Abstract
Leguminosae, Polygalaceae, Quillajaceae and Surianaceae together comprise the order Fabales. Phylogenetic relationships within Fabales remain an unsolved problem even though interfamilial relationships have been examined in a number of studies using different sampling approaches and both molecular and morphological data. In this study, we gather information from the nuclear 26S rDNA region as well as previously published data from the sqd1, matK and rbcL regions. Phylogenetic analyses were performed by maximum parsimony, maximum likelihood and Bayesian inference. Overall, the best-supported topology for the relationships among families within the order places the pair of Leguminosae and Polygalaceae as sister to the pair of Quillajaceae and Surianaceae. However, our approximately unbiased (AU) test of the combined data results has shown that none of the seven different topologies rejected. Furthermore, three topologies were not significantly different from each other. Therefore, similar to the previous studies, this study did not find well-supported dichotomous relationships among the four Fabales families. The Fabales topology was very sensitive to both data choice and the phylogenetic methods used, which may indicate a rapid-near-simultaneous evolution of the four Fabales families. Our results also show that while nuclear sqd1 can be helpful as a complementary region, both the nuclear sqd1 and rDNA 26S regions could be problematic when analyzed individually.
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Acknowledgements
We would like to thank Professor Anne Bruneau (Universite de Montreal, Canada) and Dr. Colin Hughes (Universitat Zurich, Switzerland) for their valuable suggestions, and anonymous reviewers for helpful comments. The first author also thanks Professor Darren Crayn (James Cook University, Australia) for sending some samples.
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Appendices
Appendix
Taxon sampling for the phylogenetic analyses of order Fabales based on the nuclear sqd1 and 26S rDNA, and the plastid rbcL and matK. A dash indicates the region was not sampled. Information is presented in the following order: taxon name, voucher specimen of the samples worked in this study (SOURCE); GenBank accessions: sqd1, 26S, matK, rbcL.
Leguminosae. Subfamily Duparquetioideae: Duparquetia orchidacea Baill., Bruneau 1098 (K); MG431081, MG431186, EU361937.1, —. Subfamily Cercidoideae: Adenolobus garipensis (E.Mey.) Torre & Hillc., Leistuer et al. 246 (K); —, MG431188, EU361844.1, AM234268.1. A. pechuelli (Kuntze) Torre & Hillc., Oliver et al. 6527; MG431096, MG431178, JN881353.1, —. Bauhinia syringifolia (F.Muell.) Wunderlin, Weston 2449 (NSW); —, MG431187, —, AM234267.1. B. galpinii N.E.Br., Forest 347 (NBG); MG431094, MG431172, JN881366.1, AM234262.1. Brenierea insignis Humbert, Dupuy M430 (K); —, MG431166, EU361889.1, AM234269.1. Cercis canadensis L., JBM 1397–91; MG431097, MG431189, EU361912.1, U74188.1. Griffonia physocarpa Baill., Cheek 8013 (K); MG431095, MG431190, EU361961.1, AM234265.1. Subfamily Dialioideae: Dialium guianensis (Aubl.) Sandw., Klitgaard 686 (K); MG431086, —, EU361930.1, AM234245.1. Poeppigia procera Presl., Howard 5162 (MT); MG431087, —, EU362026.1, AM234246.1. Storckiella australiensis J.H.Ross & B.Hyland, Hill et al. 2096 (K); —, —, GU321970.1, AM234249.1. Zenia insignis Chun, Manos 1418 (DUKE); —, —, EU362065.1, AF308722.1. Subfamily Detarioideae: Afzelia bella Harms., Breteler 13120; MG431085, —, EU361846.1, KC628648.1. Amherstia nobilis Wall., Baker 490 (KEP); MG431084, MG431182, EU361849.1, AM234234.1. Anthonotha macrophylla P.Beauv., Wieringa 2996 (WAG); MG431083, MG431205, EU361853.1, KC628430.1. A. pynaertii (De Wild.) Exell & Hillc., Breteler 12781 (WAG); MG431063, —, EU361854.1, —. Aphanocalyx cynometroides Oliver, Wieringa 2355 (WAG); —, MG431179, —, AM234241.1. A. djumaensis (De Wild.) J.Leonard; —, —, EU361856.1, —. A. margininervatus J.Leonard, Breteler 12,346 (WAG); MG431082, —, —, —. Brownea sp., A. Pérez and P. Alvia 38,917 QCA (K); MG431069, —, AY386932.1, U74186.1. Browneopsis ucayalina Huber, Klitgaard 684 (K); MG431089, MG431185, EU361894.1, AM234233.1. Crudia gabonensis Harms, Wieringa 2585 (WAG); —, MG431167, EU361922.1, AM234230.1. Cynometra crassifolia Benth.; —, —, KF294055.1, —. C. mannii Oliv., Bruneau 1364; MG431062, MG431177, —, AM234231.1. Detarium macrocarpum Harms., Breteler 12,528 (WAG); —, MG431195, GU321969.1, AM234239.1. Goniorrhachis marginata Taub., Cara 3585, Lewis and Klitgaard 5338; MG431136, MG431183, —, —. Hymenostegia klainei Pellegr., Wieringa 2575 (WAG); MG431061, —, —, KC628501.1. H. robusta Wieringa & Mackinder; —, —, EU361976.1, —. Intsia bijuga (Colebr.) Kuntze; —, —, EU361981.1, KF496786.1. Intsia sp., Colector. 4202; MG431060, —, —, —. Isoberlinia scheffleri (Harms) Greenway, Herendeen 16-XII-97–2 (US); —, MG431169, EU361983.1, AM234240.1. Macrolobium acaciifolium (Benth.) Benth.; —, —, —, U74191.1. M. archeri Cowan, Klitgaard 683; MG431059, —, —, —. M. bifolium (Aubl.) Pers.; —, —, EU361996.1, —. Saraca declinata (Jack) Miq., Manos 1417 (DUKE); MG431080, —, EU362033.1, JX856761.1. Tamarindus indica L., JBM 2138–76 (MT); MG431088, MG431184, EU362056.1, AB378732.1. Subfamily Caesalpinioideae: Acrocarpus fraxinifolius Arn., Manos 1416 (DUKE); —, MG431154, GU321971.1, AY904371.1. Archidendron hirsutum I.Nielsen, Douglas 625 (MEL); MG431110, MG431157, EU361860.1, AM234253.1. Caesalpinia decapetala (Roth) Alson, Herendeen and Mbago 19-XII-97–1 (US); KF379299.1, —, KF379248.1, —. C. pulcherrima (L.) Sw; KF379321.1, —, EU361906.1, U74190.1. Calliandra juzepczukii Standl.; —, —, EU812019.1, —. C. trinervia Benth., Klitgaard 622 (K); MG431072, MG431160, —, —. Calpocalyx dinklagei Harms., Breteler 15,461 (WAG); MG431107, MG431155, EU361907.1, AM234257.1. Cassia grandis L. f., Smith 2061 (MT); MG431065, —, —, —. Cedrelinga cateniformis (Ducke) Ducke, T.D. Pennington, A. Daza and A. Muellner 17,761 MOL (K) (sqd1)/Klitgaard 698 (K) (26S); MG431074, MG431159, AF521818.1, AM234256.1. Ceratoniasiliqua L., Wieringa 3341 (WAG); —, MG431194, AY386852.1, U74203.1. Chamaecrista fasciculata (Michx.) Greene; —, —, AY386955.1, U74187.1. C. nictitans (L.) Moench var. jaliscensis (Greenman) Irwin & Barnaby, Klitgaard 654; MG431098, MG431181, —, —. Colvillea racemosa Bojer; KF379329.1, —, EU361916.1, AY904425.1. Conzattia multiflora Standl.; KF379326.1, —, AY386918.2, AY904416.1. Delonix boiviniana (Baill.) Capuron, Bruneau 1365 (MT); KF379330.1, —, KF379239.1, —. D. floribunda (Baill.) Capuron, Bruneau 1393 (MT); KF379331.1, —, KF379240.1, AY904421.1. D. pumila Du Puy, Phillipson & R.Rabev., Bruneau 1411 (MT); KF379328.1, —, KF379237.1, AY904424.1. D. regia (Boj. ex Hook.) Raf; KF379327.1, —, KF379238.1, AY904419.1. D. velutina Capuron, Bruneau 1354 (MT); KF379324.1, —, KF379236.1, AY904423.1. Denisophytum madagascariense R.Vig.; KF379301.1, —, KF379246.1, —. Erythrostemon calycinus (Benth.) L.P.Queiroz, Lewis 1885 (K); —, MG431176, —, —. E. ivorense A.Chev., Breteler 15,446 (WAG); MG431092, —, EU361948.1, U74205.1. Gleditsia sinensis Lam., Haston V200305; —, —, —, AY904374.1. G. triacanthos L., JBM 2327–82 (sqd1)/ JBM 2674–95 (MT) (26S); MG431093, MG431173, EU361958.1, —. Guilandina bonduc L.; KF379298.1, —, KF379242.1, —. Gymnocladus dioica (L.) Koch, JBM 1830–72 (sqd1)/ JBM 2099–88 (MT) (26S); MG431066, MG431174, EU361966.1, U74193.1. Inga edulis Mart.; —, —, EU361980.1, —. I. nouragensis Poncy; —, —, —, JQ626021.1. Inga sp., Klitgaard 677 (K); MG431075, MG431193, —, —. Mezoneuron scortechinii F.Muell., Wieringa 4195 (WAG); MG431134, —, —, —. Mimosa colombiana Britton & Killip, A.M. Torres 21,343 (K); MG431073, —, DQ790603.1, —. M. pudica L.; —, —, —, KJ008941.1. Moullava digyna (Rottl.) E.Gagnon & G.P.Lewis, comb. nov., Lewis 2067 (K); MG431135, —, EU361902.1, —. Parkia multijuga Benth., Klitgaard 697 (K); MG431109, MG431161, EU362018.1, AM234251.1. Parkinsonia aculeata L., Spellenberg and Brouillet 12,704 (MT); KF379325.1, MG431168, —, —. P. raimondoi Brenan; —, —, —, AY904413.1. P. florida (Benth. ex A.Gray) S.Watson; —, —, AY386856.2, —. Pentaclethra macroloba (Willd.) Kuntze, B. Boyle et al. 6720 (K) (sqd1)/ DeWilde 11,496 (WAG) (26S); MG431108, MG431156, AY386904.1, —. P. macrophylla Benth.; —, —, —, AM234250.1. Poincianella palmeri (S.Watson) E.Gagnon & G.P.Lewis, comb. nov., Lewis et al. 2065 (K); MG431133, —, —, —. Pterogyne nitens Tul., Herendeen 13- XII-97–1 (US); MG431090, MG431171, EU362031.1, AY904377.1. Senna alata (L.) Roxb., Bruneau 1076 (K); MG431064, MG431180, EU362042.1, U74250.1. Tara spinosa (Molina) Britton & Rose; KF379323.1, —, —, —. Umtiza listerina T.Sim, Schrire 2602 (K); MG431091, MG431175, EU362062.1, AM234237.1. Vachellia caven (Molina) Seigler & Ebinger, JBM 386–89 (MT); —, MG431191, AF274131.1, Z70145.1. Zapoteca tetragona (Willd.) H.M.Hern., Klitgaard 649 (K); —, MG431158, AF523097.1, JQ592095.1. Subfamily Papilionoideae: Arachis hypogaea L.; FJ824608.1, —, EU307349, U74247.1. Astragalus laxmannii var. robustior (Hook.) Barneby & S.L.Welsh; —, —, —, JX848460.1. A. lusitanicus Lam., J.R. Edmondson and M.A.S. McClintock 2803 (K); MG431068, —, —, —. A. mongholicus Bunge; —, —, EF685993.1, —. Baphia nitida Afzel. ex Lodd., Bruneau s.n. (LBG); MG431103, MG431162, EU361867.1, AM234261.1. Bobgunnia fistuloides (Harms) J.H.Kirkbr. & Wiersema, Breteler 14,870 (WAG); MG431071, MG431165, EU361885.1, AM234258.1. Cadia purpurea (G.Piccioli) Aiton; —, —, JX295932.1, U74192.1. C. pubescens Bojer ex Baker, L.J. Dorr, L.C. Barnett, and R. Brooks 3279 (K); MG431104, —, —, —. Cladrastis kentukea (Dum.Cours.) Rudd; —, —, AF142694.1, —. C. sinensis Hemsl., E. Punethalengam s.n. (K); MG431105, —, —, Z95551.1. Dalbergia congestiflora Pittier; —, —, AF142696.1, —. D. hupeana Hance; —, —, —, U74236.1. D. yunnanensis Franch., Sino-British Exp. to Cangshan 1981 (K); MG431099, —, —, —. Exostyles venusta Spreng., Klitgaard 24 (K); MG431067, —, JX152591.1, —. Lecointea peruviana J.F.Macbr., B.B. Klitgaard 679 (K); MG431106, MG431163, JX295927.1, AM234260.1. Lotus corniculatus L.Cowan., R.S. MFF128 (K); MG431100, —, HM049505.1, U74213.1. Sclerolobium sp., Klitgaard 687 (K); —, MG431170, AM234242.1, —. Lupinus luteus L. (ABH 31,123); MG431101, —, HM851129.1, HM850145.1. Sophora chrysophylla (Salisb.) Seem. —, GU256432.1, —, —. S. microphylla Aiton, N.A. Smith (AK); MG431070, —, —, —. Swartzia cadiosperma Spruce ex. Benth., Klitgaard 664 (K); MG431102, MG431164, EU362053.1, AM234259.1. Wisteria sinensis (Sims) DC.; FN675910.1, —, AF142732.1, Z95544.1. Polygalaceae: Tribe Xanthophylleae: Xanthophyllum octandrum Domin, Forster 9554 (NY); —, MG431137, —, AM234229.1. Xanthophyllum sp., Coode 7760 (K); MG431076, —, EU604044.1, —. Tribe Carpolobieae: Atroxima afzeliana (Oliv. ex Chodat) Stapf, Jongkind 4281 (WAG); —, MG431150, EU604049.1, AM234175.1. Carpolobia alba G.Don., Cable 747 (K); MG431114, MG431145, EU604053.1, AM234176.1. Tribe Moutabea: Eriandra fragrans P.Royen & Steenis. R. Pullen 7234 (K); MG431115, MG431146, EU604051.1, AM234170.1. Moutabea aculeata (Ruiz & Pav.) Poepp. & Endl., Smith 1522 (US); —, MG431149, —, AM234169.1. M. guianensis Aubl.; —, —, JQ626362.1, —. Tribe Polygaleae: Bredemeyera colletioides (Phil.) Chodat, Guaglianone et al. 1587 (NY); —, MG431148, —, AM234171.1. B. floribunda Willd., Bello 742 (COL) (sqd1)/ Irwin et al. 27,995 (NY) (26S); MG431113, MG431147, EU596520.1, EU644699.1. Comesperma esulifolium (Gand.) Telford 12,350 (CANB); —, MG431192, EU596516.1, AM234179.1. Monnina xalapensis Kunth, Chase 963 (K); —, MG431151, EU604047.1, AM234184.1. Muraltia alba Levyns, Goldblatt 9515 (MO); —, MG431144, —, —. M. heisteria (L.) DC. —, —, —, AJ829698.1. M. spinosa (L.) Dumort, Chase 281 (K); —, MG431152, —, —. M. thunbergii Eckl. & Zeyh., Forest 250 (K, NBG); MG431111, —, AM889730.1, —. Polygala acuminata Willd., Wurdack 1818 (NY); —, MG431141, —, AM234195.1. P. alpicola Rupr., Chase 11,747 (K); —, MG431139, EU604041.1, AM234191.1. P. californica Nutt.; —, —, AY386842.1, —. P. chamaebuxus (L.) var. grandiflora Chase 11,323 (K); —, MG431142, —, —. P. cowellii (Britton) S.F. Blake; —, —, —, AM234199.1. P. ligustrioides A. St. Hil. Harley et al. 20,751 (K); —, MG431143, —, AM234202.1. P. senega L., Brouillet 99–11 (MT); —, MG431138, —, —. Polygala sp., Bello 48; MG431112, —, —, —. P. vulgaris L., Fay 316 (K); —, MG431140, EU604046.1, AM234193.1. Securidaca diversifolia (L.) S.F.Blake, Chase 2998 (MICH); —, —, JQ588837.1, AM234225.1. Surianaceae: Cadellia pentastylis F.Muell., Thompson and Robin s.n. (K); MG431116, MG431196, EU604056.1, L29491.1. Guilfoylia monostylis (Benth.) F. Muell., Fernando and Wannan s.n. (UNSW 21,246); —, MG431203, EU604031.1, L29494.1. Recchia mexicana Moc. & Sessé ex DC., no voucher (see Forest, 2004); —, MG431153, EU604045.1, AM234270.1. Suriana maritima L.; —, —, AY386950.1, U07680.1. Stylobasium spathulatum Desf., Latz. 13,213 (K); MG431117, MG431204, EU604032.1, U06828.1. Quillajaceae: Quillaja saponaria Molina, M.W. Chase 10,931 (K) (sqd1)/ Morgan 2146 (WS) (26S); MG431077, —, AY386843.1, U06822.1. Outgroups. Zygophyllales: Krameria ixine Lofling., Fernandez 22,529 (COK); MG431078, —, EU604050.1, EU644679.1. K. lanceolata Torr., Chase 103 (MICH); —, MG431198, —, —. Zygophyllum rosowii Bunge D1507; —, —, JF956824.1, JF944812.1. Z. xanthoxylum (Bunge) Maxim. Chase 1700 (K); —, MG431197, —, —. Celastrales: Celastrus orbiculatus Thunb., M.W. Chase 2274 (K); MG431079, AF222357.1, EF135517.1, AY788194.1. Oxalidales: Eucryphia lucida (Labill.) Baill.; —, AF036494.1, —, —. Malpighiales: Licania alba (Bernoulli) Cuatrec.; —, KJ414473.1, —, —. Viola suavis M.Bieb.; AM503808.1, —, —, —. V. chaerophylloides (Regel) W.Becker; —, —, JQ950581.1, JQ950611.1. Rosales: Colubrina arborescens (Mill.) Sarg., M.J.M. Christenhusz 5714; MG431131, —, —, —. C. asiatica (L.) Brongn.; —, DQ146521.1, —, —. Elaeagnus commutata Bernh. ex Rydb.; —, —, —, JX848456.1. Elaeagnus sp., M.W. Chase 2414 (K); MG431130, AF479235.1, —, —. E. umbellata Thunb.; —, —, AY257529.1, —. Ficus sp., Moore 315; —, —, —, EU002278.1. F. benjamina L.; FN675916.1, —, JQ773509.1, —. F. tikoua Bureau; —, JF317386.1, —, —. Fragaria × ananassa (Weston) Duchesne; —, X58118, —, U06805.1. Fragaria vesca L.; XM_004290997.1, —, AF288102.1, —. Hippophae rhamnoides L., M.J. Crawley MJC150; MG431129, JF317389.1, JF317428.1, JF317488.1. Humulus lupulus L.Fay, M.F. MFF341 (K); MG431128, AY686777.1, AY257528.1, AF206777.1. Gironniera sp., Puradyatmika 10,455 (BO, MAN, FRE, K, L, CANB, A, SING, BRI, BISH); MG431132, —, —, —. G. subaequalis Planch.; —, —, AF345319.1, AF500340.1. Malus domestica Borkh.; XM_008395413.1, —, AM042561.1, —. M. spectabilis (Aiton) Borkh.; —, —, —, JQ391363.1. Prunus armeniaca L.; FN675931.1, —, HQ235101.1, KF154869.1. P. avium (L.) L.; FN675932.1, —, AM503828.1, HQ235394.1. P. cerasus L.; FN675933.1, —, FJ899111.1, HQ235416.1. P. domestica L.; FN675934.1, —, FJ899110.1, L01947.2. P. persica (L.) Stokes; FN675912.1, AY935820.1, AF288117.1, AF411493.1. Shepherdia argentea (Pursh) Nutt., Chase 3176 (K); —, MG431201, —, AJ225787.1. S. canadensis (L.) Nutt.; —, —, KC475874.1, —. Fagales: Alnus glutinosa (L.) Gaertn; —, AF479106, KF419025.1, EU644678.1. Betula pendula Roth AM503778.1, —, AY372014.1, KF418943.1. Casuarina equisetifolia L., P.J. Edwards 4011 (K); MG431119, —, AY033837.1, AY033859.1. Juglans nigra L.; —, AF479105.1, —, U00437.1. J. regia L.Fay, M.F. et al. MFF416 (K); MG431118, —, AF118038.1, —. Morella cerifera (L.) Small; —, AF479247.1, —, —. M. nana (A.Chev.) J.Herb.; —, —, KF419020.1, —. M. quercifolia (L.) Killick, M.F. Fay s.n. (K); MG431120, —, —, —. M. rubra Lour; —, —, —, KF418924.1. Myrica gale L., M.F. Fay MFF 238 (K); MG431123, —, AY191715.1, AJ626757.1. Nothofagus alpina (Poepp. & Endl.) Oerst.; —, —, —, L13342.2. N. antarctica (G.Forst.) Oerst.; —, —, AY263924.1, —. N. obliqua (Mirb.) Oerst., M.W. Chase 33,143 (K) (1000 Plant Genomes Project); MG431121, —, —, —. Platycarya strobilacea Siebold & Zucc., Herbarium Kewense Cultivated Plants s.n. (K); MG431122, —, AY147100.1, AY263933.1. Ticodendron incognitum Gómez-Laur. & L.D.Gómez, R.K. Brummitt and R. Aizprua 21,139 (K); MG431124, —, U92855.1, AF061197.1. Trigonobalanus verticillata Forman, Chase 595 (K); —, MG431202, AB084771.1, AB084768.1. Cucurbitales: Abobra tenuifolia (Gillies ex Hook. & Arn.) Cogn., Chase 915 (K); —, MG431200, DQ536629.1, AF008961.1. Begonia glabra Aubl., Chase 945 (K); —, MG431199, —, —. B. ulmifolia Willd.; —, —, GU397115.1, —. B. metallica W.G.Sm. × Begonia sanguinea Raddi; —, —, —, L12670.1. Bolbostemma paniculatum (Maxim.) Franquet, TCMK 854 (K); MG431125, —, DQ469139.1, DQ501255.1. Corynocarpus laevigatus J.R.Forst. & G.Forst., M.W. Chase 236 (NCU); MG431126, AF479110.1, AY968448.1, AF148994.1. Cucumis sativus L.; XM_004167788.1, —, DQ536662.1, L21937.1. Datisca cannabina L., M.W. Chase 2745; MG431127, AY968410.1, AB016467.1, L21939.1.
Information on Electronic Supplementary Material
Online resource 1. sqd1 sequence alignment in nexus format.
Online resource 2. 26S sequence alignment in nexus format.
Online resource 3. sqd1 + 26S sequence alignment in nexus format.
Online resource 4. matK + rbcL sequence alignment in nexus format.
Online resource 5. sqd1 + matK sequence alignment in nexus format.
Online resource 6. sqd1 + matK + rbcL sequence alignment in nexus format.
Online resource 7. sqd1 + 26S + matK sequence alignment in nexus format.
Online resource 8. sqd1 + 26S + matK + rbcL sequence alignment in nexus format.
Online resource 9. Maximum likelihood tree of the nuclear sqd1 data set. Outgroup taxa, Polygalaceae, Surianaceae, Quillajaceae and Leguminosae are indicated.
Online resource 10. Maximum likelihood tree of the nuclear 26S data set. Outgroup taxa, Polygalaceae, Surianaceae, Quillajaceae and Leguminosae are indicated.
Online resource 11. Maximum likelihood tree of the combined nuclear sqd1 + 26S data sets. Outgroup taxa, Polygalaceae, Surianaceae, Quillajaceae and Leguminosae are indicated.
Online resource 12. Maximum likelihood tree of the combined plastid matK + rbcL data sets. Outgroup taxa, Polygalaceae, Surianaceae, Quillajaceae and Leguminosae are indicated.
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Aygoren Uluer, D., Hawkins, J.A. & Forest, F. Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA. Plant Syst Evol 306, 66 (2020). https://doi.org/10.1007/s00606-020-01691-7
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DOI: https://doi.org/10.1007/s00606-020-01691-7