Comparative phylogeography of the Smilax hispida group (Smilacaceae) in eastern Asia and North America - Implications for allopatric speciation, causes of diversity disparity, and origins of temperate elements in Mexico

Molecular Phylogenetics and Evolution

Volumn 68, Issue 2, 2013, Pages 300-311

  Zhao, Yunpeng ^a   Qi, Zhechen ^a   Ma, Weiwei ^a   Dai, Qiongyan ^a   Li, Pan ^a   Cameron, Kenneth M ^b   Lee, Joongku ^c   Xiang, Qiu Yun Jenny ^d   Fu, Chengxin ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Comparative phylogeography; Diversification rate; Eastern Asian North American disjunction; Origin of Mexican temperate plants; Smilax hispida group; Species delineation

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; FAR EAST; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; MEXICO; MOLECULAR EVOLUTION; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PHYLOGEOGRAPHY; PLANT GENE; PLASTID GENOME; SMILACACEAE; SPECIES DIFFERENTIATION;

DNA, CHLOROPLAST; EVOLUTION, MOLECULAR; FAR EAST; GENES, PLANT; GENETIC SPECIATION; GENETIC VARIATION; GENOME, PLASTID; HAPLOTYPES; MEXICO; MODELS, GENETIC; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PHYLOGEOGRAPHY; SMILACACEAE;

MYA; SMILACACEAE; SMILAX; SMILAX HISPIDA;

EID: 84878110606     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.03.025     Document Type: Article

References (85)

1. Axelrod D.I. Evolution and biogeography of Madrean-Tethyan sclerophyll vegetation. Ann. Mo. Bot. Gard. 1975, 62:280-334.
2. Braun E. Deciduous Forests of Eastern North America 1950, Blakiston, Philadelphia.
3. Caicedo A.L., Schaal B.A. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Mol. Ecol. 2004, 13:1871-1882.
4. Cameron K.M., Fu C. A nuclear rDNA phylogeny of Smilax (Smilacaceae). Aliso 2006, 22:598-605.
5. Carstens B.C., Brunsfeld S.J., Demboski J.R., Good J.M., Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution 2005, 59:1639-1652.
6. Castelloe J., Templeton A.R. Root probabilities for intraspecific gene trees under neutral coalescent theory. Mol. Phylogenet. Evol. 1994, 3:102-113.
7. Chavez R.P. Estudio palinologico de las floras fosiles del Miocene inferior y principios del Mioceno medio de la region de Pichucalco, Chiapas, Mexico. Acta Botánica Mexicana 1993, 24:1-96.
8. Chen S., Qiu Y., Wang A., Cameron K.M., Fu C. A phylogenetic analysis of the Smilacaceae based on morphological data. Acta Phytotaxon. Sin. 2006, 44:113-125.
9. Chen X.Q., Koyama T. Smilax. Flora of China 2000, 96-115. Science Press, Beijing. C.Y. Wu, P.H. Raven, D.Y. Hong (Eds.).
10. Clement M., Posada D., Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 2000, 9:1657-1660.
11. Cranston K.A., Hurwitz B., Ware D., Stein L., Wing R.A. Species trees from highly incongruent gene trees in rice. Syst. Biol. 2009, 58:489-500.
12. Cummings M.P., Neel M.C., Shaw K.L., Otto S. A genealogical approach to quantifying lineage divergence. Evolution 2008, 62:2411-2422.
13. Deevey E. Biogeography of the Pleistocene. Geol. Soc. Am. Bull. 1949, 60:1315-1416.
14. Donoghue M.J., Smith S.A. Patterns in the assembly of temperate forests around the northern hemisphere. Philos. Trans. Roy. Soc. B 2004, 359:1633-1644.
15. Douglas N.A., Wall W.A., Xiang Q.Y., et al. Recent vicariance and the origin of the rare, edaphically specialized Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from phylogenetic and coalescent analyses. Mol. Ecol. 2011, 20:2901-2915.
16. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
17. Drummond, A.J., Ashton, B., Cheung, M., et al., 2009. Geneious v4. 8. http://www.geneious.com.
18. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
19. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1994, 10:315-319.
20. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 1988, 22:521-565.
21. Fu C., Kong H., Qiu Y., Cameron K.M. Molecular phylogeny of the East Asian-North American disjunct Smilax sect. Nemexia (Smilacaceae). Int. J. Plant Sci. 2005, 166:301-309.
22. Graham A. History of the arborescent temperate element in the northern Latin American biota. Vegetation and Vegetational History of Northern Latin America 1973, 301-314. Elsevier Scientific Publishing Co., New York. A. Graham (Ed.).
23. Graham A. The Tertiary history of the northern temperate element in the northern Latin American biota. Am. J. Bot. 1999, 86:32-38.
24. Graur D., Martin W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 2004, 20:80-86.
25. Harris A.J., Xiang Q.Y., Thomas D.T. Phylogeny, origin, and biogeographic history of Aesculus L. (Sapindales) - an update from combined analysis of DNA sequences, morphology, and fossils. Taxon 2009, 58:108-126.
26. Ho S.Y.W., Phillips M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 2009, 58:367-380.
27. Holmes W.C. Smilacaceae. Flora of North America 2002, 468-478. Oxford University Press, New York. Flora of North America Editorial Committee (Ed.).
28. Hudson R.R., Turrelli M. Stochasticity overrules the 'three-times rule': genetic drift, genetic draft, and coalescent times for nuclear loci versus mitochondrial data. Evolution 2003, 57:182-190.
29. Izhaki I., Safriel U.N. The effect of some Mediterranean scrubland frugivores upon germination patterns. J. Ecol. 1990, 78:56-65.
30. Jaramillo-Correa J.P., Beaulieu J., Khasa D.P., Bousquet J. Inferring the past from the present phylogeographic structure of North American forest trees: seeing the forest for the genes. Can. J. For. Res. 2009, 39:286-307.
31. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
32. Kelchner S.A. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Mo. Bot. Gard. 2000, 87:482-498.
33. Krefting L.W., Roe E.I. The role of some birds and mammals in seed germination. Ecol. Monogr. 1949, 19:269-286.
34. Latham R.E., Ricklefs R.E. Continental comparisons of temperate-zone tree species diversity. Species Diversity in Ecological Communities 1993, 294-314. University of Chicago Press, Chicago, IL. R.E. Ricklefs, D. Schluter (Eds.).
35. Li E.X., Sun Y., Qiu Y.X., et al. Phylogeography of two East Asian species in Croomia (Stemonaceae) inferred from chloroplast DNA and ISSR fingerprinting variation. Mol. Phylogenet. Evol. 2008, 49:702-714.
36. Li M., Wunder J., Bissoli G., et al. Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 2008, 24:727-745.
37. Li P., Qi Z., Chen S., Cameron K.M., Fu C. Smilax ligneoriparia sp. nov.: a link between herbaceous and woody Smilax (Smilacaceae) based on morphology, karyotype and molecular phylogenetic data. Taxon 2011, 4:1104-1112.
38. Librado P., Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451.
39. Liu J., Sun Y., Ge X., Gao L., Qiu Y. Phylogeographic studies of plants in China: advances in the past and directions in the future. J. Syst. Evol. 2012, 50:267-275.
40. Mann P., Rogers R., Gahagan L. Overview of plate tectonic history and its unsolved tectonic problem. Central America: Geology, Resources, and Natural Hazards 2007, 205-241. Balkema, Leiden, The Netherlands. J. Bundschuh, G. Alvarado (Eds.).
41. Manos P.S., Donoghue M.J. Progress in northern hemisphere phytogeography: an introduction. Int. J. Plant Sci. 2001, 162:S1-S2.
42. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, pp. 1-8.
43. Milne R.I., Abbott R.J. The origin and evolution of tertiary relict floras. Adv. Bot. Res. 2002, 38:281-314.
44. Morris A.B., Ickert-Bond S.M., Brunson D.B., Soltis D.E., Soltis P.S. Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua, Altingiaceae). Mol. Ecol. 2008, 17:3889-3900.
45. Pfeiffer, W., Stamatakis, A., 2010. Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. In: Ninth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010), Atlanta.
46. Pons O., Petit R.J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 1996, 144:1237-1245.
47. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
48. Qi X., Chen C., Comes H.P., et al. Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian tertiary relict Cercidiphyllum (Cercidiphyllaceae). New Phytol. 2012, 196:617-630.
49. Qi, Z., Li, P., Zhao, Y., Cameron, K., Fu, C., 2012b. Molecular phylogeny and biogeography of Smilacaceae (Liliales), a cosmopolitan family of monocots. In: BSA Annual Conference, Columbus, Ohio.
50. Qian H., Ricklefs R.E. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 2000, 407:180-182.
51. Qiu Y., Fu C., Comes H.P. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of quaternary climate and environmental change in the world's most diverse temperate flora. Mol. Phylogenet. Evol. 2011, 59:225-244.
52. Qiu Y.X., Sun Y., Zhang X.P., et al. Molecular phylogeography of East Asian Kirengeshoma (Hydrangeaceae) in relation to quaternary climate change and landbridge configurations. New Phytol. 2009, 183:480-495.
53. Rambaut, A., Drummond, A.J., 2009. Tracer v1.5. http://tree.bio.ed.ac.uk/software/tracer/.
54. Raven P.H., Axelrod D.I. Angiosperm biogeography and past continental movements. Ann. Mo. Bot. Gard. 1974, 61:539-673.
55. Ree R.H., Smith S.A. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 2008, 57:4-14.
56. Robertson D.R., Christy J.H., Collin R., et al. The Smithsonian Tropical Research Institute: marine research, education, and conservation in Panama. Smithsonian Contrib. Mar. Sci. 2009, 38:73-93.
57. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
58. Rosa S.G.T., Ferreira A.G. Germination of medicinal plant: Smilax campestris Griseb. (salsaparrilha). Acta Hort. 1999, 502:105-112.
59. Sakalidis M.L., Hardy G.E.S.J., Burgess T.I. Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum-Neofusicoccum ribis species complex. Mol. Phylogenet. Evol. 2011, 60:333-344.
60. Sessa E.B., Zimmer E.A., Givnish T.J. Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). Am. J. Bot. 2012, 99:730-750.
61. Shao M.N., Xu S.J., Li N., Qu B., Fan H.Y. Preliminary study on the germination character of Smilax riparia seed. J. Anhui Agr. Sci. 2006, 34:6616-6617.
62. Shaw J., Lickey E.B., Beck J.T., et al. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005, 92:142-166.
63. Shaw J., Lickey E.B., Schilling E.E., Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 2007, 94:275-288.
64. Silvestro D., Schnitzler J., Zizka G. A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evol. Biol. 2011, 11:311.
65. Small R.L., Ryburn J.A., Cronn R.C., Seelanan T., Wendel J.F. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. Am. J. Bot. 1998, 85:1301-1315.
66. Sobel J.M., Chen G.F., Watt L.R., Schemske D.W. The biology of speciation. Evolution 2010, 64:295-315.
67. Soltis D.E., Morris A.B., McLachlan J.S., Manos P.S., Soltis P.S. Comparative phylogeography of unglaciated eastern North America. Mol. Ecol. 2006, 15:4261-4293.
68. Soltis D.E., Tago-Nakazawa M., Xiang Q., et al. Phylogenetic relationships and evolution in Chrysosplenium (Saxifragaceae) based on matK sequence data. Am. J. Bot. 2001, 88:883-893.
69. Svenning J. Deterministic Plio-Pleistocene extinctions in the European cool-temperate tree flora. Ecol. Lett. 2003, 6:646-653.
70. *and other methods). Version 4.0b10 2002, Sinauer Associates, Sunderland, Massachusetts.
71. Wall W.A., Douglas N.A., Xiang Q.Y., et al. Evidence for range stasis during the latter Pleistocene for the Atlantic coastal plain endemic genus, Pyxidanthera Michaux. Mol. Ecol. 2010, 19:4302-4314.
72. Wen J. Evolution of eastern Asian and eastern North American disjunctions in flowering plants. Annu. Rev. Ecol. Syst. 1999, 30:421-455.
73. Wen J. Evolution of eastern Asian-eastern North American biogeographic disjunctions: a few additional issues. Int. J. Plant Sci. 2001, 162:S117-S122.
74. Wen J., Shi S., Jansen R.K., Zimmer E.A. Phylogeny and Biogeography of Aralia sect. Aralia (Araliaceae). Am. J. Bot. 1998, 85:866-875.
75. Wen J., Xiang Q.Y., Qian H., et al. Intercontinental and intracontinental biogeography - patterns and methods. J Syst. Evol. 2009, 47:327-329.
76. Xiang Q., Soltis D.E., Soltis P.S. The eastern Asian and eastern and western North American floristic disjunction: congruent phylogenetic patterns in seven diverse genera. Mol. Phylogenet. Evol. 1998, 10:178-190.
77. Xiang Q., Soltis D.E., Soltis P.S., Manchester S.R., Crawford D.J. Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates. Mol. Phylogenet. Evol. 2000, 15:462-472.
78. Xiang Q., Zhang W.H., Ricklefs R.E., et al. Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America. Evolution 2004, 58:2175-2184.
79. Xiang Q.Y., Soltis D.E. Dispersal-vicariance analyses of intercontinental disjuncts: historical biogeographical implications for angiosperms in the northern hemisphere. Int. J. Plant Sci. 2001, 162:S29-S39.
80. Xiang Q.Y., Thomas D.T., Zhang W., Manchester S.R., Murrell Z. Species level phylogeny of the genus Cornus (Cornaceae) based on molecular and morphological evidence - implications for taxonomy and tertiary intercontinental migration. Taxon 2006, 55:9-30.
81. Xie L., Yi T.S., Li R., Li D.Z., Wen J. Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the northern hemisphere. Mol. Phylogenet. Evol. 2010, 56:675-689.
82. Xu T.T., Abbott R.J., Milne R.I., et al. Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions. BMC Evol. Biol. 2010, 10:194.
83. Yi T., Miller A.J., Wen J. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the northern hemisphere. Mol. Phylogenet. Evol. 2004, 33:861-879.
84. Yu Y., Harris A.J., He X. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Mol. Phylogenet. Evol. 2010, 56:848-850.
85. Yu, Y., Harris, A.J., He, X.J., 2011. RASP (Reconstruct Ancestral State in Phylogenies) 2.0 Beta. http://mnh.scu.edu.cn/soft/blog/RASP.