recent common ancestor (MRCA) or stem relatives of Cercidoideae, and evolved to having an entire lamina in Cercis. If the Tanzanian fossils are a possible stem- relative of Cercidoideae, we consider the oldest definitive crown group fossil evidence to be the recently described Cercis fossil leaves and fruits from the Late Eocene of Oregon (Jia &

Manchester, 2014), at c. 36 Ma (calibration C, a slightly older minimum age than used by

Bruneau et al. (2008) and Simon et al. (2009)).

Bifoliolate leaves from the same fossil site in Tanzania as the Bauhinia fossil were ascribed to Aphanocalyx (Detarioideae) (Herendeen & Jacobs, 2000) based on distinctive venation patterns, after comparing the leaves to all extant legume genera with bifoliolate leaves. The fossil was used to calibrate the stem lineage of that genus by Bruneau et al.

(2008) and Simon et al. (2009). The genus is deeply nested within Detarioideae, also meaning that the difference between age estimates from calibrated and uncalibrated analyses is large (46.0 vs 4.4 Ma; Bruneau et al., 2008: Table 3). While venation patterns can be

4 diagnostic in many cases, they are often variable even within modern genera and likely to be homoplasious. Therefore, these fossils might also represent an extinct lineage, possibly a stem relative of Detarioideae, that had evolved similar leaf morphology to extant

Aphanocalyx. Moreover, the author of the most recent taxonomic account of Aphanocalyx

(Wieringa, 1999), Jan Wieringa, does not accept this fossil as belonging to the genus. It also does not fit with the morphology-based phylogeny of Aphanocalyx which shows that bifoliolate leaves have evolved recently and are derived within Aphanocalyx (Wieringa, 1999). In general, leaflet numbers are highly variable across Detarioideae, so relatives of fossils should not be sought only among other bifoliolate taxa.

Further evidence of Detarioideae from the Eocene is found at two localities within the

Claiborne Formation in western Tennessee, USA. Fruits and leaflets from those sites are ascribed to the genus Crudia (Herendeen & Dilcher, 1990). As for the Aphanocalyx fossil, the affinities of the fossils were carefully evaluated before concluding that they are related to

Crudia. Bruneau et al. (2008) and Simon et al. (2009) used this fossil to calibrate the stem of

Crudia at 45 Ma, but as for the Aphanocalyx fossil age, an uncalibrated analysis finds a far younger age (6.9 Ma; Bruneau et al., 2008: Table 3). It is possible that in this case, an extinct detarioid lineage may have evolved morphological features similar to extant Crudia species independently. The raised venation on the fruit valves and twisted petiolules that most strongly resemble Crudia, for example, are both homoplasious across Detarioideae.

Fossil wood, flowers and amber of Aulacoxylon sparnacense, which has previously been interpreted as related to the extant genus Daniellia (Detarioideae), from the Early

Eocene of the Paris basin (De Franceschi & De Ploëg, 2003), provide the most convincing evidence of fossils representing Early to Middle Eocene crown group members of

Detarioideae. The fossil wood has vestured pits and resin canals, like modern resin-producing

5 Detarioideae and the amber deposits are chemically similar to the Dominican ambers.

Bruneau et al. (2008) considered the wood and flowers similar to Daniellia, but suggested they could also belong to a different genus of resin-producing Detarieae. However, it is also possible that resin-production was already present in stem-relatives of Detarioideae. This is quite likely given that this trait is homoplasious across the resin-producing clade, having apparently been independently gained or lost several times, with only about half of the extant genera in the clade producing resin (Fougère-Danezan et al., 2007). If the production of resin evolved in the ancestral lineage of Detarioideae it would not require many more losses to account for the absence of the trait in the other lineages of the subfamily, because the resin- producing clade branches deeply within Detarioideae and the basal relationships of the subfamily are poorly resolved and understood (Bruneau et al., 2008; de la Estrella et al.,

2018). Furthermore, the large majority of genera in the subfamily are confined to the large clade of Amherstieae, so perhaps only a single additional loss of the trait in the lineage leading to this clade could have produced this homoplasious pattern. This makes it possible that the Paris basin fossils belong to an extinct genus belonging to the stem group of

Detarioideae. Therefore, the Aulacoxylon fossils can be used either to calibrate the stem node of the resin producing clade (calibration Gg, as was done by Bruneau et al, (2008) and Simon et al., (2009) or the stem node of Detarioideae (calibration G), with a minimum age of 53 Ma .

For the disputed age of Dominican amber (Iturralde-Vinent & MacPhee, 1996), an intermediate age of 24 Ma was chosen by Bruneau et al. (2008), which was followed by

Simon et al. (2009), but it is preferable to not consider an intermediate age as a valid minimum, but rather to use the minimum age that was estimated for Mexican amber that includes flowers of Hymenaea mexicana, the extinct species that presumably produced the amber (Poinar & Brown, 2002), and we calibrate the Detarieae s.s. stem node with a

6 minimum age of 22.5 Ma (calibration F, a more inclusive node than in Bruneau et al, (2008) and Simon et al., (2009), and a different fossil age).

The calibration of the stem group of Styphnolobium and Cladrastis (calibration I2) is the same as used in Bruneau et al. (2008) and Simon et al. (2009), but the minimum age was updated to 37.8 Ma according to the latest version of the Geologic Time Scale (v. 4.0;

Gradstein et al., 2012), representing the end of the Middle Eocene (end of the Bartonian).

Calibration M2 is the same as used in Simon et al., (2009) but since Robinia itself is not sampled here, we place it on the stem node of the robinioid clade (represented here by Lotus japonicus) and update the minimum age to the Eocene-Oligocene boundary at 33.9 Ma.

Bruneau et al. (2008) and Simon et al. (2009) also set the ages of several fossil calibrations at the midpoint of the Eocene, at 45 Ma. This led to a bias that was observable in an LTT plot of legumes (Koenen et al., 2013), and here we prefer to use the minimum boundary ages for these fossils. Although most of these calibrations are not used in our analyses due to sparser taxon sampling, we use one of these fossils, Acacia-like polyads, to calibrate the minimum stem age of the clade including all Acacia s.l. segregates at 33.9 Ma, the Eocene-Oligocene boundary (calibration Q, same node but younger age than Bruneau et al, (2008) and Simon et al., (2009)). Finally, we add calibration Q2, based on Australian

Oligocene polyads with pseudocolpi (Miller et al., 2013), which suggest affinity with Acacia s.s., and we calibrate the stem node of that genus with a minimum age of 23 Ma, the

Oligocene-Miocene boundary.

Alternative Calibrations for Detarioideae and Cercidoideae

7 In the analysis with “alternative prior 1”, calibration C was replaced with a minimum age of 46

Ma on the stem of Bauhinia, based on fossil leaves from Tanzania (Herendeen & Jacobs,

2000; discussed above). Calibration Gg was applied on the stem of the resin-producing clade

(i.e. the crown node of Detarioideae) instead of on the stem node of Detarioideae. Calibration

Hg is taken from Bruneau et al. (2008) and Simon et al. (2009), and is added in the alternative analysis to specify a minimum age of 46 Ma on the stem of Anthonotha, based on fossil leaves assigned to the closely related genus Aphanocalyx from Tanzania (Herendeen &

Jacobs, 2000; but see above).

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10 Table S1. Accession information for the taxa included in the chloroplast alignment.

Genbank accession Taxon Herbarium voucher Comments number Abarema jupunba M.F. Simon 1600 (CEN) XXXXXXXXXX Newly sequenced Acacia koa see Table S1. Transcriptome Acacia ligulata LN555649.2 Transcriptome, available at Acrocarpus fraxinifolius https://ics.hutton.ac.uk/tropiTree/ Ambriansyah & Arifin Adenanthera pavonina XXXXXXXXXX Newly sequenced AA295 (K) S.L.A. Donkpegan 27 Afzelia africana KX673213 (BRLU) S.L.A. Donkpegan 626 Afzelia bipindensis XXXXXXXXXX Newly sequenced (BRLU) Ajuga reptans KF709391 Albizia adianthifolia J.J. Wieringa 6278 (WAG) XXXXXXXXXX Newly sequenced Albizia julibrissin E. Koenen 601 (Z) XXXXXXXXXX Newly sequenced; Transcriptome Anthonotha fragrans see Table S1. Newly sequenced; Transcriptome Apios americana KF856618 Arabidopsis thaliana AP000423 Arachis hypogaea KJ468094 Arachis ipaensis GBIW00000000 Transcriptome Aralia undulata R. Li 551 (KUN) KC456163 Archidendron lucidum Wang & Lin 2534 (L) XXXXXXXXXX Newly sequenced Transcriptome, available at Astragalus membranaceus http://dx.doi.org/10.5061/dryad.ff1tq Astragalus propinquus Transcriptome, OneKP: MYMP, available at http://www.onekp.com/public_data.html Azadirachta indica KF986530 Transcriptome, available at Bauhinia tomentosa see Table S1. http://dx.doi.org/10.5061/dryad.ff1tq Transcriptome, OneKP: TVSH, available at Bituminaria bituminosa see Table S1. http://www.onekp.com/public_data.html EU002159, EU002172, EU002205, EU002275, EU002299, EU002388, Bulnesia arborea M.J. Moore 334 (FLAS) EU002478, GQ998005-GQ998073, HQ664597 Buxus microphylla EF380351 L.P. Queiroz 15542 Calliandra hygrophila XXXXXXXXXX Newly sequenced (HUEFS) Carica papaya EU431223 Ceratonia siliqua KJ468096 Cercis canadensis KF856619 Transcriptome, available at Chamaecrista fasciculata see Table S1. http://dx.doi.org/10.5061/dryad.ff1tq Chidlowia sanguinea J.J. Wieringa 4338 (WAG) XXXXXXXXXX Newly sequenced Chrysobalanus icaco KJ414480 Cicer arietinum EU835853 Citrus sinensis DQ864733 Transcriptome, available at Cladrastis lutea http://dx.doi.org/10.5061/dryad.ff1tq Transcriptome, available at Codariocalyx motorius http://dx.doi.org/10.5061/dryad.ff1tq Coffea arabica EF044213 Cojoba arborea M.F. Simon 1545 (CEN) XXXXXXXXXX Newly sequenced Kew living collection 1993- Colvillea racemosa XXXXXXXXXX Newly sequenced 224 (K) Transcriptome, available at Copaifera officinalis http://dx.doi.org/10.5061/dryad.ff1tq Cucumis sativus AJ970307 Daucus carota DQ898156 Transcriptome, available at Desmanthus illlinoiensis http://dx.doi.org/10.5061/dryad.ff1tq Dialium guineense T. van Andel 4184 (WAG) XXXXXXXXXX Newly sequenced Dichrostachys cinerea O. Maurin 256 (JRAU) XXXXXXXXXX Newly sequenced Dimorphandra J.R. Igançi 877 (RB) XXXXXXXXXX Newly sequenced macrostachya Diptychandra aurantiaca J.R.I. Wood 26513 (K) XXXXXXXXXX Newly sequenced Distemonanthus G. Dauby 728 (BRLU) XXXXXXXXXX Newly sequenced benthamianus Duparquetia orchidacea J.J. Wieringa 7805 (L) XXXXXXXXXX Newly sequenced Entada abyssinica MSB 0133199 (K) XXXXXXXXXX Newly sequenced; Transcriptome Entada rheedei E. Koenen 496 (Z) XXXXXXXXXX Newly sequenced Erythrophleum ivorense J.J. Wieringa 5487 (WAG) XXXXXXXXXX Newly sequenced Erythrostemon gilliesii R. Steeves 852 (MT) XXXXXXXXXX Newly sequenced Eucalyptus grandis HM347959 EU002160, EU002170, EU002193, EU002277, EU002321, EU002409, Euonymus americanus W. Judd 8071 (FLAS) EU002500, GQ998147-GQ998219, HQ664608 Fagopyrum esculentum EU254477 Faidherbia albida O. Maurin 3495 (JRAU) XXXXXXXXXX Newly sequenced Garcinia mangostana HQ331601, HQ331906, HQ332057, HQ848709, JX661816, JX661859, JX661902, JX661944, JX661980, JX662020, JX662065, JX662109, JX662151, JX662196, JX662237, JX662279, JX662320, JX662359, JX662399, JX662434, JX662467, JX662502, JX662543, JX662580, JX662622, JX662666, JX662710, JX662752, JX662799, JX662841, JX662880, JX662914, JX662955, JX662996, JX663032, JX663071, JX663104, JX663149, JX663196, JX663237, JX663280, JX663322, JX663365, JX663410, JX663583, JX663630, JX663677, JX663721, JX663763, JX663804, JX663841, JX663874, JX663915, JX663962, JX664006, JX664049, JX664091, JX664127, JX664165, JX664209, JX664252, JX664297, JX664341, JX664385, JX664458, JX664495, JX664535, JX664580, JX664623, JX664659, JX664694, JX664726, JX664771, JX664812, JX664852, JX664895, JX664939, JX665004, KF783277, U92876, U92877, U92878 Transcriptome, OneKP: VHZV, available at Gleditsia sinensis http://www.onekp.com/public_data.html Transcriptome, available at Gleditsia triacanthos http://dx.doi.org/10.5061/dryad.ff1tq Transcriptome, available at Gliricidia sepium https://ics.hutton.ac.uk/tropiTree/ Glycine canescens KC893635 Glycine max DQ317523 Glycyrrhiza glabra KF201590 Transcriptome, available at Glycyrrhiza lepidota http://dx.doi.org/10.5061/dryad.ff1tq Gompholobium Transcriptome, OneKP: VLNB, available at polymorphum http://www.onekp.com/public_data.html Gossypium hirsutum DQ345959 Guibourtia ehie F. Tosso 272 (BRLU) XXXXXXXXXX Newly sequenced Guibourtia tessmannii XXXXXXXXXX Newly sequenced Guilfoylia monostylis P.I. Forster 28103 (Z) XXXXXXXXXX Newly sequenced Transcriptome, available at Gymnocladus dioicus http://dx.doi.org/10.5061/dryad.ff1tq Haematoxylum brasiletto KJ468097 Helianthus annuus DQ383815 Hymenostegia brachyura Zenker 4481 (WAG) XXXXXXXXXX Newly sequenced Hymenostegia felicis Jacques-Félix 5129 (WAG) XXXXXXXXXX Newly sequenced Indigofera tinctoria KJ468098 Inga leiocalycina T.D. Pennington 13822 (K) KT428296 Inga spectabilis T.D. Pennington 15061 (K) XXXXXXXXXX Newly sequenced Intsia bijuga KX673214 Lathyrus graminifolius KJ806193 Lathyrus sativus HM029371 Lens culinaris KF186232 Leucaena trichandra KT428297 Libidibia coriaria KJ468095 Lotus japonicus AP002983 Lupinus luteus KC695666 Transcriptome, OneKP: CMFF, available at Lupinus polyphyllus http://www.onekp.com/public_data.html Macadamia integrifolia KF862711 Manihot esculenta EU117376 Medicago hybrida KJ850240 Medicago truncatula AC093544 Microlobius foetidus C.E. Hughes 1219 (FHO) XXXXXXXXXX Newly sequenced; Transcriptome Millettia pinnata JN673818 L.P. Queiroz 15498 Mimosa tenuiflora XXXXXXXXXX Newly sequenced (HUEFS) Morus indica DQ226511 Nelumbo nucifera JQ336993 Nerium oleander W. Judd 8076 (FLAS) KJ953907 Newtonia hildebrandtii O. Maurin 2457 (JRAU) XXXXXXXXXX Newly sequenced Oenothera biennis EU262889 Olea europaea GU228899 EU002165, EU002186, EU002248, EU002282, EU002350, EU002438, EU002528, Oxalis latifolia M.J. Moore 316 (FLAS) GQ998511-GQ998580, HQ664602, KF783277, U92876, U92877, U92878 Pachyelasma tessmannii J.J. Wieringa 5229 (WAG) XXXXXXXXXX Newly sequenced Pachyrhizus erosus KJ468100 Paeonia obovata KJ206533 Parkia panurensis J.R. Igançi 842 (RB) XXXXXXXXXX Newly sequenced Pelargonium alternans KF240617 Peltophorum africanum Koenen 601 (Z) XXXXXXXXXX Newly sequenced Galeuchet & Balthazar 10 Pentaclethra macrophylla XXXXXXXXXX Newly sequenced (Z) Phaseolus vulgaris DQ886273 Piptadeniastrum E. Koenen 152 (WAG) XXXXXXXXXX Newly sequenced africanum Pisum sativum HM029370 Pithecellobium dulce B. Marazzi 309 (?) XXXXXXXXXX Newly sequenced Poeppigia procera Hernández 558 (Z) XXXXXXXXXX Newly sequenced Polygala lutea EF489041 Populus trichocarpa KF753634 Primula poissonii KF753634 Prioria balsamifera XXXXXXXXXX Newly sequenced; Transcriptome Prosopis alba see Table S1. Transcriptome Prosopis glandulosa KJ468101 Prunus persica HQ336405 Quercus rubra JX970937 Transcriptome, available at Quillaja saponaria http://dx.doi.org/10.5061/dryad.ff1tq Ranunculus macranthus DQ359689 Robinia pseudoacacia KJ468102 Samanea saman C.E. Hughes 421 (FHO) XXXXXXXXXX Newly sequenced Sapindus mukorossi KM454982 Kew living collection 2011- Saraca indica XXXXXXXXXX Newly sequenced 1421 (K) Schotia brachypetala R. Steeves 846 (MT) XXXXXXXXXX Newly sequenced Sedum sarmentosum JX427551 Senegalia ataxacantha C. Jongkind 10603 (WAG) XXXXXXXXXX Newly sequenced Transcriptome, available at Senna hebecarpa http://dx.doi.org/10.5061/dryad.ff1tq Transcriptome, available at Senna siamea https://ics.hutton.ac.uk/tropiTree/ Transcriptome, available at Sesbania macrantha https://ics.hutton.ac.uk/tropiTree/ Transcriptome, available at Sesbania sesban https://ics.hutton.ac.uk/tropiTree/ Silene latifolia JF715055 Solanum lycopersicum KP331414 Styphnolobium japonicum see Table S1. Transcriptome, available at https://www.hindawi.com/journals/bmri/2014/75 0961/sup/ Swartzia emarginata M.P. Morim 576 (RB) XXXXXXXXXX Newly sequenced Tachigali odoratissima M.P. Morim 562 (RB) XXXXXXXXXX Newly sequenced Tamarindus indica KJ468103 Theobroma cacao HQ244500 Transcriptome, available at Tipuana tipu https://ics.hutton.ac.uk/tropiTree/ Trachelium caeruleum EU090187 Trifolium aureum KC894708 Trifolium repens KC894706 Trochodendron aralioides KC608753 Vaccinium macrocarpon JQ757046 Vachellia tortilis E. Koenen 603 (Z) XXXXXXXXXX Newly sequenced Vicia faba KF042344 Vicia sativa KJ850242 Vigna radiata GQ893027 Vigna unguiculata JQ755301 Vitis vinifera DQ424856 Transcriptome, OneKP: RMWJ, available at Wisteria floribunda http://www.onekp.com/public_data.html Transcriptome, available at Xanthocercis zambesiaca http://dx.doi.org/10.5061/dryad.ff1tq Xanthophyllum P. Herendeen H.416 (?) XXXXXXXXXX Newly sequenced eurhynchum Xylia hoffmannii E. Koenen 402 (Z) XXXXXXXXXX Newly sequenced Zenia insignis Averyanov et al. 5748 (?) XXXXXXXXXX Newly sequenced Table S2. Accession information for the taxa included in the nuclear genomic and transcriptomic data set.

Taxon Source Citation Acacia koa Genbank BioProject: PRJNA268386 Ishihara et al. Acrocarpus fraxinifolius TropiTree: https://ics.hutton.ac.uk/tropiTree/ Russel et al. 2014 Afzelia bella Genbank BioProject: XXXXXXXXXX Newly sequenced Albizia julibrissin Genbank BioProject: XXXXXXXXXX Newly sequenced Alnus serrulata Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Amaranthus hypochondriacus Phytozome v11: v1.0 Clouse et al. 2016 Anthonotha fragrans Genbank BioProject: XXXXXXXXXX Newly sequenced Apios americana Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Aquilegia coerulea Phytozome v11: v3.1 Filiault et al. 2018 Arabidopsis thaliana Phytozome v11: TAIR10 Lamesch et al. 2012 Arachis ipaensis Peanutbase.org: K30076.a1.M1 Bertioli et al. 2016 Astragalus membranaceus Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Bauhinia tomentosa Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Bituminaria bituminosa OneKP: TVSH Wicket et al. 2014 Cajanus cajan http://gigadb.org/dataset/100028 Varshney et al. 2012 Cannabis sativa Genbank BioProject: PRJNA74271 van Bakel et al. 2011 Carica papaya Phytozome v11: ASGPBv4.0 Ming et al. 2008 Castanea mollissima https://www.hardwoodgenomics.org/Genome-assembly/1962958 Not available Cercis canadensis Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Chamaecrista fasciculata Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Cicer arietinum http://gigadb.org/dataset/100076 Varshney et al. 2013 Citrus sinensis Phytozome v11: v1.1 Wu et al. 2014 Cladrastis lutea Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Codariocalyx motorius Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Copaifera officinalis Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Cucumis sativus Phytozome v11: v1.0 Not available Desmanthus illinoensis Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Elaeocarpus photiniifolia Genbank BioProject: PRJDA67329 Sugai et al. 2012 Entada abyssinica Genbank BioProject: XXXXXXXXXX Newly sequenced Eucalyptus grandis Phytozome v11: v2.0 Bartholomé et al. 2015 Fragaria vesca Phytozome v11: v1.1 Shulaev et al. 2011 Gleditsia triacanthos Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Glycine max Phytozome v11: Wm82.a2.v1 Schmutz et al. 2010 Glycyrrhiza lepidota Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Gossypium raimondii Phytozome v11: v2.1 Paterson et al. 2012 Gymnocladus dioicus Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Inga spectabilis https://doi.org/10.5061/dryad.r9c12 Nicholls et al. 2015 Juglans regia https://www.hardwoodgenomics.org/Genome-assembly/2209485 Martínez‐García et al. 2016 Lactuca sativa Genbank BioProject: PRJNA65477 Not available Lathyrus sativus Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Lens culinaris Genbank BioProject: PRJNA65667 Kaur et al. 2011 Linum usitatissimum Phytozome v11: v1.0 Wang et al. 2012 Lotus japonicus http://www.plantgdb.org/LjGDB/ Sato et al. 2008 Lupinus angustifolius Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Lupinus polyphyllus Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Manihot esculenta Phytozome v11: v6.1 Bredeson et al. 2016 Medicago truncatula Phytozome v11: Mt4.0v1 Young et al. 2011 Microlobius foetidus Genbank BioProject: XXXXXXXXXX Newly sequenced Mimulus guttatus Phytozome v11: v2.0 Hellsten et al. 2013 Morus notabilis Genbank BioProject: PRJNA202089 (assembly version ASM41409v2) He et al. 2013 Nelumbo nucifera Genbank BioProject: PRJNA264089 (assembly version 1.1) Ming et al. 2013 Paeonia lactiflora Genbank BioProject: PRJNA245064 Zhang et al. 2015 Panax ginseng Genbank BioProject: PRJNA173906 Li et al. 2013 Papaver somniferum Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Phaseolus vulgaris Phytozome v11: v1.0 Schmutz et al. 2014 Pisum sativum Genbank BioProject: PRJNA211622 Duarte et al. 2014 Polygala lutea Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Populus trichocarpa Phytozome v11: v3.0 Tuskan et al. 2006 Primula veris https://doi.org/10.5061/dryad.2s200 Nowak et al. 2015 Prioria balsamifera Genbank BioProject: XXXXXXXXXX Newly sequenced Prosopis alba Genbank BioProject: PRJNA218545 Torales et al. 2013 International Peach Genome

Prunus persica Phytozome v11: v2.1 Initiative et al., 2013 Punica granatum Genbank BioProject: PRJNA231033 Ophir et al. 2014 Quillaja saponaria Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Salix purpurea Phytozome v11: v1.0 Zhou et al. 2018 Senna hebecarpa Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Solanum tuberosum Phytozome v11: v3.4 Sharma et al. 2013 Styphnolobium japonicum https://www.hindawi.com/journals/bmri/2014/750961/sup/ Zhu et al. 2014 Theobroma cacao Phytozome v11: v1.1 Motamayor et al. 2013 Trifolium pratense Genbank BioProject: PRJNA219226 Yates et al. 2014 Tripterygium wilfordii Genbank BioProject: PRJNA218574 Not available Vicia faba Genbank BioProject: PRJNA81211 Kaur et al. 2012 Vigna radiata ftp://plantgenomics.snu.ac.kr/mungbean_data/ Kang et al. 2014 Vitis vinifera Phytozome v11: Genoscope.12X Jaillon et al. 2007 Xanthocercis zambesiaca Dryad: http://dx.doi.org/10.5061/dryad.ff1tq Cannon et al. 2015 Zenia insignis Genbank BioProject: PRJNA285444 Not available

Phytozome is available at https://phytozome.jgi.doe.gov OneKP data is available at http://www.onekp.com/public_data.html

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>50% >80% Clade ML bootstrap support bootstrap support bipartitions of best supported topology Leguminosae (node A) 2669 2254 1660 Cerc + Detar (node B) 744 325 48 Cercidoideae (node C) 1815 1705 1394 Detarioideae (node D) 3041 2918 2585 Pap + Caes + Dial (node E) 794 360 91 Pap + Caes (node F) 599 231 42 Caesalpinioideae (node G) 2114 1712 1151 Papilionoideae (node H) 2456 1957 1248 conflicting bipartitions Pap + Caes + Dial + Detar 625 258 34 Pap + Caes + Dial + Cerc 546 194 20 Caes + Dial 448 132 16 Pap + Dial 446 133 20 Dial + Detar 307 96 4 Dial + Cerc 295 93 7 Caes + Dial + Cerc + Detar 247 47 4 Pap + Caes + Cerc + Detar 234 46 2 Dial + Cerc + Detar 202 21 1 Caes + Detar 200 44 3 Pap + Dial + Cerc + Detar 196 29 4 Pap + Detar 189 41 2 Pap + Cerc 173 30 2 Caes + Cerc 163 37 2 Pap + Caes + Detar 153 27 1 Caes + Dial + Detar 134 11 0 Pap + Caes + Cerc 132 15 0 Caes + Cerc + Detar 127 14 0 Pap + Dial + Detar 122 12 1 Caes + Dial + Cerc 121 16 0 Pap + Cerc + Detar 115 9 0 Pap + Dial + Cerc 110 12 0 Table S4. Age intervals specified for the fossil calibration priors under different alternative priors.

Calibration Definition MRCA taxon 1 MRCA taxon 2 Prior Alternative prior 1 Alternative prior 2 eudicots normal normal normal (mean 126.0, stdev (mean 126.0, stdev (mean 126.0, stdev 26 CG eudicots Aquilegia coerulea Medicago truncatula 1.0) 1.0) 1.0) uniform uniform uniform (min 113.0, max (min 113.0, max (min 113.0, max 27 CG Ranunculales Aquilegia coerulea Papaver somniferum 126.0) 126.0) 126.0) uniform uniform uniform (min 100.0, max (min 100.0, max (min 100.0, max 38 CG Pentapetalae Nelumbo nucifera Medicago truncatula 126.0) 126.0) 126.0) uniform uniform uniform (min 89.8, max (min 89.8, max (min 89.8, max 48 SG Ericales Primula veris Solanum tuberosum 126.0) 126.0) 113.0) uniform uniform uniform (min 83.6, max (min 83.6, max (min 83.6, max 94 SG Myrtaceae Eucalyptus grandis Punica granatum 126.0) 126.0) 100.0) uniform uniform uniform (min 89.8, max (min 89.8, max (min 89.8, max 105 SG Brassicales Carica papaya Theobroma cacao 126.0) 126.0) 100.0) uniform uniform uniform (min 49.4, max (min 49.4, max (min 49.4, max 112 CG Rosaceae Fragaria vesca Prunus persica 126.0) 126.0) 66.0) uniform uniform uniform (min 66.0, max (min 66.0, max (min 66.0, max 116 SG Cannabaceae Cannabis sativa Morus notabilis 126.0) 126.0) 83.6) uniform uniform uniform (min 64.4, max (min 64.4, max (min 64.4, max 122 SG Juglandaceae Alnus serrulata Juglans regia 126.0) 126.0) 83.6) uniform uniform uniform (min 37.8, max (min 37.8, max (min 37.8, max 133 SG Populus Populus trichocarpa Salix purpurea 126.0) 126.0) 56.0) uniform uniform uniform (min 83.6, max (min 83.6, max (min 83.6, max X14 SG Fagales Alnus serrulata Medicago truncatula 126.0) 126.0) 126.0) legumes

A SG Leguminosae Medicago truncatula Quillaja saponaria uniform uniform uniform (min 63.5, max (min 63.5, max (min 63.5, max 126.0) 126.0) 100.0) uniform uniform (min 36.0, max (min 36.0, max C SG Cercis Cercis canadensis Bauhinia tomentosa 126.0) 83.6) uniform (min 46.0, max C& SG Bauhinia Bauhinia tomentosa Cercis canadensis 126.0) uniform uniform uniform (min 22.5, max (min 22.5, max (min 22.5, max F CG Resin-producing clade Copaifera officinalis Prioria balsamifera 126.0) 126.0) 66.0) uniform uniform (min 53.0, max (min 53.0, max G SG Detarioideae Copaifera officinalis Bauhinia tomentosa 126.0) 83.6) uniform (min 53.0, max G& SG Resin-producing clade Copaifera officinalis Anthonotha fragrans 126.0) uniform (min 46.0, max H& CG Amherstieae Afzelia bella Anthonotha fragrans 126.0) uniform uniform uniform Styphnolobium (min 37.8, max (min 37.8, max (min 37.8, max I2 SG Styphnolobium/Cladrastis japonicum Medicago truncatula 126.0) 126.0) 66.0) uniform uniform uniform (min 33.9, max (min 33.9, max (min 33.9, max M2 SG Robinioid clade Lotus japonicus Medicago truncatula 126.0) 126.0) 66.0) uniform uniform uniform (min 33.9, max (min 33.9, max (min 33.9, max Q SG Acacieae/Ingeae Albizia julibrissin Prosopis alba 126.0) 126.0) 66.0) uniform uniform uniform (min 23.0, max (min 23.0, max (min 23.0, max Q2 SG Acacia s.s. Acacia koa Albizia julibrissin 126.0) 126.0) 56.0) uniform uniform uniform (min 58.0, max (min 58.0, max (min 58.0, max Z SG Caesalpinioideae Albizia julibrissin Medicago truncatula 126.0) 126.0) 83.6) Table S5. Node age estimates and priors (95% HPD intervals) of nodes A-H in the different analyses.

Node A B C D E F G H

Clade Leguminosae Cerc+Detar Cercidoideae Detarioideae Dial+Caes+Pap Caes+Pap Caesalpinioideae Papilionoideae

Standard prior

Marginal prior 79.37 - 109.20 54.56 - 99.48 36.00 - 80.55 28.91 - 87.21 73.77 - 106.04 68.16 - 101.69 56.31 - 95.76 58.85 - 96.39

UCLN 65.47 - 86.45 57.50 - 80.75 36.00 - 53.97 25.47 - 42.98 63.51 - 84.73 60.64 - 81.67 54.11 - 74.49 55.19 - 73.58

RLC 73.46 - 81.18 68.06 - 75.69 39.34 - 46.74 31.52 - 36.43 69.77 - 77.35 68.05 - 75.45 55.76 - 63.75 49.05 - 54.38 strict clock 66.94 - 69.55 60.45 - 63.87 36.00 - 36.66 26.25 - 28.71 65.60 - 68.22 64.90 - 67.48 56.01 - 59.12 56.89 - 59.47

FLC 3 clocks 65.99 - 68.85 60.79 - 64.20 36.00 - 36.85 27.69 - 30.59 63.77 - 66.52 62.78 - 65.43 56.09 - 59.04 47.39 - 50.03

FLC 6 clocks 65.74 - 68.81 60.70 - 64.40 36.00 - 36.86 27.53 - 30.94 63.53 - 66.47 62.57 - 65.43 56.10 - 59.20 47.24 - 49.86

FLC 8 clocks 64.63 - 67.64 60.24 - 64.79 36.00 - 52.41 27.00 - 49.18 62.72 - 65.61 61.86 - 64.65 55.53 - 58.51 46.98 - 49.60

Alternative prior 1 (Bruneau et al. 2008 for Cercidoideae and Detarioideae)

Marginal prior 81.60 - 110.20 63.87 - 103.63 46.00 - 85.81 53.00 - 90.89 75.00 - 106.55 69.90 - 103.35 57.41 - 97.38 60.69 - 98.39

FLC 8 clocks 64.81 - 67.96 64.06 - 67.35 57.35 - 63.89 55.38 - 63.49 63.08 - 65.94 62.16 - 64.90 55.73 - 58.76 46.96 - 49.59

Alternative prior 2 (tighter maxima)

Marginal prior 73.30 - 96.56 56.01 - 83.60 36.00 - 71.11 28.75 - 75.30 66.75 - 90.79 64.04 - 83.60 53.37 - 81.05 54.12 - 79.22

UCLN 66.92 - 76.45 60.43 - 72.34 36.01 - 50.55 39.85 - 52.84 63.48 - 71.28 61.45 - 69.38 54.20 - 63.50 47.59 - 55.25

Alternative prior 3 (reduced taxon sampling)

Marginal prior 72.85 - 106.32 53.45 - 95.52 36.00 - 78.70 29.28 - 85.30 64.01 - 100.04 58.03 - 91.93 38.95 - 83.49 46.50 - 86.28

UCLN 64.72 - 79.69 57.35 - 75.43 36.00 - 53.18 25.40 - 39.20 62.29 - 76.62 60.08 - 74.12 49.28 - 66.70 49.68 - 64.63 Ranunculus macranthus Macadamia integrifolia 99 Nelumbo nucifera Buxus microphylla 94 Trochodendron aralioides Fagopyrum esculentum 100 Silene latifolia Vaccinium macrocarpon 100 100 Primula poissonii 98 Helianthus annuus 100 100 Trachelium caeruleum 100 Daucus carota 100 Aralia undulata 100 Ajuga reptans 100 Olea europaea 100 100 Solanum lycopersicum 78 Coffea arabica 100 Nerium oleander Vitis vinifera Sedum sarmentosum 100 Paeonia obovata Oenothera biennis 100 90 Eucalyptus grandis 63 Bulnesia arborea 71 Pelargonium alternans 70 Sapindus mukorossi 54 100 Azadirachta indica 100 Citrus sinensis 100 Gossypium hirsutum 100 Theobroma cacao 100 Carica papaya 100 Arabidopsis thaliana 100 Oxalis latifolia 90 Euonymus americanus 93 Garcinia mangostana 20 Manihot esculenta 100 Populus trichocarpa 73 Chrysobalanus icaco 71 Cucumis sativus 89 Quercus rubra 67 Prunus persica 100 Morus indica Guilfoylia monostylis 100 78 Polygala lutea 100 Xanthophyllum eurhynchum Quillaja saponaria 100 Cercis canadensis 100 Bauhinia tomentosa Prioria balsamifera 72 99 Copaifera officinalis 100 Guibourtia ehie 100 100 Guibourtia tessmannii Schotia brachypetala

100 30 Saraca indica Afzelia africana 100 100 Intsia bijuga 61 98 Afzelia bipindensis Anthonotha fragrans 58 Tamarindus indica 100 Hymenostegia brachyura 100 58 Hymenostegia felicis Duparquetia orchidacea Poeppigia procera 100 Zenia insignis 100 Dialium guineense 99 Distemonanthus benthamianus Swartzia emarginata Xanthocercis zambesiaca 100 Cladrastis lutea 100 75 Styphnolobium japonicum 91 Lupinus luteus 100 Lupinus polyphyllus 99 64 Tipuana tipu 100 Arachis ipaensis 100 Arachis hypogaea Gompholobium polymorphum 100 100 Indigofera tinctoria 89 Millettia pinnata 100 Apios americana 100 Codariocalyx motorius 100 Phaseolus vulgaris 67 100 Vigna radiata 100 100 Vigna unguiculata Pachyrhizus erosus 100 93 Bituminaria bituminosa 99 Glycine max 100 Glycine canescens Robinia pseudoacacia 100 Gliricidia sepium 99 Lotus japonicus 100 37 Sesbania macrantha 100 100 Sesbania sesban Glycyrrhiza lepidota 100 Glycyrrhiza glabra 100 Wisteria floribunda Astragalus propinquus 100 75 Astragalus membranaceus 100 Cicer arietinum Medicago hybrida 100 100 Medicago truncatula Trifolium aureum 100 100 Trifolium repens

96 Pisum sativum 100 Lathyrus sativus 100 100 Lathyrus graminifolius Lens culinaris 94 Vicia sativa 100 Vicia faba Ceratonia siliqua 97 Acrocarpus fraxinifolius Gymnocladus dioicus 100 100 Gleditsia sinensis 100 Gleditsia triacanthos Chamaecrista fasciculata 83 100 Senna hebecarpa 100 Senna siamea Haematoxylum brasiletto 100 100 Libidibia coriaria 100 Erythrostemon gilliesii Diptychandra aurantiaca 86 57 Tachigali odoratissima 92 Dimorphandra macrostachya 47 Colvillea racemosa 91 96 Peltophorum africanum Pachyelasma tessmannii Erythrophleum ivorense 100 Chidlowia sanguinea 24 56 Pentaclethra macrophylla Adenanthera pavonina 100 100 Xylia hoffmannii 52 Piptadeniastrum africanum 85 Entada rheedei 100 Entada abyssinica 45 Newtonia hildebrandtii Prosopis alba 100 100 Prosopis glandulosa Dichrostachys cinerea 100 85 Leucaena trichandra 80 Desmanthus illlinoiensis 62 Vachellia tortilis 81 Parkia panurensis 53 Mimosa tenuiflora 75 Microlobius foetidus 81 Senegalia ataxacantha 100 Calliandra hygrophila 100 Faidherbia albida 100 Cojoba arborea Pithecellobium dulce 100 Abarema jupunba 5927 Archidendron lucidum 46 Acacia koa 92 100 Acacia ligulata Inga spectabilis 100 Inga leiocalycina 45 Samanea saman 91 Albizia adianthifolia 87 Albizia julibrissin

Figure S1. ML topology as inferred by RAxML from amino acid alignment of chloroplast genes under the LG4X model. Numbers on nodes indicate bootstrap percentages estimated from 1000 replicates. Ranunculus macranthus Macadamia integrifolia 1 Nelumbo nucifera Buxus microphylla 0.99 Trochodendron aralioides Fagopyrum esculentum 1 Silene latifolia Primula poissonii 1 1 Vaccinium macrocarpon 1 Aralia undulata 1 1 Daucus carota 1 Helianthus annuus 1 Trachelium caeruleum 1 Ajuga reptans 1 Olea europaea 1 1 Solanum lycopersicum 0.99 Coffea arabica 1 Nerium oleander Vitis vinifera Paeonia obovata 1 Sedum sarmentosum 1 Pelargonium alternans Eucalyptus grandis 1 0.98 Oenothera biennis 0.73 Sapindus mukorossi 0.89 1 Azadirachta indica 1 Citrus sinensis 1 Arabidopsis thaliana 1 Carica papaya 1 1 Gossypium hirsutum 1 Theobroma cacao Bulnesia arborea Euonymus americanus 0.5 Oxalis latifolia 1 Garcinia mangostana 1 1 Manihot esculenta Chrysobalanus icaco 0.51 Populus trichocarpa 0.89 Cucumis sativus 0.99 Quercus rubra 0.81 Morus indica 1 Prunus persica 1 Polygala lutea 1 Xanthophyllum eurhynchum Guilfoylia monostylis 1 Quillaja saponaria Bauhinia tomentosa 0.65 1 Cercis canadensis Prioria balsamifera 0.92 1 Copaifera officinalis 1 Guibourtia ehie 1 1 Guibourtia tessmannii Schotia brachypetala

1 0.9 Saraca indica Afzelia africana 1 1 Afzelia bipindensis 0.99 1 Intsia bijuga Anthonotha fragrans 0.54 Tamarindus indica 1 Hymenostegia brachyura 1 0.98 Hymenostegia felicis Duparquetia orchidacea Poeppigia procera 1 Zenia insignis 1 Dialium guineense 1 Distemonanthus benthamianus Swartzia emarginata Xanthocercis zambesiaca 1 Cladrastis lutea 1 1 Styphnolobium japonicum 0.98 Lupinus luteus 1 Lupinus polyphyllus 0.95 1 Tipuana tipu 1 Arachis hypogaea 1 Arachis ipaensis Gompholobium polymorphum 1 1 Indigofera tinctoria 0.99 Millettia pinnata 1 Apios americana 1 Codariocalyx motorius 1 Phaseolus vulgaris 0.91 1 Vigna radiata 1 1 Vigna unguiculata Pachyrhizus erosus 1 1 Bituminaria bituminosa 1 Glycine canescens 1 Glycine max Sesbania macrantha 1 Sesbania sesban 1 Lotus japonicus 1 0.7 Gliricidia sepium 1 1 Robinia pseudoacacia Glycyrrhiza glabra 1 Glycyrrhiza lepidota 1 Wisteria floribunda Astragalus membranaceus 1 0.99 Astragalus propinquus 1 Cicer arietinum Medicago hybrida 1 1 Medicago truncatula Trifolium repens 1 1 Trifolium aureum

1 Pisum sativum 1 Lathyrus graminifolius 1 1 Lathyrus sativus Lens culinaris 1 Vicia faba 1 Vicia sativa Acrocarpus fraxinifolius 1 Ceratonia siliqua Gymnocladus dioicus 1 1 Gleditsia sinensis 1 Gleditsia triacanthos Chamaecrista fasciculata 1 1 Senna hebecarpa 1 Senna siamea Haematoxylum brasiletto 1 1 Erythrostemon gilliesii 1 Libidibia coriaria 0.99 Tachigali odoratissima 1 Dimorphandra macrostachya 0.86 Colvillea racemosa 1 1 Peltophorum africanum Diptychandra aurantiaca Pachyelasma tessmannii 0.98 Erythrophleum ivorense 1 Chidlowia sanguinea Pentaclethra macrophylla 0.89 0.85 Adenanthera pavonina 1 Xylia hoffmannii 0.64 Piptadeniastrum africanum 0.99 Entada abyssinica 1 1 Entada rheedei Newtonia hildebrandtii Prosopis alba 1 1 Prosopis glandulosa Dichrostachys cinerea 1 1 Desmanthus illlinoiensis 0.88 Leucaena trichandra 1 Parkia panurensis 0.54 Vachellia tortilis 1 Microlobius foetidus 0.96 Mimosa tenuiflora 1 Senegalia ataxacantha 1 Calliandra hygrophila 1 Faidherbia albida 1 Cojoba arborea 1 Pithecellobium dulce Abarema jupunba 0.95 Archidendron lucidum 0.82 Acacia koa 1 1 Acacia ligulata Inga leiocalycina 1 Inga spectabilis 0.99 Samanea saman 1 Albizia adianthifolia 1 Albizia julibrissin

Figure S2. Bayesian majority-rule consensus tree inferred with Phylobayes from amino acid alignment of chloroplast genes under the CATGTR model. Numbers on nodes indicate posterior probabilities (pp) from 9000 post-burn-in MCMC cycles. Ranunculus macranthus Nelumbo nucifera 10 Macadamia integrifolia Buxus microphylla 35 Trochodendron aralioides Fagopyrum esculentum 100 Silene latifolia Primula poissonii 100 100 Vaccinium macrocarpon Aralia undulata 100 99 100 Daucus carota 100 Helianthus annuus 100 Trachelium caeruleum 100 Olea europaea 100 Ajuga reptans 100 Solanum lycopersicum 100 2 Nerium oleander 100 Coffea arabica Vitis vinifera 60 Paeonia obovata 100 Sedum sarmentosum Pelargonium alternans 98 Oenothera biennis 100 Eucalyptus grandis 100 100 Sapindus mukorossi 100 Azadirachta indica 100 Citrus sinensis 100 Carica papaya 100 Arabidopsis thaliana 100 Theobroma cacao 100 100 Gossypium hirsutum Bulnesia arborea Oxalis latifolia 100 Euonymus americanus 100 Garcinia mangostana 34 100 Populus trichocarpa 100 Manihot esculenta 40 Chrysobalanus icaco Cucumis sativus 94 92 Quercus rubra 95 Morus indica 100 Prunus persica Guilfoylia monostylis 52 Quillaja saponaria 100 24 Polygala lutea 100 Xanthophyllum eurhynchum Bauhinia tomentosa 100 Cercis canadensis 100 Schotia brachypetala 100 Prioria balsamifera 100 Copaifera officinalis 100 Guibourtia tessmannii 100 100 Guibourtia ehie

100 Saraca indica Intsia bijuga 100 100 Afzelia africana 87 100 Afzelia bipindensis Anthonotha fragrans 95 Tamarindus indica 100 Hymenostegia felicis 100 66 Hymenostegia brachyura Duparquetia orchidacea Poeppigia procera 100 Zenia insignis 100 Distemonanthus benthamianus 100 Dialium guineense Swartzia emarginata Xanthocercis zambesiaca 100 Cladrastis lutea 100 100 Styphnolobium japonicum 92 Lupinus luteus 100 Lupinus polyphyllus 98 100 Tipuana tipu 100 Arachis hypogaea 100 Arachis ipaensis Gompholobium polymorphum 100 100 Indigofera tinctoria 89 Millettia pinnata 100 Apios americana 100 Codariocalyx motorius 100 Phaseolus vulgaris 100 100 Vigna unguiculata 100 100 Vigna radiata Pachyrhizus erosus 100 Bituminaria bituminosa 100 100 Glycine max 100 Glycine canescens Gliricidia sepium 100 Robinia pseudoacacia 100 Lotus japonicus 100 100 Sesbania sesban 100 Sesbania macrantha 100 Wisteria floribunda 95 Glycyrrhiza lepidota 100 Glycyrrhiza glabra 100 Astragalus membranaceus 100 Astragalus propinquus 100 Cicer arietinum Medicago truncatula 100 100 Medicago hybrida Trifolium repens 100 100 Trifolium aureum

100 Lens culinaris 100 Vicia faba 100 100 Vicia sativa Pisum sativum 100 Lathyrus sativus 100 Lathyrus graminifolius Ceratonia siliqua 100 Acrocarpus fraxinifolius Gymnocladus dioicus 100 100 Gleditsia triacanthos 100 Gleditsia sinensis Chamaecrista fasciculata 100 100 Senna siamea 100 Senna hebecarpa Haematoxylum brasiletto 100 100 Libidibia coriaria 100 Erythrostemon gilliesii Tachigali odoratissima 100 100 Dimorphandra macrostachya 100 Peltophorum africanum 100 100 Colvillea racemosa Diptychandra aurantiaca 99 Erythrophleum ivorense Pachyelasma tessmannii 100 Pentaclethra macrophylla 64 51 Chidlowia sanguinea Xylia hoffmannii 100 100 Adenanthera pavonina 94 Piptadeniastrum africanum 100 Entada abyssinica 100 Entada rheedei 94 Newtonia hildebrandtii Prosopis alba 100 100 Prosopis glandulosa 100 Dichrostachys cinerea 100 Leucaena trichandra 100 Desmanthus illlinoiensis 93 Vachellia tortilis 100 Parkia panurensis Microlobius foetidus 100 99 Mimosa tenuiflora 100 Senegalia ataxacantha 100 Calliandra hygrophila 100 Faidherbia albida 100 Cojoba arborea Pithecellobium dulce 100 Abarema jupunba 77 49 Archidendron lucidum 91 Acacia ligulata 100 100 Acacia koa Inga leiocalycina 100 Inga spectabilis 48 Samanea saman 100 Albizia adianthifolia 100 Albizia julibrissin

Figure S3. ML topology as inferred by RAxML from nucleotide alignment of chloroplast genes under the GTR + G model. Numbers on nodes indicate bootstrap percentages estimated from 1000 replicates. Ranunculus macranthus Macadamia integrifolia 1 Nelumbo nucifera Buxus microphylla 0.81 Trochodendron aralioides Fagopyrum esculentum 1 Silene latifolia Primula poissonii 1 1 Vaccinium macrocarpon Aralia undulata 1 1 1 Daucus carota 1 Helianthus annuus 1 Trachelium caeruleum 1 Ajuga reptans 1 Olea europaea 1 Solanum lycopersicum 1 0.89 Coffea arabica 1 Nerium oleander Vitis vinifera 0.71 Paeonia obovata 1 Sedum sarmentosum Pelargonium alternans 0.5 Eucalyptus grandis 1 Oenothera biennis 1 1 Sapindus mukorossi 1 Azadirachta indica 1 Citrus sinensis 1 Arabidopsis thaliana 1 Carica papaya 1 Gossypium hirsutum 1 1 Theobroma cacao Bulnesia arborea Euonymus americanus 0.58 Oxalis latifolia 1 Chrysobalanus icaco 0.53 1 Populus trichocarpa 1 Garcinia mangostana 0.53 Manihot esculenta Cucumis sativus 1 0.65 Quercus rubra 1 Morus indica 1 Prunus persica Guilfoylia monostylis 1 0.8 Polygala lutea 1 Xanthophyllum eurhynchum Quillaja saponaria Bauhinia tomentosa 1 1 Cercis canadensis Prioria balsamifera 1 Copaifera officinalis 1 0.51 Guibourtia ehie 1 1 Guibourtia tessmannii Schotia brachypetala

0.7 Saraca indica Afzelia africana 1 1 Afzelia bipindensis 1 0.5 1 Intsia bijuga Anthonotha fragrans 1 Tamarindus indica 1 Hymenostegia brachyura 1 Hymenostegia felicis Duparquetia orchidacea Poeppigia procera 1 Zenia insignis 1 Dialium guineense 1 Distemonanthus benthamianus Swartzia emarginata Xanthocercis zambesiaca 1 Cladrastis lutea 1 1 Styphnolobium japonicum 0.99 Lupinus luteus 1 Lupinus polyphyllus 0.87 1 Tipuana tipu 1 Arachis hypogaea 1 Arachis ipaensis Gompholobium polymorphum 1 1 Indigofera tinctoria 1 Millettia pinnata 1 Apios americana 1 Codariocalyx motorius 1 Phaseolus vulgaris 1 1 Vigna radiata 1 1 Vigna unguiculata Pachyrhizus erosus 1 1 Bituminaria bituminosa 1 Glycine canescens 1 Glycine max Gliricidia sepium 1 Robinia pseudoacacia 1 Lotus japonicus 1 0.96 Sesbania macrantha 1 1 Sesbania sesban Glycyrrhiza glabra 1 Glycyrrhiza lepidota 1 Wisteria floribunda Astragalus membranaceus 1 0.99 Astragalus propinquus 1 Cicer arietinum Medicago hybrida 1 1 Medicago truncatula Trifolium repens 1 1 Trifolium aureum

1 Pisum sativum 1 Lathyrus graminifolius 1 1 Lathyrus sativus Lens culinaris 1 Vicia faba 1 Vicia sativa Acrocarpus fraxinifolius 1 Ceratonia siliqua Gymnocladus dioicus 1 1 Gleditsia sinensis 1 Gleditsia triacanthos Chamaecrista fasciculata 1 1 Senna hebecarpa 1 Senna siamea Haematoxylum brasiletto 1 1 Erythrostemon gilliesii 1 Libidibia coriaria 1 Tachigali odoratissima 1 Dimorphandra macrostachya 0.96 Colvillea racemosa 1 1 Peltophorum africanum Diptychandra aurantiaca 1 Erythrophleum ivorense Pachyelasma tessmannii 1 Chidlowia sanguinea 0.83 0.77 Pentaclethra macrophylla Adenanthera pavonina 1 1 Xylia hoffmannii 1 Piptadeniastrum africanum 1 Entada abyssinica 1 Entada rheedei 1 Newtonia hildebrandtii Prosopis alba 1 1 Prosopis glandulosa Dichrostachys cinerea 1 1 Desmanthus illlinoiensis 1 Leucaena trichandra 1 Vachellia tortilis 1 Parkia panurensis 1 Microlobius foetidus 1 Mimosa tenuiflora 1 Senegalia ataxacantha 1 Calliandra hygrophila 1 Faidherbia albida 1 Cojoba arborea Pithecellobium dulce 1 0.83 Abarema jupunba 1 Archidendron lucidum 1 Acacia koa 1 1 Acacia ligulata Inga leiocalycina 1 Inga spectabilis 0.98 Samanea saman 1 Albizia adianthifolia 1 Albizia julibrissin

Figure S4. Bayesian majority-rule consensus tree inferred with Phylobayes from nucleotide alignment of chloroplast genes under the CATGTR model. Numbers on nodes indicate the posterior probabilities (pp) from 9000 post-burn-in MCMC cycles. Papaver somniferum Ranunculales 1.00 Aquilegia coerulea Nelumbo nucifera Proteales Amaranthus hypochondriacus 0.89 Primula veris 1.00 0.93 Solanum tuberosum 0.93 Mimulus guttatus 0.91 Asterids Lactuca sativa 0.74 Panax ginseng 0.96 Paeonia lactiflora 0.00 Saxifragales Vitis vinifera Vitales Punica granatum 0.94 Eucalyptus grandis Myrtales 0.70 Tripterygium wilfordii 0.87 Manihot esculenta Celastrales Pentapetalae 0.94 Linum usitatissimum 0.97 Populus trichocarpa Malphigiales 0.59 1.00 0.83 Salix purpurea Elaeocarpus photiniifolia Oxalidales 0.80 Citrus sinensis Carica papaya Sapindales 0.82 0.75 Arabidopsis thaliana Brassicales 0.92 Theobroma cacao 1.00 0.61 Gossypium raimondii Malvales Cucumis sativus Cucurbitales 0.68 Prunus persica 0.98 Fragaria vesca 0.88 Rosales Cannabis sativa 1.00 Morus notabilis Fagales 0.50 Castanea mollissima 0.97 Juglans regia 0.91 Polygalaceae Alnus serrulata Polygala lutea 0.08 Quillajaceae 0.19 Quillaja saponaria Bauhinia tomentosa 0.98 Nitrogen-fixing Cercis canadensis Cercidoideae 0.85 Anthonotha fragrans 0.97 0.94 Afzelia bella clade 1.00 Prioria balsamifera Detarioideae 0.94 Copaifera officinalis 0.98 Zenia insignis Acrocarpus fraxinifolius Dialioideae Gleditsia triacanthos 0.95 Fabales 0.97 Gymnocladus dioicus 0.97 Chamaecrista fasciculata Cassia 0.78 0.65 Rosids Senna hebecarpa clade 0.98 Entada abyssinica 0.99 Prosopis alba 0.98 Desmanthus illinoensis 0.70 0.98 Microlobius foetidus 0.98 Acacia koa 0.98 Inga spectabilis Caesalpinioideae 0.94 Albizia julibrissin mimosoids Xanthocercis zambesiaca Styphnolobium japonicum 0.97 0.97 Cladrastis lutea Arachis ipaensis 0.83 0.93 Lupinus angustifolius 1.00 Lupinus polyphyllus Apios americana Codariocalyx motorius 0.96 0.98 0.46 Cajanus cajan 0.83 Vigna radiata Millettioid 0.98 Phaseolus vulgaris clade 0.79 0.94 Bituminaria bituminosa 0.95 Glycine max Lotus japonicus 0.95 Glycyrrhiza lepidota Papilionoideae 0.65 Astragalus membranaceus 0.99 Cicer arietinum Medicago truncatula Inverted 0.98 0.90

Trifolium pratense repeat 50Kb inversion clade 0.96 Lens culinaris lacking −0.39 Vicia faba clade 1.00 Lathyrus sativus 0.95 Pisum sativum

Figure S5. ML topology as inferred by RAxML from a concatenated alignment of 1,103 nuclear genes, under the LG4X model. Numbers on nodes indicate Internode Certainty All (ICA) values, as estimated from gene trees of the same 1,103 genes. Aquilegia coerulea 1.00 Ranunculales Papaver somniferum Nelumbo nucifera Proteales Amaranthus hypochondriacus 1.00 Primula veris 1.00 1.00 Solanum tuberosum 1.00 Mimulus guttatus 1.00 Panax ginseng Asterids 1.00 Lactuca sativa 1.00 Paeonia lactiflora Saxifragales Vitis vinifera Vitales Eucalyptus grandis 1.00 Punica granatum Myrtales Tripterygium wilfordii 0.91 0.64 0.98 Manihot esculenta Celastrales 1.00 Linum usitatissimum Pentapetalae 0.76 Populus trichocarpa Malphigiales 1.00 1.00 Salix purpurea Elaeocarpus photiniifolia Oxalidales 0.68 Citrus sinensis Arabidopsis thaliana Sapindales 0.75 1.00 Carica papaya Brassicales 1.00 0.97 Gossypium raimondii 1.00 Theobroma cacao Malvales Cucumis sativus Fragaria vesca Cucurbitales 1.00 1.00 Prunus persica 1.00 Rosales Morus notabilis 1.00 Cannabis sativa Fagales 1.00 Castanea mollissima 1.00 Alnus serrulata 1.00 Juglans regia Quillajaceae Quillaja saponaria 1.00 Polygala lutea Polygalaceae Cercis canadensis 1.00 1.00 Bauhinia tomentosa Cercidoideae Nitrogen-fixing 0.91 Prioria balsamifera 1.00 Copaifera officinalis clade 1.00 Afzelia bella Detarioideae 1.00 Anthonotha fragrans 1.00 Zenia insignis Acrocarpus fraxinifolius Dialioideae Gleditsia triacanthos Fabales 1.00 1.00 Gymnocladus dioicus 1.00 Chamaecrista fasciculata 1.00 1.00 Cassia Senna hebecarpa clade Rosids 1.00 Entada abyssinica 1.00 Prosopis alba 1.00 Desmanthus illinoensis 0.96 0.67 Microlobius foetidus 1.00 Acacia koa 1.00 Albizia julibrissin 0.88 mimosoids Inga spectabilis Caesalpinioideae Xanthocercis zambesiaca Cladrastis lutea 1.00 1.00 Styphnolobium japonicum Arachis ipaensis 0.92 1.00 Lupinus polyphyllus 1.00 Lupinus angustifolius Apios americana Cajanus cajan 1.00 1.00 0.58 Codariocalyx motorius Millettioid 1.00 Phaseolus vulgaris 1.00 Vigna radiata clade 1.00 1.00 Glycine max 1.00 Bituminaria bituminosa Lotus japonicus 1.00 Glycyrrhiza lepidota

1.00 Astragalus membranaceus Papilionoideae 1.00 Cicer arietinum Inverted Medicago truncatula 1.00 1.00 repeat

Trifolium pratense 50Kb inversion clade 1.00 Lens culinaris lacking 0.67 Vicia faba 1.00 clade Pisum sativum 1.00 Lathyrus sativus

Figure S6. Bayesian gene jackknifing majority-rule consensus tree inferred with Phylobayes from a concatenated alignment of 1,103 nuclear genes. Numbers on nodes indicate posterior probabilities (pp), averaged over 500 posterior trees each, for 25 replicates (12,500 posterior trees in total). 1 Aquilegia coerulea 65.91 Papaver somniferum Nelumbo nucifera Amaranthus hypochondriacus 1 40.08 Primula veris 1 1 Panax ginseng 1 59 51.37 65.91 1 Lactuca sativa 40.58 1 Mimulus guttatus 63.59 Solanum tuberosum

1 0.62 Paeonia lactiflora 35.65 Asterids 79.51 Vitis vinifera 1 Punica granatum 79.95 Eucalyptus grandis Tripterygium wilfordii 0.76 1 35.35 42.8 Linum usitatissimum 0.92 1 38.82 65.46 Manihot esculenta 1 38.88 Pentapetalae 1 1 Populus trichocarpa 48.38 99.68 Salix purpurea Elaeocarpus photiniifolia 0.69 38.87 Citrus sinensis 1 0.68 1 Gossypium raimondii 61.06 39.28 97.65 1 Theobroma cacao 40.91 1 Carica papaya 46.7 Arabidopsis thaliana Cucumis sativus

1 Fragaria vesca 94.09 Prunus persica 1 1 49.05 59.78 Rosids 1 Cannabis sativa 86 Morus notabilis 0.36 Castanea mollissima 34.88 1 85.47 1 Alnus serrulata 55.54 Juglans regia 1 37.67 Polygala lutea Nitrogen-fixing Quillaja saponaria 1 1 Cercis canadensis 77.42 94.36 clade Bauhinia tomentosa Cercidoideae 0.95 0.95 36.7 1 Prioria balsamifera 37.93 53.74 1 Copaifera officinalis 98.49 1 Anthonotha fragrans Detarioideae 56.18 Afzelia bella 1 Zenia insignis 88.3 Dialioideae Fabales Acrocarpus fraxinifolius Gymnocladus dioicus 1 1 94.57 74.22 Gleditsia triacanthos 1 1 Senna hebecarpa 44.19 1 47.61 52.13 Chamaecrista fasciculata Cassia clade 1 65.6 Entada abyssinica

1 0.39 Prosopis alba 84.64 36.35 Desmanthus illinoensis 0.58 1 34.66 87.77 Microlobius foetidus 1 57.57 Acacia koa 1 85.84 1 Inga spectabilis mimosoids 43.43 Albizia julibrissin Caesalpinioideae Xanthocercis zambesiaca Styphnolobium japonicum 1 1 88.15 85.48 Cladrastis lutea 1 Arachis ipaensis 51.03 1 Lupinus polyphyllus 99.55 1 Lupinus angustifolius 72.55 Apios americana 1 0.62 94.79 Codariocalyx motorius 35.7 1 Cajanus cajan 40.18 0.42 1 Vigna radiata Millettioid 33.93 95.79 1 1 Phaseolus vulgaris clade 58.46 50.56 1 Bituminaria bituminosa 68.13 Glycine max Lotus japonicus 1 64.09 Glycyrrhiza lepidota 1 Astragalus membranaceus 58.33

1 Cicer arietinum Papilionoideae 70.58 1 1 Trifolium pratense Inverted 90.71 43.03 Medicago truncatula repeat 50Kb inversion clade 1 77.24 1 Pisum sativum 56.85 lacking 1 Lathyrus sativus 96.32 clade 0.64 Lens culinaris 36.23 Vicia faba

Figure S7. Phylogeny estimated under the multi-species coalescent with ASTRAL. Support values indicated represent local posterior probability (blue rectangles) and quartet support (yellow rectangles). Nelumbo nucifera@pep12653 Nelumbo nucifera@pep6438 Cucumis sativus@pep11153 Vitis vinifera@pep5952 100 Lactuca sativa@pep876 Eucalyptus grandis@pep33852 22 Mimulus guttatus@pep981 70 100 Punica granatum@pep52461 Citrus sinensis@pep5555 33 31 100 Prunus persica@pep26402 Carica papaya@pep15732 93 36 Arabidopsis thaliana@AT1G27320 1 64 Morus notabilis@pep10996 98 Prunus persica@pep23928 Cannabis sativa@pep16975 23 Gossypium raimondii@pep23727 99 22 Citrus sinensis@pep5766 Theobroma cacao@pep27466 9 Castanea mollissima@pep31256 100 72 Gossypium raimondii@pep16031 100 52 Juglans regia@pep21850 73 Theobroma cacao@pep28606 Alnus serrulata@pep28894 Tripterygium wilfordii@pep4370 Eucalyptus grandis@pep24038 21 86 39 1 Punica granatum@pep54067 Mimulus guttatus@pep12424 2 98 5 Cucumis sativus@pep18983 Solanum tuberosum@pep8398 55 Morus notabilis@pep4078 17 100 Manihot esculenta@pep25994 2 Cannabis sativa@pep25660 Salix purpurea@pep12141 Manihot esculenta@pep8730 98 10 100 Linum usitatissimum@pep28142 Populus trichocarpa@pep839 15 31 100 Amaranthus hypochondriacus@pep20716 Salix purpurea@pep13717 4 Salix purpurea@pep15057 100 3 100 Populus trichocarpa@pep33286 Populus trichocarpa@pep34794 100 Salix purpurea@pep29519 Castanea mollissima@pep13894 100 Populus trichocarpa@pep11650 86 Juglans regia@pep20249 Bauhinia tomentosa@pep28734 53 Cercidoideae Alnus serrulata@pep23320 Zenia insignis@pep27070 Anthonotha fragrans@pep40473 Dialioideae Bauhinia tomentosa@pep11086 25 98 Cercidoideae Afzelia bella@pep20849 Anthonotha fragrans@pep29999 100 60 31 74 Copaifera officinalis@pep28719 100 96 Detarioideae Copaifera officinalis@pep24710 Detarioideae A Prioria balsamifera@pep14237 98 Anthonotha fragrans@pep30001 Acrocarpus fraxinifolius@pep15409 99 Entada abyssinica@pep35577 100 Prioria balsamifera@pep5052 53 81 Detarioideae B 100 Prosopis alba@pep28348 99 Copaifera officinalis@pep2783 97 Microlobius foetidus@pep10313 Caesalpinioideae Acrocarpus fraxinifolius@pep12136 73 Inga spectabilis@pep30535 88 Acacia koa@pep36766 98 Acacia koa@pep31068 Arachis ipaensis@pep12510 100 Caesalpinioideae 29 Inga spectabilis@pep27731 60 Glycyrrhiza lepidota@pep33029 23 Styphnolobium japonicum@pep27019 100 Astragalus membranaceus@pep29344 Cicer arietinum@pep13001 Arachis ipaensis@pep18576 97 100 Trifolium pratense@pep5130 92 95 Lupinus angustifolius@pep23514 Medicago truncatula@Medtr3g085130 1 Papilionoideae A 64 Lotus japonicus@pep21759 97 91 Vicia faba@pep21782 100 Lathyrus sativus@pep23640 56 Cicer arietinum@pep4519 98 61 Pisum sativum@pep28232 100 Pisum sativum@pep28963 Styphnolobium japonicum@pep35673 62 Trifolium pratense@pep11149 Glycyrrhiza lepidota@pep33028 92 100 100 Medicago truncatula@Medtr5g040710 1 65 Cicer arietinum@pep15233 100 Papilionoideae Medicago truncatula@Medtr8g080770 1 Vigna radiata@pep16145 97 100 Apios americana@pep30778 Phaseolus vulgaris@pep26562 Codariocalyx motorius@pep23608 100 Papilionoideae B 100 Codariocalyx motorius@pep29133 34 Glycine max@pep42115 66 Bituminaria bituminosa@pep36236 25 Apios americana@pep9855 47 Cajanus cajan@pep376 12 Glycine max@pep43512 43 Phaseolus vulgaris@pep24022 42 100 A Cajanus cajan@pep45354 B Vigna radiata@pep10279

Nelumbo nucifera@pep538 Cannabis sativa@pep7635 Vitis vinifera@pep11180 42 Paeonia lactiflora@pep13030 46 67 Castanea mollissima@pep25000 Lactuca sativa@pep22648 Prunus persica@pep20979 Carica papaya@pep25065 46 Castanea mollissima@pep28614 34 6 24 Alnus serrulata@pep28472 Gossypium raimondii@pep25338 62 Juglans regia@pep29951 4 97 Eucalyptus grandis@pep25350 Theobroma cacao@pep27751 31 26 40 Gossypium raimondii@pep24717 72 Theobroma cacao@pep23048 Populus trichocarpa@pep7162 13 Cannabis sativa@pep28328 54 19 Citrus sinensis@pep11970 20 Morus notabilis@pep18333 11 Solanum tuberosum@pep11910 38 23 Citrus sinensis@pep480 Mimulus guttatus@pep19037 4 11 Manihot esculenta@pep18288 Juglans regia@pep14713 48 Salix purpurea@pep12562 100 Populus trichocarpa@pep32557 61 Castanea mollissima@pep30768 Quillaja saponaria@pep17221 22 Bauhinia tomentosa@pep15826 88 Cercidoideae A Alnus serrulata@pep12361 Prioria balsamifera@pep2128 94 68 Afzelia bella@pep27295 Detarioideae A Juglans regia@pep9904 80 79 Microlobius foetidus@pep51263 100 Albizia julibrissin@pep1932 Fragaria vesca@pep28419 100 Caesalpinioideae A 3 43 Acacia koa@pep19005 59 Xanthocercis zambesiaca@pep18551 Prunus persica@pep10398 Styphnolobium japonicum@pep23820 58 87 Glycyrrhiza lepidota@pep22647 Quillaja saponaria@pep29629 40 Lotus japonicus@pep37960 Arachis ipaensis@pep13186 64 Cicer arietinum@pep528 11 68 63 Medicago truncatula@Medtr2g020190 1 Trifolium pratense@pep28289 100 Pisum sativum@pep16999 100 100 Lathyrus sativus@pep22427 100 35 62 Medicago truncatula@Medtr2g029450 1 Vicia faba@pep14694 Lupinus angustifolius@pep25605 62 79 100 75 Lotus japonicus@pep37608 Lupinus polyphyllus@pep18828 27 Cajanus cajan@pep17076 Cajanus cajan@pep1401 61 Papilionoideae A 99 Phaseolus vulgaris@pep22908 67 Vigna radiata@pep9397 Bituminaria bituminosa@pep19689 61 100 Codariocalyx motorius@pep12789 A Papilionoideae 72 37 Glycine max@pep14222 61 Glycine max@pep14474 Bituminaria bituminosa@pep12878 66 Zenia insignis@pep3529 Vigna radiata@pep15899 89 69 Acacia koa@pep27540 Dialioideae 97 Phaseolus vulgaris@pep14 97 Inga spectabilis@pep28695 61 Microlobius foetidus@pep24462 68 Albizia julibrissin@pep21101 Caesalpinioideae B Cercis canadensis@pep20170 48 100 100 Entada abyssinica@pep18726 Bauhinia tomentosa@pep7015 Cercidoideae Bauhinia tomentosa@pep7989 18 Anthonotha fragrans@pep26428 Cercidoideae B 34 Entada abyssinica@pep41964 90 Copaifera officinalis@pep25880 53 Prioria balsamifera@pep13539 Detarioideae B 100 31 Acacia koa@pep17295 Cladrastis lutea@pep15924 100 Caesalpinioideae Xanthocercis zambesiaca@pep18282 100 Microlobius foetidus@pep50271 94 Apios americana@pep17345 36 Phaseolus vulgaris@pep25665 86 Styphnolobium japonicum@pep15214 8 Bituminaria bituminosa@pep26354 6 Cajanus cajan@pep32271 Arachis ipaensis@pep3936 51 40 Glycine max@pep31223 99 Codariocalyx motorius@pep6651 63 Medicago truncatula@Medtr8g028060 1 Lotus japonicus@pep28953 Papilionoideae B 100 20 Cicer arietinum@pep20299 75 Glycyrrhiza lepidota@pep22649 72 Papilionoideae B 63 Astragalus membranaceus@pep26877 Medicago truncatula@Medtr4g094742 1 Lotus japonicus@pep7328 90 39 Cicer arietinum@pep14411 55 86 Cajanus cajan@pep23316 Pisum sativum@pep4173 96 100 Lathyrus sativus@pep1494 C Glycine max@pep11904 D

Nelumbo nucifera@pep546 Amaranthus hypochondriacus@pep8549 Vitis vinifera@pep16546 19 Solanum tuberosum@pep13773 Mimulus guttatus@pep6519 97 63 Lactuca sativa@pep8741 57 96 48 Mimulus guttatus@pep18796 Lactuca sativa@pep13791 Primula veris@pep4197 Eucalyptus grandis@pep4183 97 24 Paeonia lactiflora@pep20287 73 Cucumis sativus@pep2796 Vitis vinifera@pep6102 Punica granatum@pep45567 25 Cannabis sativa@pep21046 56 96 11 Eucalyptus grandis@pep12615 91 Morus notabilis@pep15673 Manihot esculenta@pep22425 47 Castanea mollissima@pep22322 Linum usitatissimum@pep12286 79 22 65 Populus trichocarpa@pep21479 Juglans regia@pep5847 26 96 Salix purpurea@pep32716 22 100 Salix purpurea@pep31207 Citrus sinensis@pep17125 76 100 Populus trichocarpa@pep3760 43 Gossypium raimondii@pep4870 56 Carica papaya@pep20998 Carica papaya@pep22885 45 Theobroma cacao@pep1974 66 Citrus sinensis@pep12151 Manihot esculenta@pep26276 40 63 28 52 Arabidopsis thaliana@AT2G43330 1 85 Linum usitatissimum@pep11767 31 Theobroma cacao@pep21550 54 66 Populus trichocarpa@pep35891 Gossypium raimondii@pep25441 100 Cucumis sativus@pep4662 Salix purpurea@pep24417 15 Prunus persica@pep25005 98 Fragaria vesca@pep8925 Cercidoideae A Polygala lutea@pep19498 Alnus serrulata@pep21508 Afzelia bella@pep11748 92 34 40 Juglans regia@pep357 100 Copaifera officinalis@pep21730 Morus notabilis@pep10861 Detarioideae A 74 Detarioideae A Cercis canadensis@pep16614 Anthonotha fragrans@pep21756 100 14 Copaifera officinalis@pep23615 Albizia julibrissin@pep36504 64 Acacia koa@pep33775 Caesalpinioideae A 69 100 Inga spectabilis@pep33036 Caesalpinioideae A 100 Arachis ipaensis@pep36380 100 Cicer arietinum@pep18858 Styphnolobium japonicum@pep10579 74 Glycine max@pep28749 34 43 Papilionoideae A 87 Xanthocercis zambesiaca@pep20065 69 Medicago truncatula@Medtr3g084110 1 44 100 Cicer arietinum@pep13044 Papilionoideae B Glycyrrhiza lepidota@pep38695 Copaifera officinalis@pep24490 Cicer arietinum@pep889 93 37 Cercis canadensis@pep16615 69 97 100 100 Medicago truncatula@Medtr2g097950 1 60 Bauhinia tomentosa@pep742 Detarioideae B Acrocarpus fraxinifolius@pep14941 81 99 Vicia faba@pep15000 58 Microlobius foetidus@pep20576 100 100 Inga spectabilis@pep10452 Cercidoideae B 71 Pisum sativum@pep39290 100 43 Albizia julibrissin@pep38063 Lathyrus sativus@pep21245 53 Acacia koa@pep32559 Caesalpinioideae B Entada abyssinica@pep9029 82 Lotus japonicus@pep9816 100 Microlobius foetidus@pep20577 Apios americana@pep16395 94 Caesalpinioideae C 48 Prosopis alba@pep24267 Codariocalyx motorius@pep4499 Microlobius foetidus@pep20579 98 45 97 100 Inga spectabilis@pep21274 Glycine max@pep14484 99 Caesalpinioideae D Acacia koa@pep10539 54 Cajanus cajan@pep8651 Prioria balsamifera@pep37746 52 43 Arachis ipaensis@pep36383 Detarioideae C Vigna radiata@pep20654 A Papilionoideae 88 Lotus japonicus@pep10902 Phaseolus vulgaris@pep7368 90 84 Medicago truncatula@Medtr1g116650 1 21 100 Copaifera officinalis@pep21733 69 Trifolium pratense@pep30510 38 Glycine max@pep29080 Papilionoideae C Bauhinia tomentosa@pep11229 Detarioideae B 72 Phaseolus vulgaris@pep16177 64 Gleditsia triacanthos@pep21831 29 Cajanus cajan@pep44735 Detarioideae D Cercidoideae Anthonotha fragrans@pep48381 65 Entada abyssinica@pep51661 48 79 Bauhinia tomentosa@pep11208 Cercidoideae C 100 Prosopis alba@pep23773 Arachis ipaensis@pep36382 100 Caesalpinioideae B 97 Glycine max@pep28786 Acacia koa@pep25517 47 33 Cajanus cajan@pep44733 10 Microlobius foetidus@pep13166 20 Cicer arietinum@pep10087 Papilionoideae D1 100 100 Albizia julibrissin@pep44736 Medicago truncatula@Medtr1g116660 1 79 Caesalpinioideae C 54 Xanthocercis zambesiaca@pep18710 Acacia koa@pep19743 35 13 Styphnolobium japonicum@pep30890 Zenia insignis@pep8072 99 Cladrastis lutea@pep18002 Dialioideae Styphnolobium japonicum@pep11646 78 Lupinus angustifolius@pep15985 35 Lotus japonicus@pep17522 Arachis ipaensis@pep7836 45 Glycyrrhiza lepidota@pep20283 83 90 Lupinus angustifolius@pep11405 54 Astragalus membranaceus@pep21540 65 52 Cicer arietinum@pep25355 Cicer arietinum@pep17197 69 Medicago truncatula@Medtr7g005910 1 88 19 96 Medicago truncatula@Medtr4g065040 1 61 Pisum sativum@pep7103 82 100 Lathyrus sativus@pep16251 Papilionoideae D2 Trifolium pratense@pep19766 Arachis ipaensis@pep16553 71 Vigna radiata@pep2699 Cajanus cajan@pep231 74 97 Phaseolus vulgaris@pep11964 Apios americana@pep16393 96 31 58 Glycine max@pep38743 Glycine max@pep46506 25 Bituminaria bituminosa@pep12263 48 22 Cajanus cajan@pep3545 Codariocalyx motorius@pep15730 18 Codariocalyx motorius@pep297 26 Vigna radiata@pep22273 43 Apios americana@pep21931 100 E F Phaseolus vulgaris@pep9481 Papilionoideae B Papilionoideae

Figure S8. Examples of homolog clusters with gene duplications in legumes that passed the bootstrap filter. Yellow stars behind nodes indicate locations of gene duplications, numbers on nodes indicate bootstrap support. The plotted gene trees are extracted from (A) cluster3675_1rr_1rr, showing a duplication subtending Detarioideae, (B) cluster1032_1rr_1rr, showing a duplication subtending Papilionoideae, (C) cluster1248_1rr_1rr and (D) cluster2941_1rr_1rr, both with a duplication subtending the legume family. Trees for (E) cluster51_7rr_1rr and (F) cluster544_1rr_1rr show evidence of more than one duplication, including one specific to Papilionoideae in the former. Papaver somniferum Ranunculales Aquilegia coerulea Nelumbo nucifera Proteales Amaranthus hypochondriacus 1/1 Primula veris 0/0 0/0 1/1 0/0 Solanum tuberosum 0/0 0/0 0/0 3/3 Mimulus guttatus Asterids 0/0 1/1 Lactuca sativa 1/1 Panax ginseng 1901/1105 284/264 0/0 Paeonia lactiflora Saxifragales 0/0 Vitis vinifera Vitales 16/16 Punica granatum 3/3 Eucalyptus grandis Myrtales 267/181 Tripterygium wilfordii 50/46 5/5 Manihot esculenta Celastrales 0/0 65/59 15/15 Linum usitatissimum Pentapetalae 24/23 Populus trichocarpa Malphigiales 45/43 1/1 2950/2676 268/194 3/3 2691/2471 Salix purpurea "gamma" 7/7 Elaeocarpus photiniifolia Oxalidales 1/1 Citrus sinensis hexaploidization 0/0 Sapindales 2/2 0/0 Carica papaya 0/0 0/0 5/5 Arabidopsis thaliana Brassicales 1/1 57/55 Theobroma cacao 429/300 40/39 Malvales 16/14 Gossypium raimondii Cucumis sativus Cucurbitales 2/2 25/24 Prunus persica 0/0 16/16 6/6 Fragaria vesca Rosales 3/3 13/10 Cannabis sativa 8/7 Morus notabilis Fagales 150/111 Castanea mollissima Salix / Populus 1/1 8/8 3/3 0/0 Juglans regia Polygalaceae WGD 0/0 Alnus serrulata 0/0 Polygala lutea 49/35 0/0 Quillaja saponaria 2/2 Quillajaceae 4/4 Bauhinia tomentosa 2/2 Cercis canadensis Cercidoideae 27/27 393/296 2/2 0/0 Anthonotha fragrans 11/11 0/0 325/316 Afzelia bella 183/181 3/3 Prioria balsamifera Detarioideae 2/2 Copaifera officinalis Detarioideae WGD 1646/1229 Zenia insignis 99/85 Dialioideae Acrocarpus fraxinifolius 81/79 2/2 Gleditsia triacanthos 11/11 0/0 Gymnocladus dioicus Rosids 31/28 Chamaecrista fasciculata 249/220 3/3 0/0 17/15 0/0 Senna hebecarpa 20/19 5/5 Entada abyssinica Leguminosae WGD 135/120 48/47 28/25 Prosopis alba 8/8 Desmanthus illinoensis 435/382 2/2 37/36 2/2 Microlobius foetidus 26/26 15/15 7/7 Acacia koa 1/1 Inga spectabilis Caesalpinioideae

3/3 mimosoids 1/1 Albizia julibrissin Xanthocercis zambesiaca 0/0 Styphnolobium japonicum 956/902 0/0 Cladrastis lutea 328/325 Arachis ipaensis 0/0 465/420 0/0 19/19 Lupinus angustifolius 160/155 13/13 Lupinus polyphyllus Papilionoideae WGD Apios americana 363/332 116/102 0/0 Codariocalyx motorius 68/65 35/34 0/0 Cajanus cajan 44/41 12/11 11/11 Vigna radiata 8/8 Phaseolus vulgaris 172/147 8/8 0/0 32/31 2/2 Bituminaria bituminosa 0/0 Glycine max Lotus japonicus 35/33 Glycyrrhiza lepidota

3/3 Papilionoideae 12/12 Astragalus membranaceus 2/2 25/23 Cicer arietinum 4/4 70/62 2/2 Medicago truncatula

22/22 1/1 Trifolium pratense inversion clade 50Kb 30/29 0/0 Lens culinaris 5/5 0/0 21/21 Vicia faba 8/8 Lathyrus sativus 3/3 1/1 Pisum sativum

Figure S9. Numbers of gene duplications mapped across the phylogeny. The topology used is the ML topology of the nuclear concatenated alignment of 1,103 genes, duplications were counted from 8,038 homolog clusters. Numbers above branches (with blue background) and below branches (with yellow background) represent numbers of duplications and numbers of homolog trees with duplications, without or with a bootstrap filter of 50%, respectively. Aquilegia coerulea 113.0027 − 120.45 Papaver somniferum Nelumbo nucifera 26124.90 − 128.25 Amaranthus hypochondriacus 100.26 − 115.86 48 Primula veris 122.59 − 126.00 38 89.80 − 104.52 Lactuca sativa 72.21 − 97.70 Mimulus guttatus 42.59 − 82.26 115.15 − 121.29 Solanum tuberosum Vitis vinifera Paeonia lactiflora 111.82 − 119.04 94 Eucalyptus grandis 83.60 − 93.79 Punica granatum

109.98 − 117.65 Citrus sinensis 92.77 − 101.07105 Carica papaya 89.80 − 94.81 Gossypium raimondii 20.23 − 63.91 97.18 − 106.31 Theobroma cacao 105.49 − 113.40 Elaeocarpus photiniifolia 89.44 − 103.41 Tripterygium wilfordii 86.98 − 101.27 Manihot esculenta 65.24 − 88.06 133 Populus trichocarpa 37.80 − 47.58 Salix purpurea 103.04 − 111.29 Cucumis sativus 116 Cannabis sativa 89.36 − 102.74 66.00 − 76.73 Morus notabilis 80.01 − 96.35 Fragaria vesca 49.40 − 73.16 112 Prunus persica 97.17 − 108.02 Castanea mollissima X14 70.40 − 88.75 Alnus serrulata 64.40 − 77.22 122 Juglans regia Quillaja saponaria 92.95 − 104.46 Bauhinia tomentosa 36.00 − 53.68 C Cercis canadensis 57.44 − 79.51 Afzelia bella 78.45 − 95.39 14.88 − 37.52 Anthonotha fragrans G 25.39 − 42.99 F Copaifera officinalis 22.50 − 35.70 Prioria balsamifera

65.51 − 85.05 A Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos 54.26 − 73.12Z 4.83 − 26.12 Gymnocladus dioicus

49.33 − 67.14 Chamaecrista fasciculata 62.42 − 82.31 18.17 − 45.35 Senna hebecarpa 44.67 − 61.09 Entada abyssinica 38.11 − 50.95 Prosopis alba 33.90Q − 41.34 Desmanthus illinoensis 59.98 − 79.71 30.21 − 39.79 Microlobius foetidus 26.86 − 36.38Q2 Acacia koa 23.00 − 27.08 Albizia julibrissin 19.76 − 26.65 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 7.12 − 29.26 55.20 − 71.82 I2 Styphnolobium japonicum Arachis ipaensis 34.91 − 56.03 Lupinus angustifolius 50.61 − 67.69 9.13 − 28.59 Lupinus polyphyllus Apios americana Cajanus cajan 45.42 − 62.84 27.53 − 44.55 19.67 − 37.23 Codariocalyx motorius 25.43 − 41.31 Bituminaria bituminosa 12.13 − 29.60 Glycine max 21.99 − 36.71 41.49 − 58.26 Phaseolus vulgaris 8.07 − 21.75 Vigna radiata M2 Lotus japonicus 36.46 − 53.58 Glycyrrhiza lepidota 31.58 − 48.99 Astragalus membranaceus 27.02 − 42.89 Cicer arietinum Medicago truncatula 19.79 − 33.90 10.67 − 23.99 Trifolium pratense 15.52 − 27.52 Lathyrus sativus 4.60 − 12.88 Pisum sativum 7.50 − 16.16 Lens culinaris 5.47 − 13.93 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S10. Chronogram estimated under the UCLN clock model. Numbers behind nodes indicate 95% HPD intervals. Substitution rate is indicated by colored branches, as indicated by the color legend, in substitutions per site per million years. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.0027 − 120.31 Papaver somniferum Nelumbo nucifera 26124.97 − 128.33 Amaranthus hypochondriacus 100.33 − 114.62 48 Primula veris 122.44 − 126.00 38 89.80 − 104.52 Lactuca sativa 71.00 − 99.58 Mimulus guttatus 30.22 − 81.69 114.37 − 120.73 Solanum tuberosum Vitis vinifera Paeonia lactiflora 111.24 − 118.39 94 Eucalyptus grandis 83.60 − 95.91 Punica granatum

109.49 − 116.96 Citrus sinensis 92.42 − 100.58105 Carica papaya 89.80 − 94.72 Gossypium raimondii 17.31 − 64.51 97.05 − 105.67 Theobroma cacao 105.15 − 112.81 Elaeocarpus photiniifolia 88.46 − 103.34 Tripterygium wilfordii 85.78 − 101.10 Manihot esculenta 59.88 − 88.83 133 Populus trichocarpa 37.80 − 48.18 Salix purpurea 102.68 − 110.54 Cucumis sativus 116 Cannabis sativa 86.86 − 102.40 66.00 − 76.34 Morus notabilis 76.91 − 95.70 Fragaria vesca 49.40 − 64.84112 Prunus persica 96.85 − 107.02 Castanea mollissima X14 70.20 − 88.55 Alnus serrulata 64.40 − 76.33 122 Juglans regia Quillaja saponaria 92.74 − 103.85 Bauhinia tomentosa 36.00 − 52.87 C Cercis canadensis 59.60 − 79.70 Afzelia bella 79.62 − 93.31 15.60 − 39.18 Anthonotha fragrans G 25.22 − 45.43 F Copaifera officinalis 22.50 − 38.57 Prioria balsamifera

69.98 − 84.50 A Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos 57.36 − 72.64Z 4.66 − 25.73 Gymnocladus dioicus

51.69 − 67.64 Chamaecrista fasciculata 67.10 − 81.44 18.76 − 45.81 Senna hebecarpa 46.50 − 61.13 Entada abyssinica 38.14 − 50.12 Prosopis alba 33.90Q − 39.85 Desmanthus illinoensis 65.67 − 79.75 30.48 − 38.31 Microlobius foetidus 27.03 − 34.93Q2 Acacia koa 23.00 − 26.66 Albizia julibrissin 19.87 − 26.27 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 7.08 − 32.66 57.08 − 70.59 I2 Styphnolobium japonicum Arachis ipaensis 34.57 − 53.79 Lupinus angustifolius 53.57 − 65.99 9.62 − 28.79 Lupinus polyphyllus Apios americana Cajanus cajan 47.68 − 60.76 26.87 − 41.32 18.37 − 35.12 Codariocalyx motorius 24.38 − 38.17 Bituminaria bituminosa 12.44 − 26.35 Glycine max 19.81 − 32.85 43.39 − 55.95 Phaseolus vulgaris 7.91 − 21.92 Vigna radiata M2 Lotus japonicus 38.53 − 51.71 Glycyrrhiza lepidota 33.59 − 46.42 Astragalus membranaceus 28.84 − 41.49 Cicer arietinum Medicago truncatula 20.66 − 32.83 9.76 − 23.10 Trifolium pratense 15.90 − 27.58 Lathyrus sativus 4.74 − 12.41 Pisum sativum 7.79 − 15.71 Lens culinaris 5.69 − 13.57 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S11. Chronogram estimated under the UCLN clock model, with alternative prior 2. Numbers behind nodes indicate 95% HPD intervals. Substitution rate is indicated by colored branches, as indicated by the color legend, in substitutions per site per million years. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.0027 − 124.70 Papaver somniferum Nelumbo nucifera 26125.69 − 127.40 Amaranthus hypochondriacus 113.93 − 118.20 48 Primula veris 125.02 − 126.00 38 104.57 − 109.28 Lactuca sativa 97.77 − 102.94 Mimulus guttatus 81.09 − 87.43 122.65 − 124.71 Solanum tuberosum Vitis vinifera Paeonia lactiflora 121.59 − 124.51 94 Eucalyptus grandis 83.60 − 85.34 Punica granatum

120.95 − 124.39 Citrus sinensis 95.42 − 99.92105 Carica papaya 89.80 − 92.46 Gossypium raimondii 43.36 − 49.13 102.35 − 107.02 Theobroma cacao 113.45 − 117.94 Elaeocarpus photiniifolia 97.52 − 103.88 Tripterygium wilfordii 96.07 − 101.93 Manihot esculenta 74.68 − 83.77 133 Populus trichocarpa 37.81 − 62.95 Salix purpurea 110.59 − 115.11 Cucumis sativus 116 Cannabis sativa 100.19 − 105.08 66.00 − 67.78 Morus notabilis 92.75 − 97.58 Fragaria vesca 61.42 − 67.66 112 Prunus persica 105.96 − 110.50 Castanea mollissima X14 75.24 − 80.61 Alnus serrulata 64.40 − 67.68 122 Juglans regia Quillaja saponaria 102.16 − 106.93 Bauhinia tomentosa 39.39 − 46.54 C Cercis canadensis 68.43 − 75.21 Afzelia bella 96.60 − 103.85 26.09 − 30.73 Anthonotha fragrans G 31.60 − 36.11 F Copaifera officinalis 26.42 − 30.67 Prioria balsamifera

73.98 − 80.72 A Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos 56.21Z − 63.37 12.34 − 21.77 Gymnocladus dioicus

48.24 − 55.39 Chamaecrista fasciculata 70.31 − 76.95 27.40 − 36.95 Senna hebecarpa 47.25 − 53.69 Entada abyssinica 44.58 − 50.33 Prosopis alba 41.77 − 48.09 Q Desmanthus illinoensis 68.26 − 74.78 39.51 − 45.74 Microlobius foetidus 35.98 − 41.05 Q2 Acacia koa 23.00 − 24.55 Albizia julibrissin 20.39 − 23.22 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 20.93 − 27.50 49.10 − 54.36 I2 Styphnolobium japonicum Arachis ipaensis 35.02 − 40.10 Lupinus angustifolius 45.66 − 50.59 10.55 − 15.85 Lupinus polyphyllus Apios americana Cajanus cajan 40.83 − 45.42 24.08 − 29.23 20.57 − 25.84 Codariocalyx motorius 23.05 − 28.16 Bituminaria bituminosa 15.76 − 19.93 Glycine max 20.30 − 24.99 36.76 − 40.95 Phaseolus vulgaris 9.25 − 12.55 Vigna radiata M2 Lotus japonicus 33.90 − 36.97 Glycyrrhiza lepidota 24.55 − 28.48 Astragalus membranaceus 21.26 − 24.85 Cicer arietinum Medicago truncatula 15.36 − 18.19 9.67 − 11.91 Trifolium pratense 11.72 − 14.08 Lathyrus sativus 3.03 − 4.41 Pisum sativum 4.00 − 5.94 Lens culinaris 3.40 − 5.40 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S12. Chronogram estimated under the RLC model. Numbers behind nodes indicate 95% HPD intervals. Substitution rate is indicated by colored branches, as indicated by the color legend, in substitutions per site per million years. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.0027 − 117.93 Papaver somniferum Nelumbo nucifera 26129.54 − 132.43 Amaranthus hypochondriacus 108.45 − 112.73 48 Primula veris 125.79 − 126.00 38 98.96 − 103.63 Lactuca sativa 92.03 − 97.02 Mimulus guttatus 73.83 − 79.84 118.09 − 120.13 Solanum tuberosum Vitis vinifera Paeonia lactiflora 116.37 − 118.58 94 Eucalyptus grandis 83.60 − 85.56 Punica granatum

115.64 − 118.01 Citrus sinensis 95.86 − 99.32105 Carica papaya 89.80 − 92.09 Gossypium raimondii 40.47 − 44.68 102.93 − 105.90 Theobroma cacao 111.78 − 114.08 Elaeocarpus photiniifolia 98.79 − 103.50 Tripterygium wilfordii 97.49 − 101.58 Manihot esculenta 79.88 − 84.33 133 Populus trichocarpa 37.80 − 37.98 Salix purpurea 109.93 − 112.23 Cucumis sativus 116 Cannabis sativa 101.52 − 104.67 66.00 − 67.83 Morus notabilis 93.93 − 97.69 Fragaria vesca 58.59 − 64.00 112 Prunus persica 106.37 − 108.94 Castanea mollissima X14 72.84 − 76.81 Alnus serrulata 64.40 − 65.06 122 Juglans regia Quillaja saponaria 102.22 − 105.34 Bauhinia tomentosa 36.00 − 36.86 C Cercis canadensis 60.81 − 64.20 Afzelia bella 80.83 − 85.21 21.89 − 25.02 Anthonotha fragrans G 27.73 − 30.60 F Copaifera officinalis 23.37 − 26.39 Prioria balsamifera

65.91A − 68.74 Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos Z 56.00 − 58.97 10.89 − 19.55 Gymnocladus dioicus

52.41 − 55.55 Chamaecrista fasciculata 63.77 − 66.52 29.93 − 38.23 Senna hebecarpa 48.63 − 52.11 Entada abyssinica 38.63 − 40.86 Prosopis alba Q33.90 − 34.35 Desmanthus illinoensis 62.74 − 65.43 30.29 − 32.99 Microlobius foetidus 28.18 − 29.85Q2 Acacia koa 23.00 − 23.13 Albizia julibrissin 17.59 − 20.63 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 14.92 − 19.46 47.37 − 50.04 I2 Styphnolobium japonicum Arachis ipaensis 33.44 − 36.29 Lupinus angustifolius 42.27 − 44.28 10.40 − 15.05 Lupinus polyphyllus Apios americana Cajanus cajan 38.91 − 40.62 21.07 − 22.85 18.11− 20.10 Codariocalyx motorius 20.45 − 22.16 Bituminaria bituminosa 13.33 − 15.23 Glycine max 18.11 − 19.80 35.69 − 36.85 Phaseolus vulgaris 9.44 − 10.88 Vigna radiata M2 Lotus japonicus 33.90 − 34.17 Glycyrrhiza lepidota 28.19 − 29.85 Astragalus membranaceus 25.09 − 26.85 Cicer arietinum Medicago truncatula 18.76 − 20.36 12.82 − 14.67 Trifolium pratense 15.32 − 16.86 Lathyrus sativus 4.74 − 6.03 Pisum sativum 6.68 − 7.92 Lens culinaris 5.85 − 7.27 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S13. Chronogram estimated under the FLC3 model. Numbers behind nodes indicate 95% HPD intervals. Clock partitions are indicated by colored branches. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.1527 − 119.86 Papaver somniferum Nelumbo nucifera 26130.15 − 133.32 Amaranthus hypochondriacus 108.05 − 112.40 48 Primula veris 125.77 − 126.00 38 98.63 − 103.27 Lactuca sativa 91.62 − 96.66 Mimulus guttatus 73.76 − 79.62 117.70 − 119.85 Solanum tuberosum Vitis vinifera Paeonia lactiflora 116.02 − 118.27 94 Eucalyptus grandis 83.60 − 85.46 Punica granatum

115.31 − 117.73 Citrus sinensis 95.50 − 98.82105 Carica papaya 89.80 − 91.63 Gossypium raimondii 39.90 − 44.14 102.19 − 105.19 Theobroma cacao 111.17 − 113.52 Elaeocarpus photiniifolia 98.08 − 102.77 Tripterygium wilfordii 96.72 − 100.85 Manihot esculenta 79.10 − 83.63 133 Populus trichocarpa 37.80 − 37.98 Salix purpurea 109.19 − 111.61 Cucumis sativus 116 Cannabis sativa 100.75 − 104.02 66.00 − 67.57 Morus notabilis 93.31 − 97.11 Fragaria vesca 57.94 − 63.52 112 Prunus persica 105.67 − 108.36 Castanea mollissima X14 72.57 − 76.43 Alnus serrulata 64.40 − 65.13 122 Juglans regia Quillaja saponaria 101.52 − 104.70 Bauhinia tomentosa 36.00 − 36.88 C Cercis canadensis 60.68 − 64.39 Afzelia bella 80.31 − 84.71 21.82 − 25.35 Anthonotha fragrans G 27.61 − 30.89 F Copaifera officinalis 23.35 − 26.66 Prioria balsamifera

65.78A − 68.79 Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos Z 56.09 − 59.22 10.81 − 19.45 Gymnocladus dioicus

52.46 − 55.71 Chamaecrista fasciculata 63.69 − 66.60 29.97 − 38.34 Senna hebecarpa 48.93 − 52.53 Entada abyssinica 38.84 − 41.20 Prosopis alba Q33.90 − 34.41 Desmanthus illinoensis 62.60 − 65.45 30.48 − 33.13 Microlobius foetidus 28.38 − 30.08Q2 Acacia koa 23.00 − 23.12 Albizia julibrissin 17.84 − 20.88 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 14.64 − 19.06 47.22 − 49.86 I2 Styphnolobium japonicum Arachis ipaensis 33.39 − 36.24 Lupinus angustifolius 42.16 − 44.17 10.33 − 15.04 Lupinus polyphyllus Apios americana Cajanus cajan 38.92 − 40.63 21.08 − 22.77 18.09 − 20.06 Codariocalyx motorius 20.42 − 22.09 Bituminaria bituminosa 13.33 − 15.19 Glycine max 18.12 − 19.79 35.64 − 36.81 Phaseolus vulgaris 9.38 − 10.85 Vigna radiata M2 Lotus japonicus 33.90 − 34.16 Glycyrrhiza lepidota 28.21 − 29.88 Astragalus membranaceus 25.11 − 26.82 Cicer arietinum Medicago truncatula 18.79 − 20.35 12.86 − 14.70 Trifolium pratense 15.31 − 16.81 Lathyrus sativus 4.75 − 6.05 Pisum sativum 6.63 − 7.86 Lens culinaris 5.85 − 7.25 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S14. Chronogram estimated under the FLC6 model. Numbers behind nodes indicate 95% HPD intervals. Cock partitions are indicated by colored branches. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.3627 − 120.20 Papaver somniferum Nelumbo nucifera 26130.04 − 133.26 Amaranthus hypochondriacus 108.05 − 112.31 48 Primula veris 125.78 − 126.00 38 98.59 − 103.24 Lactuca sativa 91.53 − 96.56 Mimulus guttatus 73.69 − 79.48 117.52 − 119.67 Solanum tuberosum Vitis vinifera Paeonia lactiflora 115.81 − 118.10 94 Eucalyptus grandis 83.60 − 85.43 Punica granatum

115.10 − 117.52 Citrus sinensis 95.34 − 98.62105 Carica papaya 89.80 − 91.53 Gossypium raimondii 39.94 − 44.24 102.02 − 105.00 Theobroma cacao 110.97 − 113.37 Elaeocarpus photiniifolia 97.87 − 102.58 Tripterygium wilfordii 96.53 − 100.59 Manihot esculenta 79.13 − 83.49 133 Populus trichocarpa 37.80 − 37.99 Salix purpurea 108.99 − 111.40 Cucumis sativus 116 Cannabis sativa 100.43 − 103.70 66.00 − 67.45 Morus notabilis 93.03 − 96.77 Fragaria vesca 57.93 − 63.43 112 Prunus persica 105.33 − 108.01 Castanea mollissima X14 72.34 − 76.22 Alnus serrulata 64.40 − 65.09 122 Juglans regia Quillaja saponaria 101.21 − 104.40 Bauhinia tomentosa 36.00 − 52.93 C Cercis canadensis 59.73 − 64.69 Afzelia bella 79.56 − 84.07 20.83 − 39.75 Anthonotha fragrans G 26.47 − 49.60 F Copaifera officinalis 22.52 − 41.94 Prioria balsamifera

64.64A − 67.77 Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos Z 55.48 − 58.53 10.73 − 19.35 Gymnocladus dioicus

51.95 − 55.12 Chamaecrista fasciculata 62.71 − 65.66 29.76 − 38.00 Senna hebecarpa 48.49 − 51.96 Entada abyssinica 38.66 − 41.00 Prosopis alba Q33.90 − 34.39 Desmanthus illinoensis 61.79 − 64.65 30.40 − 33.09 Microlobius foetidus 28.30 − 29.99Q2 Acacia koa 23.00 − 23.13 Albizia julibrissin 17.81 − 20.80 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 14.72 − 19.18 46.94 − 49.57 I2 Styphnolobium japonicum Arachis ipaensis 33.30 − 36.19 Lupinus angustifolius 42.05 − 44.05 10.22 − 14.90 Lupinus polyphyllus Apios americana Cajanus cajan 38.84 − 40.53 21.06 − 22.82 18.02 − 19.98 Codariocalyx motorius 20.40 − 22.11 Bituminaria bituminosa 13.30 − 15.17 Glycine max 18.06 − 19.74 35.63 − 36.78 Phaseolus vulgaris 9.40 − 10.84 Vigna radiata M2 Lotus japonicus 33.90 − 34.16 Glycyrrhiza lepidota 28.16 − 29.80 Astragalus membranaceus 25.08 − 26.81 Cicer arietinum Medicago truncatula 18.76 − 20.35 12.79 − 14.67 Trifolium pratense 15.30 − 16.82 Lathyrus sativus 4.75 − 6.04 Pisum sativum 6.65 − 7.87 Lens culinaris 5.82 − 7.26 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S15. Chronogram estimated under the FLC8 model. Numbers behind nodes indicate 95% HPD intervals. Cock partitions are indicated by colored branches. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. Aquilegia coerulea 113.1527 − 120.03 Papaver somniferum Nelumbo nucifera 26130.06 − 133.31 Amaranthus hypochondriacus 108.10 − 112.43 48 Primula veris 125.77 − 126.00 38 98.59 − 103.26 Lactuca sativa 91.60 − 96.64 Mimulus guttatus 73.76 − 79.67 117.64 − 119.77 Solanum tuberosum Vitis vinifera Paeonia lactiflora 115.95 − 118.20 94 Eucalyptus grandis 83.60 − 85.38 Punica granatum

115.19 − 117.59 Citrus sinensis 95.33 − 98.65105 Carica papaya 89.80 − 91.66 Gossypium raimondii 39.92 − 44.23 102.10 − 105.08 Theobroma cacao 111.07 − 113.42 Elaeocarpus photiniifolia 97.91− 102.63 Tripterygium wilfordii 96.55 − 100.63 Manihot esculenta 79.09 − 83.57 133 Populus trichocarpa 37.80 − 37.97 Salix purpurea 109.10 − 111.48 Cucumis sativus 116 Cannabis sativa 100.59 − 103.84 66.00 − 67.51 Morus notabilis 93.07 − 96.82 Fragaria vesca 57.93 − 63.39 112 Prunus persica 105.43 − 108.13 Castanea mollissima X14 72.39 − 76.33 Alnus serrulata 64.40 − 65.09 122 Juglans regia Quillaja saponaria 101.27 − 104.49 C& Bauhinia tomentosa 57.63 − 63.97 Cercis canadensis 63.85 − 67.22 Afzelia bella 79.59 − 84.08 H&46.00 − 50.84 Anthonotha fragrans 55.40 − 63.19 F Copaifera officinalis G& 46.36 − 54.47 Prioria balsamifera

64.87A − 68.17 Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos Z 55.65 − 58.77 10.67 − 19.28 Gymnocladus dioicus

52.07 − 55.35 Chamaecrista fasciculata 63.01 − 66.02 29.78 − 38.09 Senna hebecarpa 48.53 − 52.08 Entada abyssinica 38.68 − 41.05 Prosopis alba Q33.90 − 34.40 Desmanthus illinoensis 61.98 − 64.89 30.40 − 33.09 Microlobius foetidus 28.31 − 30.02Q2 Acacia koa 23.00 − 23.12 Albizia julibrissin 17.86 − 20.83 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 14.70 − 19.10 47.01 − 49.67 I2 Styphnolobium japonicum Arachis ipaensis 33.37 − 36.24 Lupinus angustifolius 42.08 − 44.08 10.28 − 14.92 Lupinus polyphyllus Apios americana Cajanus cajan 38.82 − 40.53 21.04 − 22.75 18.11 − 20.06 Codariocalyx motorius 20.41 − 22.07 Bituminaria bituminosa 13.30 − 15.15 Glycine max 18.11 − 19.75 35.66 − 36.80 Phaseolus vulgaris 9.44 − 10.88 Vigna radiata M2 Lotus japonicus 33.90 − 34.16 Glycyrrhiza lepidota 28.19 − 29.85 Astragalus membranaceus 25.07 − 26.82 Cicer arietinum Medicago truncatula 18.75 − 20.34 12.85 − 14.72 Trifolium pratense 15.32 − 16.82 Lathyrus sativus 4.75 − 6.06 Pisum sativum 6.64 − 7.86 Lens culinaris 5.80 − 7.23 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S16. Chronogram estimated under the FLC8 model, with alternative prior 1. Numbers behind nodes indicate 95% HPD intervals. Clock partitions are indicated by colored branches. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles, with alternative calibrations as red circles. Aquilegia coerulea 27113.00 − 114.75 Papaver somniferum Nelumbo nucifera 26128.29 − 130.82 Amaranthus hypochondriacus 116.66 − 119.25 48 Primula veris 125.85 − 126.00 38 109.94 − 113.14 Lactuca sativa 104.15 − 107.94 Mimulus guttatus 86.47 − 91.95 120.90 − 122.45 Solanum tuberosum Vitis vinifera Paeonia lactiflora 115.95 − 118.42 94 Eucalyptus grandis 83.60 − 84.94 Punica granatum

114.82 − 117.57 Citrus sinensis 93.79 −105 96.68 Carica papaya 89.80 − 90.59 Gossypium raimondii 38.16 − 42.11 99.98 − 102.82 Theobroma cacao 110.02 − 112.48 Elaeocarpus photiniifolia 95.40 − 100.16 Tripterygium wilfordii 94.11 − 98.20 Manihot esculenta 76.83 − 81.03 133 Populus trichocarpa 37.80 − 38.01 Salix purpurea 107.64 − 110.03 Cucumis sativus 116 Cannabis sativa 98.54 − 101.78 66.00 − 66.78 Morus notabilis 90.89 − 94.57 Fragaria vesca 55.42 − 60.68112 Prunus persica 103.59 − 106.22 Castanea mollissima X14 70.95 − 74.56 Alnus serrulata 64.40 − 64.86 122 Juglans regia Quillaja saponaria 99.70 − 102.76 Bauhinia tomentosa 36.00 − 36.66 C Cercis canadensis 60.45 − 63.87 Afzelia bella 79.68 − 83.77 20.40 − 23.30 Anthonotha fragrans G 26.25 − 28.71 F Copaifera officinalis 22.50 − 24.51 Prioria balsamifera

66.94 −A 69.55 Zenia insignis Acrocarpus fraxinifolius Gleditsia triacanthos Z 56.01 − 59.12 10.34 − 18.60 Gymnocladus dioicus

51.96− 55.26 Chamaecrista fasciculata 65.60 − 68.22 29.01 − 37.32 Senna hebecarpa 48.16 − 51.77 Entada abyssinica 38.03 − 40.21 Prosopis alba Q33.90 − 34.28 Desmanthus illinoensis 64.90 − 67.48 29.75 − 32.62 Microlobius foetidus 27.81 − 29.42Q2 Acacia koa 23.00 − 23.11 Albizia julibrissin 16.63 − 19.74 Inga spectabilis Xanthocercis zambesiaca Cladrastis lutea 14.98 − 19.72 56.89 − 59.47 I2 Styphnolobium japonicum Arachis ipaensis 45.27 − 48.85 Lupinus angustifolius 54.10 − 56.56 14.82 − 21.20 Lupinus polyphyllus Apios americana Cajanus cajan 51.63 − 54.03 32.61 − 34.93 28.21 − 30.93 Codariocalyx motorius 31.59 − 33.85 Bituminaria bituminosa 21.15 − 23.91 Glycine max 28.32 − 30.60 48.19 − 50.50 Phaseolus vulgaris 14.97 − 17.16 Vigna radiata M2 Lotus japonicus 44.92 − 47.34 Glycyrrhiza lepidota 40.27 − 42.71 Astragalus membranaceus 36.49 − 38.93 Cicer arietinum Medicago truncatula 28.32 − 30.53 19.77 − 22.50 Trifolium pratense 23.41 − 25.60 Lathyrus sativus 7.67 − 9.66 Pisum sativum 10.53 − 12.36 Lens culinaris 9.24 − 11.40 Vicia faba Lower Upper Eocene Miocene Pliocene Oligocene Paleocene

Cretaceous Paleogene Neogene 0 90 80 70 60 50 40 30 20 10 140 130 120 110 100

Figure S17. Chronogram estimated under the STRC model. Numbers behind nodes indicate 95% HPD intervals. Fossil calibrations as listed in Table 1 are indicated by blue labeled circles. .1 0.015 0.010 subst/site/My .0 0.005 0.000

bg50kb-inv asterids cerc detar mimcass rosids cercdetar mean A clock partition .1 0.015 0.010 subst/site/My .0 0.005 0.000

bg 50kb-inv asterids cerc detar mimcass rosids cercdetar mean B clock partition

Figure S18. Substitution rates as estimated in FLC8 analyses for the different clock partitions. Boxplots for each partition for (A) alternative prior 1 and (B) the “normal” prior setting. Colors correspond to the partitions as shown in Figs 5, S14, S15 and S18. x 0.35 x x

x Root − to tip length (substitutions/site) .001 .002 0.30 0.25 0.20 0.15 0.10 Vicia faba Vicia Acacia koa Acacia Vitis vinifera Afzelia bella Afzelia Glycine max Primula veris Primula Vigna radiata Vigna Juglans regia Juglans Prosopis alba Prosopis Zenia insignis Zenia Lens culinaris Polygala lutea Polygala Cajanus cajan Cajanus Lactuca sativa Carica papaya Carica Salix purpurea Salix Citrus sinensis Pisum sativum Pisum Fragaria vesca Fragaria Panax ginseng Panax Prunus persica Prunus serrulata Alnus Morus notabilis Morus Cicer arietinum Cicer Inga spectabilis lutea Cladrastis Lotus japonicus Cannabis sativa Cannabis Lathyrus sativus Lathyrus Cucumis sativus Cucumis Arachis ipaensis Arachis Albizia julibrissin Albizia Apios americana Apios Mimulus guttatus Mimulus Punica granatum Punica Paeonia lactiflora Paeonia Nelumbo nucifera Nelumbo Senna hebecarpa Senna Trifolium pratense Trifolium Quillaja saponaria Quillaja Theobroma cacao Theobroma Manihot esculenta Manihot Entada abyssinica Entada Cercis canadensis Cercis Prioria balsamifera Prioria Phaseolus vulgaris Phaseolus Eucalyptus grandis Eucalyptus Copaifera officinalis Copaifera Lupinus polyphyllus Lupinus Glycyrrhiza lepidota Glycyrrhiza Microlobius foetidus Microlobius Populus trichocarpa Populus Bauhinia tomentosa Bauhinia Solanum tuberosum Solanum Medicago truncatula Medicago Arabidopsis thaliana Arabidopsis Linum usitatissimum Linum Gleditsia triacanthos Gleditsia Anthonotha fragrans Anthonotha Tripterygium wilfordii Tripterygium Castanea mollissima Castanea Gossypium raimondii Gossypium Lupinus angustifolius Lupinus Gymnocladus dioicus Gymnocladus Codariocalyx motorius Codariocalyx Bituminaria bituminosa Bituminaria Desmanthus illinoensis Desmanthus Acrocarpus fraxinifolius Acrocarpus Elaeocarpus photiniifolia Elaeocarpus Chamaecrista fasciculata Chamaecrista Xanthocercis zambesiaca Xanthocercis Styphnolobium japonicum Styphnolobium Astragalus membranaceus Astragalus Amaranthus hypochondriacus Amaranthus A Taxon

x 0.35 x x

x Root − to tip length (substitutions/site) .001 .002 0.30 0.25 0.20 0.15 0.10 Vicia faba Vicia Acacia koa Acacia Vitis vinifera Afzelia bella Afzelia Glycine max Primula veris Primula Vigna radiata Vigna Juglans regia Juglans Prosopis alba Prosopis Zenia insignis Zenia Lens culinaris Polygala lutea Polygala Cajanus cajan Cajanus Lactuca sativa Carica papaya Carica Salix purpurea Salix Citrus sinensis Pisum sativum Pisum Fragaria vesca Fragaria Panax ginseng Panax Prunus persica Prunus serrulata Alnus Morus notabilis Morus Cicer arietinum Cicer Inga spectabilis Cladrastis lutea Cladrastis Lotus japonicus Cannabis sativa Cannabis Lathyrus sativus Lathyrus Cucumis sativus Cucumis Arachis ipaensis Arachis Albizia julibrissin Albizia Apios americana Apios Mimulus guttatus Mimulus Punica granatum Punica Paeonia lactiflora Paeonia Nelumbo nucifera Nelumbo Senna hebecarpa Senna Trifolium pratense Trifolium Quillaja saponaria Quillaja Theobroma cacao Theobroma Manihot esculenta Manihot Entada abyssinica Entada Cercis canadensis Cercis Prioria balsamifera Prioria Phaseolus vulgaris Phaseolus Eucalyptus grandis Eucalyptus Copaifera officinalis Copaifera Lupinus polyphyllus Lupinus Glycyrrhiza lepidota Glycyrrhiza Microlobius foetidus Microlobius Populus trichocarpa Populus Bauhinia tomentosa Bauhinia Solanum tuberosum Solanum Medicago truncatula Medicago Arabidopsis thaliana Arabidopsis Linum usitatissimum Linum Gleditsia triacanthos Gleditsia Anthonotha fragrans Anthonotha Tripterygium wilfordii Tripterygium Castanea mollissima Castanea Gossypium raimondii Gossypium Lupinus angustifolius Lupinus Gymnocladus dioicus Gymnocladus Codariocalyx motorius Codariocalyx Bituminaria bituminosa Bituminaria Desmanthus illinoensis Desmanthus Acrocarpus fraxinifolius Acrocarpus Elaeocarpus photiniifolia Elaeocarpus Chamaecrista fasciculata Chamaecrista Xanthocercis zambesiaca Xanthocercis Styphnolobium japonicum Styphnolobium Astragalus membranaceus Astragalus Amaranthus hypochondriacus Amaranthus B Taxon

x 0.35 x x

x Root − to tip length (substitutions/site) .001 .002 0.30 0.25 0.20 0.15 0.10 Vicia faba Vicia Acacia koa Acacia Vitis vinifera Afzelia bella Afzelia Glycine max Primula veris Primula Vigna radiata Vigna Juglans regia Juglans Prosopis alba Prosopis Zenia insignis Zenia Lens culinaris Polygala lutea Polygala Cajanus cajan Cajanus Lactuca sativa Carica papaya Carica Salix purpurea Salix Citrus sinensis Pisum sativum Pisum Fragaria vesca Fragaria Panax ginseng Panax Prunus persica Prunus serrulata Alnus Morus notabilis Morus Cicer arietinum Cicer Inga spectabilis Cladrastis lutea Cladrastis Lotus japonicus Cannabis sativa Cannabis Lathyrus sativus Lathyrus Cucumis sativus Cucumis Arachis ipaensis Arachis Albizia julibrissin Albizia Apios americana Apios Mimulus guttatus Mimulus Punica granatum Punica Paeonia lactiflora Paeonia Nelumbo nucifera Nelumbo Senna hebecarpa Senna Trifolium pratense Trifolium Quillaja saponaria Quillaja Theobroma cacao Theobroma Manihot esculenta Manihot Entada abyssinica Entada Cercis canadensis Cercis Prioria balsamifera Prioria Phaseolus vulgaris Phaseolus Eucalyptus grandis Eucalyptus Copaifera officinalis Copaifera Lupinus polyphyllus Lupinus Glycyrrhiza lepidota Glycyrrhiza Microlobius foetidus Microlobius Populus trichocarpa Populus Bauhinia tomentosa Bauhinia Solanum tuberosum Solanum Medicago truncatula Medicago Arabidopsis thaliana Arabidopsis Linum usitatissimum Linum Gleditsia triacanthos Gleditsia Anthonotha fragrans Anthonotha Tripterygium wilfordii Tripterygium Castanea mollissima Castanea Gossypium raimondii Gossypium Lupinus angustifolius Lupinus Gymnocladus dioicus Gymnocladus Codariocalyx motorius Codariocalyx Bituminaria bituminosa Bituminaria Desmanthus illinoensis Desmanthus Acrocarpus fraxinifolius Acrocarpus Elaeocarpus photiniifolia Elaeocarpus Chamaecrista fasciculata Chamaecrista Xanthocercis zambesiaca Xanthocercis Styphnolobium japonicum Styphnolobium Astragalus membranaceus Astragalus

C hypochondriacus Amaranthus Taxon

Figure S19. Root-to-tip lengths per taxon with partitions of fixed local clocks indicated. Pruned taxa with outlier root-to-tip lengths are indicated with an X, partitions are indicated with colors. (A) FLC3, (B) FLC6, (C) FLC8.