The phylogeny and biogeographic history of ashes (Fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Hinsinger, Damien Daniel ^a,b,c   Basak, Jolly ^a,f   Gaudeul, Myriam ^d   Cruaud, Corinne ^e   Bertolino, Paola ^a,b   Frascaria Lacoste, Nathalie ^a,b   Bousquet, Jean ^c  

^a UNIVERSITÉ PARIS SUD   (France)

^b CNRS   (France)

^c UNIVERSITÉ LAVAL   (Canada)

^d MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^e CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^f VISVA BHARATI UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GEOGRAPHY; OLEACEAE; PHYLOGENY;

EID: 84894293251     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080431     Document Type: Article

References (81)

1. Jaramillo-Correa JP, Beaulieu J, Khasa DP, Bousquet J (2009) Inferring the past from the present phylogeographic structure of North American forest trees: seeing the forest for the genes. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 39: 286-307.
2. Culley TM, Weller SG, Sakai AK (2002) The evolution of wind pollination in angiosperms. Trends in Ecology and Evolution 17: 361-369.
3. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95-124.
4. Wallander E (2008) Systematics of Fraxinus (Oleaceae) and evolution of dioecy. Plant Systematics and Evolution 273: 25-49.
5. Morand-Prieur M-E, Raquin C, Shykoff JA, Frascaria-Lacoste N (2003) Males outcompete hermaphrodites for seed siring success in controlled crosses in the polygamous Fraxinus excelsior (Oleaceae). American Journal of Botany 90: 949-953.
6. Via S (2002) The ecological genetics of speciation. American Naturalist 159: S1-S7.
7. Schluter D (2001) Ecology and the origin of species. Trends in Ecology and Evolution 16: 372-380.
8. Jeandroz S, Roy A, Bousquet J (1997) Phylogeny and phylogeography of the circumpolar genus Fraxinus (Oleaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA. Molecular Phylogenetics and Evolution 7: 241-251.
9. Gielly L, Taberlet P (1994) Chloroplast DNA polymorphism at the intrageneric level and plant phylogenie. Comptes-Rendus de l'Académies des Sciences de Paris, Sciences de la Vie/Life sciences 317: 685-692.
10. Wallander E, Albert VA (2000) Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data. American Journal of Botany 87: 1827-1841.
11. Bouillé M, Bousquet J (2005) Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. American Journal of Botany 92: 63-73.
12. Willyard A, Cronn R, Liston A (2009) Reticulate evolution and incomplete lineage sorting among the ponderosa pines. Molecular Phylogenetics and Evolution 52: 498-511.
13. Hamzeh M, Dayanandan S (2004) Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast trnT-trnF region and nuclear rDNA. American Journal of Botany 91: 1398-1408.
14. Rieseberg LH, Brouillet L (1994) Are many plant species paraphyletic ? Taxon 43: 21-32.
15. Fernandez-Manjarres JF, Gerard PR, Dufour J, Raquin C, Frascaria-Lacoste N (2006) Differential patterns of morphological and molecular hybridization between Fraxinus excelsior L. and Fraxinus angustifolia Vahl (Oleaceae) in eastern and western France. Molecular Ecology 15: 3245-3257.
16. Santamour FSJ (1962) The relation between polyploidy and morphology in white and biltmore ashes. Bulletin of the Torrey Botanical Club 89: 228-232.
17. Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276: 227-232.
18. Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, et al. (2012) Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. Plos ONE 7 (3): doi:10.1371/journal.pone.0034089
19. Li J, Alexander JH, Zhang D (2002) Paraphyletic Syringa (Oleaceae): evidence from sequences of nuclear ribosomal DNA ITS and ETS regions. Systematic Botany 27: 592-597.
20. Nickrent DL, Schuette KP, Starr EM (1994) A molecular phylogeny of Arceuthobium (Viscaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany 81: 1149-1160.
21. Wojciechowski MF, Sanderson MJ, Baldwin BG, Donoghue MJ (1993) Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany 80: 711-722.
22. Waites R, Selvadurai HR, Oliver IR, Hudson A (1998) The phantastica gene encodes a MYB transcription factor involved in growth and dorsoventrality of lateral organs in Antirrhinum. Cell 93: 779-789.
23. Kim M, McCormick S, Timmermans M, Sinha N (2003) The expression domain of phantastica determines leaflet placement in compound leaves. Nature 424: 438-443.
24. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18: 7213-7218.
25. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7: 544-548.
26. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5 113. doi:10.1186/1471-2105-5- 1131471-2105-5-113 [pii]
27. Rambaut A (1996) Sequence Alignment Editor v2.0a11. Available from http://tree.bio.ed.ac.uk/software/seal/. Oxford University, Oxford, England
28. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
29. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
30. Sullivan J, Joyce P (2005) Model selection in phylogenetics. Annual Review of Ecology, Evolution and Systematics 36: 445-466.
31. Huelsenbeck JP, Rannala B (2004) Frequentist properties of bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53: 904-913.
32. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
33. Rambaut A, Drummond AJ (2005) Tracer v1.5. Available from http://tree.bio.ed.ac.uk/software/tracer/. Oxford University, Oxford, England
34. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
35. Call VB, Dilcher DL (1992) Investigations of angiosperms from the Eocene of southeastern North America: samaras of Fraxinus wilcoxiana Berry. Review of Palaeobotany and Palynology 74: 249-266.
36. Magallon-Puebla S, Crane PR, Herendeen PS (1999) Phylogenetic pattern, diversity, and diversification of eudicots. Annals of the Missouri Botanical Garden 86: 297-372.
37. Manchester SR (1999) Biogeographical relationships of North American Tertiary floras. Annals of the Missouri Botanical Garden 86: 472-522.
38. Palamarev E (1989) Paleobotanical evidences of the Tertiary history and origin of the Mediterranean sclerophyll dendroflora. Plant Systematics and Evolution 162: 93-107.
39. Kay KM, Whittall JB, Hodges SA (2006) A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evolutionary Biology 6: 36.
40. Rambaut A (2009) FigTree v1.3.1. Available from http://tree.bio.ed.ac.uk/ software/figtree/. Oxford University, Oxford, England
41. R Development Core Team (2010) R: A language and environment for statistical computing v2.12.1. Available from http://www.R-project.org. Vienna, Austria
42. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
43. Ree RH, Smith SA (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14.
44. Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292: 686-693.
45. Maddison WP, Maddison DR (2011) Mesquite: a modular system for evolutionary analysis v2.75. Available from http://mesquiteproject.org.
46. Schluter D, Price T, Mooers AO, Ludwig D (1997) Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
47. Pybus OG, Harvey PH (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B-Biological Sciences 267: 2267-2272.
48. Rabosky DL (2006) Likelihood methods for inferring temporal shifts in diversification rates. Evolution 60: 1152-1164.
49. Nakaike T (1972) A synoptical study on the genus Fraxinus from Japan, Korea and Formosa. Bulletin of the National Science Museum (Tokyo) 15: 475-512.
50. Wei Z, Green PS (1996) Fraxinus. In: Wu Z, Raven PH, editors. Flora of China. Saint-Louis, Missouri: Science Press, Missouri Botanical Garden. pp. 273-279.
51. Yonekura K (2005) Taxonomic notes on vascular plants in Japan and its adjacent regions (I). - New combinations and new names of japanese plants-. Journal of japanese Botany 80: 323-333.
52. Miller GN (1955) The genus Fraxinus, the ashes, in North America, North of Mexico.: Cornell University. 64 p.
53. Nesom GL (2010) Geography of unifoliolate taxa of Fraxinus (Oleaceae). Phytoneuron 17: 1-6.
54. Nesom GL (2010) Notes on Fraxinus profunda (Oleaceae). Phytoneuron 32: 1-6.
55. Nesom GL (2010) Observations on Fraxinus albicans Buckley (Oleaceae), the correct botanical name for Texas ash. Phytoneuron 33: 1-12.
56. Nesom GL (2010) Taxonomic notes on Fraxinus berlandieriana and F. velutina (Oleaceae). Phytoneuron 34: 1-8.
57. Nesom GL (2010) Taxonomic status of Fraxinus coriacea (Oleaceae). Phytoneuron 37: 1-9.
58. Nesom GL (2010) Notes on Fraxinus cuspidata and F. gooddingii (Oleaceae). Phytoneuron 38: 1-14.
59. Nesom GL (2010) Taxonomy of the water ashes: Fraxinus caroliniana, F. cubensis, and F. pauciflora (Oleaceae). Phytoneuron 39: 1-13.
60. Nesom GL (2010) Fraxinus biltmoreana and Fraxinus smallii (Oleaceae), forest trees of the eastern United States. Phytoneuron 51: 1-30.
61. Regal PJ (1982) Pollination by wind and animals: Ecology of geographic patterns. Annual Review of Ecology and Systematics 13: 497-524.
62. Besnard G, Rubio de Casas R, Christin P-A, Vargas P (2009) Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times. Annals of Botany 104: 143-160.
63. Lee HL, Jansen RK, Chumley TW, Kim KJ (2007) Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Molecular Biology and Evolution 24: 1161-1180.
64. Wang Q, Ferguson DK, Feng GP, Ablaev AG, Wang YF, et al. (2010) Climatic change during the Palaeocene to Eocene based on fossil plants from Fushun, China. Palaeogeography, Palaeoclimatology, Palaeoecology 295: 323-331.
65. Jung SH, Lee SJ (2009) Fossil-winged fruits of Fraxinus (Oleaceae) and Liriodendron (Magnoliaceae) from the Duho formation, Pohang basin, Korea. Acta Geologica Sinica-English Edition 83: 845-852.
66. Donoghue MJ, Smith SA (2004) Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 359: 1633-1644.
67. Wen J (1999) Evolution of Eastern Asian and Eastern North American disjunct distributions in flowering plants. Annual Review of Ecology and Systematics 30: 421-455.
68. Muller J (1981) Fossil pollen records of extant angiosperms. The Botanical Review 47: 1-142.
69. Miller KG, Kominz MA, Browning JV, Wright JD, Mountain GS, et al. (2005) The Phanerozoic record of global sea-level change. Science 310: 1293-1298.
70. Donoghue MJ, Bell CD, Li J (2001) Phylogenetic patterns in Northern Hemisphere plant geography. International Journal of Plant Sciences 162: S41-S52.
71. Yihong W (1995) Study on ecology of Fraxinus mandshurica. Journal of Forestry Research 6: 61-64.
72. Nie Z-L, Sun H, Beardsley PM, Olmstead RG, Wen J (2006) Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae). American Journal of Botany 93: 1343-1356.
73. Wolfe JA (1975) Some aspects of plant geography of the Northern Hemisphere during the late Cretaceous and Tertiary. Annals of the Missouri Botanical Garden 62: 264-279.
74. Magri D, Fineschi S, Bellarosa R, Buonamici A, Sebastiani F, et al. (2007) The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean. Molecular Ecology 16: 5259-5266.
75. Havill NP, Campbell CS, Vining TF, LePage B, Bayer RJ, et al. (2009) Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Systematic Botany 33: 478-789.
76. Sang T, Crawford D, Stuessy T (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136.
77. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Annual Review of Ecology, Evolution and Systematics 37: 187-214.
78. Vamosi JC, Vamosi SM (2004) The role of diversification in causing the correlates of dioecy. Evolution 58: 723-731.
79. Chen C-H, Huang J-P, Tsai C-C, Chaw S-M (2009) Phylogeny of Calocedrus (Cupressaceae), an eastern Asian and western North American disjunct gymnosperm genus, inferred from nuclear ribosomal nrITS sequences. Botanical Studies 50: 425-433.
80. Lopez de Heredia U, Jiménez P, Collada C, Simeone MC, Bellarosa R, et al. (2007) Multi-marker phylogeny of three evergreen oaks reveals vicariant patterns in the Western Mediterranean. Taxon 56: 1199-1209.
81. Nie Z-L, Sun H, Manchester SR, Meng Y, Luke Q, et al. (2012) Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae). BMC Evolutionary Biology 12: 17.