Table 1.
Accessions of Rubus species and outgroup (Waldsteinia fragarioides) used in this study.
| Species | Ploidy | USDA GRIN subgenus classification | Focke subgenus classification | Region of origin | Group (1–8) | Voucher |
|---|---|---|---|---|---|---|
| R. deliciosus Torr. | 2x | Anoplobatus | Anoplobatus | North America | 2 | PI 553184/CRUB 1021.001 |
| R. odoratus L. | 2x | Anoplobatus | Anoplobatus | North America | 2 | Alice R14, MAINE |
| R. parviflorus Nutt. | 2x | Anoplobatus | Anoplobatus | North America | 2 | PI 553785/CRUB 13.001 |
| R. trilobus Thunb. | 2x | Anoplobatus | Anoplobatus | South America | 2 | Ruiz 889, MO |
| R. calycinus Wall. Ex D. Don | 6x | Chamaebatus | Chamaebatus | Asia | 5 | Alice et al. (2008) Now Vouchered at WKU 04-07 |
| R. nivalis Douglas | 2x | Chamaebatus | Chamaebatus | North America | 8 | PI 679726/CRUB 1374.001 PL |
| R. pectinellus Maxim.* | 6x | Chamaebatus | Chamaebatus | Asia | n/a | Jutila and Fujino 680, MO |
| R. pectinarioides | 4x | Chamaebatus* | n/a | Asia | 5 | Alice et al. (2008) Vouchered WKU 04-25 |
| R. sengorensis | 4x | Chamaebatus* | n/a | Asia | 5 | Alice et al. (2008) Vouchered WKU 04-33 |
| R. chamaemorus L. | 8x | Chamaemorus | Chamaemorus | North America/Northern Europe | 1 | Alice R17, MAINE |
| R. geoides Sm. | 4x | Comaropsis | Comaropsis | South America | 8 | Dudley et al. 1538a, MO |
| R. arcticus L. | 2x | Cylactis | Cylactis | North America/Northern Europe | 3 | T. Eriksson 701, S |
| R. humulifolius C. A. Mey. | 4x | Cylactis | Cylactis | Asia | 4 | PI 553242/CRUB 1173.001 PL |
| R. saxatilis L. | 4x | Cylactis | Cylactis | Europe/Asia | 7 | PI 370230/CRUB 918.001 PL |
| R. lasiococcus A. Gray | 2x | Cylactis | Dalibarda | North America | 1 | Merello et al. 827, MO |
| R. pedatus Sm. | 2x | Cylactis | Dalibarda | North America/Asia | 1 | Alice 96-1, MAINE |
| R. fockeanus Kurz | 4x | Cylactis | Dalibarda | Asia | 5 | PI 606537/CRUB 1960.000 SD |
| R. pubescens Raf. | 2x | Cylactis | North America | 3 | Alice R15, MAINE | |
| R. treutleri Hook. f. | 4x | Dalibardastrum | Dalibardastrum | Asia | 5 | Alice et al. (2008) Now Vouchered at WKU 04-09 |
| R. tricolor Focke | 4x | Dalibardastrum | Dalibardastrum | Asia | 5 | Alice 97-2, MAINE |
| R. amphidasys Focke | 6x | Dalibardastrum | Malachobatus | Asia | 5 | PI 618397/CRUB 1693.001 PL |
| R. nepalensis (Hook.f) Kuntze | 4x | Dalibardastrum | n/a | Asia | 5 | Alice 97-1, MAINE |
| R. gunnianus Hook. | 4x | Diemenicus | Dalibarda | Australia | 8 | Wells 96-1, MAINE |
| R. trifidus Thunb. | 2x | Idaeobatus | Anoplobatus | Asia | 4 | PI 554051/CRUB 3.001 PL |
| R. parvifolius L. | 2x | Idaeobatus | Asia | 7 | PI 553813/CRUB 5.001 PL | |
| R. hawaiensis A. Gray | 2x | Idaeobatus | Idaeobatus | North America (Hawaii) | 3 | PI 553214/CRUB 399.001 PL |
| R. spectabilis Pursh | 2x | Idaeobatus | Idaeobatus | North America | 3 | PI 553980/CRUB 4.001 PL |
| R. crataegifolius Bunge | 2x | Idaeobatus | Idaeobatus | Asia | 4 | PI 553173/CRUB 16.001 PL |
| R. ellipticus Sm. | 2x | Idaeobatus | Idaeobatus | Asia | 4 | PI 553190/CRUB 1052.001 PL |
| R. illecebrosus Focke | 2x | Idaeobatus | Idaeobatus | Asia | 4 | PI 553643/CRUB 838.001 PL |
| R. palmatus Thunb. | 2x | Idaeobatus | Idaeobatus | Asia | 4 | PI 553782/CRUB 2.002 PL |
| R. rosifolius Sm. | 2x | Idaeobatus | Idaeobatus | Asia | 4 | Eurard 11660, MO |
| R. pentagonus Wall. Ex Focke | 4x | Idaeobatus | idaeobatus | Asia | 5 | Alice et al. (2008) Vouchered WKU 04-06 |
| R. thomsonii Focke | 4x | Idaeobatus | idaeobatus | Asia | 5 | Alice et al. (2008) Vouchered WKU 04-31 |
| R. alexeterius Focke | 2x | Idaeobatus | Idaeobatus | Asia | 7 | Alice et al. (2008) Vouchered WKU 04-23 |
| R. coreanus Miq. | 2x | Idaeobatus | Idaeobatus | Asia | 7 | PI 618447/CRUB 1438.001 PL |
| R. idaeus L. | 2x | Idaeobatus | Idaeobatus | Europe/Asia | 7 | T. Eriksson 735, S |
| R. innominatus S. Moore | 2x | Idaeobatus | Idaeobatus | Asia | 7 | PI 553646/CRUB 1039.001 PL |
| R. lasiostylus Focke | 2x | Idaeobatus | Idaeobatus | Asia | 7 | PI 553668/CRUB 425.001 PL |
| R. leucodermis Douglas ex Torr. & A. Gray | 2x | Idaeobatus | Idaeobatus | North America | 7 | PI 553673/CRUB 14.001 PL |
| R. niveus Thunb. | 2x | Idaeobatus | Idaeobatus | Asia | 7 | PI 553723/CRUB 269.001 PL |
| R. occidentalis L. | 2x | Idaeobatus | Idaeobatus | North America | 7 | AliceR16,MAINE |
| R. phoenicolasius Maxim. | 2x | Idaeobatus | Idaeobatus | Asia | 7 | Alice96-2,MAINE |
| R. pungens Cambess. | 2x | Idaeobatus | Idaeobatus | Asia | 7 | PI 553849/CRUB 46.002 PL |
| R. sachalinensis H. Lév. | 4x | Idaeobatus | Idaeobatus | Asia | 7 | PI 553866/CRUB 626.001 PL |
| R. strigosus Michx. | 2x | Idaeobatus | Idaeobatus | North America | 7 | Maine Alice R8 |
| R. macraei A. Gray | 6x | Idaeobatus | n/a | North America (Hawaii) | 6 | Gardners. n., HPDL207 |
| Logan | 6x | Idaeorubus | n/a | Cultivar | 7 | PI 553258/CRUB 81.001 PL |
| Boysen | 7x | Idaeorubus | n/a | Cultivar | 8 | PI 553341/CRUB 1108.001 |
| Marion | 6x | Idaeorubus | n/a | Cultivar | 8 | PI 553254/CRUB 385.001 PL |
| R. assamensis Focke | 4x | Malachobatus | Malachobatus | Asia | 5 | PI 618433/CRUB 1701.001 PL |
| R. ichangensis Hemsl. & Kuntze | 4x | Malachobatus | Malachobatus | Asia | 5 | PI 618453/CRUB 1606.001 PL |
| R. irenaeus Focke | 6x | Malachobatus | Malachobatus | Asia | 5 | PI 618550/CRUB 1607.001 PL |
| R. lambertianus Ser. | 4x | Malachobatus | Malachobatus | Asia | 5 | Boufford and Bartholomew 23955, MO |
| R. lineatus Reinw. | 4x | Malachobatus | Malachobatus | Asia | 5 | Grierson and Long 1950, GH |
| R. clinocephalus Focke | 4x | Malachobatus | Malachobatus | Asia | 5 | PI 606459/CRUB 1642.001 PL |
| R. tephrodes Hance | 4x | Malachobatus | Malachobatus | Asia | 5 | Yao 9231, MO |
| R. australis G. Forst. | 4x | Micranthobatus | Lampobatus | New Zealand | 8 | Gardner 1539, MO |
| R. parvus Buchanan | 4x | Micranthobatus | Lampobatus | New Zealand | 8 | Alice 97-3, MAINE |
| R. moorei F. Muell. | 4x | Micranthobatus* | Lampobatus | Australia | 8 | Streimann 8207, GH |
| R. calophyllus | 4x | n/a | Malachobatus | Asia | 5 | Alice et al. (2008) Vouchered WKU 04-24 |
| R. repens (L.) Kuntze | 2x | n/a | Dalibarda | North America | 1 | Alice 97-4, MAINE |
| R. ursinus × R. armeniacus(1) | 8x | n/a | n/a | North America | 8 | Alice personal collection |
| R. ursinus × R. armeniacus(6) | 8x | n/a | n/a | North America | 8 | Alice personal collection |
| R. acanthophyllus Focke | 6x | n/a | Orobatus | South America | 8 | Alice and Cantrell are collectors in Ecuador WKU 07-11 |
| W. fragarioides (Michx.) Tratt. | 2x | n/a | n/a | North America | Outgroup | Hill & Soblo 21384, GH |
| R. glabratus Kunth | 6x | Orobatus | Orobatus | South America | 8 | PI 548901/CRUB 1251.004 PL |
| R. loxensis Benth. | 6x | Orobatus | Orobatus | South America | 8 | Alice and Cantrell are collectors in Ecuador WKU 07-17 |
| R. roseus Poir. | 6x | Orobatus | Orobatus | South America | 8 | Luteyn and Quezada 14402, MO |
| R. laegaardii Romol. | 6x | Orobatus* | n/a | South America | 8 | Voucher WKU 07-15 |
| R. hispidus L. * | 2x | Rubus (= Eubatus) | Eubatus | North America | n/a | Alice R9, MAINE |
| R. caesius L. | 4x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 6 | Karlen 243, S |
| R. ursinus Cham. Et. Schltdl. (2) | 8x | Rubus (= Eubatus) | Eubatus | North America | 6 | PI 604641 CRUB 1857.001 PL |
| R. ursinus(3) | 12x | Rubus (= Eubatus) | Eubatus | North America | 6 | PI 554067/CRUB 197.001 PL |
| R. ursinus(4) | 13x | Rubus (= Eubatus) | Eubatus | North America | 6 | USDA Accession no longer exists |
| R. ursinus(5) | 6x | Rubus (= Eubatus) | Eubatus | North America | 6 | PI 604641/CRUB 1857.001 PL |
| R. allegheniensis Porter | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice R1, MAINE |
| R. argutus Link | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice & Judd 15, MAINE |
| R. armeniacus Focke | 4x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 8 | PI 618579/CRUB 45.001 PL |
| R. bifrons Vest | 4x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 8 | Alice 98-9, MAINE |
| R. canadensis L. | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice & Campbell 98-10, MAINE |
| R. caucasicus Focke | 4x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 8 | PI 553143/CRUB 54.001 PL |
| R. coriifolius Liebm. | 2x | Rubus (= Eubatus) | Eubatus | Americas | 8 | Vouchered WKU 06-05 |
| R. cuneifolius Pursh | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice 5, MAINE |
| R. flagellaris Willd. | 4-9x | Rubus (= Eubatus) | Eubatus | North America | 8 | PI 553787/CRUB 61.001 PL |
| R. laciniatus Willd. | 4x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 8 | PI 618548/CRUB 1596.001 PL |
| R. robustus C. Presl | 2x | Rubus (= Eubatus) | Eubatus | Americas | 8 | Steinbach 247, GH |
| R. setosus Bigelow | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice 113, MAINE |
| R. trivialis Michx. | 2x | Rubus (= Eubatus) | Eubatus | North America | 8 | Alice 33, MAINE |
| R. ulmifolius Schott | 2x | Rubus (= Eubatus) | Eubatus | Europe/Asia | 8 | 190-84, MOR |
| R. urticifolius Poir. | 2x | Rubus (= Eubatus) | Eubatus | Americas | 8 | PI 548929/CRUB 1288.001 PL |
| R. glaucus Benth. | 4x | Rubus (= Eubatus) | Idaeobatus | South America | 6 | PI 548906/CRUB 1293.001 PL |
| R. eriocarpus Liebm. | 2x | Rubus (= Eubatus) | Idaeobatus | South America | 7 | Vouchered WKU 06-12 |
| R. pensilvanicus Poir. | 4x | Rubus (= Eubatus) | n/a | North America | 8 | Alice R5, MAINE |
Species marked with an asterisk in the “Species” column did not sequence well and were not included in the results. Subgenera classifications in Focke and the USDA GRIN network are reported. Subgenera marked with an asterisk in the “USDA GRIN Subgenus Classification” column are not listed in GRIN. Focke subg. Eubatus has been renamed to subg. Rubus. Current classifications were curated from other publications (Barneby, 1988; Bean, 1995; Romoleroux et al., 1996; Sutherland, 2005). Herbarium vouchers with collector, number, and herbarium (Holmgren et al., 1990) or PI numbers for accessions of plants housed in the living collection at USDA NCGR Corvallis are given. MOR refers to the living collection at Morton Arboretum, Lisle, IL. HPDL refers to the Native Hawaiian Plants DNA library (Morden et al., 1996). The geographic origin for each accession is listed by continent or region. Ploidy data was collected from flow cytometry data, multiple publications, and the Missouri Botanical Garden index of plant chromosome number database (Thompson, 1995; Thompson, 1997; Meng and Finn, 2002; Hummer et al., 2015). Eight major phylogenetic groups were identified in nuclear sequence analyses. The group in which each species is found is listed.