Phylogeny and biogeography of wild roses with specific attention to polyploids

Annals of Botany

Volumn 115, Issue 2, 2015, Pages 275-291

  Fougère Danezan, Marie ^a,b   Joly, Simon ^c,d   Bruneau, Anne ^c   Gao, Xin Fen ^a   Zhang, Li Bing ^a,e  

^a CHENGDU INSTITUTE OF BIOLOGY   (China)

^b KEY LABORATORY OF TROPICAL FOREST ECOLOGY   (China)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

^d Montreal Botanical Garden   (Canada)

^e MISSOURI BOTANICAL GARDEN   (United States)

Author keywords

allopolyploidy; ancestral area reconstruction; biogeography; divergence time; hybridization; phylogeny; Rosa; taxonomy

Indexed keywords

BIOGEOGRAPHY; CLASSIFICATION; GEOGRAPHICAL DISTRIBUTION; NEW GENUS; PHYLOGENY; PLANT COMMUNITY; POLYPLOIDY; TAXONOMY; WILD POPULATION;

EUROPE;

ROSA; ROSA ARKANSANA;

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PLANT DNA; SPACER DNA; VEGETABLE PROTEIN;

ASIA; CHLOROPLAST; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; EUROPE; EVOLUTION; GENETICS; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NORTH AMERICA; PHYLOGENY; PHYLOGEOGRAPHY; POLYPLOIDY; ROSE;

ASIA; BIOLOGICAL EVOLUTION; CHLOROPLASTS; DNA, INTERGENIC; DNA, PLANT; EUROPE; EVOLUTION, MOLECULAR; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; INTRONS; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; PHYLOGEOGRAPHY; PLANT PROTEINS; POLYPLOIDY; ROSA; SEQUENCE ANALYSIS, DNA;

EID: 84922502440     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcu245     Document Type: Article

References (86)

1. Anonymous. 1978. Fossils of China III. Cenozoic plants of China. Beijing: Science Press.
2. Becker HF. 1963. The fossil record of the genus Rosa. Bulletin of the Torrey Botanical Club 90: 99-110.
3. Brown RP, Yang Z. 2011. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evolutionary Biology 11: 271.
4. Bruneau A, Starr JR, Joly S. 2007. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and an appraisal of current knowledge. Systematic Botany 32: 366-378.
5. Crépin F. 1889. Sketch of a new classification of roses. Journal of the Royal Horticultural Society 11: 217-228.
6. Crépin F. 1891. Nouvelle classification des roses. Journal des Roses 15: 41-43, 53-55, 76-77.
7. Cronn R, Cedroni M, Haselkorn T, Grover C,Wendel JF. 2002. PCR-mediated recombination in amplification products derived from polyploid cotton. Theoretical and Applied Genetics 104: 482-489.
8. Cutler RR. 2003. Medicinal and pharmaceutical uses. In: A Roberts, T Debener, S Gudin, eds. Encyclopedia of rose science. Amsterdam: Elsevier, 716-726.
9. De Riek J, De Cock K, Smulders MJM, Nybom H. 2013. AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae). Molecular Phylogenetics and Evolution 67: 547-559.
10. Debener T, Linde M. 2009. Exploring complex ornamental ge nomes: the rose as a model plant. Critical Reviews in Plant Science 28: 267-280.
11. Debener T, Bartels C, Mattiesch L. 1996. RAPD analysis of genetic variation between a group of rose cultivars and selected wild rose species. Molecular Breeding 2: 321-327.
12. Denk T, Grimsson F, Zetter R, Simonarson LA. 2011. Late Cainozoic floras of Iceland: 15 million years of vegetation and climate history in the northern North Atlantic. Dordrecht, The Netherlands: Springer.
13. Donoghue MJ, Smith SA. 2004. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 1633-1644.
14. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
15. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
16. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
17. Edelman D. 1975. The Eocene Germer Basin Flora of South-Central Idaho. MS thesis, University of Idaho,Moscow, Idaho.
18. Erlanson EW. 1929. Cytological conditions and evidences for hybridity in North American wild roses. Botanical Gazette 87: 443-506.
19. Erlanson EW. 1934. Experimental data for a revision of the North American wild roses. Botanical Gazette 96: 197-259.
20. Erlanson EW. 1938. Phylogeny and polyploidy in Rosa. New Phytologist 37: 72-81.
21. Grossi C, Raymond O, Jay M. 1998. Flavonoid and enzyme polymorphisms and taxonomic organisation of Rosa sections: Carolinae, Cinnamomeae, Pimpinellifoliae and Synstylae. Biochemical Systematics and Ecology 26: 857-871.
22. Gu C, Robertson KR. 2003. Rosa L. In: Team FoCe, ed. Flora of China. St. Louis, MO:Missouri Botanical Garden Press.
23. Guimarães R, Barros L, Carvalho AM, Ferreira ICFR. 2010. Studies on chemical constituents and bioactivity of Rosa micrantha: an alternative antioxidants source for food, pharmaceutical, or cosmetic application. Journal of Agricultural and Food Chemistry 58: 6277-6284.
24. Guoliang W. 2003. Ancient Chinese roses. In: A Roberts, T Debener, S Gudin, eds. Encyclopedia of rose science. Amsterdam: Elsevier, 387-395.
25. Hollick AA. 1936. The Tertiary flora of Alaska. United States Geological Survey Professional Paper 182: 1-185.
26. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
27. Iwata H, Kato T, Ohno S. 2000. Triparental origin of Damask roses. Gene 259: 53-59.
28. Jäger AK, Eldeen IMS, van Staden J. 2007. COX-1 and-2 activity of rose hip. Phytotherapy Research 21: 1251-1252.
29. Jan CH, Byrne DH, Manhart J, Wilson H. 1999. Rose germplasm analysis with RAPD markers. Hortscience 34: 341-345.
30. Jian HY, Zhang H, Tang KX, et al. 2010. Decaploidy in Rosa praelucens Byhouwer (Rosaceae) endemic to Zhongdian Plateau, Yunnan, China. Caryologia 63: 162-167.
31. Joly S. 2012. JML: testing hybridization from species trees. Molecular Ecology Resources 12: 179-184.
32. Joly S, Bruneau A. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Systematic Biology 55: 623-636.
33. Joly S, Starr JR, LewisWH, Bruneau A. 2006. Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany 93: 412-425.
34. Kellner A, Benner M, Walther H, Kunzmann L, Wissemann V, Ritz CM. 2012a. Leaf architecture of extant species of Rosa L. and the Paleogene species Rosa lignitum Heer (Rosaceae). International Journal of Plant Sciences 173: 239-250.
35. Kellner A, Ritz CM, Wissemann V. 2012b. Hybridization with invasive Rosa rugosa threatens the genetic integrity of native Rosa mollis. Botanical Journal of the Linnean Society 170: 472-484.
36. Kolarcik V, Zozomová-Lihová J, Ducár E, Mártonfi P. 2014. Evolutionary significance of hybridization in Onosma (Boraginaceae): analyses of stabilized hemisexual odd polyploids and recent sterile hybrids. Biological Journal of the Linnean Society 112: 89-107.
37. Koopman WJL, Wissemann V, De Cock K, et al. 2008. AFLP markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae). American Journal of Botany 95: 353-366.
38. Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695-1701.
39. Larkin MA, Blackshields G, Brown NP, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
40. Lewis WH. 1957. Revision of the genus Rosa in eastern North America: a review. American Rose Annual 42: 116-126.
41. Lim KY,Werlemark G,Matyasek R, et al. 2005. Evolutionary implications of permanent odd polyploidy in the stable sexual, pentaploid of Rosa canina L. Heredity 94: 501-506.
42. Matsumoto S, Kouchi M, Yabuki J, Kusunoki M, Ueda Y, Fukui H. 1998. Phylogenetic analyses of the genus Rosa using the matK sequence: molecular evidence for the narrow genetic background of modern roses. Scientia Horticulturae 77: 73-82.
43. Matsumoto S, Kouchi M, Fukui H. 2000. Phylogenetic analyses of the subgenus Eurosa using the ITS nrDNA sequence. Acta Horticulturae 521: 193-202.
44. Matsumoto S, Nishio H, Fukui H. 2001. Phylogenetic analyses of genus Rosa: polyphyly of section Pimpinellifoliae and origin of Rosa fortuniana. Acta Horticulturae 547: 357-363.
45. Meng J, Fougère-Danezan M, Zhang L-B, Li D-Z, Yi T-S. 2011. Untangling the hybrid origin of the Chinese tea roses: evidence from DNA sequences of single-copy nuclear and chloroplast genes. Plant Systematics and Evolution 297: 157-170.
46. MengQ, Liu Z, Bruch AA, Liu R, Hu F. 2012. Palaeoclimatic evolution during Eocene and its influence on oil shale mineralisation, Fushun basin, China. Journal of Asian Earth Sciences 45: 95-105.
47. MercureM, Bruneau A. 2008. Hybridization between the escaped Rosa rugosa (Rosaceae) and native R. blanda in Eastern North America. American Journal of Botany 95: 597-607.
48. Millan T, Osuna F, Cobos S, Torres A, Cubero J. 1996. Using RAPDs to study phylogenetic relationships in Rosa. Theoretical and Applied Genetics 92: 273-277.
49. Nybom H, Esselink GD,Werlemark G, Vosman B. 2004. Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC. Heredity 92: 139-150.
50. Nybom H, Esselink GD,Werlemark G, Leus L, Vosman B. 2006. Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect. Caninae. Journal of Evolutionary Biology 19: 635-648.
51. Qiu X-Q, Zhang H,Wang Q-G, et al. 2012. Phylogenetic relationships of wild roses in China based on nrDNAand matKdata. Scientia Horticulturae 140: 45-51.
52. Rambaut A, Suchard M, Xie D, Drummond AJ. 2013. Tracer v1.5. Available from http://beast.bio.ed.ac.uk/Tracer (last accessed 5 January 2013).
53. Ree RH, Smith SA. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14.
54. Rehder A. 1940. Manual of cultivated trees and shrubs hardy in North America. New York: Macmillan.
55. Ritz CM,Wissemann V. 2011. Microsatellites analyses of artificial and spontaneous dogrose hybrids reveal the hybridogenic origin of Rosa micrantha by the contribution of unreduced gametes. Journal of Heredity 102: 217-227.
56. Ritz CM, Schmuths H, Wissemann V. 2005. Evolution by reticulation: European dogroses originated by multiple hybridization across the genus Rosa. Journal of Heredity 96: 4-14.
57. Ritz CM, Koehnen I, Groth M, Theissen G, Wissemann V. 2011. To be or not to be the odd one out-allele-specific transcription in pentaploid dogroses (Rosa L. sect. Caninae (DC.) Ser). BMC Plant Biology 11: 37.
58. Roberts AV. 1977. Relationship between species in the genus Rosa, section Pimpinellifoliae. Botanical Journal of the Linnean Society 74: 309-328.
59. Roberts AV, Gladis T, Brumme H. 2009. DNA amounts of roses (Rosa L.) and their use in attributing ploidy levels. Plant Cell Reports 28: 61-71.
60. Robertson KR. 1974. Genera of Rosaceae in southeastern United-States. Journal of the Arnold Arboretum 55: 611-662.
61. Rögl F. 1999. Mediterranean and Paratethys. Facts and hypotheses of an Oligocene to Miocene paleogeography (short overview). Geologica Carpathica 50: 339-349.
62. Russell A, Samuel R, Klejna V, Barfuss MHJ, Rupp B, Chase MW. 2010. Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Annals of Botany 106: 37-56.
63. Sang T, Crawford DJ, Stuessy TF. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136.
64. Scariot V, Akkak A, Botta R. 2006. Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis. Journal of the American Society for Horticultural Science 131: 66-73.
65. Schanzer IA, Kutlunina NA. 2010. Interspecific hybridization in wild roses (Rosa L. sect. Caninae DC.). Biology Bulletin 37: 480-488.
66. Schanzer IA, Vagina AV. 2007. ISSR (inter simple sequence repeat)markers reveal natural intersectional hybridization in wild roses [Rosa L., sect. Caninae (DC.) Ser. and sect. Cinnamomeae (DC.) Ser.]. Wulfenia 14: 1-14.
67. Shaw J, Lickey E, Beck J, et al. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
68. Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparion of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94: 275-288.
69. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
70. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57: 758-771.
71. Strand A, Leebens Mack J,Milligan B. 1997. Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology 6: 113-118.
72. Taberlet P, Gielly L, Pautou G, Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
73. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
74. Werlemark G. 2000. Evidence of apomixis in hemisexual dogroses, Rosa section Caninae. Sexual Plant Reproduction 12: 353-359.
75. Werlemark G, Nybom H. 2001. Skewed distribution of morphological character scores and molecular markers in three interspecific crosses in Rosa section Caninae. Hereditas 134: 1-13.
76. Werlemark G, Uggla M, Nybom H. 1999. Morphological and RAPD markers show a highly skewed distribution in a pair of reciprocal crosses between hemisexual dogrose species, Rosa sect. Caninae. Theoretical and Applied Genetics 98: 557-563.
77. Wissemann V. 2003. Conventional taxonomy (wild roses). In: AV Roberts, T Debener, S Gudin, eds. Encyclopedia of rose science. Amsterdam: Elsevier, 111-117.
78. Wissemann V, Hellwig FH. 1997. Reproduction and hybridisation in the genus Rosa, section Caninae (Ser) Rehd. Botanica Acta 110: 251-256.
79. Wissemann V, Ritz CM. 2005. The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpB-rbcL intergenic spacer (IGS) versus conventional taxonomy. Botanical Journal of the Linnean Society 147: 275-290.
80. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences, USA 106: 13875-13879.
81. Wu S, Ueda Y, Nishihara S, Matsumoto S. 2000. Phylogenetic analysis of Japanese Rosa using matK sequences. Breeding Science 50: 275-281.
82. Wu S, Ueda Y, Nishihara S, Matsumoto S. 2001. Phylogenetic analysis of Japanese Rosa species using DNA sequences of nuclear ribosomal internal transcribed spacer (ITS). Journal of Horticultural Science and Biotechnology 76: 127-132.
83. Yi OS, Jovel EM, Towers GHN, Wahbe TR, Cho DW. 2007. Antioxidant and antimicrobial activities of native Rosa sp. from British Columbia, Canada. International Journal of Food Sciences and Nutrition 58: 178-189.
84. Yokoya K, Roberts AV, Mottley J, Lewis R, Brandham PE. 2000. Nuclear DNA amounts in roses. Annals of Botany 85: 557-561.
85. Yu Y, Harris A, He X-J. 2013. RASP (Reconstruct Ancestral State in Phylogenies) 2.1 beta. Available at http://mnh.scu.edu.cn/soft/blog/ RASP (last accessed 22 August 2013).
86. Zhang J, Esselink GD, Che D, Fougère-Danezan M, Arens P, Smulders MJM. 2013. The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat. Journal of Horticultural Science and Biotechnology 88: 85-92.