Reticulate evolutionary history of a complex group of grasses: Phylogeny of elymus StStHH allotetraploids based on three nuclear genes

PLoS ONE

Volumn 5, Issue 6, 2010, Pages

  Mason Gamer, Roberta J ^a   Burns, Melissa M ^a   Naum, Marianna ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA AMYLASE; PHOSPHOENOLPYRUVATE CARBOXYLASE; STARCH SYNTHASE;

ALLOPOLYPLOIDY; ARTICLE; ASIA; BARLEY; DIPLOIDY; ELYMUS; EUROPE; GENE SEQUENCE; GEOGRAPHIC ORIGIN; HYPOTHESIS; INTROGRESSION; MOLECULAR PHYLOGENY; NONHUMAN; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT EVOLUTION; PLANT GENE; PLANT GENOME; POACEAE; POLYPHYLY; POLYPLOIDY; TETRAPLOIDY; TREE; UNINDEXED SEQUENCE; WHEAT; CELL NUCLEUS; GENETICS; SPECIES DIFFERENCE; STATISTICAL MODEL;

ELYMUS; HORDEUM; HORDEUM JUBATUM; POACEAE; PSEUDOROEGNERIA; PSEUDOROEGNERIA SPICATA; PSEUDOROEGNERIA STRIGOSA; TRITICEAE; TRITICUM AESTIVUM;

CELL NUCLEUS; GENES, PLANT; LIKELIHOOD FUNCTIONS; PHYLOGENY; POACEAE; POLYPLOIDY; SPECIES SPECIFICITY;

EID: 77956212117     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010989     Document Type: Article

References (94)

1. Guggisberg A, Bretagnolle F, Mansion G (2006) Allopolyploid origin of the Mediterranean endemic, Centaurium bianoris (Gentianaceae), inferred by molecular markers. Systematic Botany 31: 368-379.
2. Hughes CE, Bailey CD, Harris SA (2002) Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism. American Journal of Botany 89: 1057-1073.
3. Mansion G, Zeltner L, Bretagnolle F (2005) Phylogenetic patterns and polyploidy evolution within the Mediterranean genus Centaurium (Gentianaceae-Chironieae). Taxon 54: 931-950.
4. Mummenhoff K, Franzke A, Koch MA (1997) Molecular phylogenetics of Thlaspi s.l. (Brassicaceae) based on chloroplast DNA restriction site variation and sequences of the internal transcribed spacers of nuclear ribosomal DNA. Canadian Journal of Botany 75: 469-482.
5. Seelanan T, Schnabel A, Wendel JF (1997) Congruence and consensus in the cotton tribe (Malvaceae). Systematic Botany 22: 259-290.
6. Vander Stappen J, De Laet J, Gama-López S, Van Campenhout S, Volckaert G (2002) Phylogenetic analysis of Stylostanthes (Fabaceae) based on the internal transcribed spacer region of nuclear ribosomal DNA. Plant Systematics and Evolution 234: 27-51.
7. Widmer A, Baltisberger M (1999) Molecular evidence for allopolyploid speciation and a single origin of the narrow endemic Draba ladina (Brassicaceae). American Journal of Botany 86: 1282-1289.
8. Escobar García P, Schönswetter P, Fuertes Aquilar J, Nieto Feliner G, Schneeweiss GM (2009) Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae). Molecular Phylogenetics and Evolution 50: 226-239.
9. Kim S-C, Mejias JA, Lubinsky P (2008) Molecular confirmation of the hybrid origin of the critically endangered western Mediterranean endemic Sonchus pustulatus (Asteraceae: Sonchinae). Journal of Plant Research 121: 357-364.
10. Kim S-T, Donoghue MJ (2008) Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). American Journal of Botany 95: 1122-1135.
11. Liu S-C, Lu C-T, Wang J-C (2009) Reticulate hybridization of Alpinia (Zingiberaceae) in Taiwan. Journal of Plant Research 122: 305-316.
12. Stefanović S, Costea M (2008) Reticulate evolution in the parasitic genus Cuscuta (Convolvulaceae): over and over again. Botany 86: 791-808.
13. Arnheim N (1983) Concerted evolution of multigene families. In: Nei M, Koehn RK, eds. Evolution of Genes and Proteins. Sunderland, MA: Sinauer. Pp 38-61.
14. Hamby RK, Zimmer EA (1992) Ribosomal RNA as a phylogenetic tool in plant systematics. In: Soltis PS, Soltis DE, Doyle JJ, eds. Molecular Systematics of Plants. New York: Chapman and Hall. pp 50-91.
15. Jorgensen RA, Cluster PD (1988) Modes and tempos in the evolution of nuclear ribosomal DNA: new characters for evolutionary studies and new markers for genetic and population studies. Annals of the Missouri Botanical Garden 75: 1238-1247.
16. Álvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
17. Wendel JF, Schnabel A, Seelanen T (1995) Bi-directional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences of the United States of America 92: 280-284.
18. Brysting AK, Oxelman B, Huber KT, Moulton V, Brochmann C (2007) Untangling complex histories of genome mergings in high polyploids. Systematic Biology 56: 467-476.
19. Doust AN, Penly AM, Jacobs SWL, Kellogg EA (2007) Congruence, conflict, and polyploidization shown by nuclear and chloroplast markers in the monophyletic ''bristle clade'' (Paniceae, Panicoideae, Poaceae). Systematic Botany 32: 531-544.
20. Cronn RC, Small RL, Haselkorn T, Wendel JF (2003) Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57: 2475-2489.
21. Mason-Gamer RJ (2008) Allohexaploidy, introgression, and the complex phylogenetic history on Elymus repens (Poaceae). Molecular Phylogenetics and Evolution 47: 598-611.
22. Doyle JJ, Doyle JL, Brown AHD, Palmer RG (2002) Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploidy complex: histone H3-D gene sequences. Evolution 56: 1388-1402.
23. Emshwiller E, Doyle JJ (2002) Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthase data. American Journal of Botany 89: 1042-1056.
24. Friar EA, Prince LM, Cruse-Sanders JM, McGlaughlin ME, Butterworth CA, et al. (2008) Hybrid origin and genomic mosaicism of Dubautia scabra (Hawaiian silversword alliance; Asteraceae, Madiinae). Systematic Botany 33: 589-597.
25. Ge S, Sang T, Lu B-R, Hong D-Y (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proceedings of the National Academy of Sciences of the United States of America 96: 14400-14405.
26. Järvinen P, Palme A, Morales LO, Lannenpaa M, Keinanen M, et al. (2004) Phylogenetic relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast matK sequences. American Journal of Botany 91: 1834-1845.
27. Joly S, Starr JR, Lewis WH, Bruneau A (2006) Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany 93: 412-425.
28. Lihová J, Shimizu KK, Marhold K (2006) Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene. Molecular Phylogenetics and Evolution 39: 759-786.
29. Mason-Gamer RJ (2001) Origin of North American species of Elymus (Poaceae: Triticeae) allotetraploids based on granule-bound starch synthase gene sequences. Systematic Botany 26: 757-768.
30. Popp M, Erixon P, Eggens F, Oxelman B (2005) Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae) inferred from low copy nuclear RNA polymerase introns, rDNA, and chloroplast DNA. Systematic Botany 30: 302-313.
31. Rodríguez F, Spooner DM (2009) Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploidy species. Systematic Botany 34: 207-219.
32. Smedmark JEE, Eriksson T, Bremer B (2005) Allopolyploid evolution in Geinae (Colurieae: Rosaceae) - building reticulate species trees from bifurcating gene trees. Organisms Diversity & Evolution 5: 275-283.
33. Kellogg EA, Appels R, Mason-Gamer RJ (1996) When gene trees tell different stories: the diploid genera of Triticeae (Gramineae). Systematic Botany 21: 321-347.
34. Mason-Gamer RJ, Kellogg EA (1996) Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Systematic Biology 45: 524-545.
35. Löve Á (1984) Conspectus of the Triticeae. Feddes Repertorium 95: 425-521.
36. Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization within the perennial Triticeae. In: Gustafson JP, ed. Gene manipulation in plant improvement, Proc 16th Stadler genetics symposium. New York, NY: Plenum Publishing Company. pp 209-279.
37. Dewey DR (1967) Synthetic hybrids of new world and old world Agropyrons: III. Agropyron repens X tetraploid Agropyron spicatum. American Journal of Botany 54: 93-98.
38. Dewey DR (1968) Synthetic Agropyron-Elymus hybrids: III. Elymus canadensis X Agropyron caninum, A. trachycaulum, and A. striatum. American Journal of Botany 55: 1133-1139.
39. Dewey DR (1970) Genome relations among Elymus canadensis, Elymus triticoides, Elymus dasystachyus, and Agropyron smithii. American Journal of Botany 57: 861-866.
40. Dewey DR (1974) Cytogenetics of Elymus sibiricus and its hybrids with Agropyron tauri, Elymus canadensis, and Agropyron caninum. Botanical Gazette 135: 80-87.
41. Jensen KB (1990) Cytology and morphology of Elymus pendulinus, E. pendulinus ssp. multiculmis, and E. parviglume (Poaceae: Triticeae). Botanical Gazette 151: 245-251.
42. Jensen KB (1993) Cytogenetics of Elymus magellanicus and its intra-and intergeneric hybrids with Pseudoroegneria spicata, Hordeum violaceum, E. trachycaulus, E. lanceolatus, and E. glaucus (Poaceae: Triticeae). Genome 36: 72-76.
43. Jensen KB (1996) Genome analysis of Eurasian Elymus thoroldianus, E. melantherus, and E. kokonoricus (Triticeae: Poaceae). International Journal of Plant Sciences 157: 136-141.
44. Lu B-R, Salomon B, von Bothmer R (1995) Interspecific hybridizations with Elymus confusus and E. dolichatherus, and their genomic relationships (Poaceae: Triticeae). Plant Systematics and Evolution 197: 1-17.
45. Lu B-R, von Bothmer R (1991) Production and cytogenetic analysis of the intergeneric hybrids between nine Elymus species and common wheat (Triticum aestivum L.). Euphytica 58: 81-95.
46. Lu B-R, von Bothmer R (1993) Meiotic analysis of Elymus caucasicus, E. longearistatus, and their interspecific hybrids with twenty-three Elymus species (Triticeae, Poaceae). Plant Systematics and Evolution 185: 35-53.
47. Salomon B (1993) Interspecific hybridizations in the Elymus semicostatus group (Poaceae). Genome 36: 889-905.
48. Salomon B, Lu B-R (1992) Genomic groups, morphology, and sectional delimitation in Eurasian Elymus (Poaceae, Triticeae). Plant Systematics and Evolution 180: 1-13.
49. Salomon B, Lu B-R (1994) Genomic relationships between species of the Elymus semicostatus group and Elymus sensu lato (Poaceae). Plant Systematics and Evolution 191: 199-211.
50. Dewey DR (1975) The origin of Agropyron smithii. American Journal of Botany 62: 524-530.
51. Chen Q, Conner RL, Laroche A, Thomas JB (1998) Genome analysis of Thinopyrum intermedium and Thinopyrum ponticum using genomic in situ hybridization. Genome 41: 580-586.
52. Liu Z-W, Wang RR-C (1993) Genome analysis of Elytrigia caespitosa, Lophopyrum nodosum, Pseudoroegneria geniculata ssp. scythia, and Thinopyrum intermedium (Triticeae, Gramineae). Genome 36: 102-111.
53. Zhang XY, Dong YS, Wang RR-C (1996) Characterization of genomes and chromosomes in partial amphiploids of the hybrid Triticum aestivum x Thinopyrum ponticum by in situ hybridization, isozyme analysis, and RAPD. Genome 39: 1062-1071.
54. Dewey DR (1982) Genomic and phylogenetic relationships among North American perennial Triticeae. In: Estes JR, ed. Grasses and grasslands. Norman: Oklahoma University Press. pp 51-81.
55. Mason-Gamer RJ (2007) Allopolyploids of the genus Elymus (Triticeae, Poaceae): a phylogenetic perspective. Aliso 23: 372-379.
56. Helfgott DM, Mason-Gamer RJ (2004) The evolution of North American Elymus (Triticeae, Poaceae) allotetraploids: evidence from phosphoenolpyruvate carboxylase gene sequences. Systematic Botany 29: 850-861.
57. Davis JI, Soreng RJ (2007) A preliminary phylogenetic analysis of the grass subfamily Pooideae (Poaceae), with attention to structural features of the plastidand nuclear genomes, including an intron loss in GBSSI. Aliso 23: 335-348.
58. Grass Phylogeny Working Group (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88: 372-457.
59. GonzÁlez MC, Echevarría C, Vidal J, Cejudo FJ (2002) Isolation and characterization of a wheat phosphoenolpyruvate carboxylase gene. Modelling of the encoded protein. Plant Science 162: 233-238.
60. Mason-Gamer RJ (2004) Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Systematic Biology 53: 25-37.
61. Mason-Gamer RJ (2005) The b-amylase genes of grasses and a phylogenetic analysis of the Triticeae (Poaceae). American Journal of Botany 92: 1045-1058.
62. Mason-Gamer RJ, Burns MM, Naum M (2010) Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: analysis of three nuclear genes. Molecular Phylogenetics and Evolution 54: 10-22.
63. Mason-Gamer RJ, Weil CF, Kellogg EA (1998) Granule-bound starch synthase: structure, function, and phylogenetic utility. Molecular Biology and Evolution 15: 1658-1673.
64. Rohde W, Becker D, Salamini F (1988) Structural analysis of the waxy locus from Hordeum vulgare. Nucleic Acids Research 16: 7185-7186.
65. Wagner A, Blackstone N, Cartwright P, Dick M, Misof B, et al. (1994) Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Systematic Biology 43: 250-261.
66. Bradley RD, Hillis DM (1997) Recombinant DNA sequences generated by PCR amplification. Molecular Biology and Evolution 14: 592-593.
67. 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.
68. Judo MSB, Wedel AB, Wilson C (1998) Stimulation and suppression of PCRmediated recombination. Nucleic Acids Research 26: 1819-1825.
69. Lepiniec L, Keryer E, Philippe H, Gadal P, Crétin C (1993) Sorghum phosphoenolpyruvate carboxylase gene family: structure, function, and molecular evolution. Plant Molecular Biology 21: 487-502.
70. Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Molecular Biology 35: 3-15.
71. Ziegler P (1999) Cereal beta-amylases. Journal of Cereal Science 29: 195-204.
72. Sharp PJ, Kreis M, Shewry PR, Gale MD (1988) Location of b-amylase sequences in wheat and its relatives. Theoretical and Applied Genetics 75: 286-290.
73. Mason-Gamer RJ (2007) Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective. BMC Evolutionary Biology 7: 92.
74. Kleinhofs A (1997) Integrating barley RFLP and classical marker maps. Barley Genetics Newsletter 27: 105-112.
75. Korzun V, Malyshev S, Voymokov A, Börner A (1997) RFLP-mapping of three mutant loci in rye (Secale cereale L.) and their relation to homoeologous loci within the Gramineae. Theoretical and Applied Genetics 95: 468-473.
76. Frati F, Simon C, Sullivan J, Swofford DL (1997) Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. Journal of Molecular Evolution 44: 145-158.
77. Sullivan J, Markert JA, Kilpatrick CW (1997) Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Systematic Biology 46: 426-440.
78. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, eds. Molecular systematics, 2nd edition. Sunderland: Sinauer. pp 407-514.
79. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
80. Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics 28: 437-466.
81. Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276: 227-232.
82. Rodríguez F, Oliver JL, Marín A, Meduna JR (1990) The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142: 485-501.
83. Tavaré S (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17: 57-86.
84. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro NH, ed. Mammalian protein metabolism. New York: Academic Press. pp 21-132.
85. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
86. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape split by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-170.
87. Yang Z (1993) Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10: 1396-1401.
88. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion.PhD Thesis. Austin: The University of Texas.
89. Blattner FR (2004) Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences. Molecular Phylogenetics and Evolution 33: 289-299.
90. Sun G-L, Ni Y, Daley T (2008) Molecular phylogeny of RPB2 gene reveals multiple origin, geographic distribution of H genome, and the relationship of the Y genome to other genomes of Elymus species. Molecular Phylogenetics and Evolution 46: 897-907.
91. Linde-Laursen I, Seberg O, Salomon B (1994) Comparison of the Giemsa Cbanded and N-banded karyotypes of two Elymus species, E. dentatus and E. glaucescens (Poaceae: Triticeae). Plant Systematics and Evolution 192: 165-176.
92. Jaaska V (1998) Isoenzyme data on the origin of North American allotetraploid Elymus species. In: Jaradat AA, ed. Triticeae III. Enfield, New Hampshire: Science Publishers, Inc. pp 209-216.
93. Jaaska V (1992) Isoenzyme variation in the grass genus Elymus (Poaceae). Hereditas 117: 11-22.
94. Tsujimoto H, Gill BS (1991) Repetitive DNA sequences from polyploid Elymus trachycaulus and the diploid progenitor species: detection and genomic affinity of Elymus chromatin added to wheat. Genome 34: 782-789.