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Home , Acacia anceps, Acacia cochlearis, Acacia cultriformis, Acacia cupularis, Acacia deanei, Acacia dorothea

10.1071/BT13149_AC

© CSIRO 2013

Australian Journal of 2013, 61(6), 436–445

SUPPLEMENTARY MATERIAL

Comparative dating of : combining fossils and multiple phylogenies to infer ages of clades with poor fossil records

Joseph T. MillerA,E, Daniel J. MurphyB, Simon Y. W. HoC, David J. CantrillB and David SeiglerD

ACentre for Australian National Biodiversity Research, CSIRO Industry, GPO Box 1600 Canberra, ACT 2601, .

BRoyal Botanic Gardens Melbourne, Birdwood Avenue, South Yarra, Vic. 3141, Australia.

CSchool of Biological Sciences, Edgeworth David Building, University of Sydney, Sydney, NSW 2006, Australia.

DDepartment of Plant Biology, University of Illinois, Urbana, IL 61801, USA.

ECorresponding author. Email: [email protected]

Table S1 Materials used in the study

Taxon Dataset Genbank Acacia abbreviata Maslin 2 3 JF420287 JF420065 JF420395 KC421289 KC796176 JF420499 Acacia adoxa Pedley 2 3 JF420044 AF523076 AF195716 AF195684; AF195703 Acacia ampliceps Maslin 1 KC421930 EU439994 EU811845 DC. 2 3 JF420244 JF420350 JF419919 JF420130 JF420456 Acacia aneura F.Muell. ex Benth 2 3 JF420259 JF420036 JF420366 JF419935 JF420146 KF048140 Acacia aneura F.Muell. ex Benth. 1 2 3 JF420293 JF420402 KC421323 JQ248740 JF420505 Acacia baeuerlenii Maiden & R.T.Baker 2 3 JF420229 JQ248866 JF420336 JF419909 JF420115 JF420448 Acacia beckleri Tindale 2 3 JF420260 JF420037 JF420367 JF419936 JF420147 JF420473 (Labill.) H.L.Wendl. 2 3 KC283897 KC200719 JQ943314 AF523156 KC284140 KC957934 Acacia cognata Domin 2 3 JF420246 JF420022 JF420352 JF419921 JF420132 JF420458 A.Cunn. ex G.Don 2 3 JF420278 JF420056 JF420387 KC421263 KC796172 JF420494 Domin 2 3 JF420247 JF420023 JF420353 JF419922 JF420133 JF420459 Acacia dealbata Link 2 3 JF420269 JF420378 KC421251 KC955787 JF420485 Acacia dealbata Link 2 3 KC283375 KC200761 JQ942686 KC421315 KC284195 Acacia deanei (R.T.Baker) M.B.Welch, Coombs 2 3 JF420294 JF420403 KC421329 KC955795 & McGlynn JF420506 Acacia dempsteri F.Muell. 2 3 JF420261 JF420038 KF048760 KC957123 KC955784 JF420474 Acacia dorothea Maiden 2 3 JF420232 JF420339 KC421348 KC796182 JF420450 Acacia dunnii (Maiden) Turrill 2 3 KC283351 KC200800 JQ942655 KC421282 KC284236 KC958085 Acacia epacantha (Maslin) Maslin 2 3 JF420040 JF420369 JF419939 JF420150 JF420476 Acacia euthycarpa (J.M.Black) J.M.Black 2 3 JF420282 JF420060 JF420391 KC421268 KC796174 JF420498 Acacia extensa Lindl. 2 3 JF420281 KF048784 JF420390 KC421267 KC796173 JF420497 Acacia falcata Willd. 2 3 JF420233 JQ248877 JF420340 JQ248696 JQ248759 JF420451 Acacia flexifolia A.Cunn. ex Benth. 2 3 JF420234 JQ248879 JF420341 JQ248697 JQ248761 JF420452 Acacia floribunda (Vent.) Willd. 2 3 JF420235 JQ248880 JF420342 JQ248698 JQ248762 JF420453 Acacia glaucissima Maslin 2 3 KC283357 KC200836 JQ942665 KC421293 KC284282 KC958089 Acacia gonoclada F.Muell. 2 3 JF420280 JF420058 JF420389 KC421266 KC955793 JF420496 Acacia guinetii Maslin 2 3 JF420397 KC421309 KC796177 JF420500 Acacia hakeoides A.Cunn. ex Benth. 2 3 KC283271 KC200594 JF420349 JF419918 JF420129 JF420455 Acacia hakeoides A.Cunn. ex Benth. 2 3 JF420250 JF420026 JF420356 JF419925 JF420136 JF420462 Acacia hakeoides A.Cunn. ex Benth. 2 3 JF420228 JQ248882 JF420335 JQ248701 JQ248765 JF420447 Acacia halliana Maslin 2 3 KC283279 KC200849 JQ942541 KC421209 KC284300 KC957988 Acacia heteroclita Meisn. 2 3 JF420275 KF048782 JF420384 KC421254 KC796170 JF420491 Acacia latipes Benth. 2 3 KC283362 KC200904 JQ942669 KC421297 KC284357 KC958091 Acacia leioderma Maslin 2 3 JF420286 JF420064 JF420394 KC421288 KC796175 Acacia ligulata A.Cunn. ex Benth. 2 3 JF420028 JF420358 JF419927 JF420138 JF420464 Acacia linifolia (Vent.) Willd. 2 3 JF420264 JF420043 JF420373 JF419942 JF420153 JF420479 De Wild. 2 3 KC283312 JF420379 KC421252 JF420160 KC958038 Acacia mearnsii De Wild. 2 3 JF420284 KF048786 JF420393 KC421286 JF420174 Acacia meisneri Lehm. ex Meisn 2 3 JF420271 JF420049 JF420380 JF420161 KC958044 R.Br. 2 3 JF420314 JF420093 JF420425 KF048618 KC796190 JF420527 Acacia montana Benth. 2 3 JF420297 JF420406 KC421340 JF420186 KC958128 Acacia muelleriana Maiden & R.T.Baker 2 3 JF420252 JF420029 JF420359 KF048604 JF420139 JF420465 Acacia multispicata Benth. 2 3 JF420253 JF420030 JF420360 KF048605 JF420140 JF420466 F.Muell. ex Benth. 2 3 JF420317 JF420095 JF420429 KF048620 KC955806 JF420531 Acacia neriifolia A.Cunn. ex Benth. 2 3 JF420291 JF420400 KC421320 JF420181 KC958108 Acacia pachyacra Maiden & Blakely 2 3 JF420306 KF048791 JF420417 KF048616 KC796186 JF420520 Acacia penninervis Sieber ex DC. 2 3 JF420239 JF420018 JF420385 KF048603 JF420125 Acacia penninervis Sieber ex DC. 2 3 KC283336 KC201005 JQ942636 KC421259 KC284508 Acacia pentadenia Lindl. 2 3 JF420288 JF420066 JF420396 KC421302 JF420178 Acacia perryi Pedley 2 3 JF420274 JF420052 JF420383 JF420164 KC958054 Acacia platycarpa F.Muell. 2 3 JN006090 JN006101 JN006112 JN006121 JN006132 Acacia pravifolia F.Muell. 2 3 JF420230 JF420116 JF420337 KC421347 KC958135 F.Muell. ex Benth. 2 3 JF420255 JF420032 JF420362 KF048607 JF420142 JF420468 Benth. 2 3 JF420273 JF420051 JF420382 JF420163 KC958048 DC. 2 3 JF420238 JF420017 JF420345 KF048602 JF420124 Benth. 2 3 JF420272 JF420050 JF420381 JF420162 KC958046 Acacia saligna (Labill.) H.L.Wendl. 2 3 KC283494 KC201067 JQ942906 KC955805 JF420529 Acacia spectabilis A.Cunn. ex Benth. 2 3 JF420256 JF420033 JF420363 KF048608 JF420143 JF420469 Acacia suaveolens (Sm.) Willd. 2 3 JF420266 JF420046 JF420375 KC421243 JF420156 KC958028 Acacia subrigida Maslin 2 3 JF420307 JF420086 JF420418 KF048617 KC796187 JF420521 Acacia tetragonophylla F.Muell. 2 3 KC283921 KC201123 KC956407 KC421961 KC284666 KC957963 Acacia tetragonophylla F.Muell. 2 3 KC283334 KC201122 JQ942634 KC421257 KC284665 KC958066 Acacia triptera Benth. 2 3 JF420227 JF420334 KC421327 KC796180 KC958117 Acacia triquetra Benth. 2 3 JF420257 JF420034 JF420364 KF048609 JF420144 JF420470 Acacia tumida F.Muell. ex Benth. 1 AF522986 Acacia venulosa Benth. 2 3 JF420268 JF420048 JF420377 KC421246 JF420158 KC958032 Acacia victoriae subsp. arida Pedley 2 3 DQ029310 KF048792 JF420419 KC284685 KC958213 Acacia visco Lorentz ex Griseb. 1 EU812059 AF522982 Acaciella angustissima (Mill.) Britton & Rose 1 2 EU812043 EU811979 EU440019 EU811872 var. angustissima Acaciella glauca (L.) L.Rico 1 2 EU812042 EU440018 EU811871 Acaciella tequilana (S.Watson) Britton & Rose 1 2 EU812044 EU811980 EU440020 EU811873 Albizia bermudiana ined. 1 2 EU812001 EU811943 EU439975 EU811826 Albizia harveyi Fourn. 1 2 EU812003 EU811945 EU439977 EU811828 Albizia julibrissin Durazz. 1 2 EU812010 EU811952 EU439984 EU811835 Albizia kalkora Prain 1 2 EU812063 EU811999 EU440040 EU811895 Albizia procera (Roxb.) Benth. 1 2 EU812033 EU811975 EU440009 EU811861 colubrina (Vell.) Brenan 1 2 EU812064 EU812000 EU440041 EU811896 Speg. 1 2 EU812046 EU811982 EU440022 EU811875 Caesalpinia calycina Benth. 1 EU361899 AY899691 Calliandra juzepczukii Standl. 1 2 EU812019 EU811963 EU439995 EU811846 Calliandra longipedicellata (McVaugh) 1 2 EU812004 EU811946 EU439978 EU811829 Macqueen & H.M.Hern. Chloroleucon mangense (Jacq.) Britton & Rose 1 2 EU812060 EU811996 EU440037 EU811892 Chloroleucon sp. 1 2 EU812015 EU811957 EU439989 EU811840 Cojoba filipes (Vent.) Barneby & J.W.Grimes 1 2 EU812031 EU811973 EU440007 EU811859 Desmanthus sp. 1 2 EU812035 EU811976 EU440011 EU811864 Ebenopsis ebano (Berland.) Barneby & 1 2 EU812012 EU811954 EU439986 EU811837 J.W.Grimes Faidherbia albida (Delile) A.Chev. 1 2 EU812008 EU811950 EU439981 EU811833 Faidherbia albida (Delile) A.Chev. 1 2 EU812007 EU811949 EU439982 EU811832 Gledistia_sinensis Lam. 1 2 AY386930 GQ434978 AY899686 Leucaena leucocephala (Lam.) de Wit 2 KF048595 KF048135 Leucaena leucocephala (Lam.) de Wit 1 2 EU812016 EU811958 EU439990 EU811841 Lysiloma tergeminum Benth. 1 2 EU812062 EU811998 EU440039 EU811894 Mariosousa coulteri (Benth.) Seigler & 1 2 EU812057 EU811993 EU440034 EU811889 Ebinger Mariosousa dolichostachya (S. F. Blake) 1 2 EU812056 EU811992 EU440033 EU811888 Seigler & Ebinger Mariosousa millefolia (S.Watson) Seigler & 1 2 EU812058 EU811994 EU440035 EU811890 Ebinger foetida Jacq. 1 2 EU812006 EU811948 EU439980 EU811831 Neptunia monosperma F.Muell. ex Benth. 1 2 EU812005 EU811947 EU439979 EU811830 Pararchidendron pruinosum (Benth.) 1 2 3 JF420304 JF420082 AF274127 EU811953 I.C.Nielsen EU439985 EU811836 Paraserianthes lophantha (Willd.) I.C.Nielsen 1 2 3 JF420331 KF048780 AF274128 EU811978 subsp. lophantha EU440016 EU811869 viridiflora (Kunth) Benth. 1 2 EU812020 EU811964 EU439996 EU811847 Pithecellobium unguis-cati (L.) Benth. 1 2 EU812014 EU811956 EU439988 EU811839 Prosopsis sp. 1 2 EU812013 EU811955 EU439987 EU811838 fructispina 2 EU812018 EU811960 EU439992

Senegalia brevispica ( Harms ) Seigler & 2 EU812037 EU811977 EU440013 EU811866 Ebinger Senegalia galpinii ( Burtt Davy ) Seigler & 1 EU812024 EU440000 EU811851 Ebinger Senegalia gaumeri (Blake) Britton & Rose 1 2 EU812061 EU811997 EU440038 EU811893 Senegalia gilliesii (Steud.) Seigler & Ebinger 1 EU812018 EU439992 EU811843 Senegalia mellifera subsp. detinens (Busch.) 1 2 EU812052 EU811988 EU440029 EU811883 Brenan Senegalia muricata (L.) Britton & Rose 1 2 EU812032 EU811974 EU440008 EU811860 Senegalia occidentalis (Rose) Britton & Rose 1 2 EU812055 EU811991 EU440032 EU811886 Senegalia picachensis (Brandegee) Britton & 1 2 EU812009 EU811951 EU439983 EU811834 Rose Senegalia skleroxyla (Tussac) Seigler & 1 2 EU812030 EU811972 EU440006 EU811858 Ebinger Senegalia sororia (Standl.) Britton & Rose 1 2 EU812017 EU811959 EU439991 EU811842 Senegalia vogeliana Britton & Rose 1 EU812025 EU440001 EU811852 Senna candolleana (Vogel)H.S.Irwin & 1 2 AY386848 EU361834 Barneby Sphinga acatlensis (Benth.) Barneby & 1 2 EU812028 EU811971 EU812048 EU811856 J.W.Grimes Vachelia hockii De Wild. 1 EU812038 EU440014 EU811867 choriophylla (Bentham) Seigler & 1 2 EU812041 EU440017 EU811870 Ebinger Vachellia collinsii (Safford) Seigler & Ebinger 1 2 EU812054 EU811990 EU440031 EU811885 Vachellia constricta (Bentham), Seigler & 1 2 EU812051 EU811987 EU440028 EU811881 Ebinger Vachellia cucuyo (Barneby & Zanoni) Seigler 1 2 EU812034 EU440010 EU811862 & Ebinger Vachellia grandicornuta ( Gerstner ) Seigler & 1 EU812049 EU440026 EU811879 Ebinger Vachellia macracantha (Humboldt & 1 2 EU812053 EU811989 EU440030 EU811884 Bonpland ex Willdenow) Seigler & Ebinger (L.) P.J.H.Hurter & Mabb. 1 2 AF523183 AF524993 AF522973 EU811882 Vachellia oviedoensis (R.G.García & 1 2 EU812029 EU440005 EU811857 M.M.Mejía) Seigler & Ebinger Vachellia schaffneri (S. Watson) Seigler & 1 2 AF274132 HM020818 Ebinger Vachellia vernicosa (Britton & Rose), Seigler 1 2 EU811984 EU440025 EU811878 & Ebinger Vachellia cornigera (Linnaeus.) Seigler & 1 2 EU812045 EU811981 EU440021 EU811874 Ebinger Zapoteca nervosa (Urb.) H.M.Hern 1 EU812021 EU439997 EU811848

Table S2 Divergence dates estimated in this study. The skleroxylon clade and the eight bottom rows are informal clade names Acacia sl Acacia fixed crown min medi max min medi max min media max an an n Mimosoideae 45.0 51.4 62.7 45.6 54.2 63.1 Acacia sl 45.0 49.6 59.2 45.0 50.3 59.2 Vachellia 8.9 13.7 19.0 11.0 17.2 25.8 American 7.8 11.8 16.7 5.9 14.6 19.2 Vachellia African Vachellia 3.4 7.3 12.1 9.2 12.1 21.9 Senegalia 26.3 33.4 42.0 20.0 31 41.9 Senegalia "sect. 1.6 4.9 9.8 0.9 4.9 12.0 Aculieferum" Senegalia "sect. 16.9 23.7 31.6 9.6 17.4 26.8 Monacanthea" "skleroxylon" 14.7 27.3 31.6 clade Mariosousa 8.0 17.2 32.2 5.8 16.3 30.0 Acaciella 7.2 13.2 20.0 0.4 2.8 7.4 Lysiloma/ 16.3 22.1 28.1 10.1 19.4 28.7 Cojoba Albizia ss 17.0 22.5 27.7 12.8 21.8 30.9 Calliandra 4.8 8.3 12.7 4.2 9.2 15.6 Ebenopsis/ 6.6 13.8 21.8 3.1 9.7 19.1 Pithecellobium Acacia ss 23.2 24.0 43.0 21.8 27.2 35.0 23.8 26.6 32.0 Paraserianthes Acacia 17.1 21.1 25.1 16.4 21.4 27.3 16.1 23.9 30.1 Juliflorae/ 9.2 13.7 19.0 8.0 13.2 16.5 Pluinerves Plurinerves ss 7.7 12.2 17.4 6.7 10.3 14.2 Juliflorae s.s 5.7 10.0 14.8 7.1 11.0 15.0 Victoriae/Pyrifolia 1.4 6.7 14.3 6.7 12.2 18.2 Murrayana 10.3 16.6 22.3 11.2 17.3 23.1 Pulchelloideae 13.1 17.9 23.5 12.0 18.2 24.4 Botrycephalae/ 9.0 13.3 18.0 4.8 7.6 10.7 Phyllodineae

Botrycephalae 2.1 3.4 5.0 Caesalpina_calycina 1 Gledistia_sinensis 0.98 Senna_candolleana Prosopsis_sp 0.54 Neptunia_monosperma 1 Desmanthus_sp 1 1 Leucaena_leucosephala Vachellia_nilotica 1 Vachellia_hockii Vachellia_constricta 1 1 1 Vachellia_neovenicosa 0.88 Vachellia_schaffneri Vachellia_oveidoensis 1 1 Vachellia_cucuyo 0.99 Vachellia_macracantha 1 Vachellia_collinsii 1 1 Vachellia_cornigera 0.64 Vachellia_choriophylla Piptadenia_viridflora 0.94 Anadenanthera_peregrina 1 Anadenenthara_columbrina Mimosa_foetida Senegalia_mellifera 0.95 1 Senegalia_galpinii 1 Senegalia_occidentalis 1 Senegalia_brevispica 1 1 Senegalia_fructispina 0.97 Senegalia_soraria 0.78 Senegalia_gaumeri 1 Senegalia_picachensis Mariosousa_millefolia 1 1 Mariosousa_coulteri 1 0.52 Mariosousa_dolichiostachya Senegalia_vogelianan 0.81 Acacia_visco 0.61 Senegalia_skleroxylon 1 Senegalia_muricarta Calliandra_sp 0.99 1 Calliandra_longipeicellata 1 0.82 Calliandra_juzepczukii Acaciella_glauca 1 Acaciella_tequilana 1 Acaciella_anugstisima 1 Acacia_nervosa 1 Faidherbia_albida2 1 Faidherbia_albida Lysiloma_tergemina 1 1 Cojoba_sp 1 Cojoba_filipis 1 Ebenopsis_ebano 1 Pithecellobium_unguis_cati Albizia_harveyi 1 Albizia_procera 0.43 0.76 Alibizia_kalkora 1 Albizia_bermudiana 0.9 0.98 Albizia_julibrissin Chloroleucon_mangense 1 Chloroleucon_sp 1 Parachidendron_pruinosum 1 Paraserthianthes_lopantha 0.72 Acacia_ampliceps 1 Acacia_tumida 1 Acacia_aneura

Figure S1 Bayesian phylogeny inferred from the Mimosoideae dataset, based on three genes and four fossil calibrations. Nodes are labelled with posterior probabilities. Caesalpina calycina Gledistia sinensis Senna candolleana sp Prosopsis sp Neptunia monosperma Desmanthus sp Leucaena leucocephala Leucaena leucosephala Anadenanthera peregrina Anadenenthara columbrina Piptadenia viridflora Piptadenia viridflora Vachellia schaffneri Vachellia cucuyo Vachellia oveidoensis Vachellia constricta Vachellia neovenicosa Vachellia nilotica Vachellia nilotica Vachellia grandicornata Vachellia hockii Vachellia macracantha Vachellia collinsii Vachellia choriophylla Vachellia cornigera Mimosa foetida Senegalia galpinii Senegalia mellifera Senegalia fructispina Senegalia brevispica Senegalia occidentalis Senegalia soraria Senegalia picachensis Senegalia gaumeri Senegalia muricarta Senegalia skleroxylon Mariosousa millefolia Mariosousa dolichiostachya Mariosousa coulteri Acaciella glauca Acaciella anugstisima Acaciella tequilana Calliandra sp Calliandra longipeicellata Calliandra juzepczukii Faidherbia albida2 Faidherbia albida Ebenopsis ebano Pithecellobium unguis cati Lysiloma tergemina Cojoba filipis Cojoba sp Albizia procera Albizia harveyi Alibizia kalkora Albizia julibrissin Albizia bermudiana Chloroleucon sp Chloroleucon mangense Paraserthianthes lopantha Parachidendron pruinosum A. dempsteri A. pyrifolia A. victoriae A. pravifolia A. extensa A. rostellifera A. cupularis A. ligulata A. adoxa A. perryi A. leioderma A. pentadenia A. guinetii A. hemiteles A. triquetra A. latipes A. cochlearis A. suaveolens A. subrigida A. murrayana A. pachyacra A. platycarpa A. dunnii A. tetragonophylla A. heteroclita A. glaucissima A. halliana A. aneura A. aneura A. multispicata A. abbreviata A. gonoclada A. floribunda A. flexifolia A. cognata A. venulosa A. montana A. melanoxylon A. baeuerlenii A. pycnantha A. beckleri A. euthycarpa A. amblyophylla A. meissneri A. anceps A. hakeoides A. hakeoides A. neriifolia A. pravissima A. cultriformis A. falcata A. linifolia A. dorothea A. dealbata A. penninervis A. penninervis A. spectabilis A. deanei A. mearnsii A. dealbata A. mearnsii A. muelleriana

70 .0 60 .0 50 .0 40 .0 30 .0 20 .0 10 .0 0. 0

Figure S2 Dated phylogenetic inferred from the Acacia sl dataset, based on two genes and four fossil calibrations. 1 Caesalpina calycina 0.78 Gledistia sinensis Senna candolleana 1 Prosopis sp Prosopsis sp 0.63 Neptunia monosperma 0.98 Desmanthus sp 1 1 1 Leucaena leucocephala Leucaena leucosephala 1 Anadenanthera peregrina 0.99 Anadenenthara columbrina 1 Piptadenia viridflora Piptadenia viridflora 1 Vachellia schaffneri 1 Vachellia cucuyo 0.53 Vachellia oveidoensis 0.99 Vachellia constricta 1 Vachellia neovenicosa 0.82 Vachellia nilotica 1 Vachellia nilotica Vachellia grandicornata 0.09 Vachellia hockii Vachellia macracantha 1 1 0.97 Vachellia collinsii 0.61 Vachellia choriophylla Vachellia cornigera Mimosa foetida Senegalia galpinii 1 Senegalia mellifera 0.98 Senegalia fructispina 1 Senegalia brevispica 1 Senegalia occidentalis 0.98 Senegalia soraria 1 Senegalia picachensis 1 Senegalia gaumeri 1 Senegalia muricarta 1 Senegalia skleroxylon 0.71 Mariosousa millefolia 1 Mariosousa dolichiostachya 1 Mariosousa coulteri Acaciella glauca 1 Acaciella anugstisima 0.85 0.98 0.67 Acaciella tequilana Calliandra sp 1 Calliandra longipeicellata 0.98 Calliandra juzepczukii Faidherbia albida2 1 1 Faidherbia albida Ebenopsis ebano 1 Pithecellobium unguis cati Lysiloma tergemina 1 1 Cojoba filipis 0.91 Cojoba sp Albizia procera 0.55 Albizia harveyi 0.81 Alibizia kalkora 1 Albizia julibrissin 0.79 0.71 Albizia bermudiana Chloroleucon sp 1 Chloroleucon mangense Paraserthianthes lopantha 0.98 Parachidendron pruinosum 0.77 A. dempsteri 1 A. pyrifolia A. victoriae 1 A. pravifolia A. extensa 0.59 A. rostellifera 1 1 A. cupularis 1 1 A. ligulata A. adoxa 1 A. perryi A. leioderma 0.63 0.99 1 A. pentadenia A. guinetii 1 A. hemiteles A. triquetra A. latipes 0.72 0.97 1 A. cochlearis 0.8 A. suaveolens A. subrigida 1 A. murrayana 1 A. pachyacra A. platycarpa 1 A. dunnii 0.68 A. tetragonophylla 0.57 A. heteroclita A. glaucissima 1 A. halliana A. aneura 0.84 A. aneura 0.85 A. multispicata 0.79 A. abbreviata 0.98 0.95 A. gonoclada A. floribunda A. flexifolia 0.99 A. cognata A. venulosa 1 A. montana A. melanoxylon 1 A. baeuerlenii 0.73 A. pycnantha 1 A. beckleri 0.82 A. euthycarpa A. amblyophylla 1 A. meissneri 1 A. anceps A. hakeoides 1 A. hakeoides 0.89 A. neriifolia A. pravissima A. cultriformis 0.88 0.84 0.99 A. falcata A. linifolia 0.51 A. dorothea 0.61 A. dealbata 0.95 A. penninervis A. penninervis A. spectabilis A. deanei A. mearnsii A. dealbata A. mearnsii A. muelleriana

Figure S3 Bayesian phylogeny inferred from the Acacia sl dataset, based on two genes and four fossil calibrations. Nodes are labelled with posterior probabilities. 0.85 Paraserianthes lopantha Parachidendron A. victoriae 1 0.99 A. pyrifolia A. dempsteri 1 A. pravifolia A. extensa 1 A. rostellifera

1 1 A. ligulata 1 A. cupularis A. saligna 1 A. adoxa 0.59 A. perryi 1 A. pentadenia 1 A. leioderma 1 A. hemiteles A. guinetii 0.51 0.92 A. suaveolens 1 A. triquetra 1 A. subrigida 1 A. pachyacra A. murrayana 1 A. dunnii A. platycarpa 1 1 1 A. halliana A. glaucissima 1 A. cochlearis 1 A. latipes 0.98 A. heteroclita 1 1 A. tetragonophylla A. tetragonophylla Figure S4 A. montana 1 1 A. melanoxylon 1 A. baeuerlenii A. venulosa 1 0.98 1 A. cognata 0.97 A. flexifolia 1 A. floribunda 1 A. triptera A. multispicata 1 0.53 A. gonoclada 1 A. abbreviata 1 A. aneura A. aneura 0.96 1 A. pycnantha A. beckleri 1 1 A. hakeoides A. hakeoides A. euthycarpa 0.95 1 A. anceps A. amblyophylla 1 0.94 A. meissneri 1 A. cultriformis 0.86 A. falcata 1 A. pravissima A. neriifolia 1 0.58 A. spectabilis A. linifolia A. muelleriana 0.95 0.63 1 A. mearnsii A. mearnsii 0.51 A. deanei 1 A. dealbata A. dealbata 0.75 A. dorothea A. penninervis 0.92 1 A. penninervis

Figure S4 Bayesian phylogeny inferred from the Acacia ss dataset, based on 6 genes.

Nodes are labelled with posterior probabilities.